#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
NAT10	55226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	34152413	34152413	+	Missense_Mutation	SNP	A	A	C	rs147641652		TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr11:34152413A>C	ENST00000257829.3	+	13	1504	c.1298A>C	c.(1297-1299)cAa>cCa	p.Q433P	NAT10_ENST00000531159.2_Missense_Mutation_p.Q361P|NAT10_ENST00000527971.1_Intron	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	433						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				CAGCTCCGTCAACAGAGCGCC	0.567																																																0													110.0	100.0	103.0					11																	34152413		2202	4298	6500	SO:0001583	missense	55226			AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.1298A>C	11.37:g.34152413A>C	ENSP00000257829:p.Gln433Pro		B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	37	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.752349	0.89753	.	.	ENSG00000135372	ENST00000257829;ENST00000531159	T;T	0.45276	0.9;0.9	5.53	5.53	0.82687	Domain of unknown function DUF699, exodeoxyribonuclease V alpha chain (1);	0.000000	0.85682	D	0.000000	T	0.54549	0.1865	M	0.66939	2.045	0.80722	D	1	P	0.48089	0.905	P	0.51266	0.664	T	0.58973	-0.7541	10	0.66056	D	0.02	-18.0062	15.9566	0.79891	1.0:0.0:0.0:0.0	.	433	Q9H0A0	NAT10_HUMAN	P	433;361	ENSP00000257829:Q433P;ENSP00000433011:Q361P	ENSP00000257829:Q433P	Q	+	2	0	NAT10	34108989	1.000000	0.71417	0.955000	0.39395	0.997000	0.91878	9.030000	0.93725	2.231000	0.72958	0.459000	0.35465	CAA		0.567	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		42	144	42	144
FOXJ2	55810	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	8200512	8200512	+	Silent	SNP	G	G	A			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr12:8200512G>A	ENST00000162391.3	+	7	1997	c.852G>A	c.(850-852)tcG>tcA	p.S284S	FOXJ2_ENST00000428177.2_Silent_p.S284S	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	284					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		TCCCACCCTCGAACAACTACT	0.567																																																0													45.0	51.0	49.0					12																	8200512		2203	4300	6503	SO:0001819	synonymous_variant	55810			AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"""Forkhead boxes"""	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.852G>A	12.37:g.8200512G>A			A0AVK4|B2RMP3|Q96PS9|Q9NSN5	Silent	SNP	ENST00000162391.3	37	CCDS8587.1																																																																																				0.567	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	NM_018416		9	92	9	92
PZP	5858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	9317915	9317915	+	Silent	SNP	G	G	A			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr12:9317915G>A	ENST00000261336.2	-	19	2335	c.2307C>T	c.(2305-2307)acC>acT	p.T769T	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Silent_p.T638T	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	769					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CCTTCCACTCGGTGATGGTGT	0.537																																					Melanoma(125;1402 1695 4685 34487 38571)											0													78.0	69.0	72.0					12																	9317915		2203	4300	6503	SO:0001819	synonymous_variant	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2307C>T	12.37:g.9317915G>A			A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																				0.537	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		39	114	39	114
MANSC1	54682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	12483294	12483294	+	Silent	SNP	C	C	T	rs146158847	byFrequency	TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr12:12483294C>T	ENST00000535902.1	-	4	1526	c.963G>A	c.(961-963)ccG>ccA	p.P321P	MANSC1_ENST00000396349.3_Silent_p.P287P|MANSC1_ENST00000545735.1_Silent_p.P240P			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	321	Thr-rich.					integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		TTTCTGTAAACGGTATGGTTT	0.458													C|||	20	0.00399361	0.0106	0.0086	5008	,	,		22640	0.0		0.0	False		,,,				2504	0.0															0								C		26,4380	32.6+/-62.9	1,24,2178	130.0	122.0	124.0		963	-5.9	0.0	12	dbSNP_134	124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MANSC1	NM_018050.2		1,25,6477	TT,TC,CC		0.0116,0.5901,0.2076		321/432	12483294	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	54682			AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.963G>A	12.37:g.12483294C>T			Q8NEC1|Q9NW60	Silent	SNP	ENST00000535902.1	37	CCDS8648.1																																																																																				0.458	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050		24	230	24	230
COCH	1690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	31348670	31348670	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr14:31348670T>C	ENST00000396618.3	+	6	471	c.415T>C	c.(415-417)Tcc>Ccc	p.S139P	COCH_ENST00000475087.1_Missense_Mutation_p.S139P|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000216361.4_Missense_Mutation_p.S139P|COCH_ENST00000382493.4_5'Flank|COCH_ENST00000460581.2_Missense_Mutation_p.S27P	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	139					defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		ACAAGCAGTGTCCACAGCACA	0.393																																																0													98.0	91.0	93.0					14																	31348670		2203	4300	6503	SO:0001583	missense	1690				CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"""coagulation factor C (Limulus polyphemus homolog); cochlin"", ""coagulation factor C homolog, cochlin (Limulus polyphemus)"""	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.415T>C	14.37:g.31348670T>C	ENSP00000379862:p.Ser139Pro		A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	37	CCDS9640.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.024040	0.75390	.	.	ENSG00000100473	ENST00000216361;ENST00000396618;ENST00000475087;ENST00000556908;ENST00000460581;ENST00000542225	T;T;T;T;T	0.78707	-0.19;-0.19;-0.19;-1.2;-0.04	5.74	4.53	0.55603	.	0.464465	0.24481	N	0.038142	T	0.62344	0.2420	N	0.19112	0.55	0.80722	D	1	B;B	0.34214	0.442;0.261	B;B	0.31869	0.137;0.07	T	0.63902	-0.6532	10	0.40728	T	0.16	-14.3469	11.0303	0.47769	0.0:0.0:0.2431:0.7569	.	139;139	Q96IU6;O43405	.;COCH_HUMAN	P	139;139;139;123;27;27	ENSP00000216361:S139P;ENSP00000379862:S139P;ENSP00000451528:S139P;ENSP00000452541:S123P;ENSP00000451713:S27P	ENSP00000216361:S139P	S	+	1	0	COCH	30418421	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.292000	0.43549	2.182000	0.69389	0.482000	0.46254	TCC		0.393	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		52	149	52	149
TP53	7157	hgsc.bcm.edu;broad.mit.edu	37	17	7577144	7577144	+	Missense_Mutation	SNP	A	A	C			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr17:7577144A>C	ENST00000269305.4	-	8	983	c.794T>G	c.(793-795)cTg>cGg	p.L265R	TP53_ENST00000455263.2_Missense_Mutation_p.L265R|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.L265R|TP53_ENST00000445888.2_Missense_Mutation_p.L265R|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.L265R	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	265	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		L -> M (in sporadic cancers; somatic mutation).|L -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation).|L -> Q (in sporadic cancers; somatic mutation).|L -> R (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.L265P(15)|p.0?(8)|p.L265R(5)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262_S269delGNLLGRNS(2)|p.N263fs*5(1)|p.L265del(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.L265Q(1)|p.G262fs*2(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)	GTTCCGTCCCAGTAGATTACC	0.522		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"""	42	Substitution - Missense(21)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(3)|Deletion - Frameshift(3)	large_intestine(6)|lung(5)|oesophagus(5)|breast(4)|bone(4)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|upper_aerodigestive_tract(2)|stomach(2)|urinary_tract(2)|small_intestine(1)|skin(1)|eye(1)	GRCh37	CD004355|CM971505	TP53	D|M							46.0	41.0	43.0					17																	7577144		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.794T>G	17.37:g.7577144A>C	ENSP00000269305:p.Leu265Arg		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	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848055	0.71603	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99876	-7.41;-7.41;-7.41;-7.41;-7.41;-7.41	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.64402	D	0.000001	D	0.99871	0.9939	M	0.91920	3.255	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.997;1.0;1.0	D	0.96405	0.9300	10	0.87932	D	0	-15.8832	12.9367	0.58319	1.0:0.0:0.0:0.0	.	265;265;265;265	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	R	265;265;265;265;265;254;133	ENSP00000352610:L265R;ENSP00000269305:L265R;ENSP00000398846:L265R;ENSP00000391127:L265R;ENSP00000391478:L265R;ENSP00000425104:L133R	ENSP00000269305:L265R	L	-	2	0	TP53	7517869	1.000000	0.71417	0.999000	0.59377	0.528000	0.34623	9.060000	0.93907	2.154000	0.67381	0.379000	0.24179	CTG		0.522	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		16	37	16	37
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652		TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q	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	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		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.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(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)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	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"""	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	GRCh37	CM920675	TP53	M	rs11540652	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152.0	112.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1.0	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	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.743G>A	17.37:g.7577538C>T	ENSP00000269305:p.Arg248Gln		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	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	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	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		50	46	50	46
ACACA	31	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	35600456	35600456	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr17:35600456C>T	ENST00000394406.2	-	22	2841	c.2651G>A	c.(2650-2652)cGa>cAa	p.R884Q	ACACA_ENST00000335166.5_Missense_Mutation_p.R806Q|ACACA_ENST00000360679.3_Missense_Mutation_p.R826Q|ACACA_ENST00000353139.5_Missense_Mutation_p.R921Q	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	884					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TTTCATCAATCGCTCTACCCA	0.423																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											0													142.0	138.0	139.0					17																	35600456		2203	4300	6503	SO:0001583	missense	31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.2651G>A	17.37:g.35600456C>T	ENSP00000377928:p.Arg884Gln		B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.112214	0.37242	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.9	4.9	0.64082	Acetyl-CoA carboxylase, central domain (1);	0.057254	0.64402	D	0.000005	T	0.25494	0.0620	N	0.10685	0.025	0.80722	D	1	B;B;B	0.18310	0.027;0.007;0.002	B;B;B	0.15870	0.014;0.007;0.002	T	0.05632	-1.0873	10	0.23891	T	0.37	-12.8744	17.246	0.87028	0.0:1.0:0.0:0.0	.	921;884;826	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	Q	921;826;884;908;806	ENSP00000344789:R921Q;ENSP00000353898:R826Q;ENSP00000377928:R884Q;ENSP00000335323:R806Q	ENSP00000335323:R806Q	R	-	2	0	ACACA	32674569	0.295000	0.24389	0.924000	0.36721	0.984000	0.73092	2.025000	0.41059	2.551000	0.86045	0.563000	0.77884	CGA		0.423	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		98	301	98	301
VMP1	81671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	57851219	57851219	+	Missense_Mutation	SNP	G	G	T			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr17:57851219G>T	ENST00000262291.4	+	7	997	c.687G>T	c.(685-687)gaG>gaT	p.E229D	VMP1_ENST00000545362.1_Missense_Mutation_p.E173D|VMP1_ENST00000536180.1_Missense_Mutation_p.E132D|VMP1_ENST00000537567.1_Missense_Mutation_p.E95D|VMP1_ENST00000539763.1_Missense_Mutation_p.E37D	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	229					autophagy (GO:0006914)|cell junction assembly (GO:0034329)|embryo implantation (GO:0007566)|regulation of autophagy (GO:0010506)|single organismal cell-cell adhesion (GO:0016337)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|pre-autophagosomal structure (GO:0000407)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|skin(2)	16						AATTTGAAGAGATGCTGGAAC	0.438																																																0													85.0	81.0	82.0					17																	57851219		2203	4300	6503	SO:0001583	missense	81671				CCDS11619.1	17q23.1	2014-05-20	2011-03-02	2011-03-02	ENSG00000062716	ENSG00000062716			29559	protein-coding gene	gene with protein product	"""ectopic P-granules autophagy protein 3 homolog (C. elegans)"", ""transport and golgi organization 5 homolog (Drosophila)"""	611753	"""transmembrane protein 49"""	TMEM49		11230166, 11785947	Standard	NM_030938		Approved	EPG3, TANGO5	uc002ixu.4	Q96GC9	OTTHUMG00000179882	ENST00000262291.4:c.687G>T	17.37:g.57851219G>T	ENSP00000262291:p.Glu229Asp		B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	37	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.999389	0.54147	.	.	ENSG00000062716	ENST00000262291;ENST00000537567;ENST00000539763;ENST00000536180;ENST00000545362	T;T;T	0.42513	0.97;0.97;0.97	6.04	1.74	0.24563	.	0.000000	0.85682	D	0.000000	T	0.40694	0.1127	M	0.72624	2.21	0.80722	D	1	B;B;P;B	0.38729	0.054;0.099;0.644;0.197	B;B;B;B	0.44044	0.106;0.067;0.439;0.134	T	0.13361	-1.0512	10	0.20046	T	0.44	-4.7969	5.0213	0.14363	0.2889:0.0:0.5775:0.1336	.	95;132;173;229	B4DED7;B4DGZ7;F5H2J3;Q96GC9	.;.;.;VMP1_HUMAN	D	229;95;37;132;173	ENSP00000262291:E229D;ENSP00000445130:E95D;ENSP00000444969:E132D	ENSP00000262291:E229D	E	+	3	2	VMP1	55206001	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.452000	0.35156	0.102000	0.17638	0.563000	0.77884	GAG		0.438	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938		14	107	14	107
SPIRE1	56907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	12493109	12493109	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr18:12493109C>T	ENST00000409402.4	-	8	1418	c.1151G>A	c.(1150-1152)cGg>cAg	p.R384Q	SPIRE1_ENST00000464481.1_5'UTR|SPIRE1_ENST00000309836.5_Missense_Mutation_p.R187Q|SPIRE1_ENST00000410092.3_Missense_Mutation_p.R384Q|SPIRE1_ENST00000453447.2_Missense_Mutation_p.R264Q|SPIRE1_ENST00000383356.2_Missense_Mutation_p.R225Q	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						TGATACAGGCCGCAGCTTTCT	0.458																																																0													113.0	104.0	107.0					18																	12493109		2203	4300	6503	SO:0001583	missense	56907			AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"""spire homolog 1 (Drosophila)"", ""spire family actin nucleation factor 1"""			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1151G>A	18.37:g.12493109C>T	ENSP00000387266:p.Arg384Gln			Missense_Mutation	SNP	ENST00000409402.4	37	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	C	36	5.875821	0.97055	.	.	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836;ENST00000383356	T;T;T;T;T	0.57752	0.42;0.86;0.92;0.47;0.38	5.22	5.22	0.72569	.	0.156254	0.53938	D	0.000049	T	0.65606	0.2707	M	0.70275	2.135	0.58432	D	0.999999	D;P;D	0.58970	0.984;0.864;0.981	B;P;P	0.51833	0.427;0.681;0.505	T	0.70425	-0.4875	10	0.72032	D	0.01	-8.4915	19.2222	0.93801	0.0:1.0:0.0:0.0	.	384;187;384	Q08AE8-2;B4DWX0;Q08AE8	.;.;SPIR1_HUMAN	Q	264;384;384;187;225	ENSP00000407050:R264Q;ENSP00000387266:R384Q;ENSP00000387226:R384Q;ENSP00000309661:R187Q;ENSP00000372847:R225Q	ENSP00000309661:R187Q	R	-	2	0	SPIRE1	12483109	1.000000	0.71417	0.992000	0.48379	0.945000	0.59286	7.107000	0.77047	2.606000	0.88127	0.644000	0.83932	CGG		0.458	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818		13	102	13	102
CALR	811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	13050007	13050007	+	Missense_Mutation	SNP	C	C	G			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr19:13050007C>G	ENST00000316448.5	+	2	224	c.151C>G	c.(151-153)Ctc>Gtc	p.L51V		NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	51	N-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	CAAATTCGTTCTCAGTTCCGG	0.527											OREG0025278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													49.0	44.0	45.0					19																	13050007		2203	4299	6502	SO:0001583	missense	811			M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"""Sicca syndrome antigen A (autoantigen Ro; calreticulin)"", ""autoantigen Ro"""	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.151C>G	19.37:g.13050007C>G	ENSP00000320866:p.Leu51Val	684	Q6IAT4|Q9UDG2	Missense_Mutation	SNP	ENST00000316448.5	37	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	C	16.85	3.236787	0.58886	.	.	ENSG00000179218	ENST00000316448	T	0.48201	0.82	5.6	4.57	0.56435	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.41971	0.1182	L	0.46741	1.465	0.80722	D	1	B	0.18013	0.025	B	0.23574	0.047	T	0.23762	-1.0179	10	0.28530	T	0.3	-25.8264	13.1621	0.59550	0.0:0.9218:0.0:0.0782	.	51	P27797	CALR_HUMAN	V	51	ENSP00000320866:L51V	ENSP00000320866:L51V	L	+	1	0	CALR	12911007	1.000000	0.71417	0.522000	0.27862	0.878000	0.50629	4.899000	0.63245	1.366000	0.46076	0.561000	0.74099	CTC		0.527	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		4	28	4	28
HNRNPL	3191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	39334685	39334685	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr19:39334685T>C	ENST00000221419.5	-	5	1136	c.770A>G	c.(769-771)tAt>tGt	p.Y257C	HNRNPL_ENST00000600873.1_Missense_Mutation_p.Y124C|AC008982.2_ENST00000600473.1_RNA	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	257	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			ACAGCCAGAATAGATATCAGC	0.517																																																0													143.0	131.0	135.0					19																	39334685		2203	4300	6503	SO:0001583	missense	3191			X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.770A>G	19.37:g.39334685T>C	ENSP00000221419:p.Tyr257Cys		A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	37	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399617	0.83120	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750;ENST00000423415;ENST00000536292	.	.	.	5.71	5.71	0.89125	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.060637	0.64402	D	0.000002	T	0.81206	0.4774	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84447	0.0586	9	0.87932	D	0	.	14.963	0.71171	0.0:0.0:0.0:1.0	.	257	P14866	HNRPL_HUMAN	C	257;124;124;124;185	.	ENSP00000221419:Y257C	Y	-	2	0	HNRNPL	44026525	1.000000	0.71417	0.951000	0.38953	0.957000	0.61999	7.964000	0.87933	2.176000	0.68965	0.455000	0.32223	TAT		0.517	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			22	231	22	231
SPAG17	200162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	118523986	118523986	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr1:118523986T>C	ENST00000336338.5	-	43	5976	c.5911A>G	c.(5911-5913)Agt>Ggt	p.S1971G	SPAG17_ENST00000492438.1_5'UTR	NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1971						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTAGGCACACTTGAGGATTTC	0.343																																																0													108.0	107.0	107.0					1																	118523986		2203	4300	6503	SO:0001583	missense	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5911A>G	1.37:g.118523986T>C	ENSP00000337804:p.Ser1971Gly		Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	5.100	0.204164	0.09704	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.19105	2.17	4.85	0.449	0.16619	.	2.393730	0.01166	N	0.006753	T	0.04272	0.0118	L	0.34521	1.04	0.09310	N	1	B	0.16166	0.016	B	0.16722	0.016	T	0.22034	-1.0228	10	0.13470	T	0.59	.	3.6505	0.08201	0.0:0.2414:0.2164:0.5423	.	1971	Q6Q759	SPG17_HUMAN	G	1971;451	ENSP00000337804:S1971G	ENSP00000337804:S1971G	S	-	1	0	SPAG17	118325509	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.161000	0.16481	-0.095000	0.12351	-0.321000	0.08615	AGT		0.343	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		32	203	32	203
C21orf2	755	hgsc.bcm.edu;ucsc.edu	37	21	45750795	45750795	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr21:45750795C>T	ENST00000339818.4	-	6	760	c.553G>A	c.(553-555)Gcc>Acc	p.A185T	AP001062.7_ENST00000448927.1_RNA|AP001062.8_ENST00000422357.1_RNA|C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Missense_Mutation_p.A184T|C21orf2_ENST00000397956.3_Missense_Mutation_p.A184T	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	185					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		TCATCCTGGGCGCCGCTGCTG	0.677																																																0													15.0	16.0	15.0					21																	45750795		2192	4295	6487	SO:0001583	missense	0			Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.553G>A	21.37:g.45750795C>T	ENSP00000344566:p.Ala185Thr		A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	.	.	.	.	.	.	.	.	.	.	C	1.399	-0.578712	0.03854	.	.	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.36878	1.66;1.23;1.66	4.08	-8.16	0.01061	.	1.216450	0.05964	N	0.641080	T	0.13415	0.0325	N	0.02011	-0.69	0.39669	D	0.970739	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.38394	-0.9663	10	0.10902	T	0.67	-0.5012	14.9422	0.71003	0.0:0.122:0.0919:0.7861	.	184;184;185;144	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	T	185;184;184	ENSP00000344566:A185T;ENSP00000381047:A184T;ENSP00000317302:A184T	ENSP00000317302:A184T	A	-	1	0	C21orf2	44575223	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.371000	0.01074	-3.824000	0.00102	-1.769000	0.00663	GCC		0.677	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		8	25	8	25
TRABD	80305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	50636413	50636413	+	Missense_Mutation	SNP	G	G	A	rs375342223		TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr22:50636413G>A	ENST00000303434.4	+	8	952	c.833G>A	c.(832-834)cGg>cAg	p.R278Q	TRABD_ENST00000380909.4_Missense_Mutation_p.R278Q|TRABD_ENST00000395827.1_Missense_Mutation_p.R278Q|TRABD_ENST00000395829.1_Missense_Mutation_p.R278Q|SELO_ENST00000380903.2_5'Flank|RP3-402G11.26_ENST00000608025.1_RNA	NM_025204.2	NP_079480.2	Q9H4I3	TRABD_HUMAN	TraB domain containing	278										breast(1)|central_nervous_system(1)|large_intestine(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	7		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)		GAGCTGCCTCGGGCCTCTGAC	0.697													G|||	1	0.000199681	0.0	0.0	5008	,	,		10387	0.0		0.0	False		,,,				2504	0.001															0								G	GLN/ARG	0,4402		0,0,2201	55.0	52.0	53.0		833	4.9	0.0	22		53	1,8595	1.2+/-3.3	0,1,4297	no	missense	TRABD	NM_025204.2	43	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	278/377	50636413	1,12997	2201	4298	6499	SO:0001583	missense	80305			AL449244	CCDS14086.1	22q13.33	2006-07-06			ENSG00000170638	ENSG00000170638			28805	protein-coding gene	gene with protein product						12477932	Standard	NM_025204		Approved	PP2447	uc003bjs.1	Q9H4I3	OTTHUMG00000044644	ENST00000303434.4:c.833G>A	22.37:g.50636413G>A	ENSP00000305664:p.Arg278Gln		Q19CC5|Q96ED8|Q9H7N1|Q9UGX6|Q9UGX7	Missense_Mutation	SNP	ENST00000303434.4	37	CCDS14086.1	.	.	.	.	.	.	.	.	.	.	G	9.292	1.050821	0.19827	0.0	1.16E-4	ENSG00000170638	ENST00000380909;ENST00000303434;ENST00000395827;ENST00000395829	.	.	.	4.95	4.95	0.65309	.	0.249082	0.42420	D	0.000711	T	0.37156	0.0993	L	0.40543	1.245	0.33320	D	0.567235	D;P	0.58620	0.983;0.589	B;B	0.38880	0.284;0.058	T	0.49031	-0.8981	9	0.13853	T	0.58	-21.2873	18.1891	0.89802	0.0:0.0:1.0:0.0	.	232;278	Q9H4I3-2;Q9H4I3	.;TRABD_HUMAN	Q	278	.	ENSP00000305664:R278Q	R	+	2	0	TRABD	48978540	1.000000	0.71417	0.041000	0.18516	0.026000	0.11368	4.905000	0.63286	2.287000	0.76781	0.561000	0.74099	CGG		0.697	TRABD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316987.1	NM_025204		46	71	46	71
HOXD4	3233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	177017514	177017514	+	Missense_Mutation	SNP	C	C	A			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr2:177017514C>A	ENST00000306324.3	+	2	1024	c.612C>A	c.(610-612)aaC>aaA	p.N204K	HOXD3_ENST00000468418.3_5'UTR|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	204					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		GGTTCCAGAACCGGAGGATGA	0.502																																																0													87.0	89.0	88.0					2																	177017514		2203	4300	6503	SO:0001583	missense	3233				CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"""Homeoboxes / ANTP class : HOXL subclass"""	5138	protein-coding gene	gene with protein product		142981	"""homeo box D4"""	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.612C>A	2.37:g.177017514C>A	ENSP00000302548:p.Asn204Lys		B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	37	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217469	0.58560	.	.	ENSG00000170166	ENST00000306324	D	0.99382	-5.8	5.27	1.42	0.22433	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99560	0.9842	H	0.97874	4.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99069	1.0833	10	0.87932	D	0	.	9.8153	0.40849	0.0:0.7191:0.0:0.2809	.	204	P09016	HXD4_HUMAN	K	204	ENSP00000302548:N204K	ENSP00000302548:N204K	N	+	3	2	HOXD4	176725760	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	2.160000	0.42348	-0.020000	0.14032	0.561000	0.74099	AAC		0.502	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			19	161	19	161
ZDBF2	57683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	207169636	207169636	+	Silent	SNP	G	G	A	rs143619911	byFrequency	TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr2:207169636G>A	ENST00000374423.3	+	5	770	c.384G>A	c.(382-384)acG>acA	p.T128T		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	128							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.T128T(1)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGGAAGGCACGCAGGAGGTTT	0.453													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18580	0.0		0.0	False		,,,				2504	0.0															1	Substitution - coding silent(1)	breast(1)						G		5,3807		0,5,1901	64.0	61.0	62.0		384	-4.3	0.0	2	dbSNP_134	62	0,8256		0,0,4128	no	coding-synonymous	ZDBF2	NM_020923.1		0,5,6029	AA,AG,GG		0.0,0.1312,0.0414		128/2355	207169636	5,12063	1906	4128	6034	SO:0001819	synonymous_variant	57683			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.384G>A	2.37:g.207169636G>A			Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																				0.453	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		13	67	13	67
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	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			46	103	46	103
EXOC2	55770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	572531	572531	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr6:572531G>A	ENST00000230449.4	-	13	1567	c.1432C>T	c.(1432-1434)Ctc>Ttc	p.L478F	EXOC2_ENST00000448181.3_Missense_Mutation_p.L73F	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	478					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		TCACTGAAGAGGCTTCCATTA	0.438																																																0													92.0	85.0	88.0					6																	572531		2203	4300	6503	SO:0001583	missense	55770			AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1432C>T	6.37:g.572531G>A	ENSP00000230449:p.Leu478Phe		B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	37	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.786011	0.70337	.	.	ENSG00000112685	ENST00000230449;ENST00000448181	T	0.49432	0.78	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.27663	0.0680	L	0.52364	1.645	0.80722	D	1	P	0.41313	0.745	B	0.39935	0.314	T	0.04946	-1.0916	10	0.22706	T	0.39	-12.0904	12.2818	0.54767	0.0899:0.0:0.91:0.0	.	478	Q96KP1	EXOC2_HUMAN	F	478;73	ENSP00000230449:L478F	ENSP00000230449:L478F	L	-	1	0	EXOC2	517531	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.285000	0.65633	2.379000	0.81126	0.563000	0.77884	CTC		0.438	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303		14	81	14	81
ZFAT	57623	hgsc.bcm.edu;broad.mit.edu	37	8	135614421	135614421	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr8:135614421T>C	ENST00000377838.3	-	6	1715	c.1541A>G	c.(1540-1542)gAc>gGc	p.D514G	ZFAT_ENST00000520214.1_Missense_Mutation_p.D502G|ZFAT_ENST00000520356.1_Missense_Mutation_p.D502G|ZFAT_ENST00000523399.1_Missense_Mutation_p.D452G|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520727.1_Missense_Mutation_p.D502G|ZFAT_ENST00000429442.2_Missense_Mutation_p.D502G	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	514					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CTGTAGCTGGTCCCCCAGAGC	0.617																																																0													21.0	22.0	22.0					8																	135614421		1894	4111	6005	SO:0001583	missense	57623			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.1541A>G	8.37:g.135614421T>C	ENSP00000367069:p.Asp514Gly		B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	12.34	1.908077	0.33721	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.11385	2.85;2.78;2.78;2.78;2.78;2.84	6.04	2.69	0.31865	.	0.435687	0.25042	N	0.033596	T	0.04907	0.0132	N	0.04880	-0.145	0.30027	N	0.813788	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.09377	0.0;0.0;0.004;0.0	T	0.17961	-1.0352	10	0.40728	T	0.16	-26.7512	7.5874	0.28002	0.0:0.23:0.0:0.77	.	452;502;502;514	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	G	502;502;502;514;502;452;502	ENSP00000427879:D502G;ENSP00000427831:D502G;ENSP00000394501:D502G;ENSP00000367069:D514G;ENSP00000428483:D502G;ENSP00000429091:D452G	ENSP00000367069:D514G	D	-	2	0	ZFAT	135683603	0.996000	0.38824	0.995000	0.50966	0.948000	0.59901	1.735000	0.38176	0.638000	0.30545	0.460000	0.39030	GAC		0.617	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		5	79	5	79
DIAPH2	1730	hgsc.bcm.edu;broad.mit.edu	37	X	96639008	96639008	+	Missense_Mutation	SNP	A	A	T			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chrX:96639008A>T	ENST00000324765.8	+	25	3457	c.3110A>T	c.(3109-3111)cAg>cTg	p.Q1037L	DIAPH2_ENST00000355827.4_Missense_Mutation_p.Q1037L|DIAPH2_ENST00000373061.3_Missense_Mutation_p.Q1037L|DIAPH2_ENST00000373049.4_Missense_Mutation_p.Q1037L|DIAPH2_ENST00000373054.4_Missense_Mutation_p.Q1033L			O60879	DIAP2_HUMAN	diaphanous-related formin 2	1037					actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						TTAGAACGCCAGAAGAAAAAG	0.313																																																0													61.0	54.0	56.0					X																	96639008		2203	4299	6502	SO:0001583	missense	1730			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"""diaphanous (Drosophila, homolog) 2"", ""diaphanous homolog 2 (Drosophila)"""			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.3110A>T	X.37:g.96639008A>T	ENSP00000321348:p.Gln1037Leu		A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Missense_Mutation	SNP	ENST00000324765.8	37	CCDS14467.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.700002	0.68501	.	.	ENSG00000147202	ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885	D;D;D;D;D	0.82255	-1.59;-1.58;-1.52;-1.53;-1.59	4.52	4.52	0.55395	Actin-binding FH2/DRF autoregulatory (1);	0.000000	0.64402	D	0.000001	D	0.89125	0.6626	M	0.65975	2.015	0.50039	D	0.999844	D;D	0.61697	0.971;0.99	D;D	0.75020	0.932;0.985	D	0.89708	0.3910	10	0.56958	D	0.05	.	13.2344	0.59961	1.0:0.0:0.0:0.0	.	1037;1037	O60879;O60879-2	DIAP2_HUMAN;.	L	1037;1033;1037;1037;1037;1044	ENSP00000362152:Q1037L;ENSP00000362145:Q1033L;ENSP00000348082:Q1037L;ENSP00000362140:Q1037L;ENSP00000321348:Q1037L	ENSP00000321348:Q1037L	Q	+	2	0	DIAPH2	96525664	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.231000	0.78106	1.765000	0.52091	0.441000	0.28932	CAG		0.313	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		4	56	4	56
MID2	11043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	107084365	107084365	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chrX:107084365G>A	ENST00000262843.6	+	2	1018	c.470G>A	c.(469-471)tGt>tAt	p.C157Y	MID2_ENST00000443968.2_Missense_Mutation_p.C157Y	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	157					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						TGCATCACCTGTGAGGTCTCC	0.562																																																0													53.0	46.0	49.0					X																	107084365		2203	4300	6503	SO:0001583	missense	11043				CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.470G>A	X.37:g.107084365G>A	ENSP00000262843:p.Cys157Tyr		A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Missense_Mutation	SNP	ENST00000262843.6	37	CCDS14532.2	.	.	.	.	.	.	.	.	.	.	G	19.24	3.789193	0.70337	.	.	ENSG00000080561	ENST00000451923;ENST00000262843;ENST00000443968	D;D;D	0.96073	-3.9;-3.9;-3.9	5.94	5.94	0.96194	Zinc finger, B-box (1);	0.000000	0.85682	D	0.000000	D	0.98532	0.9510	H	0.96269	3.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99651	1.0991	10	0.87932	D	0	.	16.5117	0.84287	0.0:0.0:1.0:0.0	.	157;157	Q9UJV3;Q9UJV3-2	TRIM1_HUMAN;.	Y	137;157;157	ENSP00000410730:C137Y;ENSP00000262843:C157Y;ENSP00000413976:C157Y	ENSP00000262843:C157Y	C	+	2	0	MID2	106971021	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.506000	0.84524	0.600000	0.82982	TGT		0.562	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216		26	31	26	31
BRF1	2972	broad.mit.edu;ucsc.edu	37	14	105752650	105752650	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr14:105752650G>A	ENST00000546474.1	-	2	15207	c.248C>T	c.(247-249)gCg>gTg	p.A83V	BRF1_ENST00000379937.2_Intron|BRF1_ENST00000440513.3_5'UTR|BRF1_ENST00000548421.1_Missense_Mutation_p.A83V|BRF1_ENST00000327359.3_5'UTR	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	83					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		CAGGGTCTGCGCTCTCGACTC	0.587																																																0													55.0	49.0	51.0					14																	105752650		2203	4300	6503	SO:0001583	missense	2972			U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.248C>T	14.37:g.105752650G>A	ENSP00000448323:p.Ala83Val		B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Missense_Mutation	SNP	ENST00000546474.1	37	CCDS10001.1	.	.	.	.	.	.	.	.	.	.	G	5.308	0.242245	0.10077	.	.	ENSG00000185024	ENST00000546474;ENST00000548421;ENST00000345053	.	.	.	4.22	4.22	0.49857	Cyclin-like (1);	0.000000	0.85682	D	0.000000	T	0.56217	0.1970	M	0.72894	2.215	0.80722	D	1	P;P	0.52463	0.796;0.953	B;B	0.41988	0.09;0.372	T	0.64829	-0.6315	9	0.62326	D	0.03	.	11.9652	0.53031	0.0:0.0:1.0:0.0	.	83;83	Q96KX3;Q92994	.;TF3B_HUMAN	V	83	.	ENSP00000339442:A83V	A	-	2	0	BRF1	104823695	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	4.254000	0.58798	2.163000	0.67991	0.563000	0.77884	GCG		0.587	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519		3	36	3	36
TBX15	6913	broad.mit.edu;ucsc.edu	37	1	119428085	119428085	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr1:119428085G>A	ENST00000369429.3	-	8	1088	c.1079C>T	c.(1078-1080)tCg>tTg	p.S360L	TBX15_ENST00000207157.3_Missense_Mutation_p.S254L			Q96SF7	TBX15_HUMAN	T-box 15	360					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		AGAAGAAGCCGAAGGGGATGG	0.478																																																0													43.0	52.0	49.0					1																	119428085		2202	4299	6501	SO:0001583	missense	6913			AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"""T-boxes"""	11594	protein-coding gene	gene with protein product		604127	"""T-box 14"""	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.1079C>T	1.37:g.119428085G>A	ENSP00000358437:p.Ser360Leu		Q08E76|Q5JT54|Q5T9S7	Missense_Mutation	SNP	ENST00000369429.3	37		.	.	.	.	.	.	.	.	.	.	G	16.40	3.112640	0.56398	.	.	ENSG00000092607	ENST00000344218;ENST00000207157;ENST00000369429;ENST00000449873;ENST00000393149	T;T;T	0.68331	-0.32;-0.32;-0.32	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.54271	0.1848	N	0.11560	0.145	0.80722	D	1	D;D	0.69078	0.997;0.99	D;P	0.70227	0.968;0.492	T	0.52689	-0.8542	10	0.07030	T	0.85	.	19.9961	0.97386	0.0:0.0:1.0:0.0	.	157;360	E9PCG3;Q96SF7	.;TBX15_HUMAN	L	157;254;360;88;87	ENSP00000207157:S254L;ENSP00000358437:S360L;ENSP00000398625:S88L	ENSP00000207157:S254L	S	-	2	0	TBX15	119229608	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.067000	0.93955	2.744000	0.94065	0.561000	0.74099	TCG		0.478	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380		4	31	4	31
F5	2153	broad.mit.edu;ucsc.edu	37	1	169529938	169529938	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr1:169529938T>C	ENST00000367797.3	-	4	641	c.440A>G	c.(439-441)gAa>gGa	p.E147G	F5_ENST00000367796.3_Missense_Mutation_p.E147G|F5_ENST00000546081.1_Missense_Mutation_p.E10G	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	147	F5/8 type A 1.|Plastocyanin-like 1.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	ATAGGTGTATTCTCGGCCTGG	0.517																																																0													187.0	158.0	168.0					1																	169529938		2203	4300	6503	SO:0001583	missense	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.440A>G	1.37:g.169529938T>C	ENSP00000356771:p.Glu147Gly		A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.843580	0.51057	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.99023	-5.34;-5.34;-5.34	5.39	5.39	0.77823	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.664601	0.15758	N	0.246068	D	0.98629	0.9541	M	0.71036	2.16	0.37076	D	0.898771	D	0.69078	0.997	D	0.63703	0.917	D	0.99271	1.0893	9	0.49607	T	0.09	-22.9765	9.1469	0.36939	0.2786:0.0:0.0:0.7214	.	147	P12259	FA5_HUMAN	G	147;147;10	ENSP00000356771:E147G;ENSP00000356770:E147G;ENSP00000439664:E10G	ENSP00000356770:E147G	E	-	2	0	F5	167796562	0.419000	0.25449	0.324000	0.25361	0.540000	0.34992	3.221000	0.51215	2.029000	0.59856	0.477000	0.44152	GAA		0.517	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		42	297	42	297
EPHA4	2043	broad.mit.edu;ucsc.edu	37	2	222347239	222347239	+	Missense_Mutation	SNP	A	A	G			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr2:222347239A>G	ENST00000281821.2	-	5	1192	c.1151T>C	c.(1150-1152)gTc>gCc	p.V384A	EPHA4_ENST00000409938.1_Missense_Mutation_p.V384A|EPHA4_ENST00000409854.1_Missense_Mutation_p.V384A|EPHA4_ENST00000392071.4_Missense_Mutation_p.V333A	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	384	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GGTGTAGTGGACCCCACTTCC	0.512																																																0													239.0	247.0	244.0					2																	222347239		2203	4300	6503	SO:0001583	missense	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3388	protein-coding gene	gene with protein product		602188	"""EphA4"""	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.1151T>C	2.37:g.222347239A>G	ENSP00000281821:p.Val384Ala		A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.41|19.41	3.822880|3.822880	0.71028|0.71028	.|.	.|.	ENSG00000116106|ENSG00000116106	ENST00000441679|ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071;ENST00000443796	.|T;T;T;T;T	.|0.74947	.|-0.89;-0.89;-0.89;-0.87;3.68	6.06|6.06	6.06|6.06	0.98353|0.98353	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.113627	.|0.64402	.|D	.|0.000014	T|T	0.76335|0.76335	0.3973|0.3973	M|M	0.71920|0.71920	2.185|2.185	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.21147	.|0.052	.|B	.|0.26202	.|0.067	T|T	0.73799|0.73799	-0.3869|-0.3869	5|10	.|0.66056	.|D	.|0.02	.|.	16.6093|16.6093	0.84858|0.84858	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|384	.|P54764	.|EPHA4_HUMAN	P|A	121|384;384;384;333;88	.|ENSP00000281821:V384A;ENSP00000386276:V384A;ENSP00000386829:V384A;ENSP00000375923:V333A;ENSP00000395917:V88A	.|ENSP00000281821:V384A	S|V	-|-	1|2	0|0	EPHA4|EPHA4	222055483|222055483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.841000|0.841000	0.47740|0.47740	9.268000|9.268000	0.95675|0.95675	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	TCC|GTC		0.512	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			97	586	97	586
RBM33	155435	broad.mit.edu;ucsc.edu	37	7	155530752	155530752	+	Splice_Site	SNP	A	A	G			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr7:155530752A>G	ENST00000401878.3	+	11	1591		c.e11-1			NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33								nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		GTTACCTTTCAGTTTCAGGTG	0.468																																																0													104.0	104.0	104.0					7																	155530752		1932	4154	6086	SO:0001630	splice_region_variant	155435			AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.1394-1A>G	7.37:g.155530752A>G			A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Splice_Site	SNP	ENST00000401878.3	37	CCDS5941.2	.	.	.	.	.	.	.	.	.	.	A	3.953	-0.011808	0.07727	.	.	ENSG00000184863	ENST00000401878;ENST00000392761	.	.	.	5.16	2.7	0.31948	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999989	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.3277	0.04227	0.4957:0.2715:0.1019:0.1309	.	.	.	.	.	-1	.	.	.	+	.	.	RBM33	155223513	0.989000	0.36119	0.539000	0.28077	0.058000	0.15608	0.712000	0.25779	0.263000	0.21812	0.482000	0.46254	.		0.468	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	Intron	38	137	38	137
RYR3	6263	broad.mit.edu;ucsc.edu	37	15	34130251	34130251	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5143-01A-01D-1468-08	TCGA-DH-5143-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4bbefd2-808c-4646-8bee-3ab3b040b48b	ce04e1e1-0343-4378-b34e-203f88ead2a8	g.chr15:34130251T>C	ENST00000389232.4	+	89	12140	c.12070T>C	c.(12070-12072)Tac>Cac	p.Y4024H	RYR3_ENST00000415757.3_Missense_Mutation_p.Y4019H	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4024					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGTGCTAAATTACTTCGAACC	0.468																																																0													116.0	115.0	115.0					15																	34130251		1943	4149	6092	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.12070T>C	15.37:g.34130251T>C	ENSP00000373884:p.Tyr4024His		O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.358983	0.61403	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.98044	-4.68	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.98463	0.9488	M	0.75615	2.305	0.58432	D	0.999992	D;D	0.89917	0.971;1.0	D;D	0.91635	0.968;0.999	D	0.99560	1.0968	10	0.66056	D	0.02	.	15.0733	0.72056	0.0:0.0:0.0:1.0	.	4019;4024	Q15413-2;Q15413	.;RYR3_HUMAN	H	4024;4020	ENSP00000373884:Y4024H	ENSP00000354735:Y4020H	Y	+	1	0	RYR3	31917543	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	7.769000	0.85360	2.140000	0.66376	0.450000	0.29827	TAC		0.468	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			73	208	73	208
