#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
PXK	54899	broad.mit.edu	37	3	58395861	58395861	+	Silent	SNP	G	G	A			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr3:58395861G>A	ENST00000356151.2	+	16	1549	c.1440G>A	c.(1438-1440)gcG>gcA	p.A480A	PXK_ENST00000463280.1_Silent_p.A447A|PXK_ENST00000383716.3_Silent_p.A447A|PXK_ENST00000302779.5_Silent_p.A463A|PXK_ENST00000479241.1_Silent_p.A463A|PXK_ENST00000484288.1_Silent_p.A480A|PXK_ENST00000383715.4_Silent_p.A463A|PXK_ENST00000536660.1_Silent_p.A343A	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		AGCATTCAGCGAAGTACAGCA	0.433																																						uc003djz.1																			0				cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19						c.(1438-1440)gcG>gcA		Homo sapiens PX domain containing serine/threonine kinase (PXK), mRNA.							88.0	81.0	84.0					3																	58395861		2203	4300	6503	SO:0001819	synonymous_variant	54899				cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission	centrosome|cytoplasm|nucleus|plasma membrane	ATP binding|actin binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity	g.chr3:58395861G>A	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.1440G>A	3.37:g.58395861G>A						PXK_uc003djx.1_Silent_p.A480A|PXK_uc003dka.1_Silent_p.A480A|PXK_uc003dkb.1_Silent_p.A397A|PXK_uc003dkc.1_Silent_p.A463A|PXK_uc011bfe.1_Silent_p.A447A|PXK_uc010hnj.1_Silent_p.A447A|PXK_uc003dkd.1_Silent_p.A343A|PXK_uc010hnk.1_Silent_p.A254A	p.A480A	NM_017771	NP_060241	Q7Z7A4	PXK_HUMAN		BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)	15	1539	+			480			Protein kinase.			Silent	SNP	ENST00000356151.2	37	c.1440G>A	CCDS2889.1	.	.	.	.	.	.	.	.	.	.	G	7.739	0.700803	0.15172	.	.	ENSG00000168297	ENST00000479134;ENST00000495557	.	.	.	5.9	-4.12	0.03916	.	.	.	.	.	T	0.51024	0.1650	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	T	0.51293	-0.8724	4	.	.	.	0.1151	8.2699	0.31838	0.3948:0.2533:0.3519:0.0	.	.	.	.	Q	235;52	.	.	R	+	2	0	PXK	58370901	0.006000	0.16342	0.223000	0.23860	0.945000	0.59286	0.012000	0.13287	-0.435000	0.07264	-0.376000	0.06991	CGA		0.433	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771		33	41	0	0	0	1	0	33	41				
PAXBP1	94104	broad.mit.edu	37	21	34123457	34123457	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr21:34123457C>T	ENST00000331923.4	-	9	1769	c.1580G>A	c.(1579-1581)cGt>cAt	p.R527H	PAXBP1_ENST00000290178.4_Missense_Mutation_p.R527H	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	527	Necessary and sufficient for interaction with PAX7. {ECO:0000250}.				muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCAATGCGACGTTTTGCATG	0.463																																						uc002yqn.3																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(11)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	39						c.(1579-1581)cGt>cAt		Homo sapiens GC-rich sequence DNA-binding factor 1 (GCFC1), transcript variant 1, mRNA.							112.0	94.0	100.0					21																	34123457		2203	4300	6503	SO:0001583	missense	94104					cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr21:34123457C>T	AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 105"", ""GC-rich sequence DNA-binding factor candidate"""		"""chromosome 21 open reading frame 66"", ""GC-rich sequence DNA-binding factor 1"""	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.1580G>A	21.37:g.34123457C>T	ENSP00000328992:p.Arg527His					GCFC1_uc002yql.3_Missense_Mutation_p.R36H|GCFC1_uc002yqm.3_Missense_Mutation_p.R21H|GCFC1_uc002yqo.3_Non-coding_Transcript|GCFC1_uc002yqp.3_Missense_Mutation_p.R527H	p.R527H	NM_016631	NP_057715	Q9Y5B6	GCFC1_HUMAN			8	1770	-			527					D3DSE7|Q96DU8|Q9NYQ0	Missense_Mutation	SNP	ENST00000331923.4	37	c.1580G>A	CCDS13619.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629884	0.87660	.	.	ENSG00000159086	ENST00000331923;ENST00000290178	T;T	0.37058	1.65;1.22	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.60130	0.2245	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.72338	0.977;0.948;0.94	T	0.61594	-0.7031	10	0.59425	D	0.04	-11.8073	18.6815	0.91547	0.0:1.0:0.0:0.0	.	527;527;36	Q9Y5B6-2;Q9Y5B6;B3KSC0	.;GCFC1_HUMAN;.	H	527	ENSP00000328992:R527H;ENSP00000290178:R527H	ENSP00000290178:R527H	R	-	2	0	GCFC1	33045328	0.997000	0.39634	1.000000	0.80357	0.969000	0.65631	3.473000	0.53122	2.517000	0.84864	0.557000	0.71058	CGT		0.463	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		19	67	0	0	0	1	0	19	67				
MED12L	116931	broad.mit.edu	37	3	151127118	151127118	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr3:151127118C>T	ENST00000474524.1	+	38	5841	c.5803C>T	c.(5803-5805)Cag>Tag	p.Q1935*	MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1935	Gln-rich.					mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCAGCAAGCACAGGTACCCAC	0.507																																						uc003eyp.3																			0				NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128						c.(5803-5805)Cag>Tag		Homo sapiens mediator complex subunit 12-like (MED12L), mRNA.							56.0	56.0	56.0					3																	151127118		2203	4300	6503	SO:0001587	stop_gained	116931				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex		g.chr3:151127118C>T	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5803C>T	3.37:g.151127118C>T	ENSP00000417235:p.Gln1935*					MED12L_uc011bnz.2_Intron	p.Q1935*	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		37	5932	+			1935			Gln-rich.		Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Nonsense_Mutation	SNP	ENST00000474524.1	37	c.5803C>T	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	46	12.925596	0.99707	.	.	ENSG00000144893	ENST00000474524	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-2.7654	17.4518	0.87594	0.0:1.0:0.0:0.0	.	.	.	.	X	1935	.	ENSP00000417235:Q1935X	Q	+	1	0	MED12L	152609808	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.712000	0.61888	2.713000	0.92767	0.655000	0.94253	CAG		0.507	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		6	98	0	0	0	1	0	6	98				
CPT1A	1374	broad.mit.edu	37	11	68542876	68542876	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr11:68542876G>A	ENST00000265641.5	-	13	1637	c.1483C>T	c.(1483-1485)Cag>Tag	p.Q495*	CPT1A_ENST00000540367.1_Nonsense_Mutation_p.Q495*|CPT1A_ENST00000539743.1_Nonsense_Mutation_p.Q495*|CPT1A_ENST00000376618.2_Nonsense_Mutation_p.Q495*|CPT1A_ENST00000537756.2_5'Flank	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	495					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	TAGCCCAGCTGGAGGCTGTCA	0.483																																						uc001oog.4																			0				NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						c.(1483-1485)Cag>Tag		Homo sapiens carnitine palmitoyltransferase 1A (liver) (CPT1A), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	L-Carnitine(DB00583)|Perhexiline(DB01074)						128.0	113.0	118.0					11																	68542876		2200	4294	6494	SO:0001587	stop_gained	1374				carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity	g.chr11:68542876G>A	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.1483C>T	11.37:g.68542876G>A	ENSP00000265641:p.Gln495*					CPT1A_uc001oof.4_Nonsense_Mutation_p.Q495*	p.Q495*	NM_001876	NP_001867	P50416	CPT1A_HUMAN	LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		12	1653	-	Esophageal squamous(3;3.28e-14)		495					Q8TCU0|Q9BWK0	Nonsense_Mutation	SNP	ENST00000265641.5	37	c.1483C>T	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.660375	0.88154	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	.	.	.	5.12	4.14	0.48551	.	0.252005	0.40469	N	0.001095	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	12.999	0.58664	0.0:0.3499:0.6501:0.0	.	.	.	.	X	495	.	ENSP00000265641:Q495X	Q	-	1	0	CPT1A	68299452	0.948000	0.32251	0.989000	0.46669	0.362000	0.29581	2.300000	0.43620	2.550000	0.86006	0.478000	0.44815	CAG		0.483	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		51	84	0	0	0	1	0	51	84				
DMXL1	1657	broad.mit.edu	37	5	118506611	118506611	+	Missense_Mutation	SNP	G	G	T			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr5:118506611G>T	ENST00000311085.8	+	24	6205	c.6125G>T	c.(6124-6126)cGt>cTt	p.R2042L	DMXL1_ENST00000539542.1_Missense_Mutation_p.R2042L	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2042										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GTAGAACTTCGTACTTTATCT	0.358																																						uc010jcl.1																			0				breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86						c.(6124-6126)cGt>cTt		Homo sapiens Dmx-like 1 (DMXL1), mRNA.							59.0	62.0	61.0					5																	118506611		2202	4300	6502	SO:0001583	missense	1657							g.chr5:118506611G>T	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.6125G>T	5.37:g.118506611G>T	ENSP00000309690:p.Arg2042Leu					DMXL1_uc003ksd.2_Missense_Mutation_p.R2042L|DMXL1_uc021ycw.1_Missense_Mutation_p.R1869L	p.R2042L	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)	23	6306	+		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)	2042						Missense_Mutation	SNP	ENST00000311085.8	37	c.6125G>T	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.413557	0.83449	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.78126	-1.15;-1.15	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.88687	0.6504	M	0.79258	2.445	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.78314	0.991;0.967	D	0.89343	0.3655	10	0.66056	D	0.02	-15.5055	19.3932	0.94594	0.0:0.0:1.0:0.0	.	2042;2042	F5H269;Q9Y485	.;DMXL1_HUMAN	L	2042	ENSP00000309690:R2042L;ENSP00000439479:R2042L	ENSP00000309690:R2042L	R	+	2	0	DMXL1	118534510	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.577000	0.86979	0.557000	0.71058	CGT		0.358	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		43	46	0	0	0	1	0	43	46				
PCDHB6	56130	broad.mit.edu	37	5	140531054	140531054	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr5:140531054G>A	ENST00000231136.1	+	1	1216	c.1216G>A	c.(1216-1218)Gcg>Acg	p.A406T	PCDHB6_ENST00000543635.1_Missense_Mutation_p.A270T	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	406	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACAGAAGGCGCGCTGGACAG	0.483																																						uc003lir.3																			0		p.G405G(1)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84						c.(1216-1218)Gcg>Acg		Homo sapiens protocadherin beta 6 (PCDHB6), mRNA.							112.0	114.0	114.0					5																	140531054		2203	4300	6503	SO:0001583	missense	56130				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding	g.chr5:140531054G>A	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1216G>A	5.37:g.140531054G>A	ENSP00000231136:p.Ala406Thr						p.A406T	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		0	1216	+			406			Cadherin 4.		B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	c.1216G>A	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	2.570	-0.299858	0.05532	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.02682	4.2;4.2	4.59	-1.37	0.09056	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.03136	0.0092	L	0.41079	1.255	0.09310	N	1	B	0.25521	0.128	B	0.21917	0.037	T	0.36601	-0.9741	9	0.42905	T	0.14	.	11.1183	0.48273	0.0:0.4571:0.3088:0.2341	.	406	Q9Y5E3	PCDB6_HUMAN	T	270;406;191	ENSP00000438466:A270T;ENSP00000231136:A406T	ENSP00000231136:A406T	A	+	1	0	PCDHB6	140511238	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.879000	0.00716	-0.570000	0.06022	0.561000	0.74099	GCG		0.483	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		15	161	0	0	0	1	0	15	161				
TLR3	7098	broad.mit.edu	37	4	187000075	187000075	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr4:187000075G>C	ENST00000296795.3	+	3	627	c.523G>C	c.(523-525)Gag>Cag	p.E175Q	TLR3_ENST00000504367.1_5'Flank	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	175					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		AAATCTCCAAGAGCTTCTATT	0.313																																						uc003iyq.3																			0				breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29						c.(523-525)Gag>Cag		Homo sapiens toll-like receptor 3 (TLR3), mRNA.							41.0	47.0	45.0					4																	187000075		2202	4299	6501	SO:0001583	missense	7098				I-kappaB phosphorylation|MyD88-independent toll-like receptor signaling pathway|activation of NF-kappaB-inducing kinase activity|cellular response to mechanical stimulus|defense response to bacterium|defense response to virus|detection of virus|hyperosmotic response|inflammatory response|innate immune response|negative regulation of osteoclast differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of chemokine production|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|toll-like receptor 3 signaling pathway	endoplasmic reticulum membrane|endosome membrane|integral to plasma membrane	double-stranded RNA binding|transmembrane receptor activity	g.chr4:187000075G>C	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"""CD molecules"""	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.523G>C	4.37:g.187000075G>C	ENSP00000296795:p.Glu175Gln					TLR3_uc011ckz.2_5'Flank	p.E175Q	NM_003265	NP_003256	O15455	TLR3_HUMAN		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)	2	624	+		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)	175					B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	37	c.523G>C	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.616723	0.66672	.	.	ENSG00000164342	ENST00000296795;ENST00000513189;ENST00000542020	T;T	0.59638	0.31;0.25	5.48	4.59	0.56863	.	0.370309	0.34156	N	0.004210	T	0.48768	0.1518	L	0.45137	1.4	0.80722	D	1	P	0.39282	0.666	B	0.33799	0.17	T	0.56811	-0.7917	10	0.56958	D	0.05	.	15.736	0.77842	0.0:0.1366:0.8634:0.0	.	175	O15455	TLR3_HUMAN	Q	175	ENSP00000296795:E175Q;ENSP00000423386:E175Q	ENSP00000296795:E175Q	E	+	1	0	TLR3	187237069	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.201000	0.51059	2.573000	0.86826	0.650000	0.86243	GAG		0.313	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			23	30	0	0	0	1	0	23	30				
PEG3	5178	broad.mit.edu	37	19	57326078	57326078	+	Missense_Mutation	SNP	C	C	A			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr19:57326078C>A	ENST00000326441.9	-	10	4095	c.3732G>T	c.(3730-3732)atG>atT	p.M1244I	ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.M1244I|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.M1118I|PEG3_ENST00000598410.1_Missense_Mutation_p.M1120I|ZIM2_ENST00000221722.5_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1244					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TATGAAGTCTCATATGCTCAT	0.498																																						uc002qnu.2																			0				NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170						c.(3730-3732)atG>atT		Homo sapiens paternally expressed 3 (PEG3), transcript variant 4, mRNA.							51.0	46.0	48.0					19																	57326078		2203	4300	6503	SO:0001583	missense	5178				apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:57326078C>A	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3732G>T	19.37:g.57326078C>A	ENSP00000326581:p.Met1244Ile					PEG3_uc010ygr.1_Intron|PEG3_uc010ygq.1_Intron|PEG3_uc002qnr.2_Intron|PEG3_uc010etp.2_Intron|PEG3_uc010ygs.1_Intron|PEG3_uc002qnq.2_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.M1215I|PEG3_uc002qnv.2_Missense_Mutation_p.M1244I|PEG3_uc002qnw.2_Missense_Mutation_p.M1120I|PEG3_uc002qnx.2_Missense_Mutation_p.M1118I|PEG3_uc010etr.2_Missense_Mutation_p.M1244I	p.M1244I	NM_001146186	NP_001139657	Q9GZU2	PEG3_HUMAN		GBM - Glioblastoma multiforme(193;0.0269)	6	4083	-		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)	1244					A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	c.3732G>T	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694189	0.48202	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.28255	1.62;1.62	4.06	1.87	0.25490	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.358389	0.24388	N	0.038942	T	0.32010	0.0815	L	0.46885	1.475	.	.	.	B;P;P	0.49307	0.149;0.856;0.922	B;P;P	0.46718	0.103;0.525;0.525	T	0.51639	-0.8680	9	0.56958	D	0.05	-6.8134	12.3223	0.54991	0.0:0.6501:0.3499:0.0	.	1120;1244;1179	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	I	1244	ENSP00000326581:M1244I;ENSP00000403051:M1244I	ENSP00000326581:M1244I	M	-	3	0	ZIM2	62017890	0.000000	0.05858	0.002000	0.10522	0.887000	0.51463	0.755000	0.26405	0.646000	0.30693	0.655000	0.94253	ATG		0.498	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			11	81	0	0	0	1	0	11	81				
HSD17B3	3293	broad.mit.edu	37	9	99017173	99017173	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr9:99017173A>G	ENST00000375263.3	-	3	301	c.254T>C	c.(253-255)cTa>cCa	p.L85P	HSD17B3_ENST00000375262.2_Missense_Mutation_p.L85P|RNU6-1160P_ENST00000384546.1_RNA	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	85					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				AATGGCCTCTAGTTTTTCCAG	0.512																																						uc004awa.1																			0				breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13						c.(253-255)cTa>cCa		Homo sapiens hydroxysteroid (17-beta) dehydrogenase 3 (HSD17B3), mRNA.	NADH(DB00157)						123.0	91.0	102.0					9																	99017173		2203	4300	6503	SO:0001583	missense	3293				androgen biosynthetic process|male genitalia development	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity	g.chr9:99017173A>G		CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5212	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 2"""	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.254T>C	9.37:g.99017173A>G	ENSP00000364412:p.Leu85Pro					HSD17B3_uc010msc.1_Missense_Mutation_p.L85P	p.L85P	NM_000197	NP_000188	P37058	DHB3_HUMAN			2	302	-		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)	85					Q5U0Q6	Missense_Mutation	SNP	ENST00000375263.3	37	c.254T>C	CCDS6716.1	.	.	.	.	.	.	.	.	.	.	A	12.86	2.065518	0.36470	.	.	ENSG00000130948	ENST00000375263;ENST00000375262	D;D	0.94931	-3.56;-2.38	4.79	4.79	0.61399	NAD(P)-binding domain (1);	0.184069	0.38005	N	0.001842	D	0.98033	0.9352	H	0.97540	4.025	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.974;0.995	D	0.98463	1.0597	10	0.72032	D	0.01	-17.9462	10.9088	0.47097	1.0:0.0:0.0:0.0	.	85;85	Q5U0Q6;P37058	.;DHB3_HUMAN	P	85	ENSP00000364412:L85P;ENSP00000364411:L85P	ENSP00000364411:L85P	L	-	2	0	HSD17B3	98056994	1.000000	0.71417	0.819000	0.32651	0.085000	0.17905	5.435000	0.66532	2.147000	0.66899	0.533000	0.62120	CTA		0.512	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197		16	26	0	0	0	1	0	16	26				
GAK	2580	broad.mit.edu	37	4	890299	890299	+	Silent	SNP	T	T	C			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr4:890299T>C	ENST00000314167.4	-	7	800	c.690A>G	c.(688-690)gaA>gaG	p.E230E	GAK_ENST00000511163.1_Silent_p.E151E	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		AGTCTATGATTTCTGGTGTTC	0.453																																						uc003gbm.4																			0				autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39						c.(688-690)gaA>gaG		Homo sapiens cyclin G associated kinase (GAK), mRNA.							150.0	129.0	136.0					4																	890299		2203	4300	6503	SO:0001819	synonymous_variant	2580				cell cycle	Golgi apparatus|focal adhesion|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity	g.chr4:890299T>C	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.690A>G	4.37:g.890299T>C						GAK_uc003gbn.4_Silent_p.E151E|GAK_uc010ibk.1_Silent_p.E124E|GAK_uc003gbl.4_Silent_p.E94E	p.E230E	NM_005255	NP_005246	O14976	GAK_HUMAN		Colorectal(103;0.219)	6	889	-			230			Protein kinase.		Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	c.690A>G	CCDS3340.1																																																																																				0.453	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		11	59	0	0	0	1	0	11	59				
ZG16B	124220	broad.mit.edu	37	16	2880459	2880459	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr16:2880459C>T	ENST00000382280.3	+	2	204	c.125C>T	c.(124-126)aCg>aTg	p.T42M	ZG16B_ENST00000572863.1_Missense_Mutation_p.T12M	NM_145252.2	NP_660295.2	Q96DA0	ZG16B_HUMAN	zymogen granule protein 16B	42	Poly-Leu.				retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|lung(2)|ovary(1)|prostate(1)	5						CTGCTGCTCACGCTTGCCCTC	0.662																																						uc002cru.3																			0				central_nervous_system(1)|lung(2)|ovary(1)|prostate(1)	5						c.(124-126)aCg>aTg		Homo sapiens zymogen granule protein 16 homolog B (rat) (ZG16B), mRNA.							20.0	25.0	23.0					16																	2880459		2073	4213	6286	SO:0001583	missense	124220					extracellular region	sugar binding	g.chr16:2880459C>T	BC009722	CCDS10479.2	16p13.3	2014-02-12	2012-12-07		ENSG00000162078	ENSG00000162078			30456	protein-coding gene	gene with protein product	"""jacalin-like lectin domain containing 2"""		"""zymogen granule protein 16 homolog B (rat)"""			12477932	Standard	NM_145252		Approved	HRPE773, PRO1567, JCLN2	uc002cru.3	Q96DA0	OTTHUMG00000128933	ENST00000382280.3:c.125C>T	16.37:g.2880459C>T	ENSP00000371715:p.Thr42Met						p.T42M	NM_145252	NP_660295	Q96DA0	ZG16B_HUMAN			1	201	+			42			Poly-Leu.		A6NIY1|B2R4F6|Q6UW28	Missense_Mutation	SNP	ENST00000382280.3	37	c.125C>T	CCDS10479.2	.	.	.	.	.	.	.	.	.	.	c	14.77	2.634807	0.47049	.	.	ENSG00000162078	ENST00000382280	T	0.35605	1.3	3.11	2.15	0.27550	.	.	.	.	.	T	0.45617	0.1351	L	0.43923	1.385	0.21473	N	0.999671	D	0.89917	1.0	D	0.71870	0.975	T	0.15896	-1.0421	9	0.56958	D	0.05	-25.0543	5.9001	0.18962	0.0:0.856:0.0:0.144	.	42	Q96DA0	ZG16B_HUMAN	M	42	ENSP00000371715:T42M	ENSP00000371715:T42M	T	+	2	0	ZG16B	2820460	0.000000	0.05858	0.781000	0.31783	0.089000	0.18198	0.312000	0.19397	0.880000	0.35969	0.556000	0.70494	ACG		0.662	ZG16B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250912.1	NM_145252		7	5	0	0	0	1	0	7	5				
MYLK	4638	broad.mit.edu	37	3	123345699	123345699	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr3:123345699C>T	ENST00000475616.1	-	28	5203	c.5204G>A	c.(5203-5205)cGg>cAg	p.R1735Q	MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000360304.3_Missense_Mutation_p.R1735Q|MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000346322.5_Missense_Mutation_p.R1666Q|MYLK-AS1_ENST00000463408.1_RNA|MYLK_ENST00000354792.5_Missense_Mutation_p.R535Q|MYLK_ENST00000418370.2_5'Flank|MYLK_ENST00000360772.3_Missense_Mutation_p.R1684Q|MYLK_ENST00000359169.1_Missense_Mutation_p.R1684Q			Q15746	MYLK_HUMAN	myosin light chain kinase	1735	Calmodulin-binding.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CTTCTTCATCCGGTCCTTGGA	0.493																																						uc003ego.3																			0				NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113						c.(5203-5205)cGg>cAg		Homo sapiens myosin light chain kinase (MYLK), transcript variant 1, mRNA.							196.0	144.0	162.0					3																	123345699		2203	4300	6503	SO:0001583	missense	4638				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	ATP binding|actin binding|calmodulin binding|metal ion binding|myosin light chain kinase activity	g.chr3:123345699C>T	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.5204G>A	3.37:g.123345699C>T	ENSP00000418335:p.Arg1735Gln					MYLK-AS1_uc003egk.3_Intron|MYLK_uc010hrr.3_Missense_Mutation_p.R170Q|MYLK_uc011bjv.2_Missense_Mutation_p.R535Q|MYLK_uc011bjw.2_Missense_Mutation_p.R1735Q|MYLK_uc003egp.3_Missense_Mutation_p.R1666Q|MYLK_uc003egq.3_Missense_Mutation_p.R1684Q|MYLK_uc003egr.3_Missense_Mutation_p.R1615Q|MYLK_uc003egs.3_Missense_Mutation_p.R1559Q	p.R1735Q	NM_053025	NP_444253	Q15746	MYLK_HUMAN		GBM - Glioblastoma multiforme(114;0.0736)	30	5486	-		Lung NSC(201;0.0496)	1735			Calmodulin-binding.		B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	c.5204G>A	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	36	5.663878	0.96745	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T	0.66280	-0.14;-0.2;-0.14;-0.19;0.05;-0.2	5.22	5.22	0.72569	Protein kinase-like domain (1);	.	.	.	.	T	0.75302	0.3831	L	0.47190	1.495	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.998;0.979;0.998;0.997	T	0.76677	-0.2871	9	0.72032	D	0.01	.	18.9654	0.92694	0.0:1.0:0.0:0.0	.	1735;1615;1684;1666;1735	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	Q	1684;1735;1684;1666;535;1735	ENSP00000354004:R1684Q;ENSP00000353452:R1735Q;ENSP00000352088:R1684Q;ENSP00000320622:R1666Q;ENSP00000346846:R535Q;ENSP00000418335:R1735Q	ENSP00000320622:R1666Q	R	-	2	0	MYLK	124828389	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.339000	0.79282	2.732000	0.93576	0.591000	0.81541	CGG		0.493	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		13	105	0	0	0	1	0	13	105				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333	NP_004324	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		48	72	0	0	0	1	0	48	72				
TRIM47	91107	broad.mit.edu	37	17	73870808	73870808	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr17:73870808G>A	ENST00000254816.2	-	6	1699	c.1673C>T	c.(1672-1674)gCc>gTc	p.A558V	TRIM47_ENST00000587339.1_Missense_Mutation_p.A320V|RP11-552F3.9_ENST00000586076.1_RNA	NM_033452.2	NP_258411.2	Q96LD4	TRI47_HUMAN	tripartite motif containing 47	558	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22			Epithelial(20;4.23e-06)|all cancers(21;5.24e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			GAAGGCCAAGGCACGGTCAGC	0.667																																						uc002jpw.3																			0		p.R557C(1)		autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22						c.(1672-1674)gCc>gTc		Homo sapiens tripartite motif containing 47 (TRIM47), mRNA.							35.0	42.0	40.0					17																	73870808		2203	4300	6503	SO:0001583	missense	91107					cytoplasm|nucleus	zinc ion binding	g.chr17:73870808G>A	AY026763	CCDS32737.1	17q25	2013-01-09	2011-01-25			ENSG00000132481		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19020	protein-coding gene	gene with protein product		611041	"""tripartite motif-containing 47"""				Standard	NM_033452		Approved	GOA, RNF100	uc002jpw.3	Q96LD4		ENST00000254816.2:c.1673C>T	17.37:g.73870808G>A	ENSP00000254816:p.Ala558Val					TRIM47_uc002jpv.3_Missense_Mutation_p.A320V	p.A558V	NM_033452	NP_258411	Q96LD4	TRI47_HUMAN	Epithelial(20;4.23e-06)|all cancers(21;5.24e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)		5	1700	-			558			B30.2/SPRY.		Q96AD0|Q96GU5|Q9BRN7	Missense_Mutation	SNP	ENST00000254816.2	37	c.1673C>T	CCDS32737.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.647054	0.29246	.	.	ENSG00000132481	ENST00000254816	T	0.68903	-0.36	5.18	5.18	0.71444	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000009	T	0.36771	0.0979	N	0.01729	-0.75	0.20873	N	0.999835	B	0.25850	0.136	B	0.27608	0.081	T	0.13791	-1.0496	10	0.02654	T	1	.	14.3104	0.66413	0.0:0.1484:0.8516:0.0	.	558	Q96LD4	TRI47_HUMAN	V	558	ENSP00000254816:A558V	ENSP00000254816:A558V	A	-	2	0	TRIM47	71382403	0.256000	0.24012	0.996000	0.52242	0.092000	0.18411	3.069000	0.50026	2.426000	0.82243	0.561000	0.74099	GCC		0.667	TRIM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448934.1			33	56	0	0	0	1	0	33	56				
RB1	5925	broad.mit.edu	37	13	49039407	49039407	+	Missense_Mutation	SNP	C	C	T	rs187912365	byFrequency	TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr13:49039407C>T	ENST00000267163.4	+	23	2530	c.2392C>T	c.(2392-2394)Cgg>Tgg	p.R798W		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	798	Domain C; mediates interaction with E4F1.|Interaction with LIMD1.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)|p.R798fs*17(1)|p.R798W(1)|p.L797fs*1(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TTCACCCTTACGGATTCCTGG	0.408		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			C|||	4	0.000798722	0.0	0.0043	5008	,	,		14619	0.0		0.001	False		,,,				2504	0.0					uc001vcb.3		6	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	"""D, Mis, N, F, S"""	retinoblastoma gene			"""L, E, M, O"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""		29	Whole gene deletion(15)|Unknown(11)|Substitution - Missense(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	p.0?(15)|p.?(11)|p.R798fs*17(2)|p.R798W(2)|p.L797fs*1(2)	bone(11)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|eye(2)|ovary(2)|adrenal_gland(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496						c.(2392-2394)Cgg>Tgg		Homo sapiens retinoblastoma 1 (RB1), mRNA.	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	128.0	130.0	129.0		2392	4.1	1.0	13		129	0,8600		0,0,4300	yes	missense	RB1	NM_000321.2	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	798/929	49039407	1,13005	2203	4300	6503	SO:0001583	missense	5925	Hereditary Retinoblastoma	Familial Cancer Database		G1 phase of mitotic cell cycle|Ras protein signal transduction|S phase of mitotic cell cycle|androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of S phase of mitotic cell cycle|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|sister chromatid biorientation	PML body|Rb-E2F complex|SWI/SNF complex|chromatin	DNA binding|androgen receptor binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	g.chr13:49039407C>T	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2392C>T	13.37:g.49039407C>T	ENSP00000267163:p.Arg798Trp	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)					p.R798W	NM_000321	NP_000312	P06400	RB_HUMAN		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	22	2558	+		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)	798			Domain C; mediates interaction with E4F1.|Interaction with LIMD1.		A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	c.2392C>T	CCDS31973.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	C	21.0	4.075938	0.76415	2.27E-4	0.0	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.85955	-2.05	5.87	4.1	0.47936	Rb C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87144	0.6104	L	0.54323	1.7	0.52501	D	0.999954	D	0.89917	1.0	D	0.91635	0.999	D	0.88501	0.3082	10	0.87932	D	0	.	13.9886	0.64350	0.3981:0.6019:0.0:0.0	.	798	P06400	RB_HUMAN	W	777;798	ENSP00000267163:R798W	ENSP00000267163:R798W	R	+	1	2	RB1	47937408	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	4.350000	0.59392	0.780000	0.33566	0.591000	0.81541	CGG		0.408	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			24	161	0	0	0	1	0	24	161				
F9	2158	broad.mit.edu	37	X	138633271	138633271	+	Missense_Mutation	SNP	C	C	A	rs137852237		TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chrX:138633271C>A	ENST00000218099.2	+	6	578	c.571C>A	c.(571-573)Cgt>Agt	p.R191S	F9_ENST00000394090.2_Missense_Mutation_p.R153S	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	191		Cleavage; by factor XIa.	R -> C (in HEMB; moderate; Albuquerque, Cardiff-1, etc.). {ECO:0000269|PubMed:2775660}.|R -> H (in HEMB; moderate; Chapel-Hill, Chicago-2, etc.). {ECO:0000269|PubMed:6603618, ECO:0000269|PubMed:8076946}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	TAAGCTCACCCGTGCTGAGAC	0.358																																						uc004fas.1																			0				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	GRCh37	CM940536|CM940537	F9	M	rs137852237	c.(571-573)Cgt>Agt		Homo sapiens coagulation factor IX (F9), mRNA.	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)						109.0	97.0	101.0					X																	138633271		2203	4300	6503	SO:0001583	missense	2158				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	Golgi lumen|endoplasmic reticulum lumen|extracellular region|plasma membrane	calcium ion binding|serine-type endopeptidase activity	g.chrX:138633271C>A	M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"""Factor IX"", ""plasma thromboplastic component"", ""Christmas disease"", ""hemophilia B"""	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.571C>A	X.37:g.138633271C>A	ENSP00000218099:p.Arg191Ser					F9_uc004fat.1_Missense_Mutation_p.R153S	p.R191S	NM_000133	NP_000124	P00740	FA9_HUMAN			5	600	+	Acute lymphoblastic leukemia(192;0.000127)		191		R -> C (in HEMB; moderate; Albuquerque, Cardiff-1, etc.).|R -> H (in HEMB; moderate; Chapel-Hill, Chicago-2, etc.).		Cleavage; by factor XIa.	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Missense_Mutation	SNP	ENST00000218099.2	37	c.571C>A	CCDS14666.1	.	.	.	.	.	.	.	.	.	.	C	9.875	1.199980	0.22121	.	.	ENSG00000101981	ENST00000218099;ENST00000394090	D;D	0.93426	-3.22;-3.22	4.94	4.04	0.47022	.	0.411574	0.25250	N	0.032021	D	0.93035	0.7783	L	0.39397	1.21	0.36570	D	0.872959	D;P	0.64830	0.994;0.73	P;B	0.62491	0.903;0.107	D	0.91321	0.5082	10	0.22706	T	0.39	.	10.5255	0.44945	0.3505:0.6495:0.0:0.0	.	153;191	Q5FBE1;P00740	.;FA9_HUMAN	S	191;153	ENSP00000218099:R191S;ENSP00000377650:R153S	ENSP00000218099:R191S	R	+	1	0	F9	138460937	0.991000	0.36638	0.198000	0.23420	0.158000	0.22134	2.008000	0.40893	0.823000	0.34589	0.529000	0.55759	CGT		0.358	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1			12	126	0	0	0	1	0	12	126				
PNMA3	29944	broad.mit.edu	37	X	152225805	152225805	+	Silent	SNP	G	G	A			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chrX:152225805G>A	ENST00000370264.4	+	1	419	c.393G>A	c.(391-393)tcG>tcA	p.S131S	PNMA3_ENST00000370265.4_Silent_p.S131S|PNMA3_ENST00000447306.1_Silent_p.S131S			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	131					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					ccaattgttcggctccaagag	0.532													G|||	1	0.000264901	0.0	0.0	3775	,	,		13137	0.0		0.0	False		,,,				2504	0.001					uc004fhc.2																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16						c.(391-393)tcG>tcA		Homo sapiens paraneoplastic antigen MA3 (PNMA3), mRNA.							41.0	42.0	42.0					X																	152225805		2203	4300	6503	SO:0001819	synonymous_variant	29944				apoptosis	nucleolus	nucleic acid binding|zinc ion binding	g.chrX:152225805G>A	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"""Paraneoplastic Ma antigens"""	18742	protein-coding gene	gene with protein product	"""paraneoplastic cancer-testis-brain antigen"""	300675	"""paraneoplastic antigen MA3"""			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.393G>A	X.37:g.152225805G>A						PNMA3_uc022cho.1_Silent_p.S131S|PNMA3_uc004fhd.3_5'Flank	p.S131S	NM_013364	NP_037496	Q9UL41	PNMA3_HUMAN			1	729	+	Acute lymphoblastic leukemia(192;6.56e-05)		131					D3DWT7|Q9H0A4	Silent	SNP	ENST00000370264.4	37	c.393G>A	CCDS35435.2																																																																																				0.532	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364		20	73	0	0	0	1	0	20	73				
TNRC18	84629	broad.mit.edu	37	7	5401259	5401259	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DJ-A3V7-01A-11D-A23M-08	TCGA-DJ-A3V7-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c210339e-a61d-42e4-9dba-b78b2dd6a036	d3920478-36c0-454d-8847-4652bdd83241	g.chr7:5401259delG	ENST00000430969.1	-	14	4975	c.4627delC	c.(4627-4629)cgcfs	p.R1543fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.R1543fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1543							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCTCTCTTGCGGGGGGGCGAC	0.692																																						uc003soi.4																			0				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11						c.(4627-4629)cgcfs		Homo sapiens trinucleotide repeat containing 18 (TNRC18), mRNA.				32,3150		10,12,1569						3.9	1.0			15	35,6719		7,21,3349	no	frameshift	TNRC18	NM_001080495.2		17,33,4918	A1A1,A1R,RR		0.5182,1.0057,0.6743				67,9869				SO:0001589	frameshift_variant	84629						DNA binding	g.chr7:5401259delG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4627delC	7.37:g.5401259delG	ENSP00000395538:p.Arg1543fs						p.R1543fs	NM_001080495	NP_001073964	O15417	TNC18_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)	13	4976	-		Ovarian(82;0.142)	1543					A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	37	c.4627delC	CCDS47534.1																																																																																				0.692	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				2	4						2	4	---	---	---	---
