#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
YWHAG	7532	broad.mit.edu	37	7	75959220	75959220	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr7:75959220C>A	ENST00000307630.3	-	2	640	c.418G>T	c.(418-420)Gga>Tga	p.G140*		NM_012479.3	NP_036611.2	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma	140					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of neuron differentiation (GO:0045664)|regulation of signal transduction (GO:0009966)|regulation of synaptic plasticity (GO:0048167)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	insulin-like growth factor receptor binding (GO:0005159)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)|protein kinase C inhibitor activity (GO:0008426)			endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8						CTTTTCTCTCCGGTGGCCACT	0.562																																						uc011kgj.1																			0				endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8						c.(418-420)Gga>Tga		Homo sapiens tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide (YWHAG), mRNA.							137.0	137.0	137.0					7																	75959220		2203	4300	6503	SO:0001587	stop_gained	7532				G2/M transition of mitotic cell cycle|regulation of neuron differentiation|regulation of signal transduction|regulation of synaptic plasticity	cytosol	insulin-like growth factor receptor binding|protein kinase C binding|protein kinase C inhibitor activity	g.chr7:75959220C>A	AF142498	CCDS5584.1	7q11.23	2014-06-13	2013-12-03		ENSG00000170027	ENSG00000170027			12852	protein-coding gene	gene with protein product	"""14-3-3 gamma"", ""protein phosphatase 1, regulatory subunit 170"""	605356	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"""			10486217, 10433554	Standard	NM_012479		Approved	PPP1R170	uc011kgj.1	P61981	OTTHUMG00000022862	ENST00000307630.3:c.418G>T	7.37:g.75959220C>A	ENSP00000306330:p.Gly140*						p.G140*	NM_012479	NP_036611	P61981	1433G_HUMAN			1	635	-			140					O70457|P35214|Q6FH52|Q9UDP2|Q9UN99	Nonsense_Mutation	SNP	ENST00000307630.3	37	c.418G>T	CCDS5584.1	.	.	.	.	.	.	.	.	.	.	C	37	6.109776	0.97291	.	.	ENSG00000170027	ENST00000307630;ENST00000536755;ENST00000453207	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.2853	0.90112	0.0:1.0:0.0:0.0	.	.	.	.	X	140;118;100	.	ENSP00000306330:G140X	G	-	1	0	YWHAG	75797156	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	7.616000	0.83018	2.793000	0.96121	0.650000	0.86243	GGA		0.562	YWHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253002.1	NM_012479		7	143	0	0	0	1	0	7	143				
RPAP3	79657	broad.mit.edu	37	12	48091473	48091473	+	Silent	SNP	G	G	A	rs150350108		TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr12:48091473G>A	ENST00000005386.3	-	4	439	c.324C>T	c.(322-324)gaC>gaT	p.D108D	RPAP3_ENST00000432584.3_De_novo_Start_OutOfFrame|RPAP3_ENST00000380650.4_Silent_p.D108D	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	108										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					GGGTACTATCGTCTTTGTCAA	0.353																																						uc001rpr.3																			0				endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16						c.(322-324)gaC>gaT		Homo sapiens RNA polymerase II associated protein 3 (RPAP3), transcript variant 1, mRNA.							104.0	104.0	104.0					12																	48091473		2203	4300	6503	SO:0001819	synonymous_variant	79657						binding	g.chr12:48091473G>A	AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"""Tetratricopeptide (TTC) repeat domain containing"""	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.324C>T	12.37:g.48091473G>A						RPAP3_uc010slk.2_5'UTR|RPAP3_uc001rps.3_Silent_p.D108D	p.D108D	NM_024604	NP_001139548	Q9H6T3	RPAP3_HUMAN			3	440	-	Lung SC(27;0.192)		108					B4DRW9|Q6PHR5	Silent	SNP	ENST00000005386.3	37	c.324C>T	CCDS8753.1																																																																																				0.353	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604		8	99	0	0	0	1	0	8	99				
AP3M1	26985	broad.mit.edu	37	10	75883629	75883629	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr10:75883629T>C	ENST00000355264.4	-	9	1507	c.1196A>G	c.(1195-1197)tAt>tGt	p.Y399C	AP3M1_ENST00000372745.1_Missense_Mutation_p.Y399C|RP11-178G16.5_ENST00000599110.1_lincRNA	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	399	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|protein targeting to lysosome (GO:0006622)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	Rab GTPase binding (GO:0017137)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	13	Prostate(51;0.0112)					AAATGGCTTATATTTCTCCCC	0.363																																						uc001jwf.3																			0				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	13						c.(1195-1197)tAt>tGt		Homo sapiens adaptor-related protein complex 3, mu 1 subunit (AP3M1), transcript variant 1, mRNA.							206.0	188.0	194.0					10																	75883629		2203	4300	6503	SO:0001583	missense	26985				protein targeting to lysosome|vesicle-mediated transport	Golgi apparatus|clathrin adaptor complex|lysosome	protein binding	g.chr10:75883629T>C	AF092092	CCDS7342.1	10q22.1-q22.3	2008-07-07			ENSG00000185009	ENSG00000185009			569	protein-coding gene	gene with protein product		610366				10024875	Standard	NM_207012		Approved		uc001jwh.3	Q9Y2T2	OTTHUMG00000018497	ENST00000355264.4:c.1196A>G	10.37:g.75883629T>C	ENSP00000347408:p.Tyr399Cys					AP3M1_uc001jwg.3_Missense_Mutation_p.Y399C|AP3M1_uc001jwh.3_Missense_Mutation_p.Y399C|AP3M1_uc010qla.2_Missense_Mutation_p.Y345C	p.Y399C	NM_207012	NP_996895	Q9Y2T2	AP3M1_HUMAN			8	1626	-	Prostate(51;0.0112)		399			MHD.		Q5JQ12|Q9H5L2	Missense_Mutation	SNP	ENST00000355264.4	37	c.1196A>G	CCDS7342.1	.	.	.	.	.	.	.	.	.	.	T	19.42	3.823571	0.71143	.	.	ENSG00000185009	ENST00000355264;ENST00000372745	T;T	0.23552	1.9;1.9	5.8	4.63	0.57726	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.59390	0.2190	M	0.93854	3.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.992;0.995	T	0.70124	-0.4958	10	0.87932	D	0	-7.5238	12.3787	0.55295	0.1257:0.0:0.0:0.8742	.	345;399	B4DRN6;Q9Y2T2	.;AP3M1_HUMAN	C	399	ENSP00000347408:Y399C;ENSP00000361831:Y399C	ENSP00000347408:Y399C	Y	-	2	0	AP3M1	75553635	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.915000	0.69973	2.216000	0.71823	0.533000	0.62120	TAT		0.363	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048747.1			9	189	0	0	0	1	0	9	189				
C19orf44	84167	broad.mit.edu	37	19	16614022	16614022	+	Silent	SNP	C	C	T	rs138964724	byFrequency	TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr19:16614022C>T	ENST00000221671.3	+	3	1062	c.906C>T	c.(904-906)caC>caT	p.H302H	C19orf44_ENST00000594035.1_Silent_p.H302H|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	302										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						CACAGAGTCACGTTTCCAGTG	0.547													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17196	0.0		0.0	False		,,,				2504	0.0					uc002neh.1																			0				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						c.(904-906)caC>caT		Homo sapiens chromosome 19 open reading frame 44 (C19orf44), mRNA.		C		14,4392	22.3+/-47.3	0,14,2189	111.0	103.0	106.0		906	-1.5	0.0	19	dbSNP_134	106	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	C19orf44	NM_032207.2		0,14,6489	TT,TC,CC		0.0,0.3177,0.1076		302/658	16614022	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	84167							g.chr19:16614022C>T	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.906C>T	19.37:g.16614022C>T						MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_Silent_p.H302H|C19orf44_uc002neg.3_Silent_p.H302H|C19orf44_uc010eai.1_Non-coding_Transcript	p.H302H	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN			2	979	+			302					Q8N6Y7	Silent	SNP	ENST00000221671.3	37	c.906C>T	CCDS12345.1																																																																																				0.547	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		6	90	0	0	0	1	0	6	90				
CDPF1	150383	broad.mit.edu	37	22	46643010	46643010	+	Silent	SNP	G	G	A			TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr22:46643010G>A	ENST00000314567.3	-	3	645	c.222C>T	c.(220-222)ggC>ggT	p.G74G	CDPF1_ENST00000404583.1_Intron|CDPF1_ENST00000475605.1_Intron|CDPF1_ENST00000404744.1_Silent_p.G74G	NM_207327.4	NP_997210.3	Q6NVV7	CDPF1_HUMAN	cysteine-rich, DPF motif domain containing 1	74																	TACCCACCGGGCCCACACACA	0.617																																						uc003bhe.3																			0				endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						c.(220-222)ggC>ggT		Homo sapiens chromosome 22 open reading frame 40 (C22orf40), mRNA.							66.0	57.0	60.0					22																	46643010		2203	4300	6503	SO:0001819	synonymous_variant	150383							g.chr22:46643010G>A		CCDS33670.1	22q13.31	2012-07-18	2012-07-18	2012-07-18	ENSG00000205643	ENSG00000205643			33710	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 40"""	C22orf40			Standard	NM_207327		Approved	LOC150383	uc003bhe.3	Q6NVV7	OTTHUMG00000030672	ENST00000314567.3:c.222C>T	22.37:g.46643010G>A						C22orf40_uc003bhf.3_Non-coding_Transcript	p.G74G	NM_207327	NP_997210	Q6NVV7	CV040_HUMAN			2	263	-			74					A6NCA1|A9IU12|A9IU16|Q3ZCR8	Silent	SNP	ENST00000314567.3	37	c.222C>T	CCDS33670.1																																																																																				0.617	CDPF1-001	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075560.4	NM_207327		3	21	0	0	0	1	0	3	21				
HAVCR2	84868	broad.mit.edu	37	5	156533625	156533625	+	Intron	SNP	A	A	C	rs201243732	byFrequency	TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr5:156533625A>C	ENST00000307851.4	-	2	1125				HAVCR2_ENST00000522593.1_Intron|HAVCR2_ENST00000517358.1_5'Flank|CTB-120L21.1_ENST00000517708.1_RNA	NM_032782.4	NP_116171.3	Q8TDQ0	HAVR2_HUMAN	hepatitis A virus cellular receptor 2							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				cervix(1)|large_intestine(4)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATGGCATGCAAATGTCCACTC	0.423													A|||	7	0.00139776	0.0053	0.0	5008	,	,		20973	0.0		0.0	False		,,,				2504	0.0					uc003lwl.3																			0				cervix(1)|large_intestine(4)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22						c.(406-408)tTt>tGt		Homo sapiens hepatitis A virus cellular receptor 2 (HAVCR2), mRNA.		A		16,4390	23.3+/-48.9	0,16,2187	72.0	63.0	66.0			3.2	0.0	5		66	0,8600		0,0,4300	no	intron	HAVCR2	NM_032782.3		0,16,6487	CC,CA,AA		0.0,0.3631,0.123			156533625	16,12990	2203	4300	6503	SO:0001627	intron_variant	84868					integral to membrane		g.chr5:156533625A>C	AK027334	CCDS4333.1	5q34	2014-01-14			ENSG00000135077	ENSG00000135077		"""Immunoglobulin superfamily / V-set domain containing"""	18437	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 3"""	606652				11823861	Standard	NM_032782		Approved	Tim-3, TIM3, FLJ14428, TIMD3	uc003lwk.2	Q8TDQ0	OTTHUMG00000130249	ENST00000307851.4:c.394+12T>G	5.37:g.156533625A>C						HAVCR2_uc003lwk.2_Intron	p.F136C	NM_032782	NP_116171	Q8TDQ0	HAVR2_HUMAN	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		1	661	-	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	0					B2RAY2|Q8WW60|Q96K94	Missense_Mutation	SNP	ENST00000307851.4	37	c.407T>G	CCDS4333.1																																																																																				0.423	HAVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252574.2			3	36	0	0	0	1	0	3	36				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	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		3	74	0	0	0	1	0	3	74				
RPL12P38	645688	broad.mit.edu	37	17	58512596	58512596	+	RNA	SNP	G	G	A			TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr17:58512596G>A	ENST00000588627.1	-	0	761									ribosomal protein L12 pseudogene 38																		TTTTCTGCAGGGCTATTCCCT	0.483																																						uc002iyr.1																			0													Homo sapiens cDNA FLJ33664 fis, clone BRAMY2027451, moderately similar to 60S RIBOSOMAL PROTEIN L12.																																						0							g.chr17:58512596G>A			17q23.2	2013-01-23			ENSG00000213228	ENSG00000213228			36838	pseudogene	pseudogene						19123937	Standard	NG_010298		Approved				OTTHUMG00000157897		17.37:g.58512596G>A														0		-									RNA	SNP	ENST00000588627.1	37	c.762C>T																																																																																					0.483	RPL12P38-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000449464.1	NG_010298		3	55	0	0	0	1	0	3	55				
TMEM161B	153396	broad.mit.edu	37	5	87493539	87493539	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr5:87493539T>C	ENST00000296595.6	-	11	1257	c.1133A>G	c.(1132-1134)tAt>tGt	p.Y378C	TMEM161B_ENST00000512429.1_Missense_Mutation_p.Y367C|TMEM161B_ENST00000514135.1_Missense_Mutation_p.Y378C|TMEM161B_ENST00000511218.1_Missense_Mutation_p.Y169C|TMEM161B_ENST00000506536.1_Intron|TMEM161B_ENST00000515293.1_5'UTR	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	378						integral component of membrane (GO:0016021)				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		AGGCGCCACATACTGCAGTGC	0.423																																						uc003kjc.3																			0				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20						c.(1132-1134)tAt>tGt		Homo sapiens transmembrane protein 161B (TMEM161B), mRNA.							135.0	135.0	135.0					5																	87493539		2203	4300	6503	SO:0001583	missense	153396					integral to membrane		g.chr5:87493539T>C	BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.1133A>G	5.37:g.87493539T>C	ENSP00000296595:p.Tyr378Cys					TMEM161B_uc011cty.2_Missense_Mutation_p.Y367C|TMEM161B_uc010jax.3_Non-coding_Transcript|TMEM161B_uc011ctx.2_Missense_Mutation_p.Y169C	p.Y378C	NM_153354	NP_699185	Q8NDZ6	T161B_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)	10	1258	-		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)	378					Q5CZH7|Q6UWQ6	Missense_Mutation	SNP	ENST00000296595.6	37	c.1133A>G	CCDS4065.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.774543	0.90108	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000511218;ENST00000512429	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.80132	0.4567	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.82579	-0.0387	9	0.87932	D	0	-39.462	16.3839	0.83495	0.0:0.0:0.0:1.0	.	169;378	B7Z6A5;Q8NDZ6	.;T161B_HUMAN	C	378;378;169;367	.	ENSP00000296595:Y378C	Y	-	2	0	TMEM161B	87529295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.258000	0.74832	0.533000	0.62120	TAT		0.423	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354		4	85	0	0	0	1	0	4	85				
ITPR2	3709	broad.mit.edu	37	12	26572040	26572040	+	Missense_Mutation	SNP	G	G	A	rs372121234	byFrequency	TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr12:26572040G>A	ENST00000381340.3	-	50	7468	c.7052C>T	c.(7051-7053)gCg>gTg	p.A2351V	RP11-513G19.1_ENST00000535324.1_RNA	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	2351					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CAGGACATACGCCACGTGATA	0.448													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18574	0.0		0.0	False		,,,				2504	0.0					uc001rhg.3																		ETV6/ITPR2(2)	0		p.V2350M(1)		biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125						c.(7051-7053)gCg>gTg		Homo sapiens inositol 1,4,5-trisphosphate receptor, type 2 (ITPR2), mRNA.		G	VAL/ALA	1,4061		0,1,2030	89.0	97.0	95.0		7052	4.3	0.5	12		95	1,8375		0,1,4187	no	missense	ITPR2	NM_002223.2	64	0,2,6217	AA,AG,GG		0.0119,0.0246,0.0161	benign	2351/2702	26572040	2,12436	2031	4188	6219	SO:0001583	missense	3709				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity	g.chr12:26572040G>A	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.7052C>T	12.37:g.26572040G>A	ENSP00000370744:p.Ala2351Val					ITPR2_uc009zjg.1_Missense_Mutation_p.A502V	p.A2351V	NM_002223	NP_002214	Q14571	ITPR2_HUMAN			49	7469	-	Colorectal(261;0.0847)		2351					O94773	Missense_Mutation	SNP	ENST00000381340.3	37	c.7052C>T	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	3.998	-0.003084	0.07773	2.46E-4	1.19E-4	ENSG00000123104	ENST00000381340	D	0.98178	-4.77	5.22	4.31	0.51392	Ion transport (1);	0.265675	0.37530	N	0.002051	D	0.94066	0.8098	L	0.31664	0.95	0.09310	N	0.999997	B	0.13145	0.007	B	0.15484	0.013	T	0.82135	-0.0607	10	0.10377	T	0.69	.	9.0202	0.36195	0.2156:0.0:0.7844:0.0	.	2351	Q14571	ITPR2_HUMAN	V	2351	ENSP00000370744:A2351V	ENSP00000370744:A2351V	A	-	2	0	ITPR2	26463307	0.001000	0.12720	0.524000	0.27887	0.944000	0.59088	1.196000	0.32198	2.716000	0.92895	0.655000	0.94253	GCG		0.448	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		4	59	0	0	0	1	0	4	59				
MPZ	4359	broad.mit.edu	37	1	161279666	161279666	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr1:161279666delG	ENST00000533357.1	-	1	96	c.30delC	c.(28-30)cccfs	p.P10fs	MPZ_ENST00000526189.1_5'Flank|MPZ_ENST00000491222.2_5'Flank|MPZ_ENST00000360451.6_Frame_Shift_Del_p.P20fs|MPZ_ENST00000336559.4_Frame_Shift_Del_p.P10fs	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	10					cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			GGATAGGGCTGGGGCTGGATG	0.617																																						uc001gaf.4																			0				central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10						c.(28-30)cccfs		Homo sapiens myelin protein zero (MPZ), mRNA.							16.0	17.0	17.0					1																	161279666		2199	4293	6492	SO:0001589	frameshift_variant	4359				synaptic transmission	integral to plasma membrane	structural molecule activity	g.chr1:161279666delG	BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"""Immunoglobulin superfamily / V-set domain containing"""	7225	protein-coding gene	gene with protein product		159440	"""Charcot-Marie-Tooth neuropathy 1B"""	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.30delC	1.37:g.161279666delG	ENSP00000432943:p.Pro10fs						p.P10fs	NM_000530	NP_000521	P25189	MYP0_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00376)		0	97	-	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	10					Q16072|Q5VTH4|Q92677|Q9BR67	Frame_Shift_Del	DEL	ENST00000533357.1	37	c.30delC	CCDS1229.2																																																																																				0.617	MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530		2	4						2	4	---	---	---	---
SOX4	6659	broad.mit.edu	37	6	21595266	21595267	+	In_Frame_Ins	INS	-	-	GGC	rs564094826	byFrequency	TCGA-EL-A3CW-01A-11D-A19J-08	TCGA-EL-A3CW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3847f72b-5594-44f1-9624-dbbb00aa8ae0	465c59b2-9a7c-4e5b-be9c-5e9a2db9f816	g.chr6:21595266_21595267insGGC	ENST00000244745.1	+	1	1295_1296	c.501_502insGGC	c.(502-504)ggc>GGCggc	p.168_168G>GG	SOX4_ENST00000543472.1_In_Frame_Ins_p.168_168G>GG	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	168					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|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 transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			gcggccatgggggcggcggcgg	0.738														127	0.0253594	0.0923	0.0043	5008	,	,		7118	0.0		0.002	False		,,,				2504	0.0					uc003ndi.3																			0				kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6						c.(499-504)insGGC		Homo sapiens SRY (sex determining region Y)-box 4 (SOX4), mRNA.																																				SO:0001652	inframe_insertion	6659				DNA damage response, detection of DNA damage|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|T cell differentiation|canonical Wnt receptor signaling pathway|cardiac ventricle formation|cellular response to glucose stimulus|glial cell development|glial cell proliferation|limb bud formation|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein export from nucleus|negative regulation of protein ubiquitination|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|positive regulation of N-terminal peptidyl-lysine acetylation|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|positive regulation of insulin secretion|positive regulation of translation|pro-B cell differentiation|protein stabilization|skeletal system development|spinal cord motor neuron differentiation|sympathetic nervous system development	mitochondrion|nucleus	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|core promoter sequence-specific DNA binding|protein binding	g.chr6:21595266_21595267insGGC	AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"""SRY (sex determining region Y)-boxes"""	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.514_516dupGGC	6.37:g.21595273_21595275dupGGC	ENSP00000244745:p.Gly173dup						p.173_174insG	NM_003107	NP_003098	Q06945	SOX4_HUMAN	all cancers(50;0.0751)|Epithelial(50;0.155)		0	1295_1296	+	Ovarian(93;0.163)		173						In_Frame_Ins	INS	ENST00000244745.1	37	c.501_502insGGC	CCDS4547.1																																																																																				0.738	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107		3	5						3	5	---	---	---	---
