#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
VGLL1	51442	broad.mit.edu	37	X	135631112	135631112	+	Silent	SNP	C	C	T			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chrX:135631112C>T	ENST00000370634.3	+	3	749	c.579C>T	c.(577-579)ggC>ggT	p.G193G	MIR934_ENST00000401241.1_RNA	NM_016267.3	NP_057351.1	Q99990	VGLL1_HUMAN	vestigial-like family member 1	193					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;0.000127)					GCAACCCTGGCCAGATAGCTG	0.562																																						ENST00000370634.3																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20						c.(577-579)ggC>ggT		vestigial like 1 (Drosophila)							66.0	67.0	67.0					X																	135631112		2203	4300	6503	SO:0001819	synonymous_variant	51442				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription coactivator activity	g.chrX:135631112C>T	AF137387	CCDS14658.1	Xq26.3	2014-03-03	2014-03-03		ENSG00000102243	ENSG00000102243			20985	protein-coding gene	gene with protein product		300583	"""vestigial like 1 (Drosophila)"""			10518497	Standard	NM_016267		Approved	TONDU, TDU	uc004ezy.3	Q99990	OTTHUMG00000022509	ENST00000370634.3:c.579C>T	X.37:g.135631112C>T							p.G193G	NM_016267.3	NP_057351.1	Q99990	VGLL1_HUMAN			3	749	+	Acute lymphoblastic leukemia(192;0.000127)		193					Q5H915	Silent	SNP	ENST00000370634.3	37	c.579C>T	CCDS14658.1																																																																																				0.562	VGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058493.1	NM_016267		4	172	0	0	0	0.009096	0	4	172				
COX10-AS1	100874058	broad.mit.edu	37	17	13928289	13928289	+	RNA	SNP	G	G	A	rs201483912	byFrequency	TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr17:13928289G>A	ENST00000602743.1	-	0	224									COX10 antisense RNA 1																		CGGAGCCAGAGCCAGCATGGG	0.592																																						ENST00000602743.1																			0																																																			0							g.chr17:13928289G>A			17p12	2013-05-22	2012-08-15	2010-11-25	ENSG00000236088	ENSG00000236088		"""Long non-coding RNAs"""	38873	non-coding RNA	RNA, long non-coding			"""COX10 antisense RNA (non-protein coding)"", ""COX10 antisense RNA 1 (non-protein coding)"""	COX10AS, COX10-AS			Standard	NR_049718		Approved		uc002goe.1		OTTHUMG00000058771		17.37:g.13928289G>A														0	224	-									RNA	SNP	ENST00000602743.1	37																																																																																						0.592	COX10-AS1-005	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000467585.1			3	5	0	0	0	0.004672	0	3	5				
DENND4C	55667	broad.mit.edu	37	9	19360258	19360258	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr9:19360258G>A	ENST00000380432.2	+	24	4355	c.4322G>A	c.(4321-4323)aGa>aAa	p.R1441K	DENND4C_ENST00000434457.2_Missense_Mutation_p.R1726K|DENND4C_ENST00000602925.1_Missense_Mutation_p.R1677K			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1441					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TTAGGAAAAAGACCCAATCCT	0.363																																						ENST00000307015.9																			0				breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						c.(2740-2742)aGa>aAa		DENN/MADD domain containing 4C							91.0	95.0	94.0					9																	19360258		2203	4300	6503	SO:0001583	missense	55667					integral to membrane		g.chr9:19360258G>A	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.4322G>A	9.37:g.19360258G>A	ENSP00000369797:p.Arg1441Lys					DENND4C_ENST00000540671.1_Missense_Mutation_p.R771K|DENND4C_ENST00000434457.2_Missense_Mutation_p.R1726K|DENND4C_ENST00000602925.1_Missense_Mutation_p.R1677K|DENND4C_ENST00000380432.2_Missense_Mutation_p.R1441K	p.R914K			Q5VZ89	DEN4C_HUMAN			25	4493	+			1441					A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37	c.2741G>A		.	.	.	.	.	.	.	.	.	.	G	12.52	1.962511	0.34659	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.22539	1.95;1.95	5.68	3.84	0.44239	.	0.114139	0.56097	D	0.000033	T	0.18593	0.0446	L	0.46157	1.445	0.33892	D	0.637434	B;B;B	0.31274	0.317;0.082;0.047	B;B;B	0.31946	0.138;0.059;0.034	T	0.23084	-1.0198	9	.	.	.	-12.0227	10.8682	0.46869	0.2057:0.0:0.7943:0.0	.	771;623;1441	B7Z660;Q5VZ89-3;Q5VZ89	.;.;DEN4C_HUMAN	K	1441;914;623;771;914;623;438	ENSP00000305795:R914K;ENSP00000443804:R771K	.	R	+	2	0	DENND4C	19350258	0.782000	0.28689	0.975000	0.42487	0.994000	0.84299	2.336000	0.43938	1.391000	0.46566	0.655000	0.94253	AGA		0.363	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		5	149	0	0	0	0.001984	0	5	149				
ARAP1	116985	broad.mit.edu	37	11	72406076	72406076	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr11:72406076T>C	ENST00000393609.3	-	27	3845	c.3643A>G	c.(3643-3645)Agg>Ggg	p.R1215G	ARAP1_ENST00000426523.1_Missense_Mutation_p.R970G|ARAP1_ENST00000455638.2_Missense_Mutation_p.R1215G|ARAP1_ENST00000334211.8_Missense_Mutation_p.R970G|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000429686.1_Missense_Mutation_p.R909G|ARAP1-AS1_ENST00000542022.1_RNA|ARAP1_ENST00000393605.3_Missense_Mutation_p.R975G|ARAP1_ENST00000359373.5_Missense_Mutation_p.R1215G	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1215	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.R975G(1)|p.R1215G(1)		cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						TCCTTCTCCCTGATGCCCACG	0.587																																					Ovarian(102;1198 1520 13195 17913 37529)	ENST00000359373.5																			2	Substitution - Missense(2)	p.R975G(1)|p.R1215G(1)	endometrium(2)	cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						c.(3643-3645)Agg>Ggg		ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1							159.0	114.0	129.0					11																	72406076		2200	4293	6493	SO:0001583	missense	116985				actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding	g.chr11:72406076T>C	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.3643A>G	11.37:g.72406076T>C	ENSP00000377233:p.Arg1215Gly					ARAP1_ENST00000429686.1_Missense_Mutation_p.R909G|ARAP1_ENST00000393609.3_Missense_Mutation_p.R1215G|ARAP1_ENST00000455638.2_Missense_Mutation_p.R1215G|ARAP1_ENST00000393605.3_Missense_Mutation_p.R975G|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000426523.1_Missense_Mutation_p.R970G|ARAP1_ENST00000334211.8_Missense_Mutation_p.R970G	p.R1215G			Q96P48	ARAP1_HUMAN			27	4494	-			1215			Ras-associating.		A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	c.3643A>G	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	T	7.560	0.664465	0.14710	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000542596	T;T;T;T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29;2.29;2.29;2.29	5.36	4.2	0.49525	Ras-association (2);	0.374927	0.28006	N	0.016979	T	0.09949	0.0244	N	0.11427	0.14	0.29129	N	0.87977	B;P;P;B;B	0.45827	0.0;0.867;0.683;0.004;0.001	B;B;B;B;B	0.42522	0.01;0.39;0.196;0.01;0.006	T	0.08207	-1.0733	10	0.23891	T	0.37	.	11.3142	0.49381	0.0:0.0:0.1527:0.8473	.	970;909;1215;1215;975	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	G	1215;1215;975;970;1215;970;909;19	ENSP00000352332:R1215G;ENSP00000390461:R1215G;ENSP00000377230:R975G;ENSP00000335506:R970G;ENSP00000377233:R1215G;ENSP00000392264:R970G;ENSP00000403127:R909G;ENSP00000441741:R19G	ENSP00000335506:R970G	R	-	1	2	ARAP1	72083724	0.306000	0.24490	1.000000	0.80357	0.450000	0.32258	1.116000	0.31221	0.846000	0.35142	0.533000	0.62120	AGG		0.587	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		3	31	0	0	0	0.004672	0	3	31				
SETD4	54093	broad.mit.edu	37	21	37420619	37420619	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr21:37420619C>T	ENST00000399215.1	-	4	1655	c.283G>A	c.(283-285)Gca>Aca	p.A95T	SETD4_ENST00000399212.1_Missense_Mutation_p.A71T|SETD4_ENST00000399205.1_Missense_Mutation_p.A71T|SETD4_ENST00000332131.4_Missense_Mutation_p.A95T|SETD4_ENST00000399201.1_Missense_Mutation_p.A71T|SETD4_ENST00000481477.1_Intron|SETD4_ENST00000399208.2_Missense_Mutation_p.A95T|SETD4_ENST00000399207.1_Missense_Mutation_p.A95T			Q9NVD3	SETD4_HUMAN	SET domain containing 4	95	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GTAATGTATGCCCCTAAGTAG	0.448																																						ENST00000399215.1																			0				autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						c.(283-285)Gca>Aca		SET domain containing 4							389.0	320.0	343.0					21																	37420619		2203	4300	6503	SO:0001583	missense	54093							g.chr21:37420619C>T	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 27"", ""chromosome 21 open reading frame 18"""	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.283G>A	21.37:g.37420619C>T	ENSP00000382163:p.Ala95Thr					SETD4_ENST00000481477.1_Intron|SETD4_ENST00000399201.1_Missense_Mutation_p.A71T|SETD4_ENST00000399207.1_Missense_Mutation_p.A95T|SETD4_ENST00000399212.1_Missense_Mutation_p.A71T|SETD4_ENST00000332131.4_Missense_Mutation_p.A95T|SETD4_ENST00000399205.1_Missense_Mutation_p.A71T|SETD4_ENST00000399208.2_Missense_Mutation_p.A95T	p.A95T			Q9NVD3	SETD4_HUMAN			4	1655	-			95			SET.		B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	c.283G>A	CCDS13640.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.273474	0.23221	.	.	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131;ENST00000399205;ENST00000399208;ENST00000399201;ENST00000399207;ENST00000424303;ENST00000429161;ENST00000446166	T;T;T;T;T;T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55	5.25	0.891	0.19224	SET domain (1);	0.867178	0.10438	N	0.674684	T	0.10809	0.0264	L	0.40543	1.245	0.19300	N	0.99997	B;B;B;B	0.09022	0.002;0.001;0.001;0.001	B;B;B;B	0.09377	0.004;0.003;0.003;0.004	T	0.40942	-0.9536	10	0.20046	T	0.44	21.3233	8.4109	0.32642	0.0:0.4064:0.4515:0.1422	.	71;95;71;95	A8MTS1;C9JWV5;Q9NVD3-3;Q9NVD3	.;.;.;SETD4_HUMAN	T	95;71;95;71;95;71;95;95;95;71	ENSP00000382163:A95T;ENSP00000382161:A71T;ENSP00000329189:A95T;ENSP00000382156:A71T;ENSP00000382159:A95T;ENSP00000382152:A71T;ENSP00000382158:A95T;ENSP00000399998:A95T;ENSP00000396837:A95T;ENSP00000413318:A71T	ENSP00000329189:A95T	A	-	1	0	SETD4	36342489	0.013000	0.17824	0.847000	0.33407	0.951000	0.60555	0.236000	0.17967	-0.134000	0.11516	0.563000	0.77884	GCA		0.448	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		5	287	0	0	0	0.001984	0	5	287				
HSD3B2	3284	broad.mit.edu	37	1	119965210	119965210	+	Silent	SNP	G	G	A			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr1:119965210G>A	ENST00000543831.1	+	4	1335	c.1086G>A	c.(1084-1086)cgG>cgA	p.R362R	HSD3B2_ENST00000369416.3_Silent_p.R362R	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	362					androgen biosynthetic process (GO:0006702)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)	p.R362R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	TTGTGGACCGGCACAAGGAGA	0.512																																						ENST00000543831.1																			1	Substitution - coding silent(1)	p.R362R(1)	kidney(1)	breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27						c.(1084-1086)cgG>cgA		hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	NADH(DB00157)|Trilostane(DB01108)						45.0	41.0	42.0					1																	119965210		2203	4300	6503	SO:0001819	synonymous_variant	3284				androgen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity	g.chr1:119965210G>A	BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5218	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 2"""	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.1086G>A	1.37:g.119965210G>A						HSD3B2_ENST00000369416.3_Silent_p.R362R	p.R362R	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	4	1335	+	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)	362					A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Silent	SNP	ENST00000543831.1	37	c.1086G>A	CCDS902.1																																																																																				0.512	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198		4	65	0	0	0	0.000602	0	4	65				
MAST1	22983	broad.mit.edu	37	19	12951846	12951846	+	Missense_Mutation	SNP	A	A	C			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr19:12951846A>C	ENST00000251472.4	+	3	253	c.214A>C	c.(214-216)Acc>Ccc	p.T72P	MAST1_ENST00000591495.1_Missense_Mutation_p.T68P	NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						CTCCCCCAACACCCCCGCCCA	0.642																																						ENST00000251472.4																			0				NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						c.(214-216)Acc>Ccc		microtubule associated serine/threonine kinase 1							88.0	93.0	91.0					19																	12951846		2203	4300	6503	SO:0001583	missense	22983				cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	g.chr19:12951846A>C	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.214A>C	19.37:g.12951846A>C	ENSP00000251472:p.Thr72Pro					MAST1_ENST00000591495.1_Missense_Mutation_p.T68P	p.T72P	NM_014975.2	NP_055790.1	Q9Y2H9	MAST1_HUMAN			3	253	+			72						Missense_Mutation	SNP	ENST00000251472.4	37	c.214A>C	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.953944	0.53293	.	.	ENSG00000105613	ENST00000251472;ENST00000542153	T	0.32023	1.47	5.97	4.95	0.65309	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.560295	0.18178	N	0.149231	T	0.21062	0.0507	N	0.25060	0.705	0.34163	D	0.668871	B;B;B	0.19583	0.037;0.0;0.001	B;B;B	0.25405	0.06;0.008;0.005	T	0.18745	-1.0327	10	0.72032	D	0.01	-19.9269	6.2897	0.21053	0.7581:0.1623:0.0796:0.0	.	72;72;72	Q9Y2H9;B4DMN4;F5H2S9	MAST1_HUMAN;.;.	P	72	ENSP00000251472:T72P	ENSP00000251472:T72P	T	+	1	0	MAST1	12812846	0.125000	0.22332	0.981000	0.43875	0.995000	0.86356	1.398000	0.34554	1.069000	0.40788	0.533000	0.62120	ACC		0.642	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		8	82	0	0	0	0.003163	0	8	82				
MCF2L	23263	broad.mit.edu	37	13	113740522	113740522	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr13:113740522G>A	ENST00000375608.3	+	22	2480	c.2422G>A	c.(2422-2424)Gtg>Atg	p.V808M	MCF2L_ENST00000397030.1_Missense_Mutation_p.V811M|MCF2L_ENST00000375601.3_Missense_Mutation_p.V782M|MCF2L_ENST00000535094.2_Missense_Mutation_p.V778M|MCF2L_ENST00000421756.1_Missense_Mutation_p.V782M|MCF2L_ENST00000375604.2_Missense_Mutation_p.V835M|MCF2L_ENST00000442652.2_Missense_Mutation_p.V808M|MCF2L_ENST00000434480.2_Missense_Mutation_p.V784M|MCF2L_ENST00000375597.4_Missense_Mutation_p.V776M|MCF2L_ENST00000423482.2_Missense_Mutation_p.V776M			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	808	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CCTGAAGGCCGTGAACGACTC	0.622																																						ENST00000397030.1																			0				kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8						c.(2431-2433)Gtg>Atg		MCF.2 cell line derived transforming sequence-like							91.0	74.0	80.0					13																	113740522		2203	4300	6503	SO:0001583	missense	23263				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity	g.chr13:113740522G>A	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.2422G>A	13.37:g.113740522G>A	ENSP00000364758:p.Val808Met					MCF2L_ENST00000535094.2_Missense_Mutation_p.V778M|MCF2L_ENST00000375597.4_Missense_Mutation_p.V776M|MCF2L_ENST00000375604.2_Missense_Mutation_p.V835M|MCF2L_ENST00000375608.3_Missense_Mutation_p.V808M|MCF2L_ENST00000375601.3_Missense_Mutation_p.V782M|MCF2L_ENST00000423482.2_Missense_Mutation_p.V776M|MCF2L_ENST00000442652.2_Missense_Mutation_p.V808M|MCF2L_ENST00000421756.1_Missense_Mutation_p.V782M|MCF2L_ENST00000434480.2_Missense_Mutation_p.V784M	p.V811M			O15068	MCF2L_HUMAN			21	2468	+	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)	808			DH.		A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37	c.2431G>A		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.56|19.56	3.850375|3.850375	0.71719|0.71719	.|.	.|.	ENSG00000126217|ENSG00000126217	ENST00000397017|ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	.|T;T;T;T;T;T;T;T;T;T	.|0.65178	.|-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	4.67|4.67	4.67|4.67	0.58626|0.58626	.|Dbl homology (DH) domain (5);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83926|0.83926	0.5360|0.5360	M|M	0.92649|0.92649	3.33|3.33	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.80764	.|0.977;0.977;0.99;0.987;0.985;0.994	D|D	0.88732|0.88732	0.3237|0.3237	5|10	.|0.87932	.|D	.|0	.|.	17.635|17.635	0.88119|0.88119	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|776;778;835;740;776;808	.|E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.|.;.;.;.;.;MCF2L_HUMAN	H|M	438|808;808;835;811;778;782;782;784;776;776;619	.|ENSP00000364758:V808M;ENSP00000401422:V808M;ENSP00000364754:V835M;ENSP00000380225:V811M;ENSP00000440374:V778M;ENSP00000397285:V782M;ENSP00000364751:V782M;ENSP00000407722:V784M;ENSP00000405639:V776M;ENSP00000364747:V776M	.|ENSP00000364747:V776M	R|V	+|+	2|1	0|0	MCF2L|MCF2L	112788523|112788523	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.234000|0.234000	0.25298|0.25298	9.574000|9.574000	0.98184|0.98184	2.157000|2.157000	0.67596|0.67596	0.196000|0.196000	0.17591|0.17591	CGT|GTG		0.622	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			3	43	0	0	0	0.004672	0	3	43				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			0							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		3	60	0	0	0	0.004672	0	3	60				
RP9	6100	broad.mit.edu	37	7	33139017	33139017	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr7:33139017G>C	ENST00000297157.3	-	3	232	c.215C>G	c.(214-216)cCa>cGa	p.P72R		NM_203288.1	NP_976033.1	Q8TA86	RP9_HUMAN	retinitis pigmentosa 9 (autosomal dominant)	72	PIM1-binding. {ECO:0000250}.				cognition (GO:0050890)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|signal recognition particle receptor complex (GO:0005785)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P72R(2)		large_intestine(3)|lung(3)|urinary_tract(1)	7			GBM - Glioblastoma multiforme(11;0.0403)			TGGTACATCTGGTATGCAATC	0.483																																						ENST00000297157.3																			2	Substitution - Missense(2)	p.P72R(2)	urinary_tract(1)|lung(1)	large_intestine(3)|lung(3)|urinary_tract(1)	7						c.(214-216)cCa>cGa		retinitis pigmentosa 9 (autosomal dominant)							157.0	142.0	147.0					7																	33139017		2203	4300	6503	SO:0001583	missense	6100				RNA splicing	nucleus	nucleic acid binding|protein binding|zinc ion binding	g.chr7:33139017G>C	AX016710	CCDS5440.1	7p14.3	2014-01-28			ENSG00000164610	ENSG00000164610			10288	protein-coding gene	gene with protein product	"""Pim-1 kinase associated protein"""	607331				8513323	Standard	NM_203288		Approved	PAP-1	uc003tdm.3	Q8TA86	OTTHUMG00000152988	ENST00000297157.3:c.215C>G	7.37:g.33139017G>C	ENSP00000297157:p.Pro72Arg						p.P72R	NM_203288.1	NP_976033.1	Q8TA86	RP9_HUMAN	GBM - Glioblastoma multiforme(11;0.0403)		3	232	-			72			PIM1-binding (By similarity).			Missense_Mutation	SNP	ENST00000297157.3	37	c.215C>G	CCDS5440.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243312	0.79912	.	.	ENSG00000164610	ENST00000297157;ENST00000448915	T;D	0.85484	-1.2;-1.99	3.43	3.43	0.39272	.	0.000000	0.85682	U	0.000000	D	0.90027	0.6886	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91308	0.5072	10	0.66056	D	0.02	-35.7261	15.7391	0.77870	0.0:0.0:1.0:0.0	.	72	Q8TA86	RP9_HUMAN	R	72;38	ENSP00000297157:P72R;ENSP00000411577:P38R	ENSP00000297157:P72R	P	-	2	0	RP9	33105542	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.918000	0.92759	1.862000	0.54008	0.563000	0.77884	CCA		0.483	RP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328914.1	NM_203288		5	80	0	0	0	0.000602	0	5	80				
CDC40	51362	broad.mit.edu	37	6	110528751	110528751	+	Missense_Mutation	SNP	C	C	A			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr6:110528751C>A	ENST00000368932.1	+	5	550	c.449C>A	c.(448-450)gCt>gAt	p.A150D	CDC40_ENST00000368930.1_Missense_Mutation_p.A150D|CDC40_ENST00000307731.1_Missense_Mutation_p.A150D			O60508	PRP17_HUMAN	cell division cycle 40	150					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)	p.A150D(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		CAAGTGTCTGCTAAATATATT	0.269																																						ENST00000368932.1																			1	Substitution - Missense(1)	p.A150D(1)	kidney(1)	breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18						c.(448-450)gCt>gAt		cell division cycle 40							94.0	106.0	102.0					6																	110528751		2201	4290	6491	SO:0001583	missense	51362				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm		g.chr6:110528751C>A	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"""WD repeat domain containing"""	17350	protein-coding gene	gene with protein product		605585	"""cell division cycle 40 homolog (yeast)"", ""cell division cycle 40 homolog (S. cerevisiae)"""			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.449C>A	6.37:g.110528751C>A	ENSP00000357928:p.Ala150Asp					CDC40_ENST00000368933.1_Missense_Mutation_p.A150D|CDC40_ENST00000307731.1_Missense_Mutation_p.A150D|CDC40_ENST00000368930.1_Missense_Mutation_p.A150D	p.A150D			O60508	PRP17_HUMAN		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)	5	550	+		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)	150					B2RBC5|O75471|Q5SRN0|Q9UPG1	Missense_Mutation	SNP	ENST00000368932.1	37	c.449C>A	CCDS5081.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.60|12.60	1.987752|1.987752	0.35036|0.35036	.|.	.|.	ENSG00000168438|ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731;ENST00000439165;ENST00000453107|ENST00000431461	T;T;T;T|.	0.60920|.	0.28;0.15;0.15;0.28|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	0.360512|.	0.35349|.	N|.	0.003280|.	T|.	0.30230|.	0.0758|.	N|N	0.03608|0.03608	-0.345|-0.345	0.45046|0.45046	D|D	0.998061|0.998061	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|.	0.35475|.	-0.9787|.	10|.	0.10636|.	T|.	0.68|.	-15.4556|-15.4556	20.1739|20.1739	0.98173|0.98173	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	150|.	O60508|.	PRP17_HUMAN|.	D|X	150;150;150;150;150;47|42	ENSP00000357928:A150D;ENSP00000357929:A150D;ENSP00000357926:A150D;ENSP00000304370:A150D|.	ENSP00000304370:A150D|.	A|C	+|+	2|3	0|2	CDC40|CDC40	110635444|110635444	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.478000|5.478000	0.66806|0.66806	2.774000|2.774000	0.95407|0.95407	0.585000|0.585000	0.79938|0.79938	GCT|TGC		0.269	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		5	135	1	0	0.00116845	0.001168	0.00211781	5	135				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	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)	ENST00000288602.6	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(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)	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		v-raf murine sarcoma viral oncogene homolog B	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_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	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		18	56	0	0	0	0.010504	0	18	56				
NUDT5	11164	broad.mit.edu	37	10	12215790	12215790	+	Silent	SNP	G	G	A			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr10:12215790G>A	ENST00000491614.1	-	6	707	c.312C>T	c.(310-312)acC>acT	p.T104T	NUDT5_ENST00000378940.3_Silent_p.T104T|NUDT5_ENST00000537776.1_Silent_p.T104T|NUDT5_ENST00000378927.3_Silent_p.T104T|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000378937.3_Silent_p.T117T			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	104	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				CTGCTTCTGGGGTTTCACCAT	0.458																																						ENST00000491614.1																			0				breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8						c.(310-312)acC>acT		nudix (nucleoside diphosphate linked moiety X)-type motif 5							154.0	160.0	158.0					10																	12215790		2203	4300	6503	SO:0001819	synonymous_variant	11164				D-ribose catabolic process|ribonucleoside diphosphate catabolic process	intracellular	ADP-ribose diphosphatase activity|magnesium ion binding	g.chr10:12215790G>A	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.312C>T	10.37:g.12215790G>A						NUDT5_ENST00000378937.3_Silent_p.T117T|NUDT5_ENST00000378940.3_Silent_p.T104T|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000378927.3_Silent_p.T104T|NUDT5_ENST00000537776.1_Silent_p.T104T	p.T104T			Q9UKK9	NUDT5_HUMAN			6	707	-		Renal(717;0.228)	104			Nudix hydrolase.		A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	37	c.312C>T	CCDS7089.1																																																																																				0.458	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1			73	148	0	0	0	0.014410	0	73	148				
TSPAN4	7106	broad.mit.edu	37	11	865530	865530	+	Silent	SNP	G	G	A	rs371470307		TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr11:865530G>A	ENST00000397404.1	+	6	607	c.348G>A	c.(346-348)caG>caA	p.Q116Q	TSPAN4_ENST00000397406.1_Silent_p.Q116Q|TSPAN4_ENST00000397408.1_Silent_p.Q116Q|TSPAN4_ENST00000409543.2_Silent_p.Q116Q|TSPAN4_ENST00000397396.1_Silent_p.Q52Q|TSPAN4_ENST00000397397.2_Silent_p.Q116Q|TSPAN4_ENST00000397411.2_Silent_p.Q116Q|TSPAN4_ENST00000409531.1_Silent_p.Q135Q|TSPAN4_ENST00000346501.4_Intron|TSPAN4_ENST00000525201.1_Silent_p.Q52Q	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN	tetraspanin 4	116					protein complex assembly (GO:0006461)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	antigen binding (GO:0003823)|integrin binding (GO:0005178)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGTATGCCCAGCAAGACCTGA	0.667																																						ENST00000397404.1																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3						c.(346-348)caG>caA		tetraspanin 4		G	,,,,,,	1,4405	2.1+/-5.4	0,1,2202	37.0	36.0	37.0		348,348,348,348,348,156,348	0.1	0.5	11		37	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TSPAN4	NM_001025234.1,NM_001025235.1,NM_001025236.1,NM_001025237.1,NM_001025238.1,NM_001025239.1,NM_003271.4	,,,,,,	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,	116/239,116/239,116/239,116/239,116/239,52/175,116/239	865530	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	0				protein complex assembly	integral to plasma membrane		g.chr11:865530G>A	AF022813	CCDS7721.1, CCDS41589.1	11p15.5	2013-02-14	2005-03-21	2005-03-21	ENSG00000214063	ENSG00000214063		"""Tetraspanins"""	11859	protein-coding gene	gene with protein product		602644	"""transmembrane 4 superfamily member 7"""	TM4SF7		9360996	Standard	XM_005253102		Approved	NAG-2, TSPAN-4, TETRASPAN	uc001lsf.1	O14817	OTTHUMG00000133305	ENST00000397404.1:c.348G>A	11.37:g.865530G>A						TSPAN4_ENST00000397397.2_Silent_p.Q116Q|TSPAN4_ENST00000346501.4_Intron|TSPAN4_ENST00000397396.1_Silent_p.Q52Q|TSPAN4_ENST00000397408.1_Silent_p.Q116Q|TSPAN4_ENST00000397411.2_Silent_p.Q116Q|TSPAN4_ENST00000525201.1_Silent_p.Q52Q|TSPAN4_ENST00000409531.1_Silent_p.Q135Q|TSPAN4_ENST00000397406.1_Silent_p.Q116Q|TSPAN4_ENST00000409543.2_Silent_p.Q116Q	p.Q116Q	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	6	607	+		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	116					Q6IAP6	Silent	SNP	ENST00000397404.1	37	c.348G>A	CCDS7721.1																																																																																				0.667	TSPAN4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257102.2			3	27	0	0	0	0.004672	0	3	27				
KMT2C	58508	broad.mit.edu	37	7	151970890	151970891	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DJ-A2PS-01A-11D-A18F-08	TCGA-DJ-A2PS-10A-01D-A18F-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96c450fe-4e43-43b3-9adc-6549c6fff902	dd8e6cf7-7163-4b83-a429-6f19ce5690b3	g.chr7:151970890_151970891insT	ENST00000262189.6	-	7	1129_1130	c.911_912insA	c.(910-912)cagfs	p.Q304fs	KMT2C_ENST00000355193.2_Frame_Shift_Ins_p.Q304fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	304					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AATGATACATCTGGGTACATTT	0.436																																						ENST00000355193.2																			0											c.(910-912)catfs		lysine (K)-specific methyltransferase 2C																																				SO:0001589	frameshift_variant	58508							g.chr7:151970890_151970891insT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.912dupA	7.37:g.151970891_151970891dupT	ENSP00000262189:p.Gln304fs					KMT2C_ENST00000262189.6_Frame_Shift_Ins_p.H304fs	p.H304fs							7	1129_1130	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Ins	INS	ENST00000262189.6	37	c.911_912insA	CCDS5931.1																																																																																				0.436	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			8	166						8	166	---	---	---	---
