#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
CDYL2	124359	broad.mit.edu	37	16	80718510	80718510	+	Silent	SNP	A	A	G			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr16:80718510A>G	ENST00000570137.2	-	2	696	c.541T>C	c.(541-543)Ttg>Ctg	p.L181L	CDYL2_ENST00000562812.1_Silent_p.L181L|CDYL2_ENST00000566173.1_Silent_p.L181L|CDYL2_ENST00000562753.1_5'UTR|CDYL2_ENST00000563890.1_Silent_p.L181L	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	181						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						TGATCATTCAAATCCAAGCCA	0.512																																						uc002ffs.3																			0				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						c.(541-543)Ttg>Ctg		Homo sapiens chromodomain protein, Y-like 2 (CDYL2), mRNA.							124.0	110.0	114.0					16																	80718510		2203	4300	6503	SO:0001819	synonymous_variant	124359					nucleus	catalytic activity|protein binding	g.chr16:80718510A>G	AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.541T>C	16.37:g.80718510A>G			Somatic					p.L181L	NM_152342	NP_689555	WXS	Illumina GAIIx	Phase_I	Q8N8U2	CDYL2_HUMAN			1	646	-			181					Q7Z5I8	Silent	SNP	ENST00000570137.2	37	c.541T>C	CCDS32493.1																																																																																				0.512	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342		3	113	0	0	0	1	0	3	113				
KSR2	283455	broad.mit.edu	37	12	117962864	117962864	+	Missense_Mutation	SNP	A	A	T			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr12:117962864A>T	ENST00000339824.5	-	14	2739	c.2012T>A	c.(2011-2013)cTc>cAc	p.L671H	KSR2_ENST00000425217.1_Missense_Mutation_p.L642H|KSR2_ENST00000545002.1_5'UTR|KSR2_ENST00000302438.5_Missense_Mutation_p.L368H			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	671	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTTTCCAATGAGCTCGCCGAT	0.622																																						uc001two.2																			0				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						c.(1924-1926)cTc>cAc		Homo sapiens kinase suppressor of ras 2 (KSR2), mRNA.							60.0	65.0	64.0					12																	117962864		2091	4215	6306	SO:0001583	missense	283455				intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity	g.chr12:117962864A>T	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.2012T>A	12.37:g.117962864A>T	ENSP00000339952:p.Leu671His		Somatic					p.L642H	NM_173598	NP_775869	WXS	Illumina GAIIx	Phase_I	Q6VAB6	KSR2_HUMAN			13	1980	-	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		671					A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	37	c.1925T>A		.	.	.	.	.	.	.	.	.	.	A	17.55	3.417667	0.62622	.	.	ENSG00000171435	ENST00000425217;ENST00000339824;ENST00000302438;ENST00000542378	D;D;D	0.90069	-2.61;-2.61;-2.61	4.98	3.83	0.44106	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.059483	0.64402	D	0.000002	D	0.92071	0.7487	M	0.72624	2.21	0.43930	D	0.996583	D	0.63046	0.992	D	0.65323	0.934	D	0.90086	0.4174	10	0.34782	T	0.22	.	10.3954	0.44198	0.9234:0.0:0.0766:0.0	.	671	Q6VAB6	KSR2_HUMAN	H	642;671;368;343	ENSP00000389715:L642H;ENSP00000339952:L671H;ENSP00000305466:L368H	ENSP00000305466:L368H	L	-	2	0	KSR2	116447247	1.000000	0.71417	1.000000	0.80357	0.374000	0.29953	9.139000	0.94554	0.929000	0.37192	0.528000	0.53228	CTC		0.622	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		5	82	0	0	0	1	0	5	82				
PGM2	55276	broad.mit.edu	37	4	37836265	37836265	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr4:37836265A>G	ENST00000381967.4	+	3	375	c.275A>G	c.(274-276)cAa>cGa	p.Q92R	PGM2_ENST00000544359.1_5'UTR|PGM2_ENST00000537241.1_Intron	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	92					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						CTGGAAAAACAATTCAGTGAC	0.343																																						uc011byb.1																			0				breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						c.(274-276)cAa>cGa		Homo sapiens phosphoglucomutase 2 (PGM2), mRNA.							95.0	106.0	102.0					4																	37836265		2203	4300	6503	SO:0001583	missense	55276				glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity	g.chr4:37836265A>G	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.275A>G	4.37:g.37836265A>G	ENSP00000371393:p.Gln92Arg		Somatic				PGM2_uc011bya.1_5'UTR|PGM2_uc011byc.1_Intron	p.Q92R	NM_018290	NP_060760	WXS	Illumina GAIIx	Phase_I	Q96G03	PGM2_HUMAN			2	348	+			92					B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Missense_Mutation	SNP	ENST00000381967.4	37	c.275A>G	CCDS3443.1	.	.	.	.	.	.	.	.	.	.	A	11.84	1.758996	0.31137	.	.	ENSG00000169299	ENST00000381967	T	0.50548	0.74	6.05	4.83	0.62350	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I (1);Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);	0.511760	0.22952	N	0.053656	T	0.34513	0.0900	L	0.35542	1.07	0.21290	N	0.999732	B	0.11235	0.004	B	0.16722	0.016	T	0.11891	-1.0569	10	0.22706	T	0.39	-4.1688	9.7856	0.40675	0.8028:0.1291:0.068:0.0	.	92	Q96G03	PGM2_HUMAN	R	92	ENSP00000371393:Q92R	ENSP00000371393:Q92R	Q	+	2	0	PGM2	37512660	0.999000	0.42202	0.679000	0.29978	0.744000	0.42396	3.346000	0.52190	2.320000	0.78422	0.528000	0.53228	CAA		0.343	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290		88	112	0	0	0	1	0	88	112				
GAA	2548	broad.mit.edu	37	17	78079688	78079688	+	Silent	SNP	C	C	T	rs149814041		TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr17:78079688C>T	ENST00000302262.3	+	3	906	c.687C>T	c.(685-687)cgC>cgT	p.R229R	GAA_ENST00000390015.3_Silent_p.R229R	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	229					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	TGGACGGCCGCGTGCTGTGAG	0.657																																						uc002jxp.3																			0				autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21						c.(685-687)cgC>cgT		Homo sapiens glucosidase, alpha; acid (GAA), transcript variant 1, mRNA.	Acarbose(DB00284)	C	,,	0,4404		0,0,2202	36.0	34.0	34.0		687,687,687	-4.3	0.2	17	dbSNP_134	34	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	,,	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	,,	229/953,229/953,229/953	78079688	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	2548				cardiac muscle contraction|diaphragm contraction|glycogen catabolic process|lysosome organization|tongue morphogenesis|vacuolar sequestering|ventricular cardiac muscle tissue morphogenesis	lysosomal membrane	carbohydrate binding|maltose alpha-glucosidase activity	g.chr17:78079688C>T		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"""Pompe disease"", ""glycogen storage disease type II"""	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.687C>T	17.37:g.78079688C>T			Somatic				GAA_uc002jxo.3_Silent_p.R229R|GAA_uc002jxq.3_Silent_p.R229R	p.R229R	NM_000152	NP_001073272	WXS	Illumina GAIIx	Phase_I	P10253	LYAG_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		2	1054	+	all_neural(118;0.117)		229					Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	c.687C>T	CCDS32760.1																																																																																				0.657	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1			9	76	0	0	0	1	0	9	76				
DCC	1630	broad.mit.edu	37	18	50866169	50866169	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr18:50866169C>A	ENST00000442544.2	+	15	2867	c.2251C>A	c.(2251-2253)Cca>Aca	p.P751T	DCC_ENST00000412726.1_Missense_Mutation_p.P599T|DCC_ENST00000581580.1_Missense_Mutation_p.P406T	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	751	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TCCCTTGAACCCAAACATCGT	0.473																																						uc002lfe.2																			0				NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148						c.(2251-2253)Cca>Aca		Homo sapiens deleted in colorectal carcinoma (DCC), mRNA.							225.0	186.0	199.0					18																	50866169		2203	4300	6503	SO:0001583	missense	1630				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane		g.chr18:50866169C>A	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2251C>A	18.37:g.50866169C>A	ENSP00000389140:p.Pro751Thr		Somatic				DCC_uc010xdr.1_Missense_Mutation_p.P599T|DCC_uc010dpf.2_Missense_Mutation_p.P406T	p.P751T	NM_005215	NP_005206	WXS	Illumina GAIIx	Phase_I	P43146	DCC_HUMAN		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)	14	2867	+		all_cancers(7;0.11)|all_epithelial(6;0.00126)	751			Fibronectin type-III 4.			Missense_Mutation	SNP	ENST00000442544.2	37	c.2251C>A	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.852609	0.51270	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.57273	0.41;0.41	5.17	5.17	0.71159	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.58538	0.2129	L	0.48260	1.515	0.58432	D	0.999996	B;B;B	0.30664	0.018;0.018;0.289	B;B;B	0.43274	0.091;0.058;0.414	T	0.59653	-0.7414	10	0.52906	T	0.07	.	17.7948	0.88566	0.0:1.0:0.0:0.0	.	599;599;751	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	T	751;684;599	ENSP00000389140:P751T;ENSP00000397322:P599T	ENSP00000304146:P684T	P	+	1	0	DCC	49120167	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.541000	0.82084	2.565000	0.86533	0.655000	0.94253	CCA		0.473	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		7	96	0	0	0	1	0	7	96				
VIL1	7429	broad.mit.edu	37	2	219299353	219299353	+	Silent	SNP	G	G	A			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr2:219299353G>A	ENST00000248444.5	+	14	1693	c.1605G>A	c.(1603-1605)gcG>gcA	p.A535A	VIL1_ENST00000392114.2_Silent_p.A224A	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	535	Core.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGTCCCAGCGCGGGCCAATT	0.567																																						uc002via.3																			0				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(1603-1605)gcG>gcA		Homo sapiens villin 1 (VIL1), mRNA.							104.0	105.0	105.0					2																	219299353		2203	4300	6503	SO:0001819	synonymous_variant	7429				actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity	g.chr2:219299353G>A	X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.1605G>A	2.37:g.219299353G>A			Somatic				VIL1_uc010zke.2_Silent_p.A224A|VIL1_uc002vib.3_Silent_p.A535A	p.A535A	NM_007127	NP_009058	WXS	Illumina GAIIx	Phase_I	P09327	VILI_HUMAN		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	13	1670	+		Renal(207;0.0474)	535			Core.		B2R9A7|Q53S11|Q96AC8	Silent	SNP	ENST00000248444.5	37	c.1605G>A	CCDS2417.1																																																																																				0.567	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		4	118	0	0	0	1	0	4	118				
CCDC42	146849	broad.mit.edu	37	17	8647917	8647917	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr17:8647917C>T	ENST00000293845.3	-	1	237	c.11G>A	c.(10-12)gGc>gAc	p.G4D	CCDC42_ENST00000539522.2_Missense_Mutation_p.G4D	NM_144681.2	NP_653282.2	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42	4										kidney(1)|large_intestine(4)|lung(3)|ovary(1)	9						TTCCATGATGCCCAGACTCAT	0.612																																						uc002gln.3																			0				kidney(1)|large_intestine(4)|lung(3)|ovary(1)	9						c.(10-12)gGc>gAc		Homo sapiens coiled-coil domain containing 42 (CCDC42), transcript variant 1, mRNA.							91.0	77.0	82.0					17																	8647917		2203	4300	6503	SO:0001583	missense	146849							g.chr17:8647917C>T	AK057296	CCDS11145.1, CCDS54088.1	17p13.1	2012-05-28			ENSG00000161973	ENSG00000161973			26528	protein-coding gene	gene with protein product							Standard	NM_144681		Approved	FLJ32734, CCDC42A	uc002gln.3	Q96M95		ENST00000293845.3:c.11G>A	17.37:g.8647917C>T	ENSP00000293845:p.Gly4Asp		Somatic				CCDC42_uc002glo.3_Missense_Mutation_p.G4D	p.G4D	NM_144681	NP_653282	WXS	Illumina GAIIx	Phase_I	Q96M95	CCD42_HUMAN			0	238	-			4					Q8N6Q0	Missense_Mutation	SNP	ENST00000293845.3	37	c.11G>A	CCDS11145.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.426953	0.83667	.	.	ENSG00000161973	ENST00000293845;ENST00000539522	T;T	0.27402	1.67;1.76	5.14	5.14	0.70334	.	0.104471	0.42964	D	0.000638	T	0.36331	0.0963	N	0.19112	0.55	0.43175	D	0.994986	D	0.89917	1.0	D	0.87578	0.998	T	0.05370	-1.0889	10	0.09843	T	0.71	-26.3912	14.4624	0.67459	0.0:1.0:0.0:0.0	.	4	Q96M95	CCD42_HUMAN	D	4	ENSP00000293845:G4D;ENSP00000444359:G4D	ENSP00000293845:G4D	G	-	2	0	CCDC42	8588642	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.775000	0.47702	2.556000	0.86216	0.561000	0.74099	GGC		0.612	CCDC42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442491.1	NM_144681		34	46	0	0	0	1	0	34	46				
CDKL1	8814	broad.mit.edu	37	14	50877292	50877292	+	5'UTR	SNP	G	G	A			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr14:50877292G>A	ENST00000356146.1	-	0	110							Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)						heart development (GO:0007507)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12	all_epithelial(31;0.000746)|Breast(41;0.0102)					agtctgcaccgtagctgctag	0.498																																						uc010anu.2																			0				endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|stomach(1)	12						c.(109-111)taC>taT		Homo sapiens cyclin-dependent kinase-like 1 (CDC2-related kinase) (CDKL1), mRNA.							166.0	146.0	152.0					14																	50877292		876	1991	2867	SO:0001623	5_prime_UTR_variant	8814					cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity	g.chr14:50877292G>A	AF390028	CCDS9699.1, CCDS73637.1	14q21.3	2011-11-04			ENSG00000100490	ENSG00000100490		"""Cyclin-dependent kinases"""	1781	protein-coding gene	gene with protein product		603441				1639063, 7595554	Standard	XM_005268157		Approved	KKIALRE	uc010anu.2	Q00532	OTTHUMG00000140290	ENST00000356146.1:c.-2872C>T	14.37:g.50877292G>A			Somatic					p.Y37Y	NM_004196	NP_004187	WXS	Illumina GAIIx	Phase_I	Q00532	CDKL1_HUMAN			1	111	-	all_epithelial(31;0.000746)|Breast(41;0.0102)		0			Protein kinase.		Q2M3A4|Q6QUA0|Q8WXQ5	Silent	SNP	ENST00000356146.1	37	c.111C>T																																																																																					0.498	CDKL1-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000276873.2			4	117	0	0	0	1	0	4	117				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	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		Somatic					p.V600E	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	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		30	44	0	0	0	1	0	30	44				
TMEM63B	55362	broad.mit.edu	37	6	44119647	44119647	+	Missense_Mutation	SNP	G	G	T			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr6:44119647G>T	ENST00000259746.9	+	19	1921	c.1738G>T	c.(1738-1740)Ggc>Tgc	p.G580C	TMEM63B_ENST00000323267.6_Missense_Mutation_p.G580C			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	580					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			AGCCTTTATCGGCAACGCCAT	0.642											OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc003owr.3																			0				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35						c.(1738-1740)Ggc>Tgc		Homo sapiens transmembrane protein 63B (TMEM63B), mRNA.							111.0	80.0	91.0					6																	44119647		2203	4300	6503	SO:0001583	missense	55362					integral to membrane	nucleotide binding|protein binding	g.chr6:44119647G>T	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1738G>T	6.37:g.44119647G>T	ENSP00000259746:p.Gly580Cys		Somatic	OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	921	TMEM63B_uc003ows.3_Missense_Mutation_p.G483C|TMEM63B_uc010jyz.3_Non-coding_Transcript	p.G580C	NM_018426	NP_060896	WXS	Illumina GAIIx	Phase_I	Q5T3F8	TM63B_HUMAN	Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)		18	1802	+	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		580					B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Missense_Mutation	SNP	ENST00000259746.9	37	c.1738G>T	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	G	33	5.198558	0.94997	.	.	ENSG00000137216	ENST00000259746;ENST00000323267	T;T	0.35605	1.3;1.3	5.01	5.01	0.66863	Domain of unknown function DUF221 (1);	0.000000	0.85682	D	0.000000	T	0.63094	0.2482	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71411	-0.4601	10	0.87932	D	0	.	17.4887	0.87696	0.0:0.0:1.0:0.0	.	580	Q5T3F8	TM63B_HUMAN	C	580	ENSP00000259746:G580C;ENSP00000327154:G580C	ENSP00000259746:G580C	G	+	1	0	TMEM63B	44227625	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.578000	0.98200	2.618000	0.88619	0.460000	0.39030	GGC		0.642	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410		55	58	0	0	0	1	0	55	58				
RTTN	25914	broad.mit.edu	37	18	67872549	67872549	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr18:67872549G>C	ENST00000255674.6	-	2	320	c.34C>G	c.(34-36)Cat>Gat	p.H12D	RTTN_ENST00000437017.1_Missense_Mutation_p.H12D|RTTN_ENST00000454359.1_Missense_Mutation_p.H12D	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	12					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				GCCAGCTGATGACCTGTCAAC	0.483																																						uc002lkp.2																			0				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80						c.(34-36)Cat>Gat		Homo sapiens rotatin (RTTN), mRNA.							88.0	89.0	89.0					18																	67872549		1929	4130	6059	SO:0001583	missense	25914						binding	g.chr18:67872549G>C	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.34C>G	18.37:g.67872549G>C	ENSP00000255674:p.His12Asp		Somatic				RTTN_uc010xfb.1_5'UTR|RTTN_uc002lkq.1_Missense_Mutation_p.H12D	p.H12D	NM_173630	NP_775901	WXS	Illumina GAIIx	Phase_I	Q86VV8	RTTN_HUMAN			1	102	-		Esophageal squamous(42;0.129)	12					Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	c.34C>G	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.178865	0.57692	.	.	ENSG00000176225	ENST00000255674;ENST00000454359;ENST00000437017	T;T;T	0.61859	1.61;0.07;0.07	5.35	5.35	0.76521	Armadillo-type fold (2);	0.000000	0.64402	D	0.000001	T	0.75845	0.3905	M	0.68952	2.095	0.58432	D	0.999999	D;D	0.89917	1.0;0.994	D;P	0.91635	0.999;0.844	T	0.77667	-0.2502	10	0.66056	D	0.02	.	19.1024	0.93279	0.0:0.0:1.0:0.0	.	12;12	Q86VV8-2;Q86VV8	.;RTTN_HUMAN	D	12	ENSP00000255674:H12D;ENSP00000402352:H12D;ENSP00000399520:H12D	ENSP00000255674:H12D	H	-	1	0	RTTN	66023529	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	9.503000	0.97984	2.503000	0.84419	0.563000	0.77884	CAT		0.483	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		4	172	0	0	0	1	0	4	172				
EEF2K	29904	broad.mit.edu	37	16	22268620	22268620	+	Missense_Mutation	SNP	T	T	A			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr16:22268620T>A	ENST00000263026.5	+	8	1289	c.815T>A	c.(814-816)gTg>gAg	p.V272E		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	272	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CAGCTGATAGTGGTGGACATC	0.557																																					NSCLC(195;1411 2157 20319 27471 51856)	uc002dki.3																			0				breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29						c.(814-816)gTg>gAg		Homo sapiens eukaryotic elongation factor-2 kinase (EEF2K), mRNA.							141.0	118.0	126.0					16																	22268620		2197	4300	6497	SO:0001583	missense	29904				insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding	g.chr16:22268620T>A	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.815T>A	16.37:g.22268620T>A	ENSP00000263026:p.Val272Glu		Somatic				EEF2K_uc002dkh.3_Non-coding_Transcript	p.V272E	NM_013302	NP_037434	WXS	Illumina GAIIx	Phase_I	O00418	EF2K_HUMAN		GBM - Glioblastoma multiforme(48;0.0223)	7	1300	+			272			Alpha-type protein kinase.		Q8N588	Missense_Mutation	SNP	ENST00000263026.5	37	c.815T>A	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	T	34	5.309043	0.95629	.	.	ENSG00000103319	ENST00000263026	T	0.25749	1.78	5.87	5.87	0.94306	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.118831	0.56097	D	0.000032	T	0.64494	0.2603	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.76391	-0.2976	10	0.87932	D	0	-16.495	16.2813	0.82687	0.0:0.0:0.0:1.0	.	272	O00418	EF2K_HUMAN	E	272	ENSP00000263026:V272E	ENSP00000263026:V272E	V	+	2	0	EEF2K	22176121	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.493000	0.81493	2.244000	0.73946	0.533000	0.62120	GTG		0.557	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		6	157	0	0	0	1	0	6	157				
ZCWPW1	55063	broad.mit.edu	37	7	100014704	100014704	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr7:100014704G>A	ENST00000398027.2	-	6	711	c.464C>T	c.(463-465)aCt>aTt	p.T155I	ZCWPW1_ENST00000324725.6_Missense_Mutation_p.T34I|ZCWPW1_ENST00000490721.1_Missense_Mutation_p.T34I|ZCWPW1_ENST00000360951.4_Missense_Mutation_p.T155I	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	155							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGCATTATCAGTATCAGTAGC	0.433																																						uc003uut.3																			0				breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16						c.(463-465)aCt>aTt		Homo sapiens zinc finger, CW type with PWWP domain 1 (ZCWPW1), mRNA.							160.0	149.0	153.0					7																	100014704		1925	4135	6060	SO:0001583	missense	55063						zinc ion binding	g.chr7:100014704G>A	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"""zinc finger, CW-type with PWWP domain 1"""			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.464C>T	7.37:g.100014704G>A	ENSP00000381109:p.Thr155Ile		Somatic				ZCWPW1_uc011kjq.2_Missense_Mutation_p.T34I|ZCWPW1_uc003uur.3_Missense_Mutation_p.T34I|ZCWPW1_uc003uus.3_Missense_Mutation_p.T34I|ZCWPW1_uc011kjr.2_Missense_Mutation_p.T154I|ZCWPW1_uc003uuu.1_Missense_Mutation_p.T154I	p.T155I	NM_017984	NP_060454	WXS	Illumina GAIIx	Phase_I	Q9H0M4	ZCPW1_HUMAN			5	712	-	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		155					A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Missense_Mutation	SNP	ENST00000398027.2	37	c.464C>T	CCDS43623.1	.	.	.	.	.	.	.	.	.	.	G	2.874	-0.233407	0.05983	.	.	ENSG00000078487	ENST00000398027;ENST00000490721;ENST00000360951;ENST00000324725;ENST00000379559	T;T;T;T	0.45276	0.92;0.93;0.9;0.93	3.78	1.32	0.21799	.	0.437334	0.19518	N	0.112358	T	0.21674	0.0522	N	0.22421	0.69	0.09310	N	1	P;P;P;P;P	0.44521	0.837;0.627;0.627;0.627;0.744	B;B;B;B;B	0.38327	0.193;0.139;0.139;0.139;0.271	T	0.09185	-1.0686	9	.	.	.	-4.2503	4.2096	0.10505	0.1967:0.0:0.2274:0.5759	.	155;115;156;155;34	B4DUQ2;B4DXS7;C9J435;Q9H0M4;Q9H0M4-4	.;.;.;ZCPW1_HUMAN;.	I	155;34;155;34;156	ENSP00000381109:T155I;ENSP00000419187:T34I;ENSP00000354210:T155I;ENSP00000314880:T34I	.	T	-	2	0	ZCWPW1	99852640	0.803000	0.28956	0.026000	0.17262	0.070000	0.16714	0.593000	0.23999	0.274000	0.22072	-0.425000	0.05940	ACT		0.433	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		12	266	0	0	0	1	0	12	266				
SMARCA1	6594	broad.mit.edu	37	X	128657222	128657222	+	Silent	SNP	C	C	T			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chrX:128657222C>T	ENST00000371122.4	-	1	255	c.126G>A	c.(124-126)gcG>gcA	p.A42A	SMARCA1_ENST00000478420.1_5'UTR|SMARCA1_ENST00000371123.1_Silent_p.A42A|SMARCA1_ENST00000371121.3_Silent_p.A42A	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	42					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						CTTCGGTGGCCGCGGCGGCCG	0.667													c|||	1	0.000264901	0.0008	0.0	3775	,	,		6028	0.0		0.0	False		,,,				2504	0.0					uc011muk.1																			0				biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						c.(124-126)gcG>gcA		Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1), transcript variant 1, mRNA.							124.0	104.0	111.0					X																	128657222		2203	4300	6503	SO:0001819	synonymous_variant	6594				ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding	g.chrX:128657222C>T	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.126G>A	X.37:g.128657222C>T			Somatic				SMARCA1_uc004eun.4_Silent_p.A42A|SMARCA1_uc004eup.4_Silent_p.A42A|SMARCA1_uc011mul.1_Silent_p.A42A	p.A42A	NM_003069	NP_003060	WXS	Illumina GAIIx	Phase_I	P28370	SMCA1_HUMAN			0	239	-			42					Q5JV41|Q5JV42	Silent	SNP	ENST00000371122.4	37	c.126G>A	CCDS14612.1																																																																																				0.667	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		5	168	0	0	0	1	0	5	168				
GIT2	9815	broad.mit.edu	37	12	110433982	110433982	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EL-A3MW-01A-11D-A20C-08	TCGA-EL-A3MW-11A-11D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f349b8b-7642-4276-ad9a-5a76030309d8	ed837939-2741-45c0-90a3-8ec7995d5eb5	g.chr12:110433982delC	ENST00000355312.3	-	1	47	c.48delG	c.(46-48)gggfs	p.G16fs	GIT2_ENST00000354574.4_Frame_Shift_Del_p.G16fs|GIT2_ENST00000320063.9_Frame_Shift_Del_p.G16fs|GIT2_ENST00000553118.1_Frame_Shift_Del_p.G16fs|GIT2_ENST00000361006.5_Frame_Shift_Del_p.G16fs|GIT2_ENST00000457474.2_Frame_Shift_Del_p.G16fs|GIT2_ENST00000338373.5_Frame_Shift_Del_p.G16fs|GIT2_ENST00000547815.1_Frame_Shift_Del_p.G16fs|GIT2_ENST00000360185.4_Frame_Shift_Del_p.G16fs|GIT2_ENST00000356259.4_Frame_Shift_Del_p.G16fs|GIT2_ENST00000343646.5_Frame_Shift_Del_p.G16fs|GIT2_ENST00000551209.1_Frame_Shift_Del_p.G16fs	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	16	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						ACTCACCCGGCCCGCTGCAGT	0.731																																						uc001tps.2																			0				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						c.(46-48)gggfs		Homo sapiens G protein-coupled receptor kinase interacting ArfGAP 2 (GIT2), transcript variant 1, mRNA.							5.0	6.0	6.0					12																	110433982		2004	3927	5931	SO:0001589	frameshift_variant	9815				regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding	g.chr12:110433982delC	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4273	protein-coding gene	gene with protein product		608564	"""G protein-coupled receptor kinase interactor 2"""			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.48delG	12.37:g.110433982delC	ENSP00000347464:p.Gly16fs		Somatic				GIT2_uc001tpq.2_Frame_Shift_Del_p.G16fs|GIT2_uc001tpv.2_Frame_Shift_Del_p.G16fs|GIT2_uc001tpu.2_Frame_Shift_Del_p.G16fs|GIT2_uc001tpt.2_Frame_Shift_Del_p.G16fs|GIT2_uc010sxu.1_5'UTR|GIT2_uc001tpw.3_Frame_Shift_Del_p.G16fs|GIT2_uc010sxv.1_Frame_Shift_Del_p.G16fs	p.G16fs	NM_057169	NP_476510	WXS	Illumina GAIIx	Phase_I	Q14161	GIT2_HUMAN			0	213	-			16			Arf-GAP.		Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Frame_Shift_Del	DEL	ENST00000355312.3	37	c.48delG	CCDS9138.1																																																																																				0.731	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		2	4						2	4	---	---	---	---
