#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
THOC2	57187	broad.mit.edu	37	X	122830671	122830671	+	Missense_Mutation	SNP	G	G	C			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chrX:122830671G>C	ENST00000245838.8	-	6	398	c.367C>G	c.(367-369)Cta>Gta	p.L123V	THOC2_ENST00000355725.4_Missense_Mutation_p.L123V|THOC2_ENST00000491737.1_Missense_Mutation_p.L8V	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	123					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CGTTCCTTTAGAACTGTGTCT	0.318																																						uc004etu.3																			0				breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						c.(367-369)Cta>Gta		Homo sapiens THO complex 2 (THOC2), mRNA.							149.0	127.0	134.0					X																	122830671		1813	4066	5879	SO:0001583	missense	57187				RNA splicing|intronless viral mRNA export from host nucleus|mRNA processing	THO complex part of transcription export complex	RNA binding|protein binding	g.chrX:122830671G>C	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.367C>G	X.37:g.122830671G>C	ENSP00000245838:p.Leu123Val					THOC2_uc011muh.1_Missense_Mutation_p.L44V|THOC2_uc011mui.1_Missense_Mutation_p.L8V	p.L123V	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN			5	399	-			123					A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	37	c.367C>G	CCDS43988.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.383752	0.42308	.	.	ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737;ENST00000408933	.	.	.	5.77	1.94	0.25998	.	0.000000	0.47455	D	0.000221	T	0.79076	0.4385	M	0.84433	2.695	0.58432	D	0.999999	D;D	0.69078	0.997;0.996	D;D	0.78314	0.991;0.931	T	0.79184	-0.1908	9	0.54805	T	0.06	-5.7295	13.3716	0.60717	0.252:0.0:0.748:0.0	.	44;123	B4DKZ6;Q8NI27	.;THOC2_HUMAN	V	123;123;8;44	.	ENSP00000245838:L123V	L	-	1	2	THOC2	122658352	1.000000	0.71417	0.993000	0.49108	0.785000	0.44390	2.345000	0.44018	-0.019000	0.14055	-1.195000	0.01675	CTA		0.318	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			38	48	0	0	0	1	0	38	48				
HPX	3263	broad.mit.edu	37	11	6461365	6461365	+	Intron	SNP	A	A	C			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr11:6461365A>C	ENST00000265983.3	-	4	437				HPX_ENST00000525057.1_Intron	NM_000613.2	NP_000604.1	P02790	HEMO_HUMAN	hemopexin						cellular iron ion homeostasis (GO:0006879)|heme metabolic process (GO:0042168)|heme transport (GO:0015886)|hemoglobin metabolic process (GO:0020027)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|viral process (GO:0016032)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme transporter activity (GO:0015232)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(11)|prostate(1)	15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)		AGCCCTTTCCAGCCTGGCCCT	0.537																																						uc010rai.1																			0				endometrium(1)|large_intestine(2)|lung(11)|prostate(1)	15						c.(364-366)gcT>gcG		Homo sapiens hemopexin (HPX), mRNA.							78.0	70.0	72.0					11																	6461365		2201	4296	6497	SO:0001627	intron_variant	3263				cellular iron ion homeostasis|interspecies interaction between organisms	extracellular space	heme transporter activity|metal ion binding|protein binding	g.chr11:6461365A>C	J03048	CCDS7763.1	11p15.5-p15.4	2012-10-02			ENSG00000110169	ENSG00000110169			5171	protein-coding gene	gene with protein product		142290				2989777, 2842511	Standard	NM_000613		Approved		uc001mdg.2	P02790	OTTHUMG00000133399	ENST00000265983.3:c.336+29T>G	11.37:g.6461365A>C						HPX_uc001mdg.2_Intron|HPX_uc009yfc.2_Intron	p.A122A			P02790	HEMO_HUMAN		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)	3	427	-		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)	0			Hemopexin-like 2.		B2R957	Silent	SNP	ENST00000265983.3	37	c.366T>G	CCDS7763.1																																																																																				0.537	HPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257256.1	NM_000613		4	49	0	0	0	1	0	4	49				
ASMTL	8623	broad.mit.edu	37	X	1540713	1540713	+	Silent	SNP	C	C	T			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chrX:1540713C>T	ENST00000381317.3	-	9	1115	c.1083G>A	c.(1081-1083)gcG>gcA	p.A361A	ASMTL_ENST00000416733.2_Silent_p.A285A|ASMTL_ENST00000381333.4_Silent_p.A345A|ASMTL_ENST00000534940.1_Silent_p.A303A	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	361	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGTAGACGTTCGCTGTCTCTG	0.488													c|||	2	0.000399361	0.0015	0.0	5008	,	,		22567	0.0		0.0	False		,,,				2504	0.0					uc004cpx.2																			0				NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23						c.(1081-1083)gcG>gcA		Homo sapiens acetylserotonin O-methyltransferase-like (ASMTL), transcript variant 1, mRNA.			,,	7,4051		0,7,2022	341.0	344.0	343.0		909,1035,1083	-3.2	0.0	X		343	0,8386		0,0,4193	no	coding-synonymous,coding-synonymous,coding-synonymous	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	,,	0,7,6215	TT,TC,CC		0.0,0.1725,0.0563	,,	303/564,345/606,361/622	1540713	7,12437	2029	4193	6222	SO:0001819	synonymous_variant	8623				melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity	g.chrX:1540713C>T	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"""Pseudoautosomal regions / PAR1"""	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1083G>A	X.37:g.1540713C>T						CRLF2_uc022brt.1_Intron|ASMTL_uc004cpy.2_Silent_p.A345A|ASMTL_uc011mhe.2_Silent_p.A285A|ASMTL_uc011mhf.2_Silent_p.A303A	p.A361A	NM_004192	NP_001166944	O95671	ASML_HUMAN			8	1220	-		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)	361			ASMT-like.		B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	37	c.1083G>A	CCDS43917.1																																																																																				0.488	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		17	192	0	0	0	1	0	17	192				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333	NP_004324	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		34	35	0	0	0	1	0	34	35				
ALK	238	broad.mit.edu	37	2	29474117	29474117	+	Silent	SNP	G	G	A			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr2:29474117G>A	ENST00000389048.3	-	12	2964	c.2058C>T	c.(2056-2058)acC>acT	p.T686T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	686					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CCCCACATGTGGTGAACAGCC	0.652			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													uc002rmy.3			yes	Dom	yes	Familial neuroblastoma	2	2p23	238	"""T, Mis, A"""	anaplastic lymphoma kinase (Ki-1)			"""L, E, M"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	neuroblastoma	"""ALCL, NSCLC, Neuroblastoma"""	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	0				NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340						c.(2056-2058)acC>acT		Homo sapiens anaplastic lymphoma receptor tyrosine kinase (ALK), mRNA.	Adenosine triphosphate(DB00171)						30.0	33.0	32.0					2																	29474117		2203	4300	6503	SO:0001819	synonymous_variant	238	Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	g.chr2:29474117G>A	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.2058C>T	2.37:g.29474117G>A							p.T686T	NM_004304	NP_004295	Q9UM73	ALK_HUMAN			11	3010	-	Acute lymphoblastic leukemia(172;0.155)		686					Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	c.2058C>T	CCDS33172.1																																																																																				0.652	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		3	22	0	0	0	1	0	3	22				
ANO9	338440	broad.mit.edu	37	11	428731	428731	+	Silent	SNP	G	G	A			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr11:428731G>A	ENST00000332826.6	-	12	1095	c.1011C>T	c.(1009-1011)acC>acT	p.T337T		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	337					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						CCATGAGCAGGGTCAGGACGA	0.657																																						uc001lpi.2																			0				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						c.(1009-1011)acC>acT		Homo sapiens anoctamin 9 (ANO9), mRNA.							207.0	154.0	172.0					11																	428731		2198	4296	6494	SO:0001819	synonymous_variant	338440					chloride channel complex	chloride channel activity	g.chr11:428731G>A	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	20679	protein-coding gene	gene with protein product			"""tumor protein p53 inducible protein 5"", ""transmembrane protein 16J"""	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1011C>T	11.37:g.428731G>A						ANO9_uc001lph.2_Silent_p.T30T|ANO9_uc010qvv.1_Silent_p.T193T	p.T337T	NM_001012302	NP_001012302	A1A5B4	ANO9_HUMAN			11	1096	-			337					B3KUC4|B4E134|Q8TEN4	Silent	SNP	ENST00000332826.6	37	c.1011C>T	CCDS31326.1																																																																																				0.657	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		3	34	0	0	0	1	0	3	34				
MRGPRX4	117196	broad.mit.edu	37	11	18195430	18195430	+	Missense_Mutation	SNP	G	G	A	rs200217617		TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr11:18195430G>A	ENST00000314254.3	+	1	1047	c.627G>A	c.(625-627)atG>atA	p.M209I	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CCCGGAAGATGCCGCTGACCA	0.562																																						uc001mnv.1																			0				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						c.(625-627)atG>atA		Homo sapiens MAS-related GPR, member X4 (MRGPRX4), mRNA.							106.0	99.0	101.0					11																	18195430		2199	4293	6492	SO:0001583	missense	117196					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr11:18195430G>A	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.627G>A	11.37:g.18195430G>A	ENSP00000314042:p.Met209Ile						p.M209I	NM_054032	NP_473373	Q96LA9	MRGX4_HUMAN			0	1047	+			209					Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	c.627G>A	CCDS7831.1	.	.	.	.	.	.	.	.	.	.	G	1.037	-0.680012	0.03353	.	.	ENSG00000179817	ENST00000314254	T	0.36878	1.23	2.85	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	1.908680	0.02837	N	0.127499	T	0.21062	0.0507	N	0.10645	0.015	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.11324	-1.0592	10	0.06757	T	0.87	.	11.4502	0.50147	0.0:0.0:1.0:0.0	.	209	Q96LA9	MRGX4_HUMAN	I	209	ENSP00000314042:M209I	ENSP00000314042:M209I	M	+	3	0	MRGPRX4	18152006	0.000000	0.05858	0.002000	0.10522	0.038000	0.13279	-0.828000	0.04419	1.616000	0.50265	0.430000	0.28490	ATG		0.562	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		7	67	0	0	0	1	0	7	67				
RP1	6101	broad.mit.edu	37	8	55538950	55538950	+	Silent	SNP	G	G	T			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr8:55538950G>T	ENST00000220676.1	+	4	2656	c.2508G>T	c.(2506-2508)ccG>ccT	p.P836P		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	836					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TTTATGCACCGCAATCTCAAG	0.328																																					Colon(91;1014 1389 7634 14542 40420)	uc003xsd.1																			0				NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169						c.(2506-2508)ccG>ccT		Homo sapiens retinitis pigmentosa 1 (autosomal dominant) (RP1), mRNA.							42.0	46.0	45.0					8																	55538950		2200	4297	6497	SO:0001819	synonymous_variant	6101				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding	g.chr8:55538950G>T	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2508G>T	8.37:g.55538950G>T						RP1_uc011ldy.1_Intron	p.P836P	NM_006269	NP_006260	P56715	RP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)		3	2656	+		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	836						Silent	SNP	ENST00000220676.1	37	c.2508G>T	CCDS6160.1																																																																																				0.328	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		20	35	0	0	0	1	0	20	35				
CD5L	922	broad.mit.edu	37	1	157804272	157804272	+	Missense_Mutation	SNP	G	G	T			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr1:157804272G>T	ENST00000368174.4	-	4	739	c.643C>A	c.(643-645)Ctt>Att	p.L215I	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	215	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CAATCCTGAAGGGTTGCTTCT	0.532																																						uc001frk.4																			0				NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52						c.(643-645)Ctt>Att		Homo sapiens CD5 molecule-like (CD5L), mRNA.							62.0	53.0	56.0					1																	157804272		2203	4300	6503	SO:0001583	missense	922				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity	g.chr1:157804272G>T	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"""apoptosis inhibitor 6"", ""CD5 antigen-like (scavenger receptor cysteine rich family)"""	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.643C>A	1.37:g.157804272G>T	ENSP00000357156:p.Leu215Ile						p.L215I	NM_005894	NP_005885	O43866	CD5L_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.24)		3	786	-	all_hematologic(112;0.0378)		215			SRCR 2.		A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	c.643C>A	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.627757	0.46944	.	.	ENSG00000073754	ENST00000368174	T	0.58060	0.36	4.97	1.95	0.26073	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.179488	0.27080	N	0.021039	T	0.40247	0.1109	L	0.58925	1.835	0.09310	N	1	D	0.59357	0.985	P	0.52823	0.71	T	0.27088	-1.0084	10	0.51188	T	0.08	.	9.0118	0.36146	0.0:0.1432:0.5607:0.2961	.	215	O43866	CD5L_HUMAN	I	215	ENSP00000357156:L215I	ENSP00000357156:L215I	L	-	1	0	CD5L	156070896	0.987000	0.35691	0.002000	0.10522	0.245000	0.25701	1.852000	0.39348	0.236000	0.21180	0.655000	0.94253	CTT		0.532	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894		3	42	0	0	0	1	0	3	42				
NUTM1	256646	broad.mit.edu	37	15	34649616	34649616	+	Missense_Mutation	SNP	G	G	A	rs138691157	byFrequency	TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr15:34649616G>A	ENST00000333756.4	+	7	3478	c.3323G>A	c.(3322-3324)cGa>cAa	p.R1108Q	NUTM1_ENST00000438749.3_Missense_Mutation_p.R1126Q|NUTM1_ENST00000537011.1_Missense_Mutation_p.R1136Q	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1108						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GGAGTAGTTCGACCCTCACAG	0.587																																						uc010ucc.2										T					"""BRD3, BRD4"""		lethal midline carcinoma	BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	0				large_intestine(2)|ovary(3)|skin(2)	7						c.(3406-3408)cGa>cAa		Homo sapiens chromosome 15 open reading frame 55 (C15orf55), mRNA.		G	GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	60.0	63.0	62.0		3323	-3.2	0.0	15	dbSNP_134	62	12,8584	9.1+/-34.3	0,12,4286	yes	missense	C15orf55	NM_175741.1	43	0,13,6486	AA,AG,GG		0.1396,0.0227,0.1	benign	1108/1133	34649616	13,12985	2201	4298	6499	SO:0001583	missense	256646					cytoplasm|nucleus		g.chr15:34649616G>A	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3323G>A	15.37:g.34649616G>A	ENSP00000329448:p.Arg1108Gln					C15orf55_uc010ucd.2_Missense_Mutation_p.R1126Q|C15orf55_uc001zif.3_Missense_Mutation_p.R1108Q	p.R1136Q	NM_175741	NP_786883	Q86Y26	NUT_HUMAN		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)	7	3789	+		all_lung(180;2.78e-08)	1108					B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	c.3407G>A	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	G	10.00	1.233259	0.22626	2.27E-4	0.001396	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.58358	0.34;0.34;0.34	5.93	-3.15	0.05233	.	1.269900	0.05643	N	0.583876	T	0.34308	0.0893	L	0.28192	0.835	0.09310	N	1	B;B;B	0.22480	0.007;0.028;0.07	B;B;B	0.13407	0.004;0.009;0.003	T	0.21621	-1.0240	10	0.34782	T	0.22	.	5.5732	0.17208	0.4475:0.2524:0.3001:0.0	.	1126;1136;1108	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	Q	1136;1126;1108	ENSP00000444896:R1136Q;ENSP00000407031:R1126Q;ENSP00000329448:R1108Q	ENSP00000329448:R1108Q	R	+	2	0	C15orf55	32436908	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.015000	0.12634	-0.215000	0.10063	-0.137000	0.14449	CGA		0.587	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		5	93	0	0	0	1	0	5	93				
RAB27A	5873	broad.mit.edu	37	15	55497812	55497812	+	Missense_Mutation	SNP	G	G	A	rs144946000		TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr15:55497812G>A	ENST00000396307.2	-	6	810	c.559C>T	c.(559-561)Cgg>Tgg	p.R187W	RAB27A_ENST00000564609.1_Missense_Mutation_p.R187W|RAB27A_ENST00000569493.1_Missense_Mutation_p.R187W|RAB27A_ENST00000336787.1_Missense_Mutation_p.R187W	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	187					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		TCCACACACCGTTCCATTCGC	0.473													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19073	0.0		0.0	False		,,,				2504	0.0					uc002acr.3																			0				endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9						c.(559-561)Cgg>Tgg		Homo sapiens RAB27A, member RAS oncogene family (RAB27A), transcript variant 3, mRNA.		G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4385	2.1+/-5.4	0,1,2192	357.0	286.0	310.0		559,559,559,559	2.4	1.0	15	dbSNP_134	310	2,8582	2.2+/-6.3	0,2,4290	yes	missense,missense,missense,missense	RAB27A	NM_004580.4,NM_183234.2,NM_183235.2,NM_183236.2	101,101,101,101	0,3,6482	AA,AG,GG		0.0233,0.0228,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	187/222,187/222,187/222,187/222	55497812	3,12967	2193	4292	6485	SO:0001583	missense	5873				small GTPase mediated signal transduction	dendrite|exocytic vesicle|late endosome|lysosome|melanosome	GTP binding|GTPase activity	g.chr15:55497812G>A	U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"""RAB, member RAS oncogene"""	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.559C>T	15.37:g.55497812G>A	ENSP00000379601:p.Arg187Trp					RAB27A_uc002aco.3_Missense_Mutation_p.R187W|RAB27A_uc002acp.3_Missense_Mutation_p.R187W|RAB27A_uc002acq.3_Missense_Mutation_p.R187W	p.R187W	NM_183235	NP_899059	P51159	RB27A_HUMAN		all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)	6	801	-			187					O00195|Q6FI40|Q9UIR9|Q9Y5U3	Missense_Mutation	SNP	ENST00000396307.2	37	c.559C>T	CCDS10153.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	21.4	4.138707	0.77775	2.28E-4	2.33E-4	ENSG00000069974	ENST00000396307;ENST00000396304;ENST00000336787	T;T	0.69685	-0.42;-0.42	5.49	2.36	0.29203	.	0.055502	0.64402	D	0.000001	T	0.47875	0.1469	N	0.08118	0	0.58432	D	0.999999	D	0.67145	0.996	B	0.43728	0.429	T	0.57568	-0.7789	10	0.87932	D	0	-2.787	13.729	0.62776	0.0:0.0:0.5984:0.4016	.	187	P51159	RB27A_HUMAN	W	187;179;187	ENSP00000379601:R187W;ENSP00000337761:R187W	ENSP00000337761:R187W	R	-	1	2	RAB27A	53285104	1.000000	0.71417	0.975000	0.42487	0.992000	0.81027	3.696000	0.54757	0.632000	0.30432	0.655000	0.94253	CGG		0.473	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236		12	118	0	0	0	1	0	12	118				
SNX21	90203	broad.mit.edu	37	20	44463079	44463079	+	Silent	SNP	C	C	A			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr20:44463079C>A	ENST00000491381.1	+	2	329	c.261C>A	c.(259-261)ctC>ctA	p.L87L	SNX21_ENST00000344780.4_3'UTR|SNX21_ENST00000372542.1_Silent_p.L78L|SNX21_ENST00000462307.1_Silent_p.L87L|TNNC2_ENST00000372557.1_5'Flank|SNX21_ENST00000372541.1_Silent_p.L78L|SNX21_ENST00000342644.5_Silent_p.L87L			Q969T3	SNX21_HUMAN	sorting nexin family member 21	87					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				AGCTGCCCCTCGGGGATGGGA	0.692																																						uc002xpv.1																			0				breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7						c.(259-261)ctC>ctA		Homo sapiens sorting nexin family member 21 (SNX21), transcript variant 1, mRNA.							23.0	30.0	27.0					20																	44463079		2201	4297	6498	SO:0001819	synonymous_variant	90203				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding	g.chr20:44463079C>A	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.261C>A	20.37:g.44463079C>A						SNX21_uc002xpt.1_Silent_p.L87L|SNX21_uc002xps.1_Silent_p.L87L|SNX21_uc002xpu.1_Silent_p.L87L|SNX21_uc002xpw.1_5'UTR|SNX21_uc010zxd.1_Silent_p.L78L|SNX21_uc002xpy.1_5'Flank	p.L87L	NM_033421	NP_219489	Q969T3	SNX21_HUMAN			1	350	+		Myeloproliferative disorder(115;0.0122)	87					Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Silent	SNP	ENST00000491381.1	37	c.261C>A	CCDS13377.1																																																																																				0.692	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421		3	22	0	0	0	1	0	3	22				
ZNF702P	79986	broad.mit.edu	37	19	53472683	53472683	+	RNA	SNP	C	C	T			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr19:53472683C>T	ENST00000600068.1	-	0	489				ZNF702P_ENST00000270443.4_RNA																							CTGTCACACTCATCACACTTG	0.423																																						uc002qan.4																			0													Homo sapiens zinc finger protein 702, pseudogene (ZNF702P), non-coding RNA.																																						79986							g.chr19:53472683C>T																													19.37:g.53472683C>T														3		-									RNA	SNP	ENST00000600068.1	37	c.1818G>A																																																																																					0.423	CTD-2620I22.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000463881.1			17	19	0	0	0	1	0	17	19				
TBCCD1	55171	broad.mit.edu	37	3	186268971	186268971	+	Missense_Mutation	SNP	G	G	C			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr3:186268971G>C	ENST00000424280.1	-	7	2121	c.1642C>G	c.(1642-1644)Cct>Gct	p.P548A	TBCCD1_ENST00000479590.1_5'Flank|TBCCD1_ENST00000338733.5_Missense_Mutation_p.P548A|TBCCD1_ENST00000446782.1_Missense_Mutation_p.P452A	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	548					cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		CCTGCTGCAGGGGGTACAAGG	0.443																																						uc003fqg.3																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17						c.(1642-1644)Cct>Gct		Homo sapiens TBCC domain containing 1 (TBCCD1), transcript variant 2, mRNA.							121.0	115.0	117.0					3																	186268971		2203	4300	6503	SO:0001583	missense	55171				cell morphogenesis|maintenance of Golgi location|maintenance of centrosome location|regulation of cell migration|regulation of cell shape	spindle pole centrosome	binding	g.chr3:186268971G>C	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.1642C>G	3.37:g.186268971G>C	ENSP00000411253:p.Pro548Ala					TBCCD1_uc011bry.2_Missense_Mutation_p.P548A|TBCCD1_uc003fqh.3_Missense_Mutation_p.P452A	p.P548A	NM_018138	NP_060608	Q9NVR7	TBCC1_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)	6	1771	-	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		548					B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	37	c.1642C>G	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.193680	0.38707	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782	D;D;D	0.83914	-1.78;-1.78;-1.78	5.39	4.51	0.55191	.	0.063541	0.64402	D	0.000005	T	0.78597	0.4308	L	0.50333	1.59	0.37858	D	0.929633	B;B	0.21905	0.026;0.062	B;B	0.22601	0.04;0.019	T	0.77319	-0.2632	10	0.54805	T	0.06	-13.087	11.7007	0.51569	0.0:0.0:0.824:0.1759	.	452;548	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	A	548;548;452	ENSP00000411253:P548A;ENSP00000341652:P548A;ENSP00000397091:P452A	ENSP00000341652:P548A	P	-	1	0	TBCCD1	187751665	1.000000	0.71417	0.984000	0.44739	0.955000	0.61496	3.839000	0.55835	1.246000	0.43901	0.650000	0.86243	CCT		0.443	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138		33	44	0	0	0	1	0	33	44				
SPNS1	83985	broad.mit.edu	37	16	28990543	28990543	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr16:28990543C>T	ENST00000311008.11	+	4	889	c.512C>T	c.(511-513)gCg>gTg	p.A171V	SPNS1_ENST00000323081.8_Missense_Mutation_p.A98V|SPNS1_ENST00000561868.1_3'UTR|SPNS1_ENST00000334536.8_Missense_Mutation_p.A171V|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000352260.7_Missense_Mutation_p.A149V|SPNS1_ENST00000565975.1_Missense_Mutation_p.A216V|RP11-264B17.4_ENST00000567209.1_RNA	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	171					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						TCCACCATCGCGCCCACTCTC	0.657																																						uc010vdi.1																			0				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						c.(511-513)gCg>gTg		Homo sapiens spinster homolog 1 (Drosophila) (SPNS1), transcript variant 2, mRNA.							60.0	62.0	62.0					16																	28990543		2197	4300	6497	SO:0001583	missense	83985				lipid transport|transmembrane transport	integral to membrane|mitochondrial inner membrane	protein binding	g.chr16:28990543C>T	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.512C>T	16.37:g.28990543C>T	ENSP00000309945:p.Ala171Val					NPIPL1_uc010vct.2_Intron|SPNS1_uc002dry.2_Missense_Mutation_p.A171V|SPNS1_uc002drx.2_Missense_Mutation_p.A98V|SPNS1_uc002dsa.2_Missense_Mutation_p.A171V|SPNS1_uc002drz.2_Missense_Mutation_p.A171V|SPNS1_uc010byp.2_Missense_Mutation_p.A149V	p.A171V	NM_001142448	NP_001135922	Q9H2V7	SPNS1_HUMAN			4	652	+			171					B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Missense_Mutation	SNP	ENST00000311008.11	37	c.512C>T	CCDS10646.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.680748	0.68042	.	.	ENSG00000169682	ENST00000311008;ENST00000334536;ENST00000352260;ENST00000323081	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	4.34	4.34	0.51931	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	M	0.78801	2.425	0.80722	D	1	P;D;P;D;D	0.76494	0.942;0.989;0.867;0.999;0.998	P;P;P;D;D	0.66979	0.711;0.784;0.821;0.939;0.948	T	0.78848	-0.2042	10	0.87932	D	0	.	14.3725	0.66849	0.0:1.0:0.0:0.0	.	98;149;171;171;171	Q9H2V7-4;Q9H2V7-3;Q9H2V7;Q9H2V7-2;Q9H2V7-5	.;.;SPNS1_HUMAN;.;.	V	171;171;149;98	ENSP00000309945:A171V;ENSP00000335494:A171V;ENSP00000306050:A149V;ENSP00000318228:A98V	ENSP00000309945:A171V	A	+	2	0	SPNS1	28898044	1.000000	0.71417	0.970000	0.41538	0.024000	0.10985	7.271000	0.78506	2.261000	0.74972	0.561000	0.74099	GCG		0.657	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		33	63	0	0	0	1	0	33	63				
CAND1	55832	broad.mit.edu	37	12	67696298	67696298	+	Missense_Mutation	SNP	T	T	G			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr12:67696298T>G	ENST00000545606.1	+	8	1633	c.1196T>G	c.(1195-1197)cTt>cGt	p.L399R		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	399					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		CACGCATACCTTTCTCTTTTG	0.428																																						uc001stn.2																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35						c.(1195-1197)cTt>cGt		Homo sapiens cullin-associated and neddylation-dissociated 1 (CAND1), mRNA.							183.0	154.0	164.0					12																	67696298		2203	4300	6503	SO:0001583	missense	55832				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding	g.chr12:67696298T>G		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"""TBP interacting protein"""	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.1196T>G	12.37:g.67696298T>G	ENSP00000442318:p.Leu399Arg					CAND1_uc001sto.2_Missense_Mutation_p.L77R	p.L399R	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)	7	1633	+			399					B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	37	c.1196T>G	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675221	0.67928	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047;ENST00000544619	D;D	0.89050	-2.46;-2.46	5.65	5.65	0.86999	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91905	0.7437	L	0.42245	1.32	0.80722	D	1	D;P	0.69078	0.997;0.902	D;B	0.78314	0.991;0.367	D	0.91156	0.4957	9	.	.	.	-13.0718	16.1864	0.81955	0.0:0.0:0.0:1.0	.	399;399	Q86VP6-2;Q86VP6	.;CAND1_HUMAN	R	399;399;241;107	ENSP00000442318:L399R;ENSP00000444089:L107R	.	L	+	2	0	CAND1	65982565	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.224000	0.72265	2.281000	0.76405	0.528000	0.53228	CTT		0.428	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		6	137	0	0	0	1	0	6	137				
SNRNP70	6625	broad.mit.edu	37	19	49611420	49611420	+	Frame_Shift_Del	DEL	A	A	-			TCGA-ET-A39T-01A-11D-A19J-08	TCGA-ET-A39T-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0cbd1f35-6cf8-4768-a951-02b2ceeef3ab	a1ac32fc-556d-4096-b3db-fa8a584925f3	g.chr19:49611420delA	ENST00000598441.1	+	10	1258	c.1034delA	c.(1033-1035)gaafs	p.E345fs	SNRNP70_ENST00000221448.5_Frame_Shift_Del_p.E336fs			P08621	RU17_HUMAN	small nuclear ribonucleoprotein 70kDa (U1)	345	Arg/Asp/Glu-rich (mixed charge).				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						GGTCCAGAGGAAAAgggccgg	0.746																																						uc002pmk.3																			0				cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						c.(1033-1035)gaafs		Homo sapiens small nuclear ribonucleoprotein 70kDa (U1) (SNRNP70), mRNA.							3.0	5.0	4.0					19																	49611420		1836	3674	5510	SO:0001589	frameshift_variant	6625				nuclear mRNA splicing, via spliceosome|regulation of RNA splicing	nucleoplasm|spliceosomal complex	RNA binding|nucleotide binding|protein binding	g.chr19:49611420delA		CCDS12756.1, CCDS74417.1	19q13.3	2013-02-12	2008-10-29	2008-10-29		ENSG00000104852		"""RNA binding motif (RRM) containing"""	11150	protein-coding gene	gene with protein product		180740	"""small nuclear ribonucleoprotein 70kDa (RNP antigen)"""	RNPU1Z, RPU1, SNRP70			Standard	XM_005259177		Approved	U1-70K, Snp1	uc021uxh.1	P08621		ENST00000598441.1:c.1034delA	19.37:g.49611420delA	ENSP00000472998:p.Glu345fs					SNRNP70_uc002pmh.2_Non-coding_Transcript|SNRNP70_uc002pmm.3_Non-coding_Transcript|SNRNP70_uc021uxh.1_Frame_Shift_Del_p.K132fs	p.E345fs	NM_003089	NP_003080	P08621	RU17_HUMAN			9	1473	+			345			Arg/Asp/Glu-rich (mixed charge).		B3KUA3|P78493|P78494|Q15364|Q15686|Q15687|Q15689|Q99377|Q9UE45|Q9UE46|Q9UE47|Q9UE48|Q9UFQ6	Frame_Shift_Del	DEL	ENST00000598441.1	37	c.1034delA	CCDS12756.1																																																																																				0.746	SNRNP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466266.1	NM_003089		2	4						2	4	---	---	---	---
