#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
DRD5	1816	broad.mit.edu	37	4	9783838	9783838	+	Missense_Mutation	SNP	G	G	C	rs2227840	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr4:9783838G>C	ENST00000304374.2	+	1	581	c.185G>C	c.(184-186)tGc>tCc	p.C62S		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	62			C -> S (in dbSNP:rs2227840).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GTGCTGGTGTGCGCAGCCATC	0.662																																						ENST00000304374.2																			0				NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57						c.(184-186)tGc>tCc		dopamine receptor D5	Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)						30.0	24.0	26.0					4																	9783838		2203	4299	6502	SO:0001583	missense	0				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane		g.chr4:9783838G>C	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.185G>C	4.37:g.9783838G>C	ENSP00000306129:p.Cys62Ser						p.C62S	NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN			1	581	+			62		C -> S (in dbSNP:rs2227840).			B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	c.185G>C	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	g	15.32	2.798139	0.50208	.	.	ENSG00000169676	ENST00000304374	T	0.73047	-0.71	3.87	3.87	0.44632	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.80959	0.4724	M	0.91717	3.235	0.80722	D	1	P	0.47034	0.889	P	0.47786	0.557	D	0.86816	0.2001	10	0.87932	D	0	.	14.9917	0.71393	0.0:0.0:1.0:0.0	rs2227840	62	P21918	DRD5_HUMAN	S	62	ENSP00000306129:C62S	ENSP00000306129:C62S	C	+	2	0	DRD5	9392936	1.000000	0.71417	0.922000	0.36590	0.290000	0.27261	9.199000	0.95003	1.982000	0.57802	0.305000	0.20034	TGC		0.662	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			4	50	0	0	0	1	0	4	50				
ANKRD36	375248	broad.mit.edu	37	2	97866233	97866233	+	Missense_Mutation	SNP	A	A	G	rs573775748	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr2:97866233A>G	ENST00000461153.2	+	46	3072	c.2828A>G	c.(2827-2829)gAa>gGa	p.E943G	ANKRD36_ENST00000420699.2_Missense_Mutation_p.E943G			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	943										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						ATAACCAGAGAAAAAAAGGAT	0.333													.|||	16	0.00319489	0.0	0.0	5008	,	,		29505	0.0159		0.0	False		,,,				2504	0.0					ENST00000420699.2																			0				endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						c.(2827-2829)gAa>gGa		ankyrin repeat domain 36							120.0	124.0	123.0					2																	97866233		692	1591	2283	SO:0001583	missense	375248							g.chr2:97866233A>G	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.2828A>G	2.37:g.97866233A>G	ENSP00000419530:p.Glu943Gly					ANKRD36_ENST00000461153.2_Missense_Mutation_p.E943G	p.E943G	NM_001164315.1	NP_001157787.1	A6QL64	AN36A_HUMAN			46	3072	+			943					B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	c.2828A>G	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	10.06	1.246417	0.22796	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	T;T	0.78816	-1.21;-1.21	0.85	-0.345	0.12624	.	.	.	.	.	T	0.51261	0.1664	N	0.04636	-0.2	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38929	-0.9638	9	0.52906	T	0.07	.	3.2628	0.06854	0.3476:0.0:0.6524:0.0	.	943	A6QL64	AN36A_HUMAN	G	943;943;305	ENSP00000419530:E943G;ENSP00000391950:E943G	ENSP00000391950:E943G	E	+	2	0	ANKRD36	97229960	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	-0.388000	0.07352	-0.094000	0.12374	0.136000	0.15936	GAA		0.333	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5			7	10	0	0	0	1	0	7	10				
TLE3	7090	broad.mit.edu	37	15	70366914	70366914	+	Silent	SNP	G	G	A	rs376875838		TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr15:70366914G>A	ENST00000558939.1	-	6	1707	c.330C>T	c.(328-330)cgC>cgT	p.R110R	TLE3_ENST00000560939.1_Silent_p.R116R|TLE3_ENST00000440567.3_Silent_p.R103R|TLE3_ENST00000558379.1_Silent_p.R110R|TLE3_ENST00000559048.1_Silent_p.R116R|TLE3_ENST00000560589.1_Silent_p.R54R|TLE3_ENST00000451782.2_Silent_p.R110R|TLE3_ENST00000558201.1_Silent_p.R116R|TLE3_ENST00000539550.1_Silent_p.R44R|TLE3_ENST00000442299.2_Silent_p.R110R|TLE3_ENST00000557997.1_Silent_p.R110R|TLE3_ENST00000559929.1_Silent_p.R110R|TLE3_ENST00000557907.1_Silent_p.R110R|TLE3_ENST00000317509.8_Silent_p.R110R|TLE3_ENST00000559191.1_Intron	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	110	Gln-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CCTGCTTGGCGCGCTCCACTG	0.587																																						ENST00000558939.1																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						c.(328-330)cgC>cgT		transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)		G	,,	0,4384		0,0,2192	65.0	72.0	69.0		330,330,330	-5.6	1.0	15		69	1,8581		0,1,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	0,1,6482	AA,AG,GG		0.0117,0.0,0.0077	,,	110/770,110/773,110/761	70366914	1,12965	2192	4291	6483	SO:0001819	synonymous_variant	7090				organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding	g.chr15:70366914G>A	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.330C>T	15.37:g.70366914G>A						TLE3_ENST00000558379.1_Silent_p.R110R|TLE3_ENST00000451782.2_Silent_p.R110R|TLE3_ENST00000560939.1_Silent_p.R116R|TLE3_ENST00000559929.1_Silent_p.R110R|TLE3_ENST00000559048.1_Silent_p.R116R|TLE3_ENST00000557997.1_Silent_p.R110R|TLE3_ENST00000317509.8_Silent_p.R110R|TLE3_ENST00000442299.2_Silent_p.R110R|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000558201.1_Silent_p.R116R|TLE3_ENST00000560589.1_Silent_p.R54R|TLE3_ENST00000557907.1_Silent_p.R110R|TLE3_ENST00000440567.3_Silent_p.R103R|TLE3_ENST00000539550.1_Silent_p.R44R	p.R110R			Q04726	TLE3_HUMAN			6	1707	-			110			Gln-rich.		B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	c.330C>T	CCDS45293.1																																																																																				0.587	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078		15	9	0	0	0	1	0	15	9				
USH2A	7399	broad.mit.edu	37	1	216011417	216011417	+	Missense_Mutation	SNP	A	A	G			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr1:216011417A>G	ENST00000307340.3	-	47	9673	c.9287T>C	c.(9286-9288)gTg>gCg	p.V3096A	USH2A_ENST00000366943.2_Missense_Mutation_p.V3096A	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3096	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATTGCTTTTCACGCAGGCATA	0.368										HNSCC(13;0.011)																												ENST00000366943.2																			0				NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(9286-9288)gTg>gCg		Usher syndrome 2A (autosomal recessive, mild)							228.0	206.0	214.0					1																	216011417		2203	4300	6503	SO:0001583	missense	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:216011417A>G	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9287T>C	1.37:g.216011417A>G	ENSP00000305941:p.Val3096Ala	HNSCC(13;0.011)				USH2A_ENST00000307340.3_Missense_Mutation_p.V3096A	p.V3096A			O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	47	9673	-			3096			Fibronectin type-III 17.		Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	c.9287T>C	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.274008	0.23221	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.52983	0.64;0.64	5.01	-0.12	0.13539	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.368167	0.19296	N	0.117756	T	0.31638	0.0803	L	0.46157	1.445	0.39159	D	0.962363	B	0.12013	0.005	B	0.11329	0.006	T	0.33624	-0.9861	10	0.02654	T	1	.	9.3886	0.38359	0.7104:0.0:0.2896:0.0	.	3096	O75445	USH2A_HUMAN	A	3096	ENSP00000305941:V3096A;ENSP00000355910:V3096A	ENSP00000305941:V3096A	V	-	2	0	USH2A	214078040	0.902000	0.30710	0.994000	0.49952	0.325000	0.28411	1.499000	0.35671	-0.015000	0.14150	-0.290000	0.09829	GTG		0.368	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		4	140	0	0	0	1	0	4	140				
ARHGEF5	7984	broad.mit.edu	37	7	144060770	144060770	+	Silent	SNP	T	T	C	rs141931104		TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr7:144060770T>C	ENST00000056217.5	+	2	1182	c.1008T>C	c.(1006-1008)aaT>aaC	p.N336N	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	336					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N336N(5)		breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					CAGAAGAGAATAGGGCGGACT	0.512																																						ENST00000056217.5																			5	Substitution - coding silent(5)	p.N336N(5)	endometrium(2)|lung(1)|prostate(1)|kidney(1)	breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						c.(1006-1008)aaT>aaC		Rho guanine nucleotide exchange factor (GEF) 5		T		4,4184		0,4,2090	143.0	127.0	132.0		1008	-7.7	0.0	7	dbSNP_134	132	12,8044		0,12,4016	no	coding-synonymous	ARHGEF5	NM_005435.3		0,16,6106	CC,CT,TT		0.149,0.0955,0.1307		336/1598	144060770	16,12228	2094	4028	6122	SO:0001819	synonymous_variant	7984				intracellular signal transduction|regulation of Rho protein signal transduction	intracellular	GTP binding|protein binding|Rho guanyl-nucleotide exchange factor activity	g.chr7:144060770T>C	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.1008T>C	7.37:g.144060770T>C							p.N336N	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN			2	1182	+	Melanoma(164;0.14)		336					A6NNJ2|Q6ZML7	Silent	SNP	ENST00000056217.5	37	c.1008T>C	CCDS34771.1																																																																																				0.512	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435		5	98	0	0	0	1	0	5	98				
MTMR4	9110	broad.mit.edu	37	17	56582201	56582201	+	Missense_Mutation	SNP	C	C	T			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr17:56582201C>T	ENST00000323456.5	-	12	1362	c.1238G>A	c.(1237-1239)cGc>cAc	p.R413H	MTMR4_ENST00000579925.1_Missense_Mutation_p.R413H	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	413	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.|Substrate binding. {ECO:0000250}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTGCGGTGTGCGGTCCCAGCC	0.532																																						ENST00000323456.5																			0				breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36						c.(1237-1239)cGc>cAc		myotubularin related protein 4							131.0	124.0	127.0					17																	56582201		2203	4300	6503	SO:0001583	missense	9110					cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity	g.chr17:56582201C>T	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.1238G>A	17.37:g.56582201C>T	ENSP00000325285:p.Arg413His					MTMR4_ENST00000579925.1_Missense_Mutation_p.R413H	p.R413H	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN			12	1362	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		413			Myotubularin phosphatase.|Substrate binding (By similarity).		D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	37	c.1238G>A	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	C	33	5.211568	0.95069	.	.	ENSG00000108389	ENST00000323456	D	0.91740	-2.9	5.58	4.61	0.57282	Myotubularin phosphatase domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.050255	0.85682	N	0.000000	D	0.97892	0.9307	H	0.99600	4.65	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98781	1.0732	10	0.87932	D	0	.	13.7194	0.62717	0.0:0.9259:0.0:0.0741	.	413	Q9NYA4	MTMR4_HUMAN	H	413	ENSP00000325285:R413H	ENSP00000325285:R413H	R	-	2	0	MTMR4	53937200	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.776000	0.85560	1.503000	0.48686	0.591000	0.81541	CGC		0.532	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		4	132	0	0	0	1	0	4	132				
TBC1D3P2	440452	broad.mit.edu	37	17	60342186	60342186	+	RNA	SNP	T	T	C			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr17:60342186T>C	ENST00000581291.1	-	0	1967									TBC1 domain family, member 3 pseudogene 2											breast(2)|kidney(1)|lung(2)	5						GCTGGGGGTGTTGGGAGGGGC	0.498																																						ENST00000581291.1																			0				breast(2)|kidney(1)|lung(2)	5																																														0							g.chr17:60342186T>C			17q23.2	2009-05-14				ENSG00000188755			27783	pseudogene	pseudogene							Standard	NR_027486		Approved		uc002izq.2				17.37:g.60342186T>C														0	1967	-									RNA	SNP	ENST00000581291.1	37																																																																																						0.498	TBC1D3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445021.1	NR_027486		3	23	0	0	0	1	0	3	23				
ITGAX	3687	broad.mit.edu	37	16	31391686	31391686	+	Missense_Mutation	SNP	G	G	T			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr16:31391686G>T	ENST00000268296.4	+	27	3281	c.3160G>T	c.(3160-3162)Ggc>Tgc	p.G1054C	ITGAX_ENST00000562522.1_Missense_Mutation_p.G1054C	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	1054					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCTCAGCTTTGGCTGGGTCCG	0.652																																						ENST00000268296.4																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						c.(3160-3162)Ggc>Tgc		integrin, alpha X (complement component 3 receptor 4 subunit)							44.0	36.0	39.0					16																	31391686		2197	4300	6497	SO:0001583	missense	3687				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity	g.chr16:31391686G>T	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.3160G>T	16.37:g.31391686G>T	ENSP00000268296:p.Gly1054Cys					ITGAX_ENST00000562522.1_Missense_Mutation_p.G1054C	p.G1054C	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN			27	3281	+			1054					Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	c.3160G>T	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.731515	0.30684	.	.	ENSG00000140678	ENST00000268296	T	0.50813	0.73	4.49	2.53	0.30540	.	.	.	.	.	T	0.62816	0.2459	M	0.76002	2.32	0.29298	N	0.868902	D;D	0.89917	1.0;0.999	D;D	0.70227	0.968;0.938	T	0.55792	-0.8085	9	0.56958	D	0.05	.	6.7273	0.23363	0.2125:0.0:0.7875:0.0	.	1054;239	P20702;Q8TES5	ITAX_HUMAN;.	C	1054	ENSP00000268296:G1054C	ENSP00000268296:G1054C	G	+	1	0	ITGAX	31299187	0.001000	0.12720	0.687000	0.30102	0.197000	0.23852	0.110000	0.15437	0.630000	0.30394	-0.229000	0.12294	GGC		0.652	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		3	36	1	0	1	1	1	3	36				
IGLV2-28	28812	broad.mit.edu	37	22	23006961	23006961	+	RNA	SNP	C	C	T	rs200228350	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr22:23006961C>T	ENST00000385099.1	+	0	64																											GGCTCTGCTCCTCCTCACCCT	0.627																																						ENST00000385099.1																			0																																																			0							g.chr22:23006961C>T																													22.37:g.23006961C>T														0	64	+									RNA	SNP	ENST00000385099.1	37																																																																																						0.627	D86994.2-201	NOVEL	basic	miRNA	miRNA				3	15	0	0	0	1	0	3	15				
CYP2D7	1564	broad.mit.edu	37	22	42538870	42538870	+	RNA	SNP	A	A	C	rs2982057	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr22:42538870A>C	ENST00000428786.1	-	0	0				CYP2D7P1_ENST00000358097.4_RNA|CYP2D7P1_ENST00000433992.1_RNA|CYP2D7P1_ENST00000424775.1_RNA																							CCATAGCGCGACAGGAACACC	0.687													N|||	80	0.0159744	0.0023	0.0317	5008	,	,		11900	0.0109		0.0348	False		,,,				2504	0.0092					ENST00000358097.4																			0				endometrium(1)	1																																														0							g.chr22:42538870A>C																													22.37:g.42538870A>C						CYP2D7P1_ENST00000433992.1_RNA|CYP2D7P1_ENST00000424775.1_RNA								0	449	-									RNA	SNP	ENST00000428786.1	37			30	0.013736263736263736	1	0.0020325203252032522	5	0.013812154696132596	5	0.008741258741258742	19	0.025065963060686015	C	8.846	0.943329	0.18281	.	.	ENSG00000205702	ENST00000428297;ENST00000381321;ENST00000436260	.	.	.	3.26	3.26	0.37387	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.28613	N	0.908552	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23154	-1.0196	7	0.02654	T	1	.	8.0614	0.30635	0.2422:0.7578:0.0:0.0	rs2982057	122;32	Q6XP50;F5H167	.;.	A	121;71;32	.	ENSP00000446103:S71A	S	-	1	0	CYP2D7P1	40868814	0.299000	0.24426	0.017000	0.16124	0.002000	0.02628	0.565000	0.23578	0.961000	0.38030	-0.290000	0.09829	TCG		0.687	RP4-669P10.16-001	KNOWN	basic|exp_conf	sense_intronic	sense_intronic	OTTHUMT00000320534.1			3	37	0	0	0	1	0	3	37				
PCDH11X	27328	broad.mit.edu	37	X	91132473	91132473	+	Missense_Mutation	SNP	T	T	C			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chrX:91132473T>C	ENST00000373094.1	+	2	2079	c.1234T>C	c.(1234-1236)Ttc>Ctc	p.F412L	PCDH11X_ENST00000373097.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000373088.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000361724.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000406881.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000298274.8_Missense_Mutation_p.F412L|PCDH11X_ENST00000395337.2_Missense_Mutation_p.F412L|PCDH11X_ENST00000504220.2_Missense_Mutation_p.F412L|PCDH11X_ENST00000361655.2_Missense_Mutation_p.F412L	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	412	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						AAGGCCAGTATTCAGTAATCA	0.438																																					NSCLC(38;925 1092 2571 38200 45895)	ENST00000373094.1																			0				NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						c.(1234-1236)Ttc>Ctc		protocadherin 11 X-linked							177.0	147.0	157.0					X																	91132473		2203	4300	6503	SO:0001583	missense	27328				homophilic cell adhesion	integral to plasma membrane	calcium ion binding	g.chrX:91132473T>C	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.1234T>C	X.37:g.91132473T>C	ENSP00000362186:p.Phe412Leu					PCDH11X_ENST00000373097.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000361724.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000361655.2_Missense_Mutation_p.F412L|PCDH11X_ENST00000395337.2_Missense_Mutation_p.F412L|PCDH11X_ENST00000298274.8_Missense_Mutation_p.F412L|PCDH11X_ENST00000504220.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000406881.1_Missense_Mutation_p.F412L|PCDH11X_ENST00000373088.1_Missense_Mutation_p.F412L	p.F412L	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN			2	2079	+			412			Cadherin 4.		A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	c.1234T>C	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.716833	0.48622	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3	5.16	5.16	0.70880	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.65637	0.2710	L	0.41632	1.29	0.52501	D	0.999955	D;B;D;D;D;D;D;D	0.63880	0.991;0.189;0.991;0.991;0.991;0.993;0.991;0.982	P;B;P;P;P;D;P;P	0.64410	0.877;0.155;0.877;0.877;0.877;0.925;0.835;0.73	T	0.66870	-0.5814	10	0.51188	T	0.08	.	13.1413	0.59436	0.0:0.0:0.0:1.0	.	412;412;412;412;412;412;412;412	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	L	412	ENSP00000378746:F412L;ENSP00000362186:F412L;ENSP00000362189:F412L;ENSP00000355040:F412L;ENSP00000362180:F412L;ENSP00000423762:F412L;ENSP00000355105:F412L;ENSP00000384758:F412L;ENSP00000298274:F412L	ENSP00000298274:F412L	F	+	1	0	PCDH11X	91019129	1.000000	0.71417	0.983000	0.44433	0.977000	0.68977	7.754000	0.85163	1.695000	0.51148	0.441000	0.28932	TTC		0.438	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		8	193	0	0	0	1	0	8	193				
JAKMIP1	152789	broad.mit.edu	37	4	6083476	6083476	+	Missense_Mutation	SNP	G	G	A			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr4:6083476G>A	ENST00000282924.5	-	6	1446	c.961C>T	c.(961-963)Cgc>Tgc	p.R321C	JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.R321C|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.R321C|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.R156C|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.R156C	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	321	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCTCGTGAGCGTTTCAGCTGT	0.542																																						ENST00000409021.3																			0				NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						c.(961-963)Cgc>Tgc		janus kinase and microtubule interacting protein 1							89.0	88.0	88.0					4																	6083476		2203	4300	6503	SO:0001583	missense	152789				protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding	g.chr4:6083476G>A	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.961C>T	4.37:g.6083476G>A	ENSP00000282924:p.Arg321Cys					JAKMIP1_ENST00000410077.2_Missense_Mutation_p.R156C|JAKMIP1_ENST00000282924.5_Missense_Mutation_p.R321C|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.R156C|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.R321C	p.R321C	NM_001099433.1	NP_001092903.1	Q96N16	JKIP1_HUMAN			6	1410	-			321			Mediates association with microtubules.		A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	c.961C>T	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600087	0.87055	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.40756	1.34;1.06;1.34;1.34;1.02	4.41	4.41	0.53225	.	0.000000	0.64402	D	0.000004	T	0.66781	0.2824	M	0.79926	2.475	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999	D;P;D;D;P	0.85130	0.996;0.855;0.996;0.997;0.855	T	0.73398	-0.3995	10	0.87932	D	0	.	16.3932	0.83546	0.0:0.0:1.0:0.0	.	156;321;156;321;321	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	C	321;156;321;321;213;321;321;156	ENSP00000386711:R321C;ENSP00000387042:R156C;ENSP00000282924:R321C;ENSP00000386925:R321C;ENSP00000386745:R156C	ENSP00000282924:R321C	R	-	1	0	JAKMIP1	6134377	1.000000	0.71417	0.995000	0.50966	0.897000	0.52465	9.077000	0.94016	2.185000	0.69588	0.555000	0.69702	CGC		0.542	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		35	49	0	0	0	1	0	35	49				
UBBP4	23666	broad.mit.edu	37	17	21730916	21730916	+	Missense_Mutation	SNP	G	G	T	rs111245273	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr17:21730916G>T	ENST00000578713.1	+	1	222	c.218G>T	c.(217-219)cGg>cTg	p.R73L	UBBP4_ENST00000584398.1_Intron|UBBP4_ENST00000584755.1_Missense_Mutation_p.R73L|UBBP4_ENST00000583708.1_Intron					ubiquitin B pseudogene 4									p.R73L(24)		endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						GTCCTGCGTCGGAGAGGTGGT	0.552													.|||	27	0.00539137	0.0182	0.0029	5008	,	,		20752	0.0		0.0	False		,,,				2504	0.001					ENST00000584755.1																			24	Substitution - Missense(24)	p.R73L(24)	kidney(9)|urinary_tract(6)|endometrium(6)|prostate(3)	endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						c.(217-219)cGg>cTg																																						SO:0001583	missense	0							g.chr17:21730916G>T	X07499		17p11.2	2011-08-10				ENSG00000263563			12467	pseudogene	pseudogene						2834222	Standard	NG_002285		Approved		uc002gyy.3			ENST00000578713.1:c.218G>T	17.37:g.21730916G>T	ENSP00000464265:p.Arg73Leu					UBBP4_ENST00000583708.1_Intron|UBBP4_ENST00000578713.1_Missense_Mutation_p.R73L|UBBP4_ENST00000584398.1_Intron	p.R73L							2	615	+									Missense_Mutation	SNP	ENST00000578713.1	37	c.218G>T																																																																																					0.552	UBBP4-004	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444589.2			4	106	1	0	0.150653	1	0.154725	4	106				
DRD5	1816	broad.mit.edu	37	4	9783834	9783834	+	Missense_Mutation	SNP	G	G	A	rs113223975		TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr4:9783834G>A	ENST00000304374.2	+	1	577	c.181G>A	c.(181-183)Gtg>Atg	p.V61M		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	61					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CAACGTGCTGGTGTGCGCAGC	0.672																																						ENST00000304374.2																			0				NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57						c.(181-183)Gtg>Atg		dopamine receptor D5	Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)						29.0	24.0	26.0					4																	9783834		2203	4299	6502	SO:0001583	missense	0				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane		g.chr4:9783834G>A	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.181G>A	4.37:g.9783834G>A	ENSP00000306129:p.Val61Met						p.V61M	NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN			1	577	+			61					B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	c.181G>A	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	g	16.10	3.026645	0.54683	.	.	ENSG00000169676	ENST00000304374	D	0.84800	-1.9	3.87	3.87	0.44632	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.95191	0.8441	H	0.98901	4.365	0.58432	D	0.999999	D	0.63880	0.993	D	0.65773	0.938	D	0.97223	0.9879	10	0.87932	D	0	.	14.9917	0.71393	0.0:0.0:1.0:0.0	.	61	P21918	DRD5_HUMAN	M	61	ENSP00000306129:V61M	ENSP00000306129:V61M	V	+	1	0	DRD5	9392932	1.000000	0.71417	1.000000	0.80357	0.316000	0.28119	7.385000	0.79763	1.982000	0.57802	0.305000	0.20034	GTG		0.672	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			4	48	0	0	0	1	0	4	48				
C15orf41	84529	broad.mit.edu	37	15	37002124	37002124	+	Silent	SNP	C	C	T	rs578121665		TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr15:37002124C>T	ENST00000566621.1	+	10	928	c.678C>T	c.(676-678)caC>caT	p.H226H	C15orf41_ENST00000569302.1_Silent_p.H232H|C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000562877.1_Silent_p.H128H|C15orf41_ENST00000567389.1_Silent_p.H128H|C15orf41_ENST00000562489.1_Silent_p.H50H|C15orf41_ENST00000437989.2_Silent_p.H226H|C15orf41_ENST00000338183.4_Silent_p.H128H	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	226										kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GTAGCCACCACGCCTACCTGC	0.393													c|||	1	0.000199681	0.0008	0.0	5008	,	,		17949	0.0		0.0	False		,,,				2504	0.0					ENST00000566621.1																			0				kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12						c.(676-678)caC>caT		chromosome 15 open reading frame 41							137.0	128.0	131.0					15																	37002124		1883	4110	5993	SO:0001819	synonymous_variant	84529						protein binding	g.chr15:37002124C>T	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.678C>T	15.37:g.37002124C>T						C15orf41_ENST00000569302.1_Silent_p.H232H|C15orf41_ENST00000437989.2_Silent_p.H226H|C15orf41_ENST00000567389.1_Silent_p.H128H|C15orf41_ENST00000562489.1_Silent_p.H50H|C15orf41_ENST00000562877.1_Silent_p.H128H|C15orf41_ENST00000338183.4_Silent_p.H128H|C15orf41_ENST00000565792.1_3'UTR	p.H226H	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)	10	928	+		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)	226					B2RD87	Silent	SNP	ENST00000566621.1	37	c.678C>T	CCDS45215.1																																																																																				0.393	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499		8	134	0	0	0	1	0	8	134				
TMLHE	55217	broad.mit.edu	37	X	154774817	154774817	+	Missense_Mutation	SNP	A	A	C			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chrX:154774817A>C	ENST00000334398.3	-	2	266	c.121T>G	c.(121-123)Tgg>Ggg	p.W41G	TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.W41G	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	41					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|trimethyllysine dioxygenase activity (GO:0050353)			breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	GTATGGTGCCAATGGACAGCT	0.463																																						ENST00000334398.3																			0				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20						c.(121-123)Tgg>Ggg		trimethyllysine hydroxylase, epsilon	Succinic acid(DB00139)|Vitamin C(DB00126)						114.0	98.0	103.0					X																	154774817		2202	4292	6494	SO:0001583	missense	55217				carnitine biosynthetic process	mitochondrial matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|trimethyllysine dioxygenase activity	g.chrX:154774817A>C	AF373407, X97513	CCDS14768.1, CCDS55547.1	Xq28	2006-07-14			ENSG00000185973	ENSG00000185973			18308	protein-coding gene	gene with protein product	"""butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 2"""	300777				8908511, 11431483	Standard	NM_018196		Approved	TMLH, FLJ10727, BBOX2, XAP130	uc004fnn.3	Q9NVH6	OTTHUMG00000022674	ENST00000334398.3:c.121T>G	X.37:g.154774817A>C	ENSP00000335261:p.Trp41Gly					TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.W41G	p.W41G	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN			2	266	-	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)		41					A8K6M9|B4E3R3|Q5TZB5|Q6IA90|Q8TBT0	Missense_Mutation	SNP	ENST00000334398.3	37	c.121T>G	CCDS14768.1	.	.	.	.	.	.	.	.	.	.	A	2.182	-0.387410	0.04932	.	.	ENSG00000185973	ENST00000334398;ENST00000369439	D;T	0.82619	-1.63;-1.1	4.04	7.14E-4	0.14043	.	0.483471	0.21317	N	0.076531	T	0.67487	0.2898	L	0.41236	1.265	0.09310	N	0.999997	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.0;0.0	T	0.48927	-0.8991	10	0.26408	T	0.33	0.0072	0.793	0.01061	0.477:0.2042:0.1177:0.201	.	41;41;41	Q9NVH6-2;A8K6M9;Q9NVH6	.;.;TMLH_HUMAN	G	41	ENSP00000335261:W41G;ENSP00000358447:W41G	ENSP00000335261:W41G	W	-	1	0	TMLHE	154428011	0.964000	0.33143	0.018000	0.16275	0.012000	0.07955	0.653000	0.24902	-0.171000	0.10797	0.412000	0.27726	TGG		0.463	TMLHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058817.1	NM_018196		49	63	0	0	0	1	0	49	63				
IGLV2-28	28812	broad.mit.edu	37	22	23006960	23006960	+	RNA	SNP	C	C	A	rs199838243	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr22:23006960C>A	ENST00000385099.1	+	0	63																											GGGCTCTGCTCCTCCTCACCC	0.627																																						ENST00000385099.1																			0																																																			0							g.chr22:23006960C>A																													22.37:g.23006960C>A														0	63	+									RNA	SNP	ENST00000385099.1	37																																																																																						0.627	D86994.2-201	NOVEL	basic	miRNA	miRNA				3	15	1	0	6.4e-05	1	7.3697e-05	3	15				
MSLN	10232	broad.mit.edu	37	16	814961	814961	+	Silent	SNP	G	G	A	rs371797682		TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr16:814961G>A	ENST00000382862.3	+	7	530	c.435G>A	c.(433-435)acG>acA	p.T145T	MSLN_ENST00000545450.2_Silent_p.T145T|MSLN_ENST00000566549.1_Silent_p.T145T|MSLN_ENST00000563941.1_Silent_p.T145T	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	145					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				CCCGCATCACGAAGGCCAATG	0.701																																						ENST00000566549.1																			0				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20						c.(433-435)acG>acA		mesothelin		G	,,	1,4361	2.1+/-5.4	0,1,2180	30.0	31.0	30.0		435,435,435	-5.0	0.0	16		30	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	,,	0,1,6472	AA,AG,GG		0.0,0.0229,0.0077	,,	145/623,145/623,145/631	814961	1,12945	2181	4292	6473	SO:0001819	synonymous_variant	10232				cell adhesion	anchored to membrane|extracellular region|Golgi apparatus|plasma membrane		g.chr16:814961G>A	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.435G>A	16.37:g.814961G>A						MSLN_ENST00000382862.3_Silent_p.T145T|MSLN_ENST00000563941.1_Silent_p.T145T|MSLN_ENST00000545450.2_Silent_p.T145T	p.T145T			Q13421	MSLN_HUMAN			7	852	+		Hepatocellular(780;0.00335)	145					D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Silent	SNP	ENST00000382862.3	37	c.435G>A	CCDS32356.1																																																																																				0.701	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			13	31	0	0	0	1	0	13	31				
SLIT2	9353	broad.mit.edu	37	4	20490475	20490475	+	Silent	SNP	C	C	T			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr4:20490475C>T	ENST00000504154.1	+	8	897	c.645C>T	c.(643-645)tgC>tgT	p.C215C	SLIT2_ENST00000503837.1_Silent_p.C215C|SLIT2_ENST00000273739.5_Silent_p.C215C|SLIT2_ENST00000503823.1_Silent_p.C215C	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	215	LRRCT 1.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						ATTGTGACTGCCACCTGGCCT	0.473																																						ENST00000504154.1																			0				NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						c.(643-645)tgC>tgT		slit homolog 2 (Drosophila)							156.0	167.0	163.0					4																	20490475		2203	4300	6503	SO:0001819	synonymous_variant	9353				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding	g.chr4:20490475C>T	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.645C>T	4.37:g.20490475C>T						SLIT2_ENST00000503837.1_Silent_p.C215C|SLIT2_ENST00000503823.1_Silent_p.C215C|SLIT2_ENST00000273739.5_Silent_p.C215C	p.C215C	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN			8	897	+			215			LRRCT 1.		B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	c.645C>T	CCDS3426.1																																																																																				0.473	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			89	154	0	0	0	1	0	89	154				
MT-CO2	4513	broad.mit.edu	37	M	8027	8027	+	Missense_Mutation	SNP	G	G	A			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chrM:8027G>A	ENST00000361739.1	+	1	442	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	148			A -> T. {ECO:0000269|PubMed:8277847}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						TCCCGATTGAAGCCCCCATTC	0.468																																						ENST00000361739.1																			0				endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						c.(442-444)Gcc>Acc		mitochondrially encoded cytochrome c oxidase II																																				SO:0001583	missense	4513							g.chrM:8027G>A			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.442G>A	M.37:g.8027G>A	ENSP00000354876:p.Ala148Thr						p.A148T							1	442	+								Q37526	Missense_Mutation	SNP	ENST00000361739.1	37	c.442G>A																																																																																					0.468	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029		2	0	0	0	0	1	0	2	0				
SEMA3B	7869	broad.mit.edu	37	3	50311108	50311108	+	RNA	SNP	A	A	G			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr3:50311108A>G	ENST00000418948.1	+	0	1156							Q13214	SEM3B_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B						axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			central_nervous_system(2)|kidney(1)|lung(2)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GGGGTTGGGGAGGGGGGCAGC	0.701											OREG0015583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000418948.1																			0				central_nervous_system(2)|kidney(1)|lung(2)|skin(1)	6								sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B							16.0	20.0	19.0					3																	50311108		2011	4152	6163			7869				axon guidance|cell-cell signaling	endoplasmic reticulum|extracellular region|membrane	receptor activity	g.chr3:50311108A>G	U28369	CCDS74941.1	3p21.3	2013-01-11			ENSG00000012171	ENSG00000012171		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10724	protein-coding gene	gene with protein product		601281		SEMAA		7748561, 8633026	Standard	NM_004636		Approved	SemA, semaV, LUCA-1, sema5	uc003cyu.3	Q13214	OTTHUMG00000156970		3.37:g.50311108A>G			OREG0015583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	968					Q13214	SEM3B_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)	0	1156	+								Q6GU46|Q8TB71|Q8TDV7|Q93018|Q96GX0	RNA	SNP	ENST00000418948.1	37																																																																																						0.701	SEMA3B-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000346890.2	NM_001005914		9	47	0	0	0	1	0	9	47				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		42	47	0	0	0	1	0	42	47				
SCN11A	11280	broad.mit.edu	37	3	38991659	38991659	+	Silent	SNP	G	G	T			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr3:38991659G>T	ENST00000302328.3	-	1	393	c.195C>A	c.(193-195)ctC>ctA	p.L65L	SCN11A_ENST00000450244.1_Silent_p.L65L|SCN11A_ENST00000444237.2_Silent_p.L65L|SCN11A_ENST00000456224.3_Silent_p.L65L	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	65					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGTCGCCATAGAGCTTGGGCA	0.532																																						ENST00000302328.3																			0				NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119						c.(193-195)ctC>ctA		sodium channel, voltage-gated, type XI, alpha subunit	Cocaine(DB00907)						133.0	133.0	133.0					3																	38991659		2203	4300	6503	SO:0001819	synonymous_variant	11280				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr3:38991659G>T	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.195C>A	3.37:g.38991659G>T						SCN11A_ENST00000456224.3_Silent_p.L65L|SCN11A_ENST00000450244.1_Silent_p.L65L|SCN11A_ENST00000444237.2_Silent_p.L65L	p.L65L	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN		Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	1	393	-			65					A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	c.195C>A	CCDS33737.1																																																																																				0.532	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		4	185	1	0	0.150653	1	0.154725	4	185				
FRG1B	284802	broad.mit.edu	37	20	29628300	29628300	+	Missense_Mutation	SNP	G	G	A			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr20:29628300G>A	ENST00000278882.3	+	6	682	c.302G>A	c.(301-303)aGt>aAt	p.S101N	FRG1B_ENST00000358464.4_Missense_Mutation_p.S101N|FRG1B_ENST00000439954.2_Missense_Mutation_p.S106N			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	101								p.S101N(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GAAGCAAAAAGTAAAACAGCA	0.358																																						ENST00000278882.3																			2	Substitution - Missense(2)	p.S101N(2)	prostate(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(301-303)aGt>aAt																																						SO:0001583	missense	0							g.chr20:29628300G>A			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.302G>A	20.37:g.29628300G>A	ENSP00000278882:p.Ser101Asn					FRG1B_ENST00000439954.2_Missense_Mutation_p.S106N|FRG1B_ENST00000358464.4_Missense_Mutation_p.S101N	p.S101N							6	682	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.302G>A		.	.	.	.	.	.	.	.	.	.	g	10.56	1.384968	0.25031	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.49139	0.79	2.08	2.08	0.27032	Actin cross-linking (1);	0.125588	0.64402	N	0.000001	T	0.33265	0.0857	.	.	.	0.40357	D	0.979199	B;B	0.16802	0.003;0.019	B;B	0.16289	0.007;0.015	T	0.20605	-1.0270	9	0.33940	T	0.23	.	10.2211	0.43198	0.0:0.0:1.0:0.0	.	106;101	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	N	101;106;101	ENSP00000408863:S106N	ENSP00000278882:S101N	S	+	2	0	FRG1B	28241961	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.004000	0.40854	1.475000	0.48197	0.423000	0.28283	AGT		0.358	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		6	93	0	0	0	1	0	6	93				
NLRP3	114548	broad.mit.edu	37	1	247597549	247597549	+	Silent	SNP	C	C	T	rs200319515		TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr1:247597549C>T	ENST00000336119.3	+	5	3218	c.2472C>T	c.(2470-2472)caC>caT	p.H824H	NLRP3_ENST00000391827.2_Silent_p.H767H|NLRP3_ENST00000391828.3_Silent_p.H824H|NLRP3_ENST00000348069.2_Silent_p.H767H|NLRP3_ENST00000366497.2_Silent_p.H824H|NLRP3_ENST00000366496.2_Silent_p.H824H	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	824					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			GACTGAAGCACCTGTTGTGCA	0.587																																						ENST00000366497.2																			0				NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142						c.(2470-2472)caC>caT		NLR family, pyrin domain containing 3		C	,,,,	1,4405	2.1+/-5.4	0,1,2202	151.0	133.0	139.0		2472,2472,2301,2472,2301	-4.2	0.0	1		139	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	824/1037,824/980,767/980,824/1037,767/923	247597549	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114548				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding	g.chr1:247597549C>T	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2472C>T	1.37:g.247597549C>T						NLRP3_ENST00000336119.3_Silent_p.H824H|NLRP3_ENST00000391828.3_Silent_p.H824H|NLRP3_ENST00000348069.2_Silent_p.H767H|NLRP3_ENST00000366496.2_Silent_p.H824H|NLRP3_ENST00000391827.2_Silent_p.H767H	p.H824H	NM_001127461.2	NP_001120933.1	Q96P20	NALP3_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0141)		6	3252	+	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	881					B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	c.2472C>T	CCDS1632.1																																																																																				0.587	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		4	117	0	0	0	1	0	4	117				
PRB2	653247	broad.mit.edu	37	12	11546506	11546508	+	In_Frame_Del	DEL	TTG	TTG	-			TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr12:11546506_11546508delTTG	ENST00000389362.4	-	3	539_541	c.504_506delCAA	c.(502-507)aacaag>aag	p.N168del	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	168	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACTTCGGGACTTGTTGTCTCCTT	0.596																																						ENST00000389362.4																			0				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37						c.(502-507)aag>aa		proline-rich protein BstNI subfamily 2																																				SO:0001651	inframe_deletion	653247							g.chr12:11546506_11546508delTTG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.504_506delCAA	12.37:g.11546509_11546511delTTG	ENSP00000374013:p.Asn168del					PRB1_ENST00000546254.1_Intron	p.NK168del	NM_006248.3	NP_006239.3			OV - Ovarian serous cystadenocarcinoma(49;0.185)		3	539_541	-		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)						O00599|P02811|P04281	In_Frame_Del	DEL	ENST00000389362.4	37	c.504_506delCAA	CCDS41757.2																																																																																				0.596	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248		8	764						8	764	---	---	---	---
MED6	10001	broad.mit.edu	37	14	71067484	71067504	+	5'Flank	DEL	GGCAGGAGAGAGGCAGGGGGT	GGCAGGAGAGAGGCAGGGGGT	-	rs150061450|rs554135173	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr14:71067484_71067504delGGCAGGAGAGAGGCAGGGGGT	ENST00000256379.5	-	0	0				MED6_ENST00000554963.1_5'Flank|MED6_ENST00000440435.2_5'Flank|CTD-2540L5.5_ENST00000553982.1_lincRNA|MED6_ENST00000430055.2_5'Flank|MED6_ENST00000556044.1_5'Flank	NM_001284209.1|NM_005466.2	NP_001271138.1|NP_005457.2	O75586	MED6_HUMAN	mediator complex subunit 6						gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(2)|skin(1)	5				all cancers(60;0.00315)|BRCA - Breast invasive adenocarcinoma(234;0.00685)|OV - Ovarian serous cystadenocarcinoma(108;0.0352)		gggcggggcgggcaggagagaggcagggggtggaggtgcgg	0.71														1000	0.199681	0.1384	0.0994	5008	,	,		5273	0.4812		0.1054	False		,,,				2504	0.1605					ENST00000553982.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr14:71067484_71067504delGGCAGGAGAGAGGCAGGGGGT	BC004106	CCDS9805.1, CCDS61483.1, CCDS61484.1, CCDS73649.1	14q24.1	2013-02-28	2007-07-30		ENSG00000133997	ENSG00000133997			19970	protein-coding gene	gene with protein product		602984	"""mediator of RNA polymerase II transcription, subunit 6 homolog (S. cerevisiae)"""			9234719, 9671713	Standard	NM_001284209		Approved	NY-REN-28	uc001xmf.3	O75586	OTTHUMG00000171252		14.37:g.71067484_71067504delGGCAGGAGAGAGGCAGGGGGT	Exception_encountered													0	294	-								B4DU17|B4E2P0|O15401|Q53FE3|Q53HJ3|Q6FHQ4|Q9BTH1|Q9UHL1	RNA	DEL	ENST00000256379.5	37		CCDS9805.1																																																																																				0.710	MED6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412560.2	NM_005466		3	3						3	3	---	---	---	---
IGHJ6	28475	broad.mit.edu	37	14	106329450	106329451	+	RNA	INS	-	-	ACC	rs2338628|rs67183528|rs376479093|rs74454466	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr14:106329450_106329451insACC	ENST00000390560.2	-	0	17_18				IGHJ3_ENST00000463911.1_RNA|IGHD7-27_ENST00000439842.1_RNA|IGHJ1_ENST00000390565.1_RNA|IGHJ2_ENST00000390564.2_RNA|IGHJ4_ENST00000461719.1_RNA|IGHJ5_ENST00000488476.1_RNA					immunoglobulin heavy joining 6																		CAGACGTCCATGTAGTAGTAGT	0.54																																						ENST00000390560.2																			0																																																			0							g.chr14:106329450_106329451insACC	J00256		14q32.33	2012-02-08			ENSG00000211900	ENSG00000211900		"""Immunoglobulins / IGH locus"""	5540	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152455		14.37:g.106329450_106329451insACC														0	17_18	-									RNA	INS	ENST00000390560.2	37																																																																																						0.540	IGHJ6-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_start_NF|cds_end_NF|basic|appris_principal	IG_J_gene	IG_J_gene	OTTHUMT00000326277.1	NG_001019		9	89						9	89	---	---	---	---
CTB-134H23.3	0	broad.mit.edu	37	16	29113498	29113498	+	RNA	DEL	T	T	-	rs11366120	byFrequency	TCGA-KS-A4I1-01A-11D-A257-08	TCGA-KS-A4I1-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa5b5812-355d-4716-a55a-38071b50593c	f758e38b-90f4-4aea-9c72-2b506baf6678	g.chr16:29113498delT	ENST00000562618.1	-	0	1840				RRN3P2_ENST00000564580.1_RNA																							AGGAGGTGGAttttttttttc	0.542													|||unknown(NO_COVERAGE)	2145	0.428315	0.5507	0.4856	5008	,	,		13214	0.248		0.4334	False		,,,				2504	0.4029					ENST00000564580.1																			0																																																			0							g.chr16:29113498delT																													16.37:g.29113498delT														0	1360	+									RNA	DEL	ENST00000562618.1	37																																																																																						0.542	CTB-134H23.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433241.1			7	37						7	37	---	---	---	---
