#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
SLC12A3	6559	broad.mit.edu	37	16	56906569	56906569	+	Splice_Site	SNP	G	G	A	rs149172580		TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr16:56906569G>A	ENST00000563236.1	+	8	991	c.966G>A	c.(964-966)gcG>gcA	p.A322A	SLC12A3_ENST00000438926.2_Splice_Site_p.A322A|SLC12A3_ENST00000262502.5_Splice_Site_p.A321A|SLC12A3_ENST00000566786.1_Splice_Site_p.A321A			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	322					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CTTTTCCAGCGGACATTTTTG	0.592													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21687	0.0		0.0	False		,,,				2504	0.0					ENST00000438926.2																			0				breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						c.e8-1		solute carrier family 12 (sodium/chloride transporter), member 3	Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	G	,,	7,4389	12.9+/-30.5	0,7,2191	81.0	71.0	74.0		966,963,966	2.6	1.0	16	dbSNP_134	74	0,8600		0,0,4300	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SLC12A3	NM_000339.2,NM_001126107.1,NM_001126108.1	,,	0,7,6491	AA,AG,GG		0.0,0.1592,0.0539	,,	322/1031,321/1030,322/1022	56906569	7,12989	2198	4300	6498	SO:0001630	splice_region_variant	0				sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity	g.chr16:56906569G>A		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.965-1G>A	16.37:g.56906569G>A						SLC12A3_ENST00000566786.1_Splice_Site_p.A321_splice|SLC12A3_ENST00000563236.1_Splice_Site_p.A322_splice|SLC12A3_ENST00000262502.5_Splice_Site_p.A321_splice	p.A322_splice	NM_000339.2|NM_001126107.1|NM_001126108.1	NP_000330.2|NP_001119579.1|NP_001119580.1	P55017	S12A3_HUMAN			8	995	+			322					A8MSJ2|C9JNN9	Splice_Site	SNP	ENST00000563236.1	37	c.964_splice	CCDS58464.1																																																																																				0.592	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		Silent	18	35	0	0	0	1	0	18	35				
UTP20	27340	broad.mit.edu	37	12	101777048	101777048	+	Missense_Mutation	SNP	T	T	G	rs559137147		TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr12:101777048T>G	ENST00000261637.4	+	59	8060	c.7886T>G	c.(7885-7887)aTt>aGt	p.I2629S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2629					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CTGTCCCGGATTGCAAAACTG	0.493																																						ENST00000261637.4																			0				NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						c.(7885-7887)aTt>aGt		UTP20, small subunit (SSU) processome component, homolog (yeast)							57.0	63.0	61.0					12																	101777048		2203	4300	6503	SO:0001583	missense	27340				endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding	g.chr12:101777048T>G	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.7886T>G	12.37:g.101777048T>G	ENSP00000261637:p.Ile2629Ser						p.I2629S	NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN			59	8060	+			2629					Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	c.7886T>G	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.257892	0.59321	.	.	ENSG00000120800	ENST00000261637	T	0.04551	3.6	5.73	5.73	0.89815	.	0.330121	0.39544	N	0.001326	T	0.07413	0.0187	L	0.48642	1.525	0.39109	D	0.961433	B	0.16603	0.018	B	0.18263	0.021	T	0.14476	-1.0471	10	0.48119	T	0.1	-2.0574	16.0371	0.80638	0.0:0.0:0.0:1.0	.	2629	O75691	UTP20_HUMAN	S	2629	ENSP00000261637:I2629S	ENSP00000261637:I2629S	I	+	2	0	UTP20	100301179	1.000000	0.71417	0.153000	0.22517	0.812000	0.45895	4.739000	0.62080	2.187000	0.69744	0.523000	0.50628	ATT		0.493	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		5	63	0	0	0	1	0	5	63				
MED13L	23389	broad.mit.edu	37	12	116413488	116413488	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr12:116413488T>C	ENST00000281928.3	-	24	5626	c.5420A>G	c.(5419-5421)gAc>gGc	p.D1807G		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1807						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TGTCTGCTTGTCTTTGATTGG	0.488																																						ENST00000281928.3																			0				NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85						c.(5419-5421)gAc>gGc		mediator complex subunit 13-like							81.0	86.0	84.0					12																	116413488		2203	4300	6503	SO:0001583	missense	23389				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent			g.chr12:116413488T>C	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.5420A>G	12.37:g.116413488T>C	ENSP00000281928:p.Asp1807Gly						p.D1807G	NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.0407)	24	5626	-	all_neural(191;0.117)|Medulloblastoma(191;0.163)		1807					A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	c.5420A>G	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.513219	0.85389	.	.	ENSG00000123066	ENST00000281928	T	0.75367	-0.93	5.87	5.87	0.94306	.	0.143889	0.64402	D	0.000005	T	0.75503	0.3858	L	0.49640	1.575	0.54753	D	0.999982	P	0.43231	0.801	P	0.46510	0.519	T	0.74722	-0.3569	10	0.38643	T	0.18	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	1807	Q71F56	MD13L_HUMAN	G	1807	ENSP00000281928:D1807G	ENSP00000281928:D1807G	D	-	2	0	MED13L	114897871	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.872000	0.56085	2.371000	0.80710	0.533000	0.62120	GAC		0.488	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			6	61	0	0	0	1	0	6	61				
PTPN4	5775	broad.mit.edu	37	2	120677715	120677715	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr2:120677715C>A	ENST00000263708.2	+	12	1670	c.899C>A	c.(898-900)gCa>gAa	p.A300E	snoU13_ENST00000459555.1_RNA	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	300	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	TTGTGGAAAGCATGTGTAGAA	0.333																																						ENST00000263708.2																			0				endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30						c.(898-900)gCa>gAa		protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	Alendronate(DB00630)						125.0	124.0	124.0					2																	120677715		2203	4300	6503	SO:0001583	missense	5775					cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity	g.chr2:120677715C>A		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.899C>A	2.37:g.120677715C>A	ENSP00000263708:p.Ala300Glu						p.A300E	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN			12	1670	+			300			FERM.		B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	37	c.899C>A	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.395043	0.83011	.	.	ENSG00000088179	ENST00000263708	D	0.82255	-1.59	5.55	5.55	0.83447	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.095693	0.64402	D	0.000001	D	0.86497	0.5947	M	0.66939	2.045	0.80722	D	1	B	0.29671	0.254	B	0.40565	0.333	D	0.84392	0.0555	10	0.52906	T	0.07	.	19.6941	0.96016	0.0:1.0:0.0:0.0	.	300	P29074	PTN4_HUMAN	E	300	ENSP00000263708:A300E	ENSP00000263708:A300E	A	+	2	0	PTPN4	120394185	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	5.810000	0.69179	2.885000	0.99019	0.655000	0.94253	GCA		0.333	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			63	78	1	0	2.53126e-37	1	2.86143e-37	63	78				
WNT3A	89780	broad.mit.edu	37	1	228210473	228210473	+	Silent	SNP	C	C	T			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr1:228210473C>T	ENST00000284523.1	+	2	255	c.177C>T	c.(175-177)taC>taT	p.Y59Y	WNT3A_ENST00000366753.2_Silent_p.Y59Y	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	59					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)	p.Y59Y(1)		kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				GCAGGAACTACGTGGAGATCA	0.652																																						ENST00000284523.1																			1	Substitution - coding silent(1)	p.Y59Y(1)	ovary(1)	kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12						c.(175-177)taC>taT		wingless-type MMTV integration site family, member 3A							54.0	53.0	54.0					1																	228210473		2203	4300	6503	SO:0001819	synonymous_variant	89780				axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of neuron projection development|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|positive regulation of transcription from RNA polymerase II promoter|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity	g.chr1:228210473C>T	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.177C>T	1.37:g.228210473C>T						WNT3A_ENST00000366753.2_Silent_p.Y59Y	p.Y59Y	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN			2	255	+		Prostate(94;0.0405)	59					Q3SY79|Q3SY80|Q969P2	Silent	SNP	ENST00000284523.1	37	c.177C>T	CCDS1564.1																																																																																				0.652	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		14	28	0	0	0	1	0	14	28				
PLIN4	729359	broad.mit.edu	37	19	4510792	4510792	+	Silent	SNP	G	G	A	rs144380069	byFrequency	TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr19:4510792G>A	ENST00000301286.3	-	3	3137	c.3138C>T	c.(3136-3138)ccC>ccT	p.P1046P		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1046						cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						AGGAGGTGGCGGGGGTACTAG	0.637													N|||	16	0.00319489	0.0	0.0	5008	,	,		17541	0.001		0.006	False		,,,				2504	0.0092					ENST00000301286.3																			0				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						c.(3136-3138)ccC>ccT		perilipin 4				5,4169		0,5,2082	54.0	63.0	60.0		3138	-6.0	0.0	19	dbSNP_134	60	55,8381		0,55,4163	no	coding-synonymous	PLIN4	NM_001080400.1		0,60,6245	AA,AG,GG		0.652,0.1198,0.4758		1046/1358	4510792	60,12550	2087	4218	6305	SO:0001819	synonymous_variant	729359					lipid particle|plasma membrane		g.chr19:4510792G>A	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.3138C>T	19.37:g.4510792G>A							p.P1046P	NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN			3	3137	-			1046					A6NEI2	Silent	SNP	ENST00000301286.3	37	c.3138C>T	CCDS45927.1																																																																																				0.637	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		3	41	0	0	0	1	0	3	41				
TFE3	7030	broad.mit.edu	37	X	48896807	48896807	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chrX:48896807A>C	ENST00000315869.7	-	3	618	c.359T>G	c.(358-360)cTa>cGa	p.L120R	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	120					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GGCCCGCATTAGCTGCTGCCG	0.657			T	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""	"""papillary renal, alveolar soft part sarcoma, renal"""																																	ENST00000315869.7				Dom	yes		X	Xp11.22	7030	T	transcription factor binding to IGHM enhancer 3			E	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""		"""papillary renal, alveolar soft part sarcoma, renal"""	NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	0				central_nervous_system(1)	1						c.(358-360)cTa>cGa		transcription factor binding to IGHM enhancer 3							20.0	18.0	18.0					X																	48896807		2201	4298	6499	SO:0001583	missense	7030				humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding	g.chrX:48896807A>C	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"""Basic helix-loop-helix proteins"""	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.359T>G	X.37:g.48896807A>C	ENSP00000314129:p.Leu120Arg					TFE3_ENST00000493583.1_5'UTR	p.L120R	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN			3	618	-			120					A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	37	c.359T>G	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	A	17.13	3.311874	0.60414	.	.	ENSG00000068323	ENST00000315869	T	0.58797	0.31	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000006	T	0.73353	0.3576	M	0.71206	2.165	0.54753	D	0.999989	D	0.71674	0.998	D	0.83275	0.996	T	0.76498	-0.2937	10	0.87932	D	0	-8.8663	11.6256	0.51142	1.0:0.0:0.0:0.0	.	120	P19532	TFE3_HUMAN	R	120	ENSP00000314129:L120R	ENSP00000314129:L120R	L	-	2	0	TFE3	48783751	1.000000	0.71417	0.995000	0.50966	0.761000	0.43186	8.566000	0.90734	1.728000	0.51552	0.417000	0.27973	CTA		0.657	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		8	3	0	0	0	1	0	8	3				
SEMA4B	10509	broad.mit.edu	37	15	90764978	90764978	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr15:90764978G>A	ENST00000411539.2	+	7	1102	c.842G>A	c.(841-843)cGc>cAc	p.R281H	SEMA4B_ENST00000379122.3_Missense_Mutation_p.R276H|SEMA4B_ENST00000332496.6_Missense_Mutation_p.R281H	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	276	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			ATTGTGTCCCGCATTGCCCGC	0.552											OREG0023469	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000411539.2																			0				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12						c.(841-843)cGc>cAc		sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B							49.0	48.0	48.0					15																	90764978		2047	4195	6242	SO:0001583	missense	10509							g.chr15:90764978G>A	AB051532	CCDS45347.1	15q25	2008-07-18						"""Semaphorins"""	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.842G>A	15.37:g.90764978G>A	ENSP00000394720:p.Arg281His		OREG0023469	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1277	SEMA4B_ENST00000379122.3_Missense_Mutation_p.R276H|SEMA4B_ENST00000332496.6_Missense_Mutation_p.R281H	p.R281H	NM_198925.2	NP_945119.1			BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)		7	1102	+	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)							Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Missense_Mutation	SNP	ENST00000411539.2	37	c.842G>A	CCDS45347.1	.	.	.	.	.	.	.	.	.	.	g	32	5.159288	0.94686	.	.	ENSG00000185033	ENST00000332496;ENST00000379122;ENST00000411539	T;T;T	0.32272	1.46;1.46;1.46	5.31	5.31	0.75309	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.70228	0.3200	H	0.96943	3.91	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.81236	-0.1024	10	0.87932	D	0	.	17.9333	0.89005	0.0:0.0:1.0:0.0	.	281;276	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	H	281;276;281	ENSP00000332204:R281H;ENSP00000368417:R276H;ENSP00000394720:R281H	ENSP00000332204:R281H	R	+	2	0	SEMA4B	88565982	1.000000	0.71417	0.976000	0.42696	0.968000	0.65278	9.727000	0.98787	2.652000	0.90054	0.558000	0.71614	CGC		0.552	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925		3	30	0	0	0	1	0	3	30				
TRIO	7204	broad.mit.edu	37	5	14492733	14492733	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr5:14492733G>A	ENST00000344204.4	+	49	7714	c.7690G>A	c.(7690-7692)Gca>Aca	p.A2564T	TRIO_ENST00000344135.5_Missense_Mutation_p.A63T|TRIO_ENST00000537187.1_Missense_Mutation_p.A2388T	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2564	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CGATTACACGGCAGTGAAGGA	0.517																																						ENST00000344204.4																			0				NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118						c.(7690-7692)Gca>Aca		trio Rho guanine nucleotide exchange factor							111.0	88.0	96.0					5																	14492733		2203	4300	6503	SO:0001583	missense	7204				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity	g.chr5:14492733G>A	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.7690G>A	5.37:g.14492733G>A	ENSP00000339299:p.Ala2564Thr					TRIO_ENST00000344135.5_Missense_Mutation_p.A63T|TRIO_ENST00000537187.1_Missense_Mutation_p.A2388T	p.A2564T	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN			49	7714	+	Lung NSC(4;0.000742)		2564			SH3 2.		D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	c.7690G>A	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	34	5.339224	0.95783	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000344135	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.52	5.52	0.82312	Src homology-3 domain (2);	0.054930	0.64402	D	0.000001	T	0.69187	0.3083	L	0.34521	1.04	0.42253	D	0.991982	D	0.89917	1.0	D	0.97110	1.0	T	0.72033	-0.4412	10	0.72032	D	0.01	.	19.4741	0.94979	0.0:0.0:1.0:0.0	.	2564	O75962	TRIO_HUMAN	T	2564;2388;2251;63	ENSP00000339299:A2564T;ENSP00000446348:A2388T;ENSP00000426342:A2251T;ENSP00000339291:A63T	ENSP00000339291:A63T	A	+	1	0	TRIO	14545733	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.414000	0.97362	2.595000	0.87683	0.655000	0.94253	GCA		0.517	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		13	31	0	0	0	1	0	13	31				
PTPN4	5775	broad.mit.edu	37	2	120677714	120677714	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr2:120677714G>C	ENST00000263708.2	+	12	1669	c.898G>C	c.(898-900)Gca>Cca	p.A300P	snoU13_ENST00000459555.1_RNA	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	300	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	TTTGTGGAAAGCATGTGTAGA	0.333																																						ENST00000263708.2																			0				endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30						c.(898-900)Gca>Cca		protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	Alendronate(DB00630)						123.0	122.0	123.0					2																	120677714		2203	4300	6503	SO:0001583	missense	5775					cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity	g.chr2:120677714G>C		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.898G>C	2.37:g.120677714G>C	ENSP00000263708:p.Ala300Pro						p.A300P	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN			12	1669	+			300			FERM.		B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	37	c.898G>C	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.043362	0.75732	.	.	ENSG00000088179	ENST00000263708	D	0.82344	-1.6	5.55	3.57	0.40892	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.095693	0.64402	D	0.000001	D	0.85720	0.5762	M	0.66939	2.045	0.80722	D	1	P	0.40230	0.708	P	0.49387	0.609	D	0.84554	0.0646	10	0.46703	T	0.11	.	13.1862	0.59682	0.1084:0.0:0.8916:0.0	.	300	P29074	PTN4_HUMAN	P	300	ENSP00000263708:A300P	ENSP00000263708:A300P	A	+	1	0	PTPN4	120394184	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	5.073000	0.64395	0.756000	0.33013	0.655000	0.94253	GCA		0.333	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			64	77	0	0	0	1	0	64	77				
LOC645752	645752	broad.mit.edu	37	15	78212618	78212618	+	lincRNA	SNP	A	A	G	rs201050938	byFrequency	TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr15:78212618A>G	ENST00000565869.1	+	0	111				RP11-114H24.2_ENST00000567226.1_RNA																							TGTAACCGCCACTGGAGGACC	0.562																																						ENST00000565869.1																			0																																																			0							g.chr15:78212618A>G																													15.37:g.78212618A>G						RP11-114H24.2_ENST00000567226.1_RNA								0	111	+									RNA	SNP	ENST00000565869.1	37																																																																																						0.562	RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1			3	35	0	0	0	1	0	3	35				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	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		49	76	0	0	0	1	0	49	76				
ANKRD36C	400986	broad.mit.edu	37	2	96521777	96521777	+	Missense_Mutation	SNP	T	T	C	rs77768218		TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr2:96521777T>C	ENST00000456556.1	-	63	4316	c.4232A>G	c.(4231-4233)cAt>cGt	p.H1411R	ANKRD36C_ENST00000419039.2_Missense_Mutation_p.H438R|ANKRD36C_ENST00000420871.2_Missense_Mutation_p.H662R			Q5JPF3	AN36C_HUMAN	ankyrin repeat domain 36C	1411							ion channel inhibitor activity (GO:0008200)	p.H662R(6)|p.H1411R(3)		breast(1)|endometrium(8)|kidney(5)|lung(4)	18						AAGGTCTTCATGCTTTCTTTT	0.383																																						ENST00000456556.1																			9	Substitution - Missense(9)	p.H662R(6)|p.H1411R(3)	kidney(6)|lung(3)	breast(1)|endometrium(8)|kidney(5)|lung(4)	18						c.(4231-4233)cAt>cGt		ankyrin repeat domain 36C																																				SO:0001583	missense	400986							g.chr2:96521777T>C	AL832836		2q11.1	2013-01-10			ENSG00000174501	ENSG00000174501		"""Ankyrin repeat domain containing"""	32946	protein-coding gene	gene with protein product	"""protein immuno-reactive with anti-PTH polyclonal antibodies"""						Standard	XR_251121		Approved	DKFZp667P0924	uc002suz.1	Q5JPF3	OTTHUMG00000155211	ENST00000456556.1:c.4232A>G	2.37:g.96521777T>C	ENSP00000403302:p.His1411Arg					ANKRD36C_ENST00000419039.2_Missense_Mutation_p.H438R|ANKRD36C_ENST00000420871.2_Missense_Mutation_p.H662R	p.H1411R							63	4316	-								C9JZ08|Q15694|Q53S06|Q658V2	Missense_Mutation	SNP	ENST00000456556.1	37	c.4232A>G		.	.	.	.	.	.	.	.	.	.	t	1.211	-0.629664	0.03610	.	.	ENSG00000174501	ENST00000420871;ENST00000456556;ENST00000419039	T;T;T	0.13196	2.61;2.61;2.61	1.87	0.665	0.17896	.	.	.	.	.	T	0.05731	0.0150	N	0.14661	0.345	0.09310	N	1	B	0.21071	0.051	B	0.15870	0.014	T	0.42666	-0.9438	9	0.15952	T	0.53	.	1.8453	0.03158	0.2739:0.1735:0.0:0.5526	.	1411	Q5JPF3	AN36C_HUMAN	R	662;1411;438	ENSP00000415231:H662R;ENSP00000403302:H1411R;ENSP00000407838:H438R	ENSP00000407838:H438R	H	-	2	0	AC073995.2	95885504	1.000000	0.71417	0.011000	0.14972	0.003000	0.03518	1.050000	0.30404	0.187000	0.20147	-0.818000	0.03119	CAT		0.383	ANKRD36C-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000338799.2	NM_001010914		3	29	0	0	0	1	0	3	29				
CAPN15	6650	broad.mit.edu	37	16	601310	601310	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr16:601310T>C	ENST00000219611.2	+	8	2438	c.2075T>C	c.(2074-2076)aTg>aCg	p.M692T	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	692	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										AGGTTCCTCATGGGTGCCTCC	0.682																																						ENST00000219611.2																			0											c.(2074-2076)aTg>aCg		calpain 15							42.0	51.0	48.0					16																	601310		2198	4299	6497	SO:0001583	missense	6650							g.chr16:601310T>C	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2075T>C	16.37:g.601310T>C	ENSP00000219611:p.Met692Thr					LA16c-366D1.3_ENST00000565879.1_RNA	p.M692T	NM_005632.2	NP_005623.1					8	2438	+								B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	c.2075T>C	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	t	15.26	2.781902	0.49891	.	.	ENSG00000103326	ENST00000219611	T	0.45276	0.9	5.55	4.45	0.53987	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.65460	0.2693	M	0.86268	2.805	0.58432	D	0.999999	D	0.65815	0.995	D	0.77557	0.99	T	0.68542	-0.5381	10	0.72032	D	0.01	.	10.2506	0.43367	0.0:0.0789:0.0:0.9211	.	692	O75808	CAN15_HUMAN	T	692	ENSP00000219611:M692T	ENSP00000219611:M692T	M	+	2	0	SOLH	541311	1.000000	0.71417	0.998000	0.56505	0.683000	0.39861	7.999000	0.88496	0.933000	0.37291	0.454000	0.30748	ATG		0.682	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		14	24	0	0	0	1	0	14	24				
LIN7C	55327	broad.mit.edu	37	11	27528435	27528435	+	5'Flank	SNP	C	C	T	rs578259658		TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr11:27528435C>T	ENST00000278193.2	-	0	0				LIN7C_ENST00000524596.1_5'Flank|BDNF-AS_ENST00000530686.1_RNA|BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000500662.2_RNA|BDNF-AS_ENST00000502161.2_RNA	NM_018362.3	NP_060832.1	Q9NUP9	LIN7C_HUMAN	lin-7 homolog C (C. elegans)						exocytosis (GO:0006887)|morphogenesis of an epithelial sheet (GO:0002011)|neurotransmitter secretion (GO:0007269)|protein transport (GO:0015031)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|MPP7-DLG1-LIN7 complex (GO:0097025)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|L27 domain binding (GO:0097016)|protein domain specific binding (GO:0019904)			endometrium(2)|lung(2)|upper_aerodigestive_tract(1)	5						TGTGTCGCCGCGGCCATCAGG	0.652																																						ENST00000499008.3																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr11:27528435C>T	AK002077	CCDS7864.1	11p14	2008-07-18				ENSG00000148943			17789	protein-coding gene	gene with protein product	"""LIN-7 protein 3"""	612332				10341223	Standard	NM_018362		Approved	MALS-3, Lin7c, LIN-7C, LIN-7-C, VELI3, FLJ11215	uc001mrl.3	Q9NUP9			11.37:g.27528435C>T	Exception_encountered					BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000530686.1_RNA|BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000500662.2_RNA		NR_002832.2						0	37	+									RNA	SNP	ENST00000278193.2	37		CCDS7864.1																																																																																				0.652	LIN7C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388311.2	NM_018362		6	12	0	0	0	1	0	6	12				
ZC3H4	23211	broad.mit.edu	37	19	47572495	47572495	+	Missense_Mutation	SNP	C	C	A	rs372785889		TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr19:47572495C>A	ENST00000253048.5	-	14	2289	c.2252G>T	c.(2251-2253)cGg>cTg	p.R751L	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	751							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		TGGCTTCGGCCGGCCTGGGGG	0.677																																						ENST00000253048.5																			0				NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41						c.(2251-2253)cGg>cTg		zinc finger CCCH-type containing 4							25.0	30.0	29.0					19																	47572495		1909	4105	6014	SO:0001583	missense	23211						nucleic acid binding|zinc ion binding	g.chr19:47572495C>A	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2252G>T	19.37:g.47572495C>A	ENSP00000253048:p.Arg751Leu					ZC3H4_ENST00000594019.1_Intron	p.R751L	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)	14	2289	-		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)	751					Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	c.2252G>T	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640046	0.29157	.	.	ENSG00000130749	ENST00000253048	T	0.18174	2.23	5.17	4.11	0.48088	.	1.018400	0.07859	N	0.965990	T	0.14485	0.0350	L	0.36672	1.1	0.28761	N	0.900886	B	0.10296	0.003	B	0.10450	0.005	T	0.31943	-0.9925	10	0.11485	T	0.65	.	10.2217	0.43201	0.1528:0.6994:0.1478:0.0	.	751	Q9UPT8	ZC3H4_HUMAN	L	751	ENSP00000253048:R751L	ENSP00000253048:R751L	R	-	2	0	ZC3H4	52264335	0.994000	0.37717	1.000000	0.80357	0.936000	0.57629	1.015000	0.29963	1.361000	0.45981	0.591000	0.81541	CGG		0.677	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			11	17	1	0	7.03913e-09	1	7.62572e-09	11	17				
RUSC1	23623	broad.mit.edu	37	1	155300201	155300201	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr1:155300201C>T	ENST00000368352.5	+	10	2699	c.2548C>T	c.(2548-2550)Cgg>Tgg	p.R850W	RUSC1_ENST00000292254.4_Missense_Mutation_p.R381W|RUSC1_ENST00000462780.1_3'UTR|RUSC1_ENST00000368354.3_Missense_Mutation_p.R744W|RUSC1_ENST00000368349.4_Missense_Mutation_p.R381W|RUSC1_ENST00000368347.4_Missense_Mutation_p.R440W	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	850	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			CAGGGCAGTGCGGGCTCTCTG	0.617																																						ENST00000368352.5																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21						c.(2548-2550)Cgg>Tgg		RUN and SH3 domain containing 1							89.0	74.0	79.0					1																	155300201		2203	4300	6503	SO:0001583	missense	23623					cytoplasm|nucleolus	SH3/SH2 adaptor activity	g.chr1:155300201C>T	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.2548C>T	1.37:g.155300201C>T	ENSP00000357336:p.Arg850Trp					RUSC1_ENST00000368347.4_Missense_Mutation_p.R440W|RUSC1_ENST00000368354.3_Missense_Mutation_p.R744W|RUSC1_ENST00000292254.4_Missense_Mutation_p.R381W|RUSC1_ENST00000462780.1_3'UTR|RUSC1_ENST00000368349.4_Missense_Mutation_p.R381W	p.R850W	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		10	2699	+	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		850			SH3.		B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	37	c.2548C>T	CCDS41410.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.341654	0.41498	.	.	ENSG00000160753	ENST00000368354;ENST00000368352;ENST00000368347;ENST00000368349;ENST00000292254	T;T;T;T;T	0.37915	1.37;1.6;1.17;1.17;1.17	4.4	3.47	0.39725	Src homology-3 domain (4);	0.000000	0.41194	D	0.000929	T	0.59101	0.2169	M	0.92970	3.365	0.50313	D	0.999861	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.997;1.0;0.998;0.999	T	0.70644	-0.4815	10	0.72032	D	0.01	-28.7572	12.6539	0.56776	0.0:0.8331:0.1669:0.0	.	348;381;381;275;440;349;850	B4DQB8;Q9BVN2-2;Q5T9U9;B3KWM9;Q5T9V0;Q9BT86;Q9BVN2	.;.;.;.;.;.;RUSC1_HUMAN	W	744;850;440;381;381	ENSP00000357338:R744W;ENSP00000357336:R850W;ENSP00000357331:R440W;ENSP00000357333:R381W;ENSP00000292254:R381W	ENSP00000292254:R381W	R	+	1	2	RUSC1	153566825	0.904000	0.30761	0.888000	0.34837	0.026000	0.11368	1.884000	0.39668	1.180000	0.42898	-0.499000	0.04595	CGG		0.617	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			3	38	0	0	0	1	0	3	38				
RP11-46A10.5	0	broad.mit.edu	37	1	180934580	180934580	+	RNA	DEL	A	A	-			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr1:180934580delA	ENST00000358073.2	-	0	365																											tatatgaaccaaaaaaaATTT	0.468																																						ENST00000358073.2																			0																																																			0							g.chr1:180934580delA																													1.37:g.180934580delA														0	365	-									RNA	DEL	ENST00000358073.2	37																																																																																						0.468	RP11-46A10.5-001	KNOWN	basic	antisense	antisense	OTTHUMT00000085133.1			2	4						2	4	---	---	---	---
HLA-V	352962	broad.mit.edu	37	6	29761783	29761784	+	RNA	INS	-	-	G			TCGA-EL-A3ZT-01A-12D-A23M-08	TCGA-EL-A3ZT-11A-13D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61a33169-6990-498f-b8fa-f978c4c6de35	fc947e09-bbcf-4555-84c3-6e3fa8b5256b	g.chr6:29761783_29761784insG	ENST00000457107.1	+	0	1009_1010									major histocompatibility complex, class I, V (pseudogene)																		ggattggtgcaaagccctgctt	0.55																																						ENST00000457107.1																			0																																																			0							g.chr6:29761783_29761784insG	M96332		6p21.3	2012-10-05	2007-12-12	2007-12-12	ENSG00000181126	ENSG00000181126		"""Histocompatibility complex"""	23482	pseudogene	pseudogene			"""HLA-75 pseudogene"""	HLA-75			Standard	NG_002729		Approved	dJ377H14.4			OTTHUMG00000031277		6.37:g.29761783_29761784insG														0	1009_1010	+									RNA	INS	ENST00000457107.1	37																																																																																						0.550	HLA-V-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000105231.1	NG_002729		3	6						3	6	---	---	---	---
