#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
GPR124	25960	broad.mit.edu	37	8	37693223	37693223	+	Missense_Mutation	SNP	G	G	A	rs576854487		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr8:37693223G>A	ENST00000412232.2	+	13	1998	c.1985G>A	c.(1984-1986)cGc>cAc	p.R662H	GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	662					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			AACACCTCCCGCCCTGGAGCT	0.682													G|||	1	0.000199681	0.0	0.0	5008	,	,		12725	0.0		0.001	False		,,,				2504	0.0					ENST00000412232.2																			0				central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37						c.(1984-1986)cGc>cAc		G protein-coupled receptor 124							48.0	54.0	52.0					8																	37693223		2201	4299	6500	SO:0001583	missense	25960				central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr8:37693223G>A	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.1985G>A	8.37:g.37693223G>A	ENSP00000406367:p.Arg662His					GPR124_ENST00000315215.7_Intron	p.R662H	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		13	1998	+			662					A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	37	c.1985G>A	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	G	6.429	0.447309	0.12223	.	.	ENSG00000020181	ENST00000416514;ENST00000412232	T	0.58358	0.34	5.29	5.29	0.74685	.	0.126543	0.50627	D	0.000105	T	0.34745	0.0908	L	0.28274	0.84	0.45035	D	0.998054	B	0.27450	0.179	B	0.15052	0.012	T	0.16424	-1.0403	10	0.23891	T	0.37	-32.2337	9.6335	0.39793	0.1552:0.0:0.8448:0.0	.	662	Q96PE1	GP124_HUMAN	H	655;662	ENSP00000406367:R662H	ENSP00000406367:R662H	R	+	2	0	GPR124	37812381	0.699000	0.27786	0.981000	0.43875	0.044000	0.14063	1.904000	0.39868	2.497000	0.84241	0.655000	0.94253	CGC		0.682	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			9	82	0	0	0	0.047766	0	9	82				
PRNP	5621	broad.mit.edu	37	20	4680251	4680251	+	Missense_Mutation	SNP	A	A	G	rs1799990	byFrequency	TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr20:4680251A>G	ENST00000379440.4	+	2	672	c.385A>G	c.(385-387)Atg>Gtg	p.M129V	PRNP_ENST00000430350.2_Missense_Mutation_p.M129V	NM_000311.3|NM_001080121.1|NM_001080122.1|NM_001080123.1|NM_001271561.1|NM_183079.2	NP_000302.1|NP_001073590.1|NP_001073591.1|NP_001073592.1|NP_001258490.1|NP_898902.1	F7VJQ1	APRIO_HUMAN	prion protein	0						integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)		p.M129V(2)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14						TGGCGGCTACATGCTGGGAAG	0.547													A|||	1335	0.266573	0.3525	0.4063	5008	,	,		16338	0.0248		0.325	False		,,,				2504	0.2403					ENST00000379440.4																			2	Substitution - Missense(2)	p.M129V(2)	central_nervous_system(1)|skin(1)	central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14	GRCh37	CM890104	PRNP	M	rs1799990	c.(385-387)Atg>Gtg		prion protein	Tetracycline(DB00759)	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	1504,2902	476.6+/-357.7	261,982,960	72.0	56.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	385,385,385,385,385	2.9	1.0	20	dbSNP_89	62	2889,5711	452.0+/-362.8	486,1917,1897	yes	missense,missense,missense,missense,missense	PRNP	NM_000311.3,NM_001080121.1,NM_001080122.1,NM_001080123.1,NM_183079.2	21,21,21,21,21	747,2899,2857	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	33.593,34.1353,33.7767	benign,benign,benign,benign,benign	129/254,129/254,129/254,129/254,129/254	4680251	4393,8613	2203	4300	6503	SO:0001583	missense	5621				axon guidance|cell cycle arrest|cellular copper ion homeostasis|metabolic process|negative regulation of activated T cell proliferation|negative regulation of calcineurin-NFAT signaling pathway|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-2 production|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T cell receptor signaling pathway|protein homooligomerization|response to oxidative stress	anchored to membrane|endoplasmic reticulum|extrinsic to membrane|Golgi apparatus|membrane raft|nucleus|plasma membrane	copper ion binding|identical protein binding|microtubule binding	g.chr20:4680251A>G	M13899	CCDS13080.1	20p13	2014-06-05	2008-07-28		ENSG00000171867	ENSG00000171867		"""CD molecules"""	9449	protein-coding gene	gene with protein product	"""Creutzfeldt-Jakob disease"", ""Gerstmann-Strausler-Scheinker syndrome"", ""fatal familial insomnia"", ""p27-30"""	176640	"""prion protein (p27-30)"""	PRIP, GSS, CJD			Standard	NM_000311		Approved	CD230, PRP, AltPrP	uc002wkw.4	F7VJQ1	OTTHUMG00000031786	ENST00000379440.4:c.385A>G	20.37:g.4680251A>G	ENSP00000368752:p.Met129Val					PRNP_ENST00000430350.2_Missense_Mutation_p.M129V	p.M129V	NM_000311.3|NM_001080121.1|NM_001080122.1|NM_001080123.1|NM_001271561.1|NM_183079.2	NP_000302.1|NP_001073590.1|NP_001073591.1|NP_001073592.1|NP_001258490.1|NP_898902.1	P04156	PRIO_HUMAN			2	672	+			129		M -> V (polymorphism; determines the disease phenotype in patients who have a PrP mutation at position 178. Patients with M-129 develop FFI, those with V-129 develop CJD; dbSNP:rs1799990).	Interaction with GRB2, ERI3 and SYN1 (By similarity).			Missense_Mutation	SNP	ENST00000379440.4	37	c.385A>G	CCDS13080.1	576	0.26373626373626374	172	0.34959349593495936	140	0.3867403314917127	12	0.02097902097902098	252	0.3324538258575198	A	11.91	1.778679	0.31502	0.341353	0.33593	ENSG00000171867	ENST00000379440;ENST00000430350;ENST00000424424;ENST00000444805;ENST00000457586	D;D;D;T	0.91996	-2.95;-2.95;-2.95;-1.42	5.3	2.93	0.34026	Prion/Doppel protein, beta-ribbon domain (2);	0.219208	0.38720	N	0.001589	T	0.00012	0.0000	L	0.47716	1.5	0.30001	P	0.8160000000000001	B;B;B	0.25235	0.009;0.082;0.121	B;B;B	0.22601	0.012;0.036;0.04	T	0.04693	-1.0933	9	0.66056	D	0.02	-2.3944	5.8372	0.18613	0.6585:0.1745:0.0:0.167	rs1799990;rs17850971;rs17858648;rs52800775;rs1799990	129;129;161	B2NI04;P04156;O75942	.;PRIO_HUMAN;.	V	129;129;129;68;129	ENSP00000368752:M129V;ENSP00000399376:M129V;ENSP00000411599:M129V;ENSP00000415284:M129V	ENSP00000368752:M129V	M	+	1	0	PRNP	4628251	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.521000	0.22893	0.281000	0.22233	0.533000	0.62120	ATG		0.547	PRNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077820.2	NM_000311		4	47	0	0	0	0.009096	0	4	47				
TNRC6B	23112	broad.mit.edu	37	22	40719206	40719206	+	Silent	SNP	A	A	T			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr22:40719206A>T	ENST00000454349.2	+	23	5674	c.5463A>T	c.(5461-5463)ctA>ctT	p.L1821L	TNRC6B_ENST00000402203.1_Silent_p.L1017L|TNRC6B_ENST00000335727.9_Silent_p.L1711L|TNRC6B_ENST00000301923.9_Silent_p.L1017L	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1821					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						CTCCTTTACTACCTGGTGACC	0.517																																						ENST00000454349.2																			0				breast(1)	1						c.(5461-5463)ctA>ctT		trinucleotide repeat containing 6B							54.0	54.0	54.0					22																	40719206		1897	4122	6019	SO:0001819	synonymous_variant	23112				gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding	g.chr22:40719206A>T	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.5463A>T	22.37:g.40719206A>T						TNRC6B_ENST00000402203.1_Silent_p.L1017L|TNRC6B_ENST00000335727.8_Silent_p.L1711L|TNRC6B_ENST00000301923.9_Silent_p.L1017L	p.L1821L	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN			23	5674	+			1821					B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Silent	SNP	ENST00000454349.2	37	c.5463A>T	CCDS54533.1																																																																																				0.517	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				4	41	0	0	0	0.014758	0	4	41				
FHL3	2275	broad.mit.edu	37	1	38465013	38465013	+	Silent	SNP	G	G	A			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr1:38465013G>A	ENST00000373016.3	-	2	240	c.72C>T	c.(70-72)agC>agT	p.S24S	FHL3_ENST00000485803.1_Intron	NM_001243878.1|NM_004468.4	NP_001230807.1|NP_004459.2	Q13643	FHL3_HUMAN	four and a half LIM domains 3	24					actin cytoskeleton organization (GO:0030036)|muscle organ development (GO:0007517)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)|Z disc (GO:0030018)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AGTAGGGGCCGCTGTCTGTCT	0.547																																						ENST00000373016.3																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5						c.(70-72)agC>agT		four and a half LIM domains 3							110.0	97.0	102.0					1																	38465013		2203	4300	6503	SO:0001819	synonymous_variant	2275				muscle organ development		zinc ion binding	g.chr1:38465013G>A	BC011697	CCDS30678.1	1p34.3	2008-02-05			ENSG00000183386	ENSG00000183386			3704	protein-coding gene	gene with protein product		602790				8753811, 10226657	Standard	NM_004468		Approved	SLIM2	uc001cck.3	Q13643	OTTHUMG00000004434	ENST00000373016.3:c.72C>T	1.37:g.38465013G>A						FHL3_ENST00000485803.1_Intron	p.S24S	NM_001243878.1|NM_004468.4	NP_001230807.1|NP_004459.2	Q13643	FHL3_HUMAN			2	240	-	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)	24					D3DPT6|Q6I9T0|Q9BVA2	Silent	SNP	ENST00000373016.3	37	c.72C>T	CCDS30678.1																																																																																				0.547	FHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012958.1	NM_004468		7	49	0	0	0	0.029380	0	7	49				
PPAT	5471	broad.mit.edu	37	4	57301543	57301543	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr4:57301543G>A	ENST00000264220.2	-	1	238	c.101C>T	c.(100-102)aCt>aTt	p.T34I	PAICS_ENST00000514888.1_5'Flank|PAICS_ENST00000264221.2_5'Flank|PAICS_ENST00000399688.3_5'Flank|PAICS_ENST00000512576.1_5'Flank	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	34	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	GAGTCCCAGAGTGATCACATG	0.652																																						ENST00000264220.2																			0				cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20						c.(100-102)aCt>aTt		phosphoribosyl pyrophosphate amidotransferase	L-Glutamine(DB00130)|Thioguanine(DB00352)						77.0	75.0	76.0					4																	57301543		2203	4300	6503	SO:0001583	missense	5471				glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding	g.chr4:57301543G>A		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.101C>T	4.37:g.57301543G>A	ENSP00000264220:p.Thr34Ile						p.T34I	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN			1	238	-	Glioma(25;0.08)|all_neural(26;0.101)		34			Glutamine amidotransferase type-2.			Missense_Mutation	SNP	ENST00000264220.2	37	c.101C>T	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.900501	0.92035	.	.	ENSG00000128059	ENST00000264220	T	0.62941	-0.01	5.14	4.28	0.50868	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.046170	0.85682	D	0.000000	T	0.47060	0.1425	N	0.16130	0.375	0.58432	D	0.999999	B	0.06786	0.001	B	0.14023	0.01	T	0.44620	-0.9316	10	0.66056	D	0.02	-6.1192	14.942	0.71000	0.0:0.0:0.856:0.144	.	34	Q06203	PUR1_HUMAN	I	34	ENSP00000264220:T34I	ENSP00000264220:T34I	T	-	2	0	PPAT	56996300	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.904000	0.75708	1.356000	0.45884	0.561000	0.74099	ACT		0.652	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		18	83	0	0	0	0.069288	0	18	83				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T								NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	4	42	0	0	0	0.021553	0	4	42				
PEX7	5191	broad.mit.edu	37	6	137147485	137147485	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr6:137147485G>A	ENST00000318471.4	+	3	298	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	PEX7_ENST00000541292.1_Missense_Mutation_p.V73M|PEX7_ENST00000367756.4_Missense_Mutation_p.V73M	NM_000288.3	NP_000279.1	O00628	PEX7_HUMAN	peroxisomal biogenesis factor 7	73					endochondral ossification (GO:0001958)|ether lipid biosynthetic process (GO:0008611)|fatty acid beta-oxidation (GO:0006635)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-2 binding (GO:0005053)|protein homodimerization activity (GO:0042803)			lung(7)|prostate(1)	8	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)		TTTGTTTGATGTGACTTGGAG	0.438																																						ENST00000541292.1																			0				lung(7)|prostate(1)	8						c.(217-219)Gtg>Atg		peroxisomal biogenesis factor 7							197.0	173.0	181.0					6																	137147485		2203	4300	6503	SO:0001583	missense	5191				ether lipid biosynthetic process|protein import into peroxisome matrix	peroxisome	peroxisome matrix targeting signal-2 binding	g.chr6:137147485G>A	AF180814	CCDS5180.1	6q21-q22.2	2013-01-10			ENSG00000112357	ENSG00000112357		"""WD repeat domain containing"""	8860	protein-coding gene	gene with protein product	"""Refsum disease"""	601757				9090381, 10673331	Standard	NM_000288		Approved	PTS2R, RD	uc003qhd.3	O00628	OTTHUMG00000015650	ENST00000318471.4:c.217G>A	6.37:g.137147485G>A	ENSP00000315680:p.Val73Met					PEX7_ENST00000318471.4_Missense_Mutation_p.V73M|PEX7_ENST00000367756.4_Missense_Mutation_p.V73M	p.V73M			O00628	PEX7_HUMAN		GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)	3	303	+	Colorectal(23;0.24)		73					C0H5X6	Missense_Mutation	SNP	ENST00000318471.4	37	c.217G>A	CCDS5180.1	.	.	.	.	.	.	.	.	.	.	G	31	5.070857	0.93950	.	.	ENSG00000112357	ENST00000367756;ENST00000541292;ENST00000318471	D;T;T	0.94497	-3.44;-0.16;-0.16	5.52	5.52	0.82312	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.97195	0.9083	M	0.80847	2.515	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.97406	0.9999	10	0.72032	D	0.01	-27.8536	19.4383	0.94807	0.0:0.0:1.0:0.0	.	73	O00628	PEX7_HUMAN	M	73	ENSP00000356730:V73M;ENSP00000441004:V73M;ENSP00000315680:V73M	ENSP00000315680:V73M	V	+	1	0	PEX7	137189178	1.000000	0.71417	0.985000	0.45067	0.987000	0.75469	8.961000	0.93122	2.589000	0.87451	0.655000	0.94253	GTG		0.438	PEX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042387.2	NM_000288		17	149	0	0	0	0.033300	0	17	149				
CSMD3	114788	broad.mit.edu	37	8	113418891	113418891	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr8:113418891C>T	ENST00000297405.5	-	35	5915	c.5671G>A	c.(5671-5673)Ggc>Agc	p.G1891S	CSMD3_ENST00000455883.2_Missense_Mutation_p.G1787S|CSMD3_ENST00000343508.3_Missense_Mutation_p.G1851S|CSMD3_ENST00000352409.3_Missense_Mutation_p.G1821S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1891	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AATTCATTGCCAATTCTTCTT	0.358										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																												ENST00000297405.5																			0				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						c.(5671-5673)Ggc>Agc		CUB and Sushi multiple domains 3							110.0	105.0	106.0					8																	113418891		2203	4300	6503	SO:0001583	missense	114788					integral to membrane|plasma membrane		g.chr8:113418891C>T	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.5671G>A	8.37:g.113418891C>T	ENSP00000297405:p.Gly1891Ser	HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)				CSMD3_ENST00000352409.3_Missense_Mutation_p.G1821S|CSMD3_ENST00000455883.2_Missense_Mutation_p.G1787S|CSMD3_ENST00000343508.3_Missense_Mutation_p.G1851S	p.G1891S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN			35	5915	-			1891			Sushi 10.		Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	c.5671G>A	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	34	5.292355	0.95546	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	4.64	4.64	0.57946	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.53417	0.1795	M	0.78637	2.42	0.58432	D	0.999994	D;D;D	0.89917	1.0;0.996;1.0	D;D;D	0.97110	0.994;0.93;1.0	T	0.55566	-0.8121	10	0.48119	T	0.1	.	18.0718	0.89410	0.0:1.0:0.0:0.0	.	1787;1891;1851	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	1851;1891;1161;1787;1821	ENSP00000345799:G1851S;ENSP00000297405:G1891S;ENSP00000341558:G1161S;ENSP00000412263:G1787S;ENSP00000343124:G1821S	ENSP00000297405:G1891S	G	-	1	0	CSMD3	113488067	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.609000	0.82925	2.574000	0.86865	0.655000	0.94253	GGC		0.358	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		9	79	0	0	0	0.058154	0	9	79				
FAM63B	54629	broad.mit.edu	37	15	59113964	59113964	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr15:59113964G>A	ENST00000559228.1	+	5	1253	c.1171G>A	c.(1171-1173)Gtg>Atg	p.V391M	FAM63B_ENST00000450403.2_Missense_Mutation_p.V391M			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	391										central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						CAACCAACTAGTGGAGAAGAT	0.388																																						ENST00000559228.1																			0				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						c.(1171-1173)Gtg>Atg		family with sequence similarity 63, member B							120.0	114.0	116.0					15																	59113964		1906	4135	6041	SO:0001583	missense	54629							g.chr15:59113964G>A	AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09							26954	protein-coding gene	gene with protein product						10574461	Standard	NM_001040450		Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.1171G>A	15.37:g.59113964G>A	ENSP00000452885:p.Val391Met					FAM63B_ENST00000450403.2_Missense_Mutation_p.V391M	p.V391M			Q8NBR6	FA63B_HUMAN			5	1253	+			391					B2RTT8|Q9ULQ6	Missense_Mutation	SNP	ENST00000559228.1	37	c.1171G>A	CCDS42046.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.968022	0.92855	.	.	ENSG00000128923	ENST00000316848;ENST00000450403	T	0.52526	0.66	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.69726	0.3143	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.70714	-0.4796	10	0.56958	D	0.05	-2.6042	19.445	0.94843	0.0:0.0:1.0:0.0	.	391;391	Q8NBR6;Q8NBR6-2	FA63B_HUMAN;.	M	391	ENSP00000393231:V391M	ENSP00000326194:V391M	V	+	1	0	FAM63B	56901256	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.781000	0.99029	2.665000	0.90641	0.650000	0.86243	GTG		0.388	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1	NM_019092		7	46	0	0	0	0.047766	0	7	46				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			0							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		3	33	0	0	0	0.004672	0	3	33				
TRPM4	54795	broad.mit.edu	37	19	49713617	49713617	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr19:49713617C>T	ENST00000252826.5	+	21	3409	c.3283C>T	c.(3283-3285)Cga>Tga	p.R1095*	TRPM4_ENST00000355712.5_Nonsense_Mutation_p.R741*|TRPM4_ENST00000427978.2_Nonsense_Mutation_p.R950*	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	1095	Calmodulin-binding.				calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)	p.R1095*(1)		breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		ATTGTGCAGGCGACCCCGGAG	0.622																																						ENST00000252826.5																			1	Substitution - Nonsense(1)	p.R1095*(1)	large_intestine(1)	breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49						c.(3283-3285)Cga>Tga		transient receptor potential cation channel, subfamily M, member 4							38.0	41.0	40.0					19																	49713617		2203	4300	6503	SO:0001587	stop_gained	54795				dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding	g.chr19:49713617C>T	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.3283C>T	19.37:g.49713617C>T	ENSP00000252826:p.Arg1095*					TRPM4_ENST00000355712.5_Nonsense_Mutation_p.R741*|TRPM4_ENST00000427978.2_Nonsense_Mutation_p.R950*	p.R1095*	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)	21	3409	+		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)	1095			Calmodulin-binding.		A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Nonsense_Mutation	SNP	ENST00000252826.5	37	c.3283C>T	CCDS33073.1	.	.	.	.	.	.	.	.	.	.	C	39	7.775985	0.98483	.	.	ENSG00000130529	ENST00000252826;ENST00000427978;ENST00000355712	.	.	.	5.34	0.531	0.17108	.	0.707747	0.14145	N	0.338404	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-4.9386	8.097	0.30835	0.5257:0.3991:0.0:0.0752	.	.	.	.	X	1095;950;741	.	ENSP00000252826:R1095X	R	+	1	2	TRPM4	54405429	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.549000	0.06041	0.021000	0.15133	-0.714000	0.03626	CGA		0.622	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		7	48	0	0	0	0.029380	0	7	48				
ZNF621	285268	broad.mit.edu	37	3	40573621	40573621	+	Missense_Mutation	SNP	C	C	G	rs189638815		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr3:40573621C>G	ENST00000339296.5	+	5	812	c.360C>G	c.(358-360)aaC>aaG	p.N120K	ZNF621_ENST00000310898.1_Missense_Mutation_p.N120K|ZNF621_ENST00000431278.1_Missense_Mutation_p.N9K|ZNF621_ENST00000490457.1_Intron|ZNF621_ENST00000403205.2_Missense_Mutation_p.N120K	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	120					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		TTCTCAGGAACGTTTCTCAGC	0.413																																						ENST00000339296.5																			0				endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21						c.(358-360)aaC>aaG		zinc finger protein 621							82.0	87.0	85.0					3																	40573621		2203	4300	6503	SO:0001583	missense	285268				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr3:40573621C>G	AK127181	CCDS2693.1, CCDS74920.1	3p21.33	2013-01-08			ENSG00000172888	ENSG00000172888		"""Zinc fingers, C2H2-type"", ""-"""	24787	protein-coding gene	gene with protein product							Standard	XM_005265079		Approved	FLJ45246	uc003ckm.2	Q6ZSS3	OTTHUMG00000131389	ENST00000339296.5:c.360C>G	3.37:g.40573621C>G	ENSP00000340841:p.Asn120Lys					ZNF621_ENST00000490457.1_Intron|ZNF621_ENST00000431278.1_Missense_Mutation_p.N9K|ZNF621_ENST00000403205.2_Missense_Mutation_p.N120K|ZNF621_ENST00000310898.1_Missense_Mutation_p.N120K	p.N120K	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)	5	812	+			120					Q14DC7|Q8TE91	Missense_Mutation	SNP	ENST00000339296.5	37	c.360C>G	CCDS2693.1	.	.	.	.	.	.	.	.	.	.	c	12.11	1.840609	0.32513	.	.	ENSG00000172888	ENST00000403205;ENST00000310898;ENST00000339296;ENST00000431278;ENST00000453351	T;T;T;T;T	0.07567	3.36;5.44;3.36;3.18;5.47	3.73	-5.9	0.02275	.	0.996321	0.08128	N	0.993716	T	0.05731	0.0150	L	0.40543	1.245	0.09310	N	1	P;B;B	0.49447	0.924;0.319;0.319	B;B;B	0.35312	0.2;0.062;0.062	T	0.17592	-1.0364	10	0.18710	T	0.47	.	13.8617	0.63564	0.0:0.1742:0.0:0.8258	.	120;9;120	C9JM43;C9JZC2;Q6ZSS3	.;.;ZN621_HUMAN	K	120;120;120;9;120	ENSP00000386051:N120K;ENSP00000312144:N120K;ENSP00000340841:N120K;ENSP00000413236:N9K;ENSP00000408779:N120K	ENSP00000312144:N120K	N	+	3	2	ZNF621	40548625	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.314000	0.00516	-1.606000	0.01591	-0.880000	0.02959	AAC		0.413	ZNF621-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254178.2	NM_198484		9	74	0	0	0	0.058154	0	9	74				
ZNF345	25850	broad.mit.edu	37	19	37368055	37368055	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr19:37368055A>T	ENST00000529555.1	+	2	1111	c.323A>T	c.(322-324)cAt>cTt	p.H108L	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.H108L|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.H108L			Q14585	ZN345_HUMAN	zinc finger protein 345	108					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTTGCTTACCATCAAAGAATT	0.423																																						ENST00000529555.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24						c.(322-324)cAt>cTt		zinc finger protein 345							68.0	69.0	69.0					19																	37368055		2203	4300	6503	SO:0001583	missense	25850				negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleus	DNA binding|zinc ion binding	g.chr19:37368055A>T	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.323A>T	19.37:g.37368055A>T	ENSP00000431202:p.His108Leu					ZNF345_ENST00000589046.1_Missense_Mutation_p.H108L|ZNF345_ENST00000420450.1_Missense_Mutation_p.H108L|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000432005.2_Intron	p.H108L			Q14585	ZN345_HUMAN	COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)		2	1111	+	Esophageal squamous(110;0.183)		108						Missense_Mutation	SNP	ENST00000529555.1	37	c.323A>T	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.240005	0.58995	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000331800	D;D;T	0.86865	-2.18;-2.18;2.96	3.58	3.58	0.41010	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.95265	0.8464	H	0.97265	3.97	0.34692	D	0.725865	D	0.69078	0.997	D	0.77557	0.99	D	0.97583	1.0112	8	.	.	.	.	10.7525	0.46217	1.0:0.0:0.0:0.0	.	108	Q14585	ZN345_HUMAN	L	108	ENSP00000431216:H108L;ENSP00000431202:H108L;ENSP00000331120:H108L	.	H	+	2	0	ZNF345	42059895	0.961000	0.32948	1.000000	0.80357	0.990000	0.78478	5.848000	0.69458	1.847000	0.53656	0.459000	0.35465	CAT		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			10	36	0	0	0	0.058154	0	10	36				
HOOK3	84376	broad.mit.edu	37	8	42819533	42819533	+	Missense_Mutation	SNP	C	C	G			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr8:42819533C>G	ENST00000307602.4	+	9	895	c.695C>G	c.(694-696)tCt>tGt	p.S232C		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	232					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			CAATCTGATTCTATAGAAGAC	0.413			T	RET	papillary thyroid																																	ENST00000307602.4				Dom	yes		8	8p11.21	84376	T	hook homolog 3			E	RET		papillary thyroid		0				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31						c.(694-696)tCt>tGt		hook microtubule-tethering protein 3							109.0	106.0	107.0					8																	42819533		2203	4300	6503	SO:0001583	missense	84376				cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding	g.chr8:42819533C>G	AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"""hook homolog 3 (Drosophila)"""			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.695C>G	8.37:g.42819533C>G	ENSP00000305699:p.Ser232Cys						p.S232C	NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)		9	895	+	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	232					D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	37	c.695C>G	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799121	0.90538	.	.	ENSG00000168172	ENST00000307602	T	0.20881	2.04	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.46698	0.1406	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.77557	0.986;0.99	T	0.23332	-1.0191	10	0.66056	D	0.02	-7.4486	20.4084	0.99013	0.0:1.0:0.0:0.0	.	232;232	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	C	232	ENSP00000305699:S232C	ENSP00000305699:S232C	S	+	2	0	HOOK3	42938690	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.436000	0.80404	2.833000	0.97629	0.650000	0.86243	TCT		0.413	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410		34	34	0	0	0	0.069456	0	34	34				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	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		33	35	0	0	0	0.054565	0	33	35				
LRRC37A4P	55073	broad.mit.edu	37	17	43587576	43587576	+	RNA	SNP	A	A	G	rs2684618	byFrequency	TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr17:43587576A>G	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		tctgaaaagaaaagaaaaaaa	0.428													A|||	308	0.0615016	0.0204	0.0548	5008	,	,		16882	0.0685		0.1113	False		,,,				2504	0.0634					ENST00000253803.2																			0																																																			0							g.chr17:43587576A>G	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587576A>G						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.428	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		4	30	0	0	0	0.009096	0	4	30				
LRRN1	57633	broad.mit.edu	37	3	3887996	3887996	+	Silent	SNP	G	G	A			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr3:3887996G>A	ENST00000319331.3	+	2	2432	c.1671G>A	c.(1669-1671)tcG>tcA	p.S557S	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	557	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TAAAATGGTCGTCTGCCACCA	0.443																																						ENST00000319331.3																			0				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26						c.(1669-1671)tcG>tcA		leucine rich repeat neuronal 1							202.0	205.0	204.0					3																	3887996		2203	4300	6503	SO:0001819	synonymous_variant	57633					integral to membrane		g.chr3:3887996G>A	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.1671G>A	3.37:g.3887996G>A						SUMF1_ENST00000534863.1_Intron	p.S557S	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN		Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)	2	2432	+			557			Fibronectin type-III.		Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	c.1671G>A	CCDS33685.1																																																																																				0.443	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		32	163	0	0	0	0.064281	0	32	163				
LRRC37A4P	55073	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs202189074		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr17:43587569G>C	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		aactccgtctgaaaagaaaag	0.443																																						ENST00000253803.2																			0																																																			0							g.chr17:43587569G>C	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587569G>C						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.443	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		4	21	0	0	0	0.009096	0	4	21				
PEAK1	79834	broad.mit.edu	37	15	77474126	77474126	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr15:77474126T>C	ENST00000560626.2	-	4	618	c.143A>G	c.(142-144)aAt>aGt	p.N48S	PEAK1_ENST00000312493.4_Missense_Mutation_p.N48S|PEAK1_ENST00000558305.1_Missense_Mutation_p.N48S			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	48					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GTTACTGTGATTGGCATTAGT	0.483																																						ENST00000560626.2																			0											c.(142-144)aAt>aGt		pseudopodium-enriched atypical kinase 1							180.0	170.0	173.0					15																	77474126		1926	4111	6037	SO:0001583	missense	79834				cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding	g.chr15:77474126T>C		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.143A>G	15.37:g.77474126T>C	ENSP00000452796:p.Asn48Ser					PEAK1_ENST00000312493.4_Missense_Mutation_p.N48S|PEAK1_ENST00000558305.1_Missense_Mutation_p.N48S	p.N48S			Q9H792	PEAK1_HUMAN			4	618	-			48					Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	c.143A>G	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	T	10.41	1.341940	0.24339	.	.	ENSG00000173517	ENST00000312493	T	0.68765	-0.35	5.77	5.77	0.91146	.	0.558038	0.12692	U	0.447103	T	0.49695	0.1572	N	0.22421	0.69	0.29659	N	0.843333	B	0.22346	0.068	B	0.13407	0.009	T	0.43180	-0.9407	10	0.23891	T	0.37	-10.2808	8.1517	0.31145	0.1329:0.0:0.1388:0.7283	.	48	Q9H792	PEAK1_HUMAN	S	48	ENSP00000309230:N48S	ENSP00000309230:N48S	N	-	2	0	AC087465.1	75261181	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.362000	0.44169	2.330000	0.79161	0.528000	0.53228	AAT		0.483	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			16	124	0	0	0	0.038395	0	16	124				
KMT2C	58508	broad.mit.edu	37	7	151859891	151859891	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr7:151859891G>A	ENST00000262189.6	-	43	10989	c.10771C>T	c.(10771-10773)Cag>Tag	p.Q3591*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.Q3591*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3591					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GAATACAACTGAATGAGCGAT	0.433																																						ENST00000355193.2																			0											c.(10771-10773)Cag>Tag		lysine (K)-specific methyltransferase 2C							70.0	67.0	68.0					7																	151859891		2203	4300	6503	SO:0001587	stop_gained	58508							g.chr7:151859891G>A	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.10771C>T	7.37:g.151859891G>A	ENSP00000262189:p.Gln3591*					KMT2C_ENST00000262189.6_Nonsense_Mutation_p.Q3591*	p.Q3591*							43	10989	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	c.10771C>T	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	53|53	21.227398|21.227398	0.99938|0.99938	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	0.000000|.	0.44285|.	D|.	0.000477|.	.|T	.|0.75436	.|0.3849	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73544	.|-0.3949	.|4	0.66056|.	D|.	0.02|.	.|.	19.451|19.451	0.94867|0.94867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	3591;3591;177|1096	.|.	ENSP00000262189:Q3591X|.	Q|S	-|-	1|2	0|0	MLL3|MLL3	151490824|151490824	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.843000|0.843000	0.47879|0.47879	9.467000|9.467000	0.97671|0.97671	2.593000|2.593000	0.87608|0.87608	0.655000|0.655000	0.94253|0.94253	CAG|TCA		0.433	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			5	52	0	0	0	0.021553	0	5	52				
SRGAP2-AS1	100873165	broad.mit.edu	37	1	121137791	121137793	+	lincRNA	DEL	CCA	CCA	-	rs28552466|rs61625886|rs374710813	byFrequency	TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr1:121137791_121137793delCCA	ENST00000417218.1	+	0	0				RP11-343N15.1_ENST00000437515.1_lincRNA																							ATTTCGCCCTCCACCGCCGCCGC	0.631																																						ENST00000437515.1																			0																																																			0							g.chr1:121137791_121137793delCCA																													1.37:g.121137791_121137793delCCA														0	329	-									RNA	DEL	ENST00000417218.1	37																																																																																						0.631	AL592494.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000036739.1			6	11						6	11	---	---	---	---
CTD-2509G16.5	0	broad.mit.edu	37	14	65747997	65747997	+	lincRNA	DEL	C	C	-	rs374530281		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr14:65747997delC	ENST00000553754.1	-	0	300																											GATTTTCTTTCtttctttttt	0.488																																						ENST00000553754.1																			0																																																			0							g.chr14:65747997delC																													14.37:g.65747997delC														0	300	-									RNA	DEL	ENST00000553754.1	37																																																																																						0.488	CTD-2509G16.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000412041.1			3	3						3	3	---	---	---	---
PPM1D	8493	broad.mit.edu	37	17	58740817	58740818	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr17:58740817_58740818delCT	ENST00000305921.3	+	6	1954_1955	c.1722_1723delCT	c.(1720-1725)aactctfs	p.S575fs	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	575					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			AGCGAAAGAACTCTGTTAAACT	0.465											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																										ENST00000305921.3																			0				haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15						c.(1720-1725)aactfs		protein phosphatase, Mg2+/Mn2+ dependent, 1D																																				SO:0001589	frameshift_variant	8493				negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity	g.chr17:58740817_58740818delCT	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9277	protein-coding gene	gene with protein product	"""wild-type p53-induced phosphatase 1"", ""protein phosphatase 2C, delta isoform"""	605100	"""protein phosphatase 1D magnesium-dependent, delta isoform"""			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1722_1723delCT	17.37:g.58740819_58740820delCT	ENSP00000306682:p.Ser575fs		OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	1033		p.NS574fs	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)		6	1954_1955	+	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		574					Q53XP4|Q6P991|Q8IVR6	Frame_Shift_Del	DEL	ENST00000305921.3	37	c.1722_1723delCT	CCDS11625.1																																																																																				0.465	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620		27	81						27	81	---	---	---	---
IL11	3589	broad.mit.edu	37	19	55877466	55877466	+	Frame_Shift_Del	DEL	C	C	-	rs530006295		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr19:55877466delC	ENST00000264563.2	-	5	571	c.509delG	c.(508-510)ggcfs	p.G170fs	FAM71E2_ENST00000424985.3_5'Flank|IL11_ENST00000590625.1_Frame_Shift_Del_p.G91fs|IL11_ENST00000585513.1_Frame_Shift_Del_p.G170fs	NM_000641.3	NP_000632.1	P20809	IL11_HUMAN	interleukin 11	170					B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|fat cell differentiation (GO:0045444)|megakaryocyte differentiation (GO:0030219)|negative regulation of hormone secretion (GO:0046888)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|interleukin-11 receptor binding (GO:0005142)			large_intestine(1)|skin(1)	2	Breast(117;0.191)	Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		GGCCCTGATGCCCCCCCAGGC	0.746																																						ENST00000264563.2																			0				large_intestine(1)|skin(1)	2						c.(508-510)gcfs		interleukin 11	Oprelvekin(DB00038)			15,4075		4,7,2034	8.0	8.0	8.0			-1.5	0.2	19		8	40,7894		4,32,3931	no	frameshift	IL11	NM_000641.2		8,39,5965	A1A1,A1R,RR		0.5042,0.3667,0.4574			55877466	55,11969	2166	4234	6400	SO:0001589	frameshift_variant	3589				B cell differentiation|fat cell differentiation|megakaryocyte differentiation|negative regulation of hormone secretion|platelet activation|positive regulation of cell proliferation|positive regulation of MAPKKK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	extracellular space	cytokine activity|growth factor activity|interleukin-11 receptor binding	g.chr19:55877466delC	X58377	CCDS12923.1, CCDS59423.1	19q13.3-q13.4	2014-01-30			ENSG00000095752	ENSG00000095752		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5966	protein-coding gene	gene with protein product	"""adipogenesis inhibitory factor"", ""oprelvekin"""	147681				1386338	Standard	NM_001267718		Approved	IL-11, AGIF	uc002qks.2	P20809		ENST00000264563.2:c.509delG	19.37:g.55877466delC	ENSP00000264563:p.Gly170fs					IL11_ENST00000585513.1_Frame_Shift_Del_p.G170fs|IL11_ENST00000590625.1_Frame_Shift_Del_p.G91fs	p.G170fs	NM_000641.3	NP_000632.1	P20809	IL11_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)	5	571	-	Breast(117;0.191)	Renal(1328;0.245)	170					B4DQV5|Q96EB4	Frame_Shift_Del	DEL	ENST00000264563.2	37	c.509delG	CCDS12923.1																																																																																				0.746	IL11-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453027.1	NM_000641		2	4						2	4	---	---	---	---
EP300-AS1	101927279	broad.mit.edu	37	22	41586192	41586193	+	RNA	DEL	CA	CA	-	rs200000207|rs538168962|rs74853955|rs76554533|rs397687872|rs60941555		TCGA-DJ-A2PW-01A-11D-A19J-08	TCGA-DJ-A2PW-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6409f4a-e1fb-4831-8fe7-0a67450f615e	d33d4bc0-93b1-46ba-af93-21ad6af330f7	g.chr22:41586192_41586193delCA	ENST00000420537.1	-	0	223																											TCTTCAAAGGCaaaaaaaaaaa	0.411																																						ENST00000420537.1																			0																																																			0							g.chr22:41586192_41586193delCA																													22.37:g.41586192_41586193delCA														0	223	-									RNA	DEL	ENST00000420537.1	37																																																																																						0.411	RP1-85F18.5-001	KNOWN	basic	antisense	antisense	OTTHUMT00000320612.1			2	4						2	4	---	---	---	---
