#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
AGPAT2	10555	broad.mit.edu	37	9	139581702	139581702	+	Silent	SNP	C	C	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr9:139581702C>A	ENST00000371696.2	-	1	173	c.108G>T	c.(106-108)ctG>ctT	p.L36L	AGPAT2_ENST00000538402.1_Silent_p.L36L|AGPAT2_ENST00000371694.3_Silent_p.L36L	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	36					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CCGTGAAGCACAGCGCGCAGT	0.726																																						ENST00000371696.2																			0				endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6						c.(106-108)ctG>ctT		1-acylglycerol-3-phosphate O-acyltransferase 2							18.0	21.0	20.0					9																	139581702		1985	4005	5990	SO:0001819	synonymous_variant	10555				phosphatidic acid biosynthetic process|positive regulation of cytokine production|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity	g.chr9:139581702C>A	AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	325	protein-coding gene	gene with protein product	"""LPAAT-beta"", ""lysophosphatidic acid acyltransferase, beta"""	603100	"""Berardinelli-Seip congenital lipodystrophy"", ""1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"""	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.108G>T	9.37:g.139581702C>A						AGPAT2_ENST00000538402.1_Silent_p.L36L|AGPAT2_ENST00000371694.3_Silent_p.L36L	p.L36L	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)	1	173	-	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)	36					O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Silent	SNP	ENST00000371696.2	37	c.108G>T	CCDS7003.1																																																																																				0.726	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		7	35	1	0	0.000274275	1	0.000281894	7	35				
EIF3E	3646	broad.mit.edu	37	8	109215251	109215251	+	Missense_Mutation	SNP	C	C	T			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr8:109215251C>T	ENST00000220849.5	-	12	1322	c.1260G>A	c.(1258-1260)atG>atA	p.M420I	EIF3E_ENST00000519030.1_Missense_Mutation_p.M327I|EIF3E_ENST00000519517.1_5'Flank	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TCTCAATATTCATGGCCAACA	0.398																																					GBM(15;360 410 8460 34179 52246)	ENST00000220849.5																		EIF3E/RSPO2(6)	0				NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						c.(1258-1260)atG>atA		eukaryotic translation initiation factor 3, subunit E							153.0	139.0	144.0					8																	109215251		2203	4300	6503	SO:0001583	missense	3646				negative regulation of translational initiation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|eukaryotic translation initiation factor 3 complex|PML body	protein N-terminus binding	g.chr8:109215251C>T	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"""eukaryotic translation initiation factor 3, subunit 6 48kDa"""	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.1260G>A	8.37:g.109215251C>T	ENSP00000220849:p.Met420Ile					EIF3E_ENST00000519030.1_Missense_Mutation_p.M327I	p.M420I	NM_001568.2	NP_001559.1	P60228	EIF3E_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)		12	1322	-			420			Sufficient for interaction with MCM7.			Missense_Mutation	SNP	ENST00000220849.5	37	c.1260G>A	CCDS6308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.75|13.75	2.329402|2.329402	0.41197|0.41197	.|.	.|.	ENSG00000104408|ENSG00000104408	ENST00000522352|ENST00000220849;ENST00000519030	.|T;T	.|0.41400	.|1.0;1.0	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.035831	.|0.85682	.|D	.|0.000000	T|T	0.32793|0.32793	0.0841|0.0841	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|B	.|0.09022	.|0.002	.|B	.|0.06405	.|0.002	T|T	0.07712|0.07712	-1.0758|-1.0758	5|10	.|0.20046	.|T	.|0.44	-21.1765|-21.1765	19.8276|19.8276	0.96624|0.96624	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|420	.|P60228	.|EIF3E_HUMAN	K|I	131|420;327	.|ENSP00000220849:M420I;ENSP00000428796:M327I	.|ENSP00000220849:M420I	E|M	-|-	1|3	0|0	EIF3E|EIF3E	109284427|109284427	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.999000|5.999000	0.70665|0.70665	2.697000|2.697000	0.92050|0.92050	0.585000|0.585000	0.79938|0.79938	GAA|ATG		0.398	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		13	20	0	0	0	1	0	13	20				
PRR12	57479	broad.mit.edu	37	19	50097869	50097869	+	Missense_Mutation	SNP	A	A	G			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr19:50097869A>G	ENST00000418929.2	+	3	370	c.358A>G	c.(358-360)Aca>Gca	p.T120A		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TTCCTGGCAAACAGGTAAGCC	0.667																																						ENST00000418929.2																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11						c.(358-360)Aca>Gca		proline rich 12							30.0	35.0	34.0					19																	50097869		1930	4118	6048	SO:0001583	missense	57479						DNA binding	g.chr19:50097869A>G	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.358A>G	19.37:g.50097869A>G	ENSP00000394510:p.Thr120Ala						p.T120A	NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)	3	370	+		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)	534			Pro-rich.		E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	c.358A>G	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.216154	0.39201	.	.	ENSG00000126464	ENST00000418929	.	.	.	4.65	4.65	0.58169	.	.	.	.	.	T	0.77130	0.4085	.	.	.	0.37193	D	0.904039	D	0.71674	0.998	D	0.80764	0.994	T	0.82026	-0.0661	7	0.51188	T	0.08	.	13.1947	0.59732	1.0:0.0:0.0:0.0	.	120	Q9ULL5-3	.	A	120	.	ENSP00000394510:T120A	T	+	1	0	PRR12	54789681	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	8.284000	0.89912	1.959000	0.56917	0.460000	0.39030	ACA		0.667	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		16	36	0	0	0	1	0	16	36				
BRAP	8315	broad.mit.edu	37	12	112103497	112103497	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr12:112103497G>A	ENST00000327551.6	-	6	892	c.752C>T	c.(751-753)aCg>aTg	p.T251M	BRAP_ENST00000539060.1_Missense_Mutation_p.T102M|BRAP_ENST00000419234.4_Missense_Mutation_p.T281M			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						GTTACATAACGTTGTGAGGAT	0.582																																					Pancreas(146;846 1904 7830 25130 26065)	ENST00000419234.4																			0				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						c.(841-843)aCg>aTg		BRCA1 associated protein							158.0	103.0	122.0					12																	112103497		2203	4300	6503	SO:0001583	missense	8315				MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr12:112103497G>A	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"""RING-type (C3HC4) zinc fingers"""	1099	protein-coding gene	gene with protein product	"""impedes mitogenic signal propagation"", ""galectin-2-binding protein"""	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.752C>T	12.37:g.112103497G>A	ENSP00000330813:p.Thr251Met					BRAP_ENST00000539060.1_Missense_Mutation_p.T102M|BRAP_ENST00000327551.6_Missense_Mutation_p.T251M	p.T281M	NM_006768.3	NP_006759.3	Q7Z569	BRAP_HUMAN			6	1035	-			281					B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	37	c.842C>T		.	.	.	.	.	.	.	.	.	.	G	20.9	4.061811	0.76187	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	T;T;T	0.47177	0.85;0.85;0.85	5.22	5.22	0.72569	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	L	0.33245	0.995	0.80722	D	1	D;D	0.89917	1.0;0.988	D;P	0.83275	0.996;0.721	T	0.63550	-0.6612	10	0.62326	D	0.03	-14.9971	18.7631	0.91860	0.0:0.0:1.0:0.0	.	102;281	B4DRM1;Q7Z569	.;BRAP_HUMAN	M	281;102;251;63	ENSP00000403524:T281M;ENSP00000441659:T102M;ENSP00000330813:T251M	ENSP00000330813:T251M	T	-	2	0	BRAP	110587880	1.000000	0.71417	0.943000	0.38184	0.885000	0.51271	9.276000	0.95745	2.431000	0.82371	0.305000	0.20034	ACG		0.582	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			3	52	0	0	0	1	0	3	52				
GPR116	221395	broad.mit.edu	37	6	46826302	46826302	+	Missense_Mutation	SNP	T	T	C			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr6:46826302T>C	ENST00000283296.7	-	17	3626	c.3338A>G	c.(3337-3339)tAt>tGt	p.Y1113C	GPR116_ENST00000265417.7_Missense_Mutation_p.Y1113C|GPR116_ENST00000545669.1_Missense_Mutation_p.Y542C|GPR116_ENST00000456426.2_Missense_Mutation_p.Y971C|GPR116_ENST00000362015.4_Missense_Mutation_p.Y1113C	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	1113					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			AACCAGGCGATAGAACAGCAT	0.517																																					NSCLC(59;410 1274 8751 36715 50546)	ENST00000283296.7																			0				breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59						c.(3337-3339)tAt>tGt		G protein-coupled receptor 116							48.0	49.0	49.0					6																	46826302		2203	4300	6503	SO:0001583	missense	221395				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr6:46826302T>C	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.3338A>G	6.37:g.46826302T>C	ENSP00000283296:p.Tyr1113Cys					GPR116_ENST00000456426.2_Missense_Mutation_p.Y971C|GPR116_ENST00000265417.7_Missense_Mutation_p.Y1113C|GPR116_ENST00000362015.4_Missense_Mutation_p.Y1113C|GPR116_ENST00000545669.1_Missense_Mutation_p.Y542C	p.Y1113C	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	Lung(136;0.192)		17	3626	-			1113					O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	c.3338A>G	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320894	0.60634	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	5.38	4.19	0.49359	GPCR, family 2-like (1);	0.240498	0.29486	N	0.012007	T	0.56426	0.1984	M	0.90759	3.145	0.50313	D	0.999864	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.66630	-0.5875	10	0.87932	D	0	-22.649	11.8232	0.52252	0.1314:0.0:0.0:0.8686	.	542;668;1113;971;1113	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	C	1113;1113;1113;971;484;1113;542	ENSP00000283296:Y1113C;ENSP00000354563:Y1113C;ENSP00000412866:Y971C;ENSP00000265417:Y1113C;ENSP00000441581:Y542C	ENSP00000265417:Y1113C	Y	-	2	0	GPR116	46934261	1.000000	0.71417	0.977000	0.42913	0.918000	0.54935	7.970000	0.88000	0.941000	0.37499	0.528000	0.53228	TAT		0.517	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		3	35	0	0	0	1	0	3	35				
ADAMTS16	170690	broad.mit.edu	37	5	5237086	5237086	+	Silent	SNP	G	G	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr5:5237086G>A	ENST00000274181.7	+	14	2166	c.2028G>A	c.(2026-2028)caG>caA	p.Q676Q	ADAMTS16_ENST00000513709.1_Intron	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	676	Cys-rich.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						TTTAAGATCAGGACTTATGCA	0.353																																						ENST00000274181.7																			0				breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						c.(2026-2028)caG>caA		ADAM metallopeptidase with thrombospondin type 1 motif, 16							134.0	121.0	125.0					5																	5237086		1836	4084	5920	SO:0001819	synonymous_variant	170690				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	g.chr5:5237086G>A	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17108	protein-coding gene	gene with protein product		607510	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"""			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.2028G>A	5.37:g.5237086G>A						ADAMTS16_ENST00000513709.1_Intron	p.Q676Q	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN			14	2166	+			676			Cys-rich.		C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	c.2028G>A	CCDS43299.1																																																																																				0.353	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		7	31	0	0	0	1	0	7	31				
TSC2	7249	broad.mit.edu	37	16	2098652	2098652	+	Silent	SNP	G	G	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr16:2098652G>A	ENST00000219476.3	+	2	666	c.36G>A	c.(34-36)aaG>aaA	p.K12K	TSC2_ENST00000568454.1_Silent_p.K23K|TSC2_ENST00000353929.4_Silent_p.K12K|TSC2_ENST00000401874.2_Silent_p.K12K|TSC2_ENST00000382538.6_Intron|NTHL1_ENST00000219066.1_5'Flank|TSC2_ENST00000350773.4_Silent_p.K12K|TSC2_ENST00000439673.2_Silent_p.K12K	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	12	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CAGGCTTGAAGGAGAAGTTTA	0.502			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																													ENST00000219476.3			yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	"""D, Mis, N, F, S"""	tuberous sclerosis 2 gene			"""E, O"""		"""hamartoma, renal cell"""			0				NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56						c.(34-36)aaG>aaA		tuberous sclerosis 2							122.0	111.0	115.0					16																	2098652		2196	4299	6495	SO:0001819	synonymous_variant	7249	Tuberous Sclerosis	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity	g.chr16:2098652G>A	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.36G>A	16.37:g.2098652G>A						TSC2_ENST00000568454.1_Silent_p.K23K|TSC2_ENST00000350773.4_Silent_p.K12K|TSC2_ENST00000439673.2_Silent_p.K12K|TSC2_ENST00000353929.4_Silent_p.K12K|TSC2_ENST00000382538.6_Intron|TSC2_ENST00000401874.2_Silent_p.K12K	p.K12K	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN			2	666	+		Hepatocellular(780;0.0202)	12			Required for interaction with TSC1.		A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	c.36G>A	CCDS10458.1																																																																																				0.502	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		3	43	0	0	0	1	0	3	43				
MSL3P1	151507	broad.mit.edu	37	2	234774852	234774852	+	RNA	SNP	G	G	C			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr2:234774852G>C	ENST00000438684.1	-	0	1262					NR_024322.1		P0C860	MS3L2_HUMAN	male-specific lethal 3 homolog (Drosophila) pseudogene 1						chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)											CTGGGAAGAAGTCATCGTGGT	0.433																																						ENST00000438684.1																			0																				118.0	99.0	105.0					2																	234774852		692	1591	2283			0							g.chr2:234774852G>C	BI831020		2q37.1	2011-03-21	2011-03-21	2011-03-21	ENSG00000224287	ENSG00000224287			17837	pseudogene	pseudogene			"""male-specific lethal 3-like 2 (Drosophila)"""	MSL3L2			Standard	NR_024322		Approved		uc010znf.2	P0C860	OTTHUMG00000059126		2.37:g.234774852G>C								NR_024322.1						0	1262	-									RNA	SNP	ENST00000438684.1	37																																																																																						0.433	MSL3P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000131002.2	NR_024322		19	32	0	0	0	1	0	19	32				
C9orf9	11092	broad.mit.edu	37	9	135763731	135763731	+	Silent	SNP	C	C	T	rs537630425		TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr9:135763731C>T	ENST00000372136.3	+	4	849	c.402C>T	c.(400-402)taC>taT	p.Y134Y	C9orf9_ENST00000356311.5_Silent_p.Y134Y|C9orf9_ENST00000350499.6_Silent_p.Y134Y			Q96E40	CI009_HUMAN	chromosome 9 open reading frame 9	134						cytoplasmic microtubule (GO:0005881)		p.?(1)		cervix(1)|large_intestine(1)|lung(1)|prostate(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|GBM - Glioblastoma multiforme(294;4.84e-07)|Epithelial(140;1.28e-06)		GGAACCACTACGGCGGCGTGG	0.607																																						ENST00000372136.3																			1	Unknown(1)	p.?(1)	bone(1)	cervix(1)|large_intestine(1)|lung(1)|prostate(1)	4						c.(400-402)taC>taT		chromosome 9 open reading frame 9							90.0	73.0	79.0					9																	135763731		2203	4300	6503	SO:0001819	synonymous_variant	11092							g.chr9:135763731C>T		CCDS6955.1	9q34.13	2012-03-06			ENSG00000165698	ENSG00000165698			1367	protein-coding gene	gene with protein product							Standard	NM_018956		Approved		uc004cby.1	Q96E40	OTTHUMG00000020847	ENST00000372136.3:c.402C>T	9.37:g.135763731C>T						C9orf9_ENST00000350499.6_Silent_p.Y134Y|C9orf9_ENST00000356311.5_Silent_p.Y134Y	p.Y134Y			Q96E40	CI009_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|GBM - Glioblastoma multiforme(294;4.84e-07)|Epithelial(140;1.28e-06)	4	849	+			134					Q9UGQ0	Silent	SNP	ENST00000372136.3	37	c.402C>T																																																																																					0.607	C9orf9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000054806.1	NM_018956		18	48	0	0	0	1	0	18	48				
GOLGA8DP	100132979	broad.mit.edu	37	15	22709637	22709637	+	RNA	SNP	T	T	G	rs375512037		TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr15:22709637T>G	ENST00000314246.8	-	0	1147				RN7SL545P_ENST00000495815.2_RNA			Q0D2H9	GOG8D_HUMAN	golgin A8 family, member D, pseudogene							Golgi apparatus (GO:0005794)											CCCATCTGGTTTTTGAGTTTG	0.547																																						ENST00000314246.8																			0																																																			0							g.chr15:22709637T>G			15q11.2	2014-04-10	2011-04-15	2010-02-12	ENSG00000185182	ENSG00000185182			32376	pseudogene	pseudogene			"""golgi autoantigen, golgin subfamily a, 8D"""	GOLGA8D		12477932	Standard	NR_027407		Approved		uc010axw.2	Q0D2H9	OTTHUMG00000171882		15.37:g.22709637T>G														0	1147	-									RNA	SNP	ENST00000314246.8	37			.	.	.	.	.	.	.	.	.	.	t	4.705	0.131021	0.08981	.	.	ENSG00000185182	ENST00000341390;ENST00000314246;ENST00000317692	.	.	.	0.921	0.921	0.19403	.	.	.	.	.	T	0.23330	0.0564	.	.	.	.	.	.	B	0.10296	0.003	B	0.08055	0.003	T	0.20773	-1.0265	6	0.25751	T	0.34	.	4.1761	0.10353	0.0:0.0:0.0:1.0	.	84	F8WBT8	.	H	84;84;302	.	ENSP00000327024:N84H	N	-	1	0	AC116165.1	20261001	0.018000	0.18449	0.020000	0.16555	0.004000	0.04260	2.215000	0.42862	0.684000	0.31448	0.228000	0.17796	AAC		0.547	GOLGA8DP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415613.1	NR_027407		4	99	0	0	0	1	0	4	99				
CCDC67	159989	broad.mit.edu	37	11	93088558	93088558	+	Missense_Mutation	SNP	G	G	C			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr11:93088558G>C	ENST00000298050.3	+	3	151	c.51G>C	c.(49-51)gaG>gaC	p.E17D	CCDC67_ENST00000530053.1_3'UTR|CCDC67_ENST00000527307.1_Missense_Mutation_p.E17D	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	17					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				GTGAGGCTGAGCTTCAGGAAT	0.378																																						ENST00000298050.3																			0				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						c.(49-51)gaG>gaC		coiled-coil domain containing 67							103.0	100.0	101.0					11																	93088558		1852	4087	5939	SO:0001583	missense	159989							g.chr11:93088558G>C	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.51G>C	11.37:g.93088558G>C	ENSP00000298050:p.Glu17Asp					CCDC67_ENST00000527307.1_Missense_Mutation_p.E17D|CCDC67_ENST00000530053.1_3'UTR	p.E17D	NM_181645.3	NP_857596.2	Q05D60	CCD67_HUMAN			3	151	+		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)	17					Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	c.51G>C	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.881241	0.72294	.	.	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000532819;ENST00000527307	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.54	1.49	0.22878	.	0.000000	0.56097	D	0.000021	T	0.44808	0.1311	M	0.71206	2.165	0.32877	D	0.509997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	T	0.54899	-0.8224	10	0.66056	D	0.02	.	8.739	0.34545	0.5578:0.0:0.4422:0.0	.	17;17;9	Q05D60;E9PJR5;Q6ZRU6	CCD67_HUMAN;.;.	D	17	ENSP00000432111:E17D;ENSP00000298050:E17D;ENSP00000434635:E17D;ENSP00000433002:E17D	ENSP00000298050:E17D	E	+	3	2	CCDC67	92728206	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	1.102000	0.31050	0.023000	0.15187	0.491000	0.48974	GAG		0.378	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		8	52	0	0	0	1	0	8	52				
PPL	5493	broad.mit.edu	37	16	4935111	4935111	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr16:4935111G>A	ENST00000345988.2	-	22	3634	c.3545C>T	c.(3544-3546)cCc>cTc	p.P1182L	PPL_ENST00000590782.2_Missense_Mutation_p.P1180L	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1182					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TTCCGCCTTGGGGTCTGGCCG	0.622																																						ENST00000345988.2																			0				breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						c.(3544-3546)cCc>cTc		periplakin							95.0	88.0	90.0					16																	4935111		2197	4300	6497	SO:0001583	missense	5493				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton	g.chr16:4935111G>A	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3545C>T	16.37:g.4935111G>A	ENSP00000340510:p.Pro1182Leu					PPL_ENST00000590782.2_Missense_Mutation_p.P1180L	p.P1182L	NM_002705.4	NP_002696.3	O60437	PEPL_HUMAN			22	3634	-			1182					O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	c.3545C>T	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.187242	0.57909	.	.	ENSG00000118898	ENST00000345988	T	0.79749	-1.3	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.90889	0.7137	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91097	0.4911	10	0.59425	D	0.04	.	19.7311	0.96182	0.0:0.0:1.0:0.0	.	1182	O60437	PEPL_HUMAN	L	1182	ENSP00000340510:P1182L	ENSP00000340510:P1182L	P	-	2	0	PPL	4875112	1.000000	0.71417	1.000000	0.80357	0.500000	0.33767	9.827000	0.99397	2.677000	0.91161	0.561000	0.74099	CCC		0.622	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		31	64	0	0	0	1	0	31	64				
KCNC3	3748	broad.mit.edu	37	19	50827018	50827018	+	Missense_Mutation	SNP	G	G	C			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr19:50827018G>C	ENST00000477616.1	-	2	1486	c.1192C>G	c.(1192-1194)Ctc>Gtc	p.L398V	KCNC3_ENST00000376959.2_Missense_Mutation_p.L398V|KCNC3_ENST00000391818.2_Intron|KCNC3_ENST00000474951.1_Intron	NM_004977.2	NP_004968.2	Q14003	KCNC3_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 3	398					cell death (GO:0008219)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axolemma (GO:0030673)|axon terminus (GO:0043679)|dendrite membrane (GO:0032590)|neuromuscular junction (GO:0031594)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)	13		all_neural(266;0.057)|Ovarian(192;0.208)		OV - Ovarian serous cystadenocarcinoma(262;0.00283)|GBM - Glioblastoma multiforme(134;0.0181)	Dalfampridine(DB06637)	AGGCCCGAGAGGCCCACCTCG	0.597																																					Melanoma(91;1496 2324 50908)	ENST00000376959.2																			0				endometrium(2)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)	13						c.(1192-1194)Ctc>Gtc		potassium voltage-gated channel, Shaw-related subfamily, member 3							98.0	95.0	96.0					19																	50827018		2203	4300	6503	SO:0001583	missense	3748				cell death	voltage-gated potassium channel complex	voltage-gated potassium channel activity	g.chr19:50827018G>C	AB208930	CCDS12793.1	19q13.33	2014-09-17			ENSG00000131398	ENSG00000131398		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6235	protein-coding gene	gene with protein product		176264	"""spinocerebellar ataxia 13"""	SCA13		1740329, 8111118, 16382104	Standard	NM_004977		Approved	Kv3.3	uc002pru.1	Q14003	OTTHUMG00000044580	ENST00000477616.1:c.1192C>G	19.37:g.50827018G>C	ENSP00000434241:p.Leu398Val					KCNC3_ENST00000474951.1_Intron|KCNC3_ENST00000477616.1_Missense_Mutation_p.L398V|KCNC3_ENST00000391818.2_Intron	p.L398V			Q14003	KCNC3_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00283)|GBM - Glioblastoma multiforme(134;0.0181)	2	1355	-		all_neural(266;0.057)|Ovarian(192;0.208)	398						Missense_Mutation	SNP	ENST00000477616.1	37	c.1192C>G	CCDS12793.1	.	.	.	.	.	.	.	.	.	.	g	11.80	1.746783	0.30955	.	.	ENSG00000131398	ENST00000376959;ENST00000477616;ENST00000443843	D;D	0.98777	-5.13;-5.13	2.86	0.683	0.17998	Ion transport (1);	0.119748	0.34338	U	0.004053	D	0.97826	0.9286	L	0.38692	1.165	0.80722	D	1	D;P	0.71674	0.998;0.747	D;P	0.91635	0.999;0.678	D	0.96010	0.9001	10	0.52906	T	0.07	.	8.3161	0.32102	0.2336:0.0:0.7664:0.0	.	398;398	Q14003;E7ETH1	KCNC3_HUMAN;.	V	398;398;212	ENSP00000366158:L398V;ENSP00000434241:L398V	ENSP00000366158:L398V	L	-	1	0	KCNC3	55518830	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	5.470000	0.66756	0.543000	0.28864	-0.436000	0.05848	CTC		0.597	KCNC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314288.2	NM_004977		5	46	0	0	0	1	0	5	46				
JMJD4	65094	broad.mit.edu	37	1	227922874	227922874	+	Missense_Mutation	SNP	G	G	C	rs201975311	byFrequency	TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr1:227922874G>C	ENST00000366758.3	-	1	238	c.239C>G	c.(238-240)tCg>tGg	p.S80W	SNAP47_ENST00000315781.5_5'UTR|JMJD4_ENST00000438896.2_Missense_Mutation_p.S80W|SNAP47_ENST00000366759.4_5'UTR|JMJD4_ENST00000485807.1_5'Flank|SNAP47_ENST00000366760.1_Intron	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	80										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				GCCCGGCTCCGAGACGAAGGC	0.711													G|||	4	0.000798722	0.0	0.0014	5008	,	,		13457	0.0		0.003	False		,,,				2504	0.0					ENST00000366758.3																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9						c.(238-240)tCg>tGg		jumonji domain containing 4		G	TRP/SER,TRP/SER,	1,4053		0,1,2026	4.0	6.0	5.0		239,239,	0.5	0.0	1		5	21,7991		0,21,3985	yes	missense,missense,utr-5	JMJD4,SNAP47	NM_001161465.1,NM_023007.2,NM_053052.3	177,177,	0,22,6011	CC,CG,GG		0.2621,0.0247,0.1823	possibly-damaging,possibly-damaging,	80/448,80/464,	227922874	22,12044	2027	4006	6033	SO:0001583	missense	65094							g.chr1:227922874G>C	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.239C>G	1.37:g.227922874G>C	ENSP00000355720:p.Ser80Trp					JMJD4_ENST00000438896.2_Missense_Mutation_p.S80W|SNAP47_ENST00000366759.4_5'UTR|SNAP47_ENST00000366760.1_Intron|SNAP47_ENST00000315781.5_5'UTR	p.S80W	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN			1	238	-		Prostate(94;0.0885)	80					Q5TBZ1|Q5TBZ6|Q9H970	Missense_Mutation	SNP	ENST00000366758.3	37	c.239C>G	CCDS1561.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.04|18.04	3.534856|3.534856	0.64972|0.64972	2.47E-4|2.47E-4	0.002621|0.002621	ENSG00000081692|ENSG00000081692	ENST00000438896|ENST00000366758	.|T	.|0.14266	.|2.52	4.5|4.5	0.459|0.459	0.16678|0.16678	.|.	.|0.518516	.|0.20991	.|N	.|0.082040	T|T	0.15392|0.15392	0.0371|0.0371	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999999|0.999999	.|D;P	.|0.55385	.|0.971;0.951	.|P;P	.|0.59825	.|0.864;0.734	T|T	0.12293|0.12293	-1.0553|-1.0553	5|10	.|0.87932	.|D	.|0	-10.1325|-10.1325	11.0285|11.0285	0.47759|0.47759	0.0:0.0:0.5247:0.4753|0.0:0.0:0.5247:0.4753	.|.	.|80;80	.|Q9H9V9-2;Q9H9V9	.|.;JMJD4_HUMAN	G|W	73|80	.|ENSP00000355720:S80W	.|ENSP00000355720:S80W	R|S	-|-	1|2	2|0	JMJD4|JMJD4	225989497|225989497	0.029000|0.029000	0.19370|0.19370	0.001000|0.001000	0.08648|0.08648	0.004000|0.004000	0.04260|0.04260	1.399000|1.399000	0.34566|0.34566	0.208000|0.208000	0.20626|0.20626	0.542000|0.542000	0.68232|0.68232	CGG|TCG		0.711	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007		7	5	0	0	0	1	0	7	5				
KRTAP4-6	81871	broad.mit.edu	37	17	39296626	39296626	+	Silent	SNP	G	G	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr17:39296626G>A	ENST00000345847.4	-	1	113	c.114C>T	c.(112-114)ccC>ccT	p.P38P		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	38	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						CACAGCAGCTGGGGCGGCAGC	0.667																																						ENST00000345847.4																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						c.(112-114)ccC>ccT		keratin associated protein 4-6																																				SO:0001819	synonymous_variant	81871					keratin filament		g.chr17:39296626G>A	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.114C>T	17.37:g.39296626G>A							p.P38P	NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN			1	113	-			38			29 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].		Q9BYR1	Silent	SNP	ENST00000345847.4	37	c.114C>T	CCDS54125.1																																																																																				0.667	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1			5	102	0	0	0	1	0	5	102				
KRTAP4-6	81871	broad.mit.edu	37	17	39296674	39296674	+	Silent	SNP	G	G	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr17:39296674G>A	ENST00000345847.4	-	1	65	c.66C>T	c.(64-66)cgC>cgT	p.R22R		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	22	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						AGCAGCTGGGGCGGCAGCAGG	0.632																																						ENST00000345847.4																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						c.(64-66)cgC>cgT		keratin associated protein 4-6																																				SO:0001819	synonymous_variant	81871					keratin filament		g.chr17:39296674G>A	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.66C>T	17.37:g.39296674G>A							p.R22R	NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN			1	65	-			22			29 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].		Q9BYR1	Silent	SNP	ENST00000345847.4	37	c.66C>T	CCDS54125.1																																																																																				0.632	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1			6	76	0	0	0	1	0	6	76				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	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		6	21	0	0	0	1	0	6	21				
BAGE2	85319	broad.mit.edu	37	21	11058248	11058248	+	RNA	SNP	G	G	A	rs8130203	byFrequency	TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr21:11058248G>A	ENST00000470054.1	-	0	399							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GCAGCACAAGGATAATGATAC	0.433																																						ENST00000470054.1																			0													B melanoma antigen family, member 2							80.0	67.0	71.0					21																	11058248		692	1591	2283			85319							g.chr21:11058248G>A	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058248G>A												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	399	-								A8K925|Q08ER0	RNA	SNP	ENST00000470054.1	37																																																																																						0.433	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		5	59	0	0	0	1	0	5	59				
CDH6	1004	broad.mit.edu	37	5	31305327	31305327	+	Missense_Mutation	SNP	C	C	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr5:31305327C>A	ENST00000265071.2	+	7	1311	c.1046C>A	c.(1045-1047)gCc>gAc	p.A349D	CDH6_ENST00000514738.1_Missense_Mutation_p.A294D	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	349	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AAAGTGGAAGCCTCCAATCCT	0.463																																						ENST00000265071.2																			0				NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						c.(1045-1047)gCc>gAc		cadherin 6, type 2, K-cadherin (fetal kidney)							93.0	90.0	91.0					5																	31305327		2203	4300	6503	SO:0001583	missense	1004				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding	g.chr5:31305327C>A	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.1046C>A	5.37:g.31305327C>A	ENSP00000265071:p.Ala349Asp					CDH6_ENST00000514738.1_Missense_Mutation_p.A294D	p.A349D	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN			7	1311	+			349			Cadherin 3.		A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	37	c.1046C>A	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.630943	0.87660	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	T;T	0.58940	0.3;0.3	5.88	5.88	0.94601	Cadherin (5);Cadherin-like (1);	0.052391	0.85682	D	0.000000	D	0.84660	0.5521	H	0.96365	3.81	0.58432	D	0.999997	D;D	0.76494	0.999;0.997	D;D	0.72982	0.979;0.951	D	0.88700	0.3215	10	0.87932	D	0	.	20.2187	0.98312	0.0:1.0:0.0:0.0	.	349;349	P55285;P55285-2	CADH6_HUMAN;.	D	294;349	ENSP00000424843:A294D;ENSP00000265071:A349D	ENSP00000265071:A349D	A	+	2	0	CDH6	31341084	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.558000	0.67319	2.780000	0.95670	0.655000	0.94253	GCC		0.463	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		18	27	1	0	4.75885e-15	1	5.17875e-15	18	27				
FBXO10	26267	broad.mit.edu	37	9	37541400	37541400	+	Silent	SNP	G	G	A			TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr9:37541400G>A	ENST00000432825.2	-	2	414	c.366C>T	c.(364-366)ggC>ggT	p.G122G	RP11-613M10.8_ENST00000537239.2_3'UTR|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Intron	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	122					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		CCAAGGCACTGCCCAGGCTGT	0.552																																						ENST00000432825.2																			0				breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34						c.(364-366)ggC>ggT		F-box protein 10							119.0	122.0	121.0					9																	37541400		2054	4201	6255	SO:0001819	synonymous_variant	26267					ubiquitin ligase complex	ubiquitin-protein ligase activity	g.chr9:37541400G>A	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.366C>T	9.37:g.37541400G>A						FBXO10_ENST00000541829.1_Intron|RP11-613M10.8_ENST00000544475.1_5'UTR|RP11-613M10.8_ENST00000537239.2_3'UTR	p.G122G	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN		GBM - Glioblastoma multiforme(29;0.0107)	2	414	-			122					Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Silent	SNP	ENST00000432825.2	37	c.366C>T	CCDS47966.1																																																																																				0.552	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			5	109	0	0	0	1	0	5	109				
ZC3H15	55854	broad.mit.edu	37	2	187351112	187351113	+	Start_Codon_Ins	INS	-	-	C	rs375523117		TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr2:187351112_187351113insC	ENST00000337859.6	+	0	230_231				ZC3H15_ENST00000544130.1_5'UTR	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15						cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			TCTCCGCAATGCCCCCCAAGAA	0.609																																						ENST00000337859.6																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15								zinc finger CCCH-type containing 15																																				SO:0001582	initiator_codon_variant	55854					cytoplasm|nucleolus|plasma membrane	nucleic acid binding|zinc ion binding	g.chr2:187351112_187351113insC		CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"""Zinc fingers, CCCH-type domain containing"""	29528	protein-coding gene	gene with protein product	"""likely ortholog of mouse immediate early response, erythropoietin 4"""					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.9dupC	2.37:g.187351118_187351118dupC						ZC3H15_ENST00000544130.1_5'UTR		NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)		0	230_231	+								B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Translation_Start_Site	INS	ENST00000337859.6	37		CCDS42791.1																																																																																				0.609	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471		2	4						2	4	---	---	---	---
PODXL	5420	broad.mit.edu	37	7	131241030	131241035	+	In_Frame_Del	DEL	GGCGAC	GGCGAC	-	rs11277659|rs547816245|rs532078953	byFrequency	TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr7:131241030_131241035delGGCGAC	ENST00000378555.3	-	1	331_336	c.84_89delGTCGCC	c.(82-90)ccgtcgccc>ccc	p.28_30PSP>P	PODXL_ENST00000322985.9_In_Frame_Del_p.28_30PSP>P|PODXL_ENST00000537928.1_In_Frame_Del_p.28_30PSP>P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000541194.1_In_Frame_Del_p.28_30PSP>P			O00592	PODXL_HUMAN	podocalyxin-like	28					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)		p.P30_S31delPS(2)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					ATTCTGGGAGggcgacggcgacggcg	0.748																																						ENST00000541194.1																			2	Deletion - In frame(2)	p.P30_S31delPS(2)	prostate(2)	NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						c.(82-90)ccc>cc		podocalyxin-like																																				SO:0001651	inframe_deletion	5420				cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly	actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle		g.chr7:131241030_131241035delGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.84_89delGTCGCC	7.37:g.131241036_131241041delGGCGAC	ENSP00000367817:p.Pro30_Ser31del					PODXL_ENST00000465001.1_Intron|PODXL_ENST00000322985.9_In_Frame_Del_p.PSP28del|PODXL_ENST00000378555.3_In_Frame_Del_p.PSP28del|PODXL_ENST00000537928.1_In_Frame_Del_p.PSP28del	p.PSP28del	NM_001018111.2	NP_001018121.1	O00592	PODXL_HUMAN			1	341_346	-	Melanoma(18;0.162)		28					A6NHX8|Q52LZ7|Q53ER6	In_Frame_Del	DEL	ENST00000378555.3	37	c.84_89delGTCGCC	CCDS34755.1																																																																																				0.748	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		3	3						3	3	---	---	---	---
RP11-252A24.2	0	broad.mit.edu	37	16	74372915	74372915	+	RNA	DEL	T	T	-	rs397827801|rs11353924|rs532713769|rs398078750		TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr16:74372915delT	ENST00000429810.2	-	0	1404																											ACGTAGtttgttttttttttt	0.438																																						ENST00000429810.2																			0																																																			0							g.chr16:74372915delT																													16.37:g.74372915delT														0	1404	-									RNA	DEL	ENST00000429810.2	37																																																																																						0.438	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000434683.1			2	4						2	4	---	---	---	---
ROCK1P1	727758	broad.mit.edu	37	18	112402	112405	+	RNA	DEL	AACC	AACC	-	rs113232824|rs111811281|rs11080396		TCGA-FY-A4B3-01A-11D-A23U-08	TCGA-FY-A4B3-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fbe5a458-6112-46da-bc88-5bf6467f73bb	f27473dd-f2e2-4039-a2f4-e60e8f59a93e	g.chr18:112402_112405delAACC	ENST00000608049.1	+	0	389					NR_033770.1				Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1																		CCCTGCCCCGAACCACCCGACCCC	0.711																																						ENST00000576266.1																			0																																																			0							g.chr18:112402_112405delAACC			18p11.32	2012-10-04			ENSG00000263006	ENSG00000263006			37832	pseudogene	pseudogene							Standard	NR_033770		Approved		uc002kke.3		OTTHUMG00000177913		18.37:g.112402_112405delAACC														0	36_39	+									RNA	DEL	ENST00000608049.1	37																																																																																						0.711	ROCK1P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472417.1			4	7						4	7	---	---	---	---
