#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
TIA1	7072	broad.mit.edu	37	2	70439917	70439917	+	Silent	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr2:70439917C>T	ENST00000433529.2	-	13	1305	c.1095G>A	c.(1093-1095)ggG>ggA	p.G365G	TIA1_ENST00000445587.1_Silent_p.G264G|TIA1_ENST00000482876.1_5'Flank|TIA1_ENST00000415783.2_Silent_p.G354G|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000282574.4_Silent_p.G364G	NM_022173.2	NP_071505.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	365					apoptotic process (GO:0006915)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of translation (GO:0017148)|regulation of mRNA splicing, via spliceosome (GO:0048024)	cytoplasmic stress granule (GO:0010494)|nuclear stress granule (GO:0097165)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						TGCCATTTTGCCCTTGAGGCG	0.502																																						ENST00000433529.2																			0				endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						c.(1093-1095)ggG>ggA		TIA1 cytotoxic granule-associated RNA binding protein							141.0	126.0	131.0					2																	70439917		2203	4300	6503	SO:0001819	synonymous_variant	7072				apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding	g.chr2:70439917C>T		CCDS1900.1, CCDS1901.1	2p13	2013-02-12	2001-11-28		ENSG00000116001	ENSG00000116001		"""RNA binding motif (RRM) containing"""	11802	protein-coding gene	gene with protein product	"""T-cell-restricted intracellular antigen-1"", ""nucleolysin TIA-1 isoform p40"""	603518	"""TIA1 cytotoxic granule-associated RNA-binding protein"""			8176212, 12486009	Standard	NM_022173		Approved		uc002sgj.4	P31483	OTTHUMG00000129644	ENST00000433529.2:c.1095G>A	2.37:g.70439917C>T						TIA1_ENST00000282574.4_Silent_p.G364G|TIA1_ENST00000415783.2_Silent_p.G354G|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000445587.1_Silent_p.G264G	p.G365G	NM_022173.2	NP_071505.2	P31483	TIA1_HUMAN			13	1305	-			365					Q53SS9	Silent	SNP	ENST00000433529.2	37	c.1095G>A	CCDS1901.1																																																																																				0.502	TIA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251842.2	NM_022037		4	130	0	0	0	0.009096	0	4	130				
NPR1	4881	broad.mit.edu	37	1	153660571	153660571	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr1:153660571G>A	ENST00000368680.3	+	15	2763	c.2291G>A	c.(2290-2292)cGg>cAg	p.R764Q		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	764	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CCCCCCTTCCGGCCCTCCCTG	0.657																																					Pancreas(141;1349 1870 15144 15830 40702)	ENST00000368680.3																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42						c.(2290-2292)cGg>cAg		natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A)	Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)						50.0	53.0	52.0					1																	153660571		2203	4299	6502	SO:0001583	missense	4881				body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity	g.chr1:153660571G>A	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2291G>A	1.37:g.153660571G>A	ENSP00000357669:p.Arg764Gln						p.R764Q	NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.151)		15	2763	+	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		764			Protein kinase.		B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	c.2291G>A	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	g	22.7	4.327672	0.81690	.	.	ENSG00000169418	ENST00000368680;ENST00000428723	D	0.82433	-1.61	4.02	3.11	0.35812	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.082914	0.46758	D	0.000261	D	0.90038	0.6889	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91150	0.4952	10	0.66056	D	0.02	.	11.2084	0.48784	0.0:0.0:0.815:0.185	.	243;764	B7Z4Y7;P16066	.;ANPRA_HUMAN	Q	764;243	ENSP00000357669:R764Q	ENSP00000357669:R764Q	R	+	2	0	NPR1	151927195	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.639000	0.83342	1.071000	0.40834	-0.372000	0.07161	CGG		0.657	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		26	44	0	0	0	0.027356	0	26	44				
BCRP7	100133163	broad.mit.edu	37	22	18845995	18845995	+	3'UTR	SNP	T	T	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr22:18845995T>C	ENST00000412938.1	+	0	3353																											CATCCCGTCCTGCGCAGGCCG	0.592																																						ENST00000412938.1																			0																																																	SO:0001624	3_prime_UTR_variant	0							g.chr22:18845995T>C																												ENST00000412938.1:c.*3350T>C	22.37:g.18845995T>C														0	3353	+									RNA	SNP	ENST00000412938.1	37																																																																																						0.592	AC008132.13-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000471615.1			8	54	0	0	0	0.008291	0	8	54				
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	A	G			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr1:145367739A>G	ENST00000342960.5	+	83	10370	c.10335A>G	c.(10333-10335)aaA>aaG	p.K3445K	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	750						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.K3445K(4)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.413																																						ENST00000342960.5																			4	Substitution - coding silent(4)	p.K3445K(4)	prostate(3)|kidney(1)	NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73						c.(10333-10335)aaA>aaG		neuroblastoma breakpoint family, member 10																																				SO:0001819	synonymous_variant	100132406							g.chr1:145367739A>G	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.10335A>G	1.37:g.145367739A>G						NBPF10_ENST00000369339.2_Intron|NBPF10_ENST00000369338.1_Intron	p.K3445K	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	83	10370	+	all_hematologic(923;0.032)		3445					Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	c.10335A>G	CCDS53355.1																																																																																				0.413	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703		3	112	0	0	0	0.004672	0	3	112				
ANKEF1	63926	broad.mit.edu	37	20	10025188	10025188	+	Silent	SNP	C	C	T	rs368002362		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr20:10025188C>T	ENST00000378380.3	+	4	1022	c.693C>T	c.(691-693)ttC>ttT	p.F231F	SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000488991.1_3'UTR|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Silent_p.F231F	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	231							calcium ion binding (GO:0005509)										GAGGCTTTTTCGATGTAATAA	0.358																																						ENST00000378380.3																			0											c.(691-693)ttC>ttT		ankyrin repeat and EF-hand domain containing 1		C	,	0,4406		0,0,2203	163.0	152.0	156.0		693,693	-0.5	1.0	20		156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ANKRD5	NM_022096.4,NM_198798.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	231/777,231/777	10025188	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	63926							g.chr20:10025188C>T	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.693C>T	20.37:g.10025188C>T						SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000488991.1_3'UTR|ANKEF1_ENST00000378392.1_Silent_p.F231F|SNAP25-AS1_ENST00000603542.1_RNA	p.F231F	NM_198798.1	NP_942093.1					4	1022	+								B3KUQ0|Q9H6Y9	Silent	SNP	ENST00000378380.3	37	c.693C>T	CCDS13108.1																																																																																				0.358	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096		4	101	0	0	0	0.014758	0	4	101				
FRG1B	284802	broad.mit.edu	37	20	29628278	29628278	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr20:29628278G>A	ENST00000278882.3	+	6	660	c.280G>A	c.(280-282)Gca>Aca	p.A94T	FRG1B_ENST00000358464.4_Missense_Mutation_p.A94T|FRG1B_ENST00000439954.2_Missense_Mutation_p.A99T			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	94										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATGCAATGAAGCAGGGGACAT	0.373																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(280-282)Gca>Aca																																						SO:0001583	missense	0							g.chr20:29628278G>A			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.280G>A	20.37:g.29628278G>A	ENSP00000278882:p.Ala94Thr					FRG1B_ENST00000439954.2_Missense_Mutation_p.A99T|FRG1B_ENST00000358464.4_Missense_Mutation_p.A94T	p.A94T							6	660	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.280G>A		.	.	.	.	.	.	.	.	.	.	g	9.994	1.231660	0.22626	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.44083	0.93	2.08	2.08	0.27032	Actin cross-linking (1);	0.286587	0.39083	N	0.001478	T	0.22898	0.0553	.	.	.	0.21290	N	0.99973	B;B	0.12630	0.0;0.006	B;B	0.12156	0.002;0.007	T	0.15407	-1.0438	9	0.16420	T	0.52	.	10.2211	0.43198	0.0:0.0:1.0:0.0	.	99;94	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	T	94;99;94	ENSP00000408863:A99T	ENSP00000278882:A94T	A	+	1	0	FRG1B	28241939	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.196000	0.58407	1.475000	0.48197	0.423000	0.28283	GCA		0.373	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		5	96	0	0	0	0.004482	0	5	96				
SLC2A9	56606	broad.mit.edu	37	4	9982230	9982230	+	Missense_Mutation	SNP	C	C	T	rs147289616	byFrequency	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:9982230C>T	ENST00000264784.3	-	5	720	c.667G>A	c.(667-669)Gag>Aag	p.E223K	SLC2A9_ENST00000506583.1_Missense_Mutation_p.E194K|SLC2A9_ENST00000309065.3_Missense_Mutation_p.E194K	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	223					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	CCCAGCAGCTCGGGCAGGCCC	0.567																																						ENST00000506583.1																			0				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35						c.(580-582)Gag>Aag		solute carrier family 2 (facilitated glucose transporter), member 9		C	LYS/GLU,LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	61.0	55.0	57.0		580,667	3.8	0.8	4	dbSNP_134	57	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SLC2A9	NM_001001290.1,NM_020041.2	56,56	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	probably-damaging,probably-damaging	194/512,223/541	9982230	3,13003	2203	4300	6503	SO:0001583	missense	56606				glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity	g.chr4:9982230C>T	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.667G>A	4.37:g.9982230C>T	ENSP00000264784:p.Glu223Lys					SLC2A9_ENST00000264784.3_Missense_Mutation_p.E223K|SLC2A9_ENST00000309065.3_Missense_Mutation_p.E194K	p.E194K			Q9NRM0	GTR9_HUMAN			7	797	-			223					Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	c.580G>A	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.742241	0.49151	4.54E-4	1.16E-4	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065;ENST00000513129	T;T;T;D	0.87729	0.33;-1.4;0.33;-2.29	4.66	3.81	0.43845	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.127237	0.51477	N	0.000086	D	0.84252	0.5431	L	0.60904	1.88	0.41440	D	0.987918	B;P	0.35411	0.301;0.5	B;B	0.37198	0.112;0.243	T	0.80968	-0.1145	9	.	.	.	.	12.1394	0.53989	0.0:0.8067:0.1933:0.0	.	194;223	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	K	194;223;194;194	ENSP00000422209:E194K;ENSP00000264784:E223K;ENSP00000311383:E194K;ENSP00000426800:E194K	.	E	-	1	0	SLC2A9	9591328	0.996000	0.38824	0.784000	0.31847	0.751000	0.42716	3.454000	0.52986	0.908000	0.36671	0.650000	0.86243	GAG		0.567	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			5	49	0	0	0	0.021553	0	5	49				
PHF6	84295	broad.mit.edu	37	X	133527567	133527567	+	Missense_Mutation	SNP	G	G	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chrX:133527567G>T	ENST00000332070.3	+	4	479	c.277G>T	c.(277-279)Ggt>Tgt	p.G93C	PHF6_ENST00000370803.3_Missense_Mutation_p.G93C|PHF6_ENST00000394292.1_Missense_Mutation_p.G93C|PHF6_ENST00000370800.4_Missense_Mutation_p.G93C|PHF6_ENST00000370799.1_Missense_Mutation_p.G93C|PHF6_ENST00000416404.2_Missense_Mutation_p.G59C	NM_032458.2	NP_115834.1	Q8IWS0	PHF6_HUMAN	PHD finger protein 6	93	Extended PHD1 domain (ePHD1).				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|scaffold protein binding (GO:0097110)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(88)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(1)|skin(1)|urinary_tract(1)	103	Acute lymphoblastic leukemia(192;0.000127)					AGCAACAATTGGTTGTGATGT	0.368			"""F, N, Splice, Mis"""		ETP ALL																																Colon(100;666 1493 6344 21231 35807)	ENST00000332070.3				Rec	yes		X	Xq26.3	84295	"""F, N, Splice, Mis"""	PHD finger protein 6			L			ETP ALL		0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(88)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(1)|skin(1)|urinary_tract(1)	103						c.(277-279)Ggt>Tgt		PHD finger protein 6							195.0	168.0	177.0					X																	133527567		2203	4300	6503	SO:0001583	missense	84295				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding	g.chrX:133527567G>T	AB058726	CCDS14639.1, CCDS14640.1	Xq26	2014-09-17			ENSG00000156531	ENSG00000156531		"""Zinc fingers, PHD-type"""	18145	protein-coding gene	gene with protein product	"""centromere protein 31"""	300414	"""Borjeson-Forssman-Lehmann syndrome"""	BFLS, BORJ		12415272, 15466013	Standard	NM_032335		Approved	KIAA1823, MGC14797, CENP-31	uc004exk.3	Q8IWS0	OTTHUMG00000022453	ENST00000332070.3:c.277G>T	X.37:g.133527567G>T	ENSP00000329097:p.Gly93Cys					PHF6_ENST00000370799.1_Missense_Mutation_p.G93C|PHF6_ENST00000416404.2_Missense_Mutation_p.G59C|PHF6_ENST00000370803.3_Missense_Mutation_p.G93C|PHF6_ENST00000370800.4_Missense_Mutation_p.G93C|PHF6_ENST00000394292.1_Missense_Mutation_p.G93C	p.G93C	NM_032458.2	NP_115834.1	Q8IWS0	PHF6_HUMAN			4	479	+	Acute lymphoblastic leukemia(192;0.000127)		93					A8K230|B4E0G4|D3DTG3|E9PC97|Q5JRC7|Q5JRC8|Q96JK3|Q9BRU0	Missense_Mutation	SNP	ENST00000332070.3	37	c.277G>T	CCDS14639.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.508321	0.85282	.	.	ENSG00000156531	ENST00000370803;ENST00000332070;ENST00000394292;ENST00000370799;ENST00000416404;ENST00000370800	T;T;T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59;-0.59;-0.59	5.15	5.15	0.70609	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.86251	0.5888	M	0.86953	2.85	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.87578	0.983;0.998;0.989;0.989;0.939	D	0.88926	0.3369	10	0.87932	D	0	-13.8317	16.9007	0.86113	0.0:0.0:1.0:0.0	.	59;93;93;93;93	B4E0G4;A8K230;Q8IWS0;E9PC97;Q8IWS0-2	.;.;PHF6_HUMAN;.;.	C	93;93;93;93;59;93	ENSP00000359839:G93C;ENSP00000329097:G93C;ENSP00000377831:G93C;ENSP00000359835:G93C;ENSP00000394480:G59C;ENSP00000359836:G93C	ENSP00000329097:G93C	G	+	1	0	PHF6	133355233	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.420000	0.97426	2.284000	0.76573	0.523000	0.50628	GGT		0.368	PHF6-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058367.1	NM_032458		15	167	1	0	6.72482e-11	0.024245	1.15945e-10	15	167				
PMS2	5395	broad.mit.edu	37	7	6018249	6018249	+	Silent	SNP	A	A	G	rs1805325	byFrequency	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr7:6018249A>G	ENST00000265849.7	-	13	2358	c.2253T>C	c.(2251-2253)ttT>ttC	p.F751F	PMS2_ENST00000441476.2_Silent_p.F645F|PMS2_ENST00000382321.4_Silent_p.F350F|PMS2_ENST00000406569.3_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	751					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TAACAAAATCAAAGCCATTCT	0.393			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																													ENST00000265849.7			yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	"""Mis, N, F"""	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)			E		"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						c.(2251-2253)ttT>ttC	Direct reversal of damage;Mismatch excision repair (MMR)	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)							108.0	86.0	93.0					7																	6018249		2198	4284	6482	SO:0001819	synonymous_variant	5395	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding	g.chr7:6018249A>G		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.2253T>C	7.37:g.6018249A>G						PMS2_ENST00000382321.4_Silent_p.F350F|PMS2_ENST00000406569.3_Intron|PMS2_ENST00000441476.2_Silent_p.F645F	p.F751F	NM_000535.5	NP_000526.1	P54278	PMS2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)	13	2358	-		Ovarian(82;0.0694)	751					B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	c.2253T>C	CCDS5343.1																																																																																				0.393	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		4	26	0	0	0	0.009096	0	4	26				
KCNN3	3782	broad.mit.edu	37	1	154841828	154841828	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr1:154841828C>T	ENST00000271915.4	-	1	928	c.613G>A	c.(613-615)Ggc>Agc	p.G205S	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	210					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	AGGGGTTGGCCCTCAGTCTCG	0.632																																						ENST00000271915.3																			0				cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28						c.(613-615)Ggc>Agc		potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3							49.0	50.0	49.0					1																	154841828		2203	4300	6503	SO:0001583	missense	3782					integral to membrane	calmodulin binding	g.chr1:154841828C>T	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.613G>A	1.37:g.154841828C>T	ENSP00000271915:p.Gly205Ser						p.G205S	NM_002249.5	NP_002240.3	Q9UGI6	KCNN3_HUMAN	BRCA - Breast invasive adenocarcinoma(34;0.00819)		1	928	-	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		210					B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	c.613G>A	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	C	8.386	0.838543	0.16891	.	.	ENSG00000143603	ENST00000271915	D	0.94330	-3.4	4.75	2.72	0.32119	.	0.155049	0.30649	N	0.009166	T	0.63295	0.2499	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.63989	-0.6512	10	0.02654	T	1	-20.4673	3.0661	0.06214	0.2162:0.5562:0.0:0.2275	.	211;210	Q6JXY2;Q9UGI6	.;KCNN3_HUMAN	S	205	ENSP00000271915:G205S	ENSP00000271915:G205S	G	-	1	0	KCNN3	153108452	0.997000	0.39634	1.000000	0.80357	0.988000	0.76386	0.351000	0.20096	1.221000	0.43506	0.561000	0.74099	GGC		0.632	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		32	33	0	0	0	0.013726	0	32	33				
CGB1	114335	broad.mit.edu	37	19	49539494	49539494	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr19:49539494G>A	ENST00000301407.7	-	2	180	c.76C>T	c.(76-78)Cgg>Tgg	p.R26W	CGB1_ENST00000391869.3_Missense_Mutation_p.R26W|CTB-60B18.6_ENST00000591656.1_Intron	NM_033377.1	NP_203695.2	A6NKQ9	CGB1_HUMAN	chorionic gonadotropin, beta polypeptide 1	58						extracellular region (GO:0005576)				liver(1)|lung(1)	2		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GGGCGGCACCGTGGCCGAAGC	0.652																																						ENST00000301407.7																			0				liver(1)|lung(1)	2						c.(76-78)Cgg>Tgg		chorionic gonadotropin, beta polypeptide 1							32.0	33.0	32.0					19																	49539494		1466	2623	4089	SO:0001583	missense	114335					extracellular region	hormone activity	g.chr19:49539494G>A	S80935	CCDS12751.2	19q13.32	2012-10-03				ENSG00000267631			16721	protein-coding gene	gene with protein product		608823				6194155	Standard	NM_033377		Approved		uc002plx.3	A6NKQ9	OTTHUMG00000150186	ENST00000301407.7:c.76C>T	19.37:g.49539494G>A	ENSP00000301407:p.Arg26Trp					CTB-60B18.6_ENST00000591656.1_Intron|CGB1_ENST00000391869.3_Missense_Mutation_p.R26W	p.R26W	NM_033377.1	NP_203695.2	A6NKQ9	CGB1_HUMAN		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	2	180	-		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)	58					A4FVC8|A8MUK6	Missense_Mutation	SNP	ENST00000301407.7	37	c.76C>T	CCDS12751.2	.	.	.	.	.	.	.	.	.	.	g	2.894	-0.229075	0.06022	.	.	ENSG00000213030	ENST00000301407;ENST00000391869	D;D	0.91011	-2.77;-2.77	1.79	0.712	0.18167	.	0.221865	0.29225	N	0.012762	T	0.81394	0.4813	.	.	.	0.20563	N	0.999882	B	0.23540	0.087	B	0.14023	0.01	T	0.68405	-0.5417	9	0.37606	T	0.19	-16.6805	6.2364	0.20766	0.1778:0.0:0.8222:0.0	.	26	A6NKQ9-2	.	W	26	ENSP00000301407:R26W;ENSP00000375742:R26W	ENSP00000301407:R26W	R	-	1	2	CGB1	54231306	0.452000	0.25713	0.893000	0.35052	0.080000	0.17528	1.194000	0.32174	0.309000	0.22966	0.184000	0.17185	CGG		0.652	CGB1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316746.4	NM_033377		6	89	0	0	0	0.003080	0	6	89				
TRO	7216	broad.mit.edu	37	X	54954164	54954164	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chrX:54954164C>T	ENST00000173898.7	+	11	1940	c.1828C>T	c.(1828-1830)Cgc>Tgc	p.R610C	TRO_ENST00000375022.4_Missense_Mutation_p.R610C|TRO_ENST00000319167.8_Missense_Mutation_p.R610C|TRO_ENST00000420798.2_Missense_Mutation_p.R141C|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000399736.1_Missense_Mutation_p.R213C|TRO_ENST00000375041.2_Missense_Mutation_p.R213C	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	610	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R610C(2)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						CTGGGGCTTGCGCTCCTACCA	0.483																																						ENST00000173898.7																			2	Substitution - Missense(2)	p.R610C(2)	kidney(2)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						c.(1828-1830)Cgc>Tgc		trophinin							60.0	58.0	59.0					X																	54954164		2199	4300	6499	SO:0001583	missense	7216				embryo implantation|homophilic cell adhesion	integral to plasma membrane		g.chrX:54954164C>T	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.1828C>T	X.37:g.54954164C>T	ENSP00000173898:p.Arg610Cys					TRO_ENST00000319167.8_Missense_Mutation_p.R610C|TRO_ENST00000420798.2_Missense_Mutation_p.R141C|TRO_ENST00000375022.4_Missense_Mutation_p.R610C|TRO_ENST00000399736.1_Missense_Mutation_p.R213C|TRO_ENST00000375041.2_Missense_Mutation_p.R213C	p.R610C	NM_001039705.1	NP_001034794.1	Q12816	TROP_HUMAN			11	1940	+			610			MAGE.		B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	c.1828C>T	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.814959	0.32053	.	.	ENSG00000067445	ENST00000173898;ENST00000319167;ENST00000375022;ENST00000399736;ENST00000319179;ENST00000420798;ENST00000375041	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	3.1	2.2	0.27929	.	.	.	.	.	T	0.55816	0.1944	H	0.96301	3.8	0.50632	D	0.999886	B;D;D;B	0.89917	0.155;1.0;1.0;0.155	B;D;D;B	0.97110	0.015;1.0;0.999;0.015	T	0.54642	-0.8263	9	0.87932	D	0	.	2.9059	0.05721	0.2683:0.568:0.0:0.1637	.	213;213;610;610	B1AKE9;B1AKF1;Q96SX2;Q12816	.;.;.;TROP_HUMAN	C	610;610;610;213;213;141;213	ENSP00000173898:R610C;ENSP00000318278:R610C;ENSP00000364162:R610C;ENSP00000382641:R213C;ENSP00000405126:R141C;ENSP00000364181:R213C	ENSP00000173898:R610C	R	+	1	0	TRO	54970889	0.914000	0.31030	0.716000	0.30569	0.957000	0.61999	1.178000	0.31981	0.651000	0.30788	0.513000	0.50165	CGC		0.483	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		4	93	0	0	0	0.009096	0	4	93				
DCAF12L2	340578	broad.mit.edu	37	X	125298907	125298907	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chrX:125298907G>A	ENST00000360028.2	-	1	1027	c.1001C>T	c.(1000-1002)cCg>cTg	p.P334L	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.P334L			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	334										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						GCGCTGGCGCGGATCCAGGAA	0.617																																						ENST00000538699.1																			0				NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						c.(1000-1002)cCg>cTg		DDB1 and CUL4 associated factor 12-like 2							61.0	65.0	64.0					X																	125298907		2203	4300	6503	SO:0001583	missense	340578							g.chrX:125298907G>A	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.1001C>T	X.37:g.125298907G>A	ENSP00000353128:p.Pro334Leu					DCAF12L2_ENST00000360028.2_Missense_Mutation_p.P334L	p.P334L	NM_001013628.2	NP_001013650.1	Q5VW00	DC122_HUMAN			2	1081	-			334					B2RN42	Missense_Mutation	SNP	ENST00000360028.2	37	c.1001C>T	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.262479	0.39995	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.58652	0.32;0.32	4.05	4.05	0.47172	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.468130	0.16069	N	0.231104	T	0.37128	0.0992	N	0.13299	0.325	0.58432	D	0.999997	B	0.06786	0.001	B	0.04013	0.001	T	0.14476	-1.0471	10	0.09338	T	0.73	.	13.1427	0.59444	0.0:0.0:1.0:0.0	.	334	Q5VW00	DC122_HUMAN	L	334	ENSP00000441489:P334L;ENSP00000353128:P334L	ENSP00000353128:P334L	P	-	2	0	DCAF12L2	125126588	1.000000	0.71417	0.912000	0.35992	0.809000	0.45718	3.533000	0.53561	2.263000	0.75096	0.544000	0.68410	CCG		0.617	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		49	81	0	0	0	0.014410	0	49	81				
STC2	8614	broad.mit.edu	37	5	172752921	172752921	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr5:172752921G>A	ENST00000265087.4	-	2	1553	c.244C>T	c.(244-246)Cat>Tat	p.H82Y	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	82					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CAAATCCCATGTAAGCCCCGA	0.468																																						ENST00000265087.4																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25						c.(244-246)Cat>Tat		stanniocalcin 2							252.0	273.0	266.0					5																	172752921		2203	4300	6503	SO:0001583	missense	8614				cell surface receptor linked signaling pathway|cell-cell signaling	extracellular region	hormone activity	g.chr5:172752921G>A	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.244C>T	5.37:g.172752921G>A	ENSP00000265087:p.His82Tyr						p.H82Y	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		2	1553	-	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	82						Missense_Mutation	SNP	ENST00000265087.4	37	c.244C>T	CCDS4388.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.86|18.86	3.712879|3.712879	0.68730|0.68730	.|.	.|.	ENSG00000113739|ENSG00000113739	ENST00000265087|ENST00000520648	.|.	.|.	.|.	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	0.049753|.	0.85682|.	D|.	0.000000|.	T|T	0.67202|0.67202	0.2868|0.2868	L|L	0.41573|0.41573	1.285|1.285	0.53688|0.53688	D|D	0.999976|0.999976	P|.	0.40398|.	0.716|.	B|.	0.42319|.	0.383|.	T|T	0.62534|0.62534	-0.6834|-0.6834	9|5	0.12430|.	T|.	0.62|.	-12.9523|-12.9523	19.2864|19.2864	0.94072|0.94072	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	82|.	O76061|.	STC2_HUMAN|.	Y|I	82|35	.|.	ENSP00000265087:H82Y|.	H|T	-|-	1|2	0|0	STC2|STC2	172685527|172685527	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.476000|9.476000	0.97823|0.97823	2.559000|2.559000	0.86315|0.86315	0.655000|0.655000	0.94253|0.94253	CAT|ACA		0.468	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714		12	373	0	0	0	0.013537	0	12	373				
BMS1P20	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	A	G	rs187344612		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr22:22664606A>G	ENST00000426066.1	+	0	787					NR_027293.1				BMS1 pseudogene 20																		GTCTTCATGCAAACTTGGTAT	0.398																																						ENST00000426066.1																			0																																																			0							g.chr22:22664606A>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664606A>G								NR_027293.1						0	787	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.398	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			3	18	0	0	0	0.004672	0	3	18				
FIP1L1	81608	broad.mit.edu	37	4	54310242	54310242	+	Silent	SNP	T	T	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:54310242T>C	ENST00000337488.6	+	15	1451	c.1257T>C	c.(1255-1257)cgT>cgC	p.R419R	FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000358575.5_Silent_p.R413R|FIP1L1_ENST00000306932.6_Silent_p.R345R	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	419					mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			ATGATAGTCGTTCTGCACGTG	0.303			T	PDGFRA	idiopathic hypereosinophilic syndrome																																	ENST00000337488.6				Dom	yes		4	4q12	81608	T	FIP1 like 1 (S. cerevisiae)			L	PDGFRA		idiopathic hypereosinophilic syndrome		0				large_intestine(3)|liver(1)|ovary(1)|skin(1)	6						c.(1255-1257)cgT>cgC		factor interacting with PAPOLA and CPSF1							175.0	164.0	168.0					4																	54310242		2203	4298	6501	SO:0001819	synonymous_variant	81608				mRNA processing	nucleus	RNA binding	g.chr4:54310242T>C	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"""FIP1 like 1 (S. cerevisiae)"", ""FIP1L1 cleavage and polyadenylation specific factor subunit"""			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1257T>C	4.37:g.54310242T>C						FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000306932.6_Silent_p.R345R|FIP1L1_ENST00000358575.5_Silent_p.R413R	p.R419R	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)		15	1451	+			419					B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Silent	SNP	ENST00000337488.6	37	c.1257T>C	CCDS3491.1																																																																																				0.303	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		3	82	0	0	0	0.014758	0	3	82				
TMPRSS11F	389208	broad.mit.edu	37	4	68939712	68939712	+	Nonsense_Mutation	SNP	G	G	A	rs542655796		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:68939712G>A	ENST00000356291.2	-	4	357	c.298C>T	c.(298-300)Cga>Tga	p.R100*	UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	100	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						GAAGAATGTCGAAATATCCTA	0.244													g|||	1	0.000199681	0.0	0.0	5008	,	,		16271	0.001		0.0	False		,,,				2504	0.0					ENST00000356291.2																			0				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						c.(298-300)Cga>Tga		transmembrane protease, serine 11F							30.0	29.0	29.0					4																	68939712		2196	4293	6489	SO:0001587	stop_gained	389208				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity	g.chr4:68939712G>A	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.298C>T	4.37:g.68939712G>A	ENSP00000348639:p.Arg100*					RP11-453E17.1_ENST00000511571.1_RNA|RP11-453E17.1_ENST00000500538.2_RNA|RP11-453E17.1_ENST00000499180.2_RNA	p.R100*	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN			4	357	-			100			SEA.		A8MXX2	Nonsense_Mutation	SNP	ENST00000356291.2	37	c.298C>T	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	g	22.1	4.251053	0.80135	.	.	ENSG00000198092	ENST00000356291	.	.	.	5.53	3.8	0.43715	.	0.436137	0.19621	N	0.109909	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.3813	0.38316	0.0:0.1567:0.6804:0.1629	.	.	.	.	X	100	.	ENSP00000348639:R100X	R	-	1	2	TMPRSS11F	68622307	0.664000	0.27457	0.997000	0.53966	0.573000	0.36030	0.786000	0.26844	0.695000	0.31675	-0.121000	0.15023	CGA		0.244	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		10	16	0	0	0	0.008291	0	10	16				
PRDM9	56979	broad.mit.edu	37	5	23526762	23526762	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr5:23526762C>T	ENST00000296682.3	+	11	1747	c.1565C>T	c.(1564-1566)gCa>gTa	p.A522V		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	522					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						TCAAGAATTGCAAAAGTCAAG	0.433										HNSCC(3;0.000094)																												ENST00000296682.3																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						c.(1564-1566)gCa>gTa		PR domain containing 9							103.0	104.0	104.0					5																	23526762		2052	4230	6282	SO:0001583	missense	56979				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding	g.chr5:23526762C>T	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1565C>T	5.37:g.23526762C>T	ENSP00000296682:p.Ala522Val	HNSCC(3;0.000094)					p.A522V	NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN			11	1747	+			522					B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	c.1565C>T	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	7.919	0.738232	0.15574	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.08634	3.07	2.43	-4.86	0.03132	.	1.776670	0.03697	N	0.247961	T	0.04497	0.0123	N	0.16478	0.41	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.37798	-0.9690	10	0.21014	T	0.42	1.344	3.6377	0.08155	0.1903:0.4564:0.0:0.3534	.	522	Q9NQV7	PRDM9_HUMAN	V	522;316	ENSP00000296682:A522V	ENSP00000253473:A316V	A	+	2	0	PRDM9	23562519	0.000000	0.05858	0.000000	0.03702	0.304000	0.27724	-1.173000	0.03108	-1.217000	0.02604	-0.362000	0.07510	GCA		0.433	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		5	71	0	0	0	0.014758	0	5	71				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	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		31	59	0	0	0	0.010818	0	31	59				
MGAM	8972	broad.mit.edu	37	7	141767225	141767225	+	Intron	SNP	C	C	T	rs7778384	byFrequency	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr7:141767225C>T	ENST00000549489.2	+	38	4713				MGAM_ENST00000475668.2_Splice_Site_p.R1668R	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)						carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCCTGGAGCGCGTGAGTATGG	0.592													c|||	29	0.00579073	0.0121	0.0086	5008	,	,		14537	0.001		0.004	False		,,,				2504	0.002					ENST00000475668.2																			0				cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13						c.e42+1		maltase-glucoamylase (alpha-glucosidase)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)						68.0	55.0	59.0					7																	141767225		874	1947	2821	SO:0001627	intron_variant	8972				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity	g.chr7:141767225C>T	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4618+1957C>T	7.37:g.141767225C>T						MGAM_ENST00000549489.2_Intron	p.R1668_splice			O43451	MGA_HUMAN			42	5058	+	Melanoma(164;0.0272)		1668			Glucoamylase.		Q0VAX6|Q75ME7|Q86UM5	Splice_Site	SNP	ENST00000549489.2	37	c.5004_splice	CCDS47727.1																																																																																				0.592	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			5	26	0	0	0	0.021553	0	5	26				
CACNA1G	8913	broad.mit.edu	37	17	48680555	48680555	+	Silent	SNP	G	G	A	rs527581833		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr17:48680555G>A	ENST00000359106.5	+	21	4164	c.4164G>A	c.(4162-4164)ccG>ccA	p.P1388P	CACNA1G_ENST00000429973.2_Silent_p.P1388P|CACNA1G_ENST00000507336.1_Silent_p.P1388P|CACNA1G_ENST00000354983.4_Silent_p.P1365P|CACNA1G_ENST00000510115.1_Silent_p.P1365P|CACNA1G_ENST00000507896.1_Silent_p.P1388P|CACNA1G_ENST00000512389.1_Silent_p.P1388P|CACNA1G_ENST00000416767.4_Silent_p.P1388P|CACNA1G_ENST00000515411.1_Silent_p.P1388P|CACNA1G_ENST00000505165.1_Silent_p.P1388P|CACNA1G_ENST00000514717.1_Silent_p.P1365P|CACNA1G_ENST00000442258.2_Silent_p.P1365P|CACNA1G_ENST00000514079.1_Silent_p.P1388P|CACNA1G_ENST00000507510.2_Silent_p.P1388P|CACNA1G_ENST00000513964.1_Silent_p.P1388P|CACNA1G_ENST00000507609.1_Silent_p.P1388P|CACNA1G_ENST00000513689.2_Silent_p.P1388P|CACNA1G_ENST00000502264.1_Silent_p.P1365P|CACNA1G_ENST00000503485.1_Silent_p.P1388P|CACNA1G_ENST00000360761.4_Silent_p.P1365P|CACNA1G_ENST00000358244.5_Silent_p.P1365P|CACNA1G_ENST00000510366.1_Silent_p.P1388P|CACNA1G_ENST00000515765.1_Silent_p.P1388P|CACNA1G_ENST00000514181.1_Silent_p.P1388P|CACNA1G_ENST00000515165.1_Silent_p.P1388P|CACNA1G_ENST00000352832.5_Silent_p.P1365P	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1388					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CCCTGCGCCCGCTCAGGTGAC	0.637													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13777	0.0		0.0	False		,,,				2504	0.0					ENST00000352832.5																			0				breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47						c.(4093-4095)ccG>ccA		calcium channel, voltage-dependent, T type, alpha 1G subunit	Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)						49.0	53.0	52.0					17																	48680555		2134	4245	6379	SO:0001819	synonymous_variant	8913				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity	g.chr17:48680555G>A	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4164G>A	17.37:g.48680555G>A						CACNA1G_ENST00000503485.1_Silent_p.P1388P|CACNA1G_ENST00000515765.1_Silent_p.P1388P|CACNA1G_ENST00000515165.1_Silent_p.P1388P|CACNA1G_ENST00000442258.2_Silent_p.P1365P|CACNA1G_ENST00000514717.1_Silent_p.P1365P|CACNA1G_ENST00000507609.1_Silent_p.P1388P|CACNA1G_ENST00000514181.1_Silent_p.P1388P|CACNA1G_ENST00000514079.1_Silent_p.P1388P|CACNA1G_ENST00000513964.1_Silent_p.P1388P|CACNA1G_ENST00000513689.2_Silent_p.P1388P|CACNA1G_ENST00000416767.4_Silent_p.P1388P|CACNA1G_ENST00000429973.2_Silent_p.P1388P|CACNA1G_ENST00000360761.4_Silent_p.P1365P|CACNA1G_ENST00000507896.1_Silent_p.P1388P|CACNA1G_ENST00000512389.1_Silent_p.P1388P|CACNA1G_ENST00000510366.1_Silent_p.P1388P|CACNA1G_ENST00000505165.1_Silent_p.P1388P|CACNA1G_ENST00000507510.2_Silent_p.P1388P|CACNA1G_ENST00000358244.5_Silent_p.P1365P|CACNA1G_ENST00000507336.1_Silent_p.P1388P|CACNA1G_ENST00000510115.1_Silent_p.P1365P|CACNA1G_ENST00000515411.1_Silent_p.P1388P|CACNA1G_ENST00000502264.1_Silent_p.P1365P|CACNA1G_ENST00000354983.4_Silent_p.P1365P|CACNA1G_ENST00000359106.5_Silent_p.P1388P	p.P1365P	NM_001256334.1|NM_198376.2|NM_198379.2|NM_198387.2|NM_198388.2	NP_001243263.1|NP_938190.1|NP_938193.1|NP_938201.1|NP_938202.1	O43497	CAC1G_HUMAN	BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		20	4467	+	Breast(11;6.7e-17)		1388					D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	c.4095G>A	CCDS45730.1																																																																																				0.637	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		10	17	0	0	0	0.008291	0	10	17				
PLEKHA4	57664	broad.mit.edu	37	19	49351244	49351244	+	Silent	SNP	A	A	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr19:49351244A>C	ENST00000263265.6	-	14	2034	c.1479T>G	c.(1477-1479)ggT>ggG	p.G493G	PLEKHA4_ENST00000355496.5_Silent_p.G468G	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	493						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGCCACCCAGACCTGCCAGCG	0.592																																						ENST00000263265.6																			0				NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30						c.(1477-1479)ggT>ggG		pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4							32.0	33.0	33.0					19																	49351244		2203	4300	6503	SO:0001819	synonymous_variant	0					cytoplasm|membrane	1-phosphatidylinositol binding	g.chr19:49351244A>C	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.1479T>G	19.37:g.49351244A>C						PLEKHA4_ENST00000355496.5_Silent_p.G468G	p.G493G	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)	14	2034	-		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)	493					Q8N4M8|Q8N658	Silent	SNP	ENST00000263265.6	37	c.1479T>G	CCDS12737.1																																																																																				0.592	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			4	23	0	0	0	0.014758	0	4	23				
GTF2IRD2P1	401375	broad.mit.edu	37	7	72658179	72658179	+	RNA	SNP	T	T	C	rs62464331		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr7:72658179T>C	ENST00000425256.1	-	0	1732									GTF2I repeat domain containing 2 pseudogene 1																		cagagtgatttcggatgaatt	0.507																																						ENST00000425256.1																			0																																																			0							g.chr7:72658179T>C	AY312852		7q11.23	2010-03-19	2010-02-09	2010-02-09	ENSG00000214544	ENSG00000214544			33127	pseudogene	pseudogene			"""GTF2I repeat domain containing 2 pseudogene"""	GTF2IRD2P		15100712	Standard	NG_033736		Approved		uc003txs.1		OTTHUMG00000156803		7.37:g.72658179T>C								NR_002164.1						0	1732	-									RNA	SNP	ENST00000425256.1	37																																																																																						0.507	GTF2IRD2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345921.1	NR_002164		5	55	0	0	0	0.021553	0	5	55				
IARS	3376	broad.mit.edu	37	9	95030578	95030578	+	Missense_Mutation	SNP	G	G	C			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr9:95030578G>C	ENST00000375643.3	-	14	1575	c.1309C>G	c.(1309-1311)Cca>Gca	p.P437A	IARS_ENST00000375629.3_5'UTR|IARS_ENST00000443024.2_Missense_Mutation_p.P437A|IARS_ENST00000447699.2_Missense_Mutation_p.P327A	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	437					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	ACCAACTCTGGGACCCTGCAA	0.418																																						ENST00000375643.3																			0				breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35						c.(1309-1311)Cca>Gca		isoleucyl-tRNA synthetase	L-Isoleucine(DB00167)						135.0	131.0	133.0					9																	95030578		2203	4300	6503	SO:0001583	missense	3376				isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding	g.chr9:95030578G>C	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.1309C>G	9.37:g.95030578G>C	ENSP00000364794:p.Pro437Ala					IARS_ENST00000375629.3_5'UTR|IARS_ENST00000447699.2_Missense_Mutation_p.P327A|IARS_ENST00000443024.2_Missense_Mutation_p.P437A	p.P437A	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN			14	1575	-			437					A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	37	c.1309C>G	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.876197	0.91664	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660	T;T;T	0.53857	0.6;0.6;0.6	5.96	5.96	0.96718	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	D	0.87688	0.6240	H	0.99942	5.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93266	0.6647	10	0.87932	D	0	-13.3093	20.0142	0.97474	0.0:0.0:1.0:0.0	.	437;282	P41252;Q6P0M4	SYIC_HUMAN;.	A	437;437;327;437	ENSP00000364794:P437A;ENSP00000406448:P437A;ENSP00000415020:P327A	ENSP00000364794:P437A	P	-	1	0	IARS	94070399	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	9.641000	0.98458	2.831000	0.97527	0.650000	0.86243	CCA		0.418	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		15	139	0	0	0	0.024245	0	15	139				
GBA3	57733	broad.mit.edu	37	4	22749784	22749785	+	RNA	DEL	TA	TA	-	rs73803318|rs33941035|rs553347641	byFrequency	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr4:22749784_22749785delTA	ENST00000503442.1	+	0	377				GBA3_ENST00000511446.2_RNA|GBA3_ENST00000508166.1_RNA	NM_001128432.2	NP_001121904.1	Q9H227	GBA3_HUMAN	glucosidase, beta, acid 3 (gene/pseudogene)						carbohydrate metabolic process (GO:0005975)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	beta-galactosidase activity (GO:0004565)|beta-glucosidase activity (GO:0008422)|glycosylceramidase activity (GO:0017042)			breast(1)|kidney(2)|large_intestine(4)|lung(20)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CAGGCatatgtatatatatata	0.342														1217	0.243011	0.18	0.2882	5008	,	,		12142	0.2262		0.2594	False		,,,				2504	0.2965					ENST00000503442.1																			0				breast(1)|kidney(2)|large_intestine(4)|lung(20)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33								glucosidase, beta, acid 3 (gene/pseudogene)																																						57733				glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity	g.chr4:22749784_22749785delTA	AB017913		4p15.2	2013-05-09	2013-05-09		ENSG00000249948	ENSG00000249948	3.2.1.21		19069	protein-coding gene	gene with protein product	"""klotho-related protein"""	606619	"""glucosidase, beta, acid 3 (cytosolic)"""			11389701	Standard	NM_020973		Approved	GLUC, KLrP	uc031sdv.1	Q9H227	OTTHUMG00000160448		4.37:g.22749794_22749795delTA						GBA3_ENST00000511446.1_RNA|GBA3_ENST00000508166.1_RNA		NM_001128432.2	NP_001121904.1	Q9H227	GBA3_HUMAN			0	377	+								Q32LY7|Q3MIH4|Q53GG8|Q6NSF4|Q8NHT8|Q9H3T4|Q9H4C6	RNA	DEL	ENST00000503442.1	37																																																																																						0.342	GBA3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000360620.2			4	3						4	3	---	---	---	---
SLC22A2	6582	broad.mit.edu	37	6	160664756	160664757	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr6:160664756_160664757delAT	ENST00000366953.3	-	7	1384_1385	c.1126_1127delAT	c.(1126-1128)atcfs	p.I376fs	SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	376					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	ATCCAGGTAGATATTGTCACCT	0.535																																						ENST00000366953.3																			0				breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27						c.(1126-1128)cfs		solute carrier family 22 (organic cation transporter), member 2																																				SO:0001589	frameshift_variant	6582				body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity	g.chr6:160664756_160664757delAT	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.1126_1127delAT	6.37:g.160664758_160664759delAT	ENSP00000355920:p.Ile376fs					SLC22A2_ENST00000491092.1_5'UTR	p.I376fs	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	7	1384_1385	-		Breast(66;0.000776)|Ovarian(120;0.0303)	376					Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Frame_Shift_Del	DEL	ENST00000366953.3	37	c.1126_1127delAT	CCDS5276.1																																																																																				0.535	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058		41	56						41	56	---	---	---	---
APOA4	337	broad.mit.edu	37	11	116693873	116693873	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr11:116693873delA	ENST00000357780.3	-	1	149	c.35delT	c.(34-36)ctgfs	p.L12fs		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	12					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GACAGCCACCAGGGCCAGGGT	0.592																																						ENST00000357780.3																			0				cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20						c.(34-36)cgfs		apolipoprotein A-IV							139.0	134.0	135.0					11																	116693873		2201	4292	6493	SO:0001589	frameshift_variant	337							g.chr11:116693873delA		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.35delT	11.37:g.116693873delA	ENSP00000350425:p.Leu12fs						p.L12fs	NM_000482.3	NP_000473.2				BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)	1	149	-	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)						A8MSL6|Q14CW8|Q6Q787	Frame_Shift_Del	DEL	ENST00000357780.3	37	c.35delT	CCDS31681.1																																																																																				0.592	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482		107	140						107	140	---	---	---	---
PEX5	5830	broad.mit.edu	37	12	7338794	7338794	+	5'Flank	DEL	G	G	-	rs34548221|rs78202591|rs397851127		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr12:7338794delG	ENST00000455147.2	+	0	0				RP11-273B20.3_ENST00000543061.1_RNA|RP11-273B20.3_ENST00000545794.1_RNA	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5						cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						cctgttgagaggggggactga	0.502													?|GGGGGG|GGGGG|unsure	1968	0.392971	0.1278	0.6556	5008	,	,		21746	0.3998		0.5109	False		,,,				2504	0.4366					ENST00000545794.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr12:7338794delG	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"""Tetratricopeptide (TTC) repeat domain containing"""	9719	protein-coding gene	gene with protein product		600414	"""peroxisome receptor 1"""	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542			12.37:g.7338794delG	Exception_encountered					RP11-273B20.3_ENST00000543061.1_RNA								0	279	-								A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	RNA	DEL	ENST00000455147.2	37		CCDS44823.1																																																																																				0.502	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319		3	5						3	5	---	---	---	---
CHORDC2P	317775	broad.mit.edu	37	14	90203668	90203668	+	RNA	DEL	C	C	-	rs12897726|rs144915275		TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr14:90203668delC	ENST00000555070.1	-	0	170																											CTCTTTCTTTCtttttttttt	0.368																																						ENST00000555070.1																			0																																																			0							g.chr14:90203668delC																													14.37:g.90203668delC														0	170	-									RNA	DEL	ENST00000555070.1	37																																																																																						0.368	RP11-33N16.3-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000411023.1			5	8						5	8	---	---	---	---
RP11-439I14.2	0	broad.mit.edu	37	16	64770704	64770705	+	lincRNA	INS	-	-	CCAGTGATGGTCACCT	rs200421189|rs71143515|rs377231404|rs145408521|rs140029302	byFrequency	TCGA-FE-A235-01A-11D-A16O-08	TCGA-FE-A235-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe317172-c1fd-4d34-a694-ef2be40ff0e4	93ec843a-30ab-4881-ac2a-7bfcd79d5e67	g.chr16:64770704_64770705insCCAGTGATGGTCACCT	ENST00000564293.1	+	0	453_454																											TGTCACCACTGCCACCTTGTTC	0.371														3288	0.65655	0.8434	0.5144	5008	,	,		21531	0.6052		0.5537	False		,,,				2504	0.6636					ENST00000564293.1																			0																																																			0							g.chr16:64770704_64770705insCCAGTGATGGTCACCT																													16.37:g.64770704_64770705insCCAGTGATGGTCACCT														0	453_454	+									RNA	INS	ENST00000564293.1	37																																																																																						0.371	RP11-439I14.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000422725.1			3	4						3	4	---	---	---	---
