#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
LOC101927079	101927079	broad.mit.edu	37	15	22332570	22332570	+	RNA	SNP	T	T	C	rs551210093		TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr15:22332570T>C	ENST00000558896.1	+	0	377																											CCCATGCTCATCTGCTCCAAT	0.398																																						ENST00000558896.1																			0																																																			0							g.chr15:22332570T>C																													15.37:g.22332570T>C														0	377	+									RNA	SNP	ENST00000558896.1	37																																																																																						0.398	RP11-69H14.6-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000417625.1			4	194	0	0	0	1	0	4	194				
ATP2B4	493	broad.mit.edu	37	1	203671203	203671203	+	Missense_Mutation	SNP	C	C	G			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:203671203C>G	ENST00000357681.5	+	7	2056	c.933C>G	c.(931-933)aaC>aaG	p.N311K	ATP2B4_ENST00000367218.3_Missense_Mutation_p.N311K|ATP2B4_ENST00000391954.2_Missense_Mutation_p.N311K|ATP2B4_ENST00000367219.3_Intron|ATP2B4_ENST00000341360.2_Missense_Mutation_p.N311K	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	311					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AAAATCGCAACAAAGGTAACC	0.418											OREG0014124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000357681.5																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56						c.(931-933)aaC>aaG		ATPase, Ca++ transporting, plasma membrane 4							137.0	132.0	134.0					1																	203671203		2203	4300	6503	SO:0001583	missense	493				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding	g.chr1:203671203C>G	M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"""ATPases / P-type"""	817	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 4"""	108732	"""matrix-remodelling associated 1"""	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.933C>G	1.37:g.203671203C>G	ENSP00000350310:p.Asn311Lys		OREG0014124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2138	ATP2B4_ENST00000367218.3_Missense_Mutation_p.N311K|ATP2B4_ENST00000367219.3_Intron|ATP2B4_ENST00000341360.2_Missense_Mutation_p.N311K|ATP2B4_ENST00000391954.2_Missense_Mutation_p.N311K	p.N311K	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	BRCA - Breast invasive adenocarcinoma(75;0.109)		7	2056	+	all_cancers(21;0.071)|all_epithelial(62;0.228)		311					B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000357681.5	37	c.933C>G	CCDS1440.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.382999	0.61845	.	.	ENSG00000058668	ENST00000357681;ENST00000367218;ENST00000391954;ENST00000341360	D;D;D;D	0.92446	-3.04;-3.04;-3.03;-3.04	5.65	4.7	0.59300	ATPase, P-type, ATPase-associated domain (1);	.	.	.	.	D	0.89976	0.6871	N	0.04508	-0.205	0.58432	D	0.999994	B;B;D	0.69078	0.011;0.004;0.997	B;B;D	0.79108	0.022;0.012;0.992	D	0.90272	0.4308	9	0.37606	T	0.19	-29.4326	14.8862	0.70570	0.144:0.856:0.0:0.0	.	311;311;311	P23634;P23634-6;B1APW5	AT2B4_HUMAN;.;.	K	311	ENSP00000350310:N311K;ENSP00000356187:N311K;ENSP00000375816:N311K;ENSP00000340930:N311K	ENSP00000340930:N311K	N	+	3	2	ATP2B4	201937826	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.323000	0.59221	2.673000	0.90976	0.557000	0.71058	AAC		0.418	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		16	29	0	0	0	1	0	16	29				
UBBP4	23666	broad.mit.edu	37	17	21731144	21731144	+	Missense_Mutation	SNP	T	T	G	rs375625296		TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr17:21731144T>G	ENST00000578713.1	+	1	450	c.446T>G	c.(445-447)cTg>cGg	p.L149R	UBBP4_ENST00000584398.1_3'UTR|UBBP4_ENST00000583708.1_3'UTR|UBBP4_ENST00000584755.1_Missense_Mutation_p.L149R					ubiquitin B pseudogene 4									p.L149R(18)		endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						GTCCTGCGTCTGAGAGGTGGT	0.542																																						ENST00000584755.1																			18	Substitution - Missense(18)	p.L149R(18)	endometrium(12)|prostate(6)	endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						c.(445-447)cTg>cGg																																						SO:0001583	missense	0							g.chr17:21731144T>G	X07499		17p11.2	2011-08-10				ENSG00000263563			12467	pseudogene	pseudogene						2834222	Standard	NG_002285		Approved		uc002gyy.3			ENST00000578713.1:c.446T>G	17.37:g.21731144T>G	ENSP00000464265:p.Leu149Arg					UBBP4_ENST00000584398.1_3'UTR|UBBP4_ENST00000578713.1_Missense_Mutation_p.L149R|UBBP4_ENST00000583708.1_3'UTR	p.L149R							2	843	+									Missense_Mutation	SNP	ENST00000578713.1	37	c.446T>G																																																																																					0.542	UBBP4-004	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444589.2			4	92	0	0	0	1	0	4	92				
COPA	1314	broad.mit.edu	37	1	160261696	160261696	+	Silent	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:160261696G>A	ENST00000241704.7	-	30	3400	c.3171C>T	c.(3169-3171)tgC>tgT	p.C1057C	COPA_ENST00000368069.3_Silent_p.C1066C	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	1057					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGTACTCACGGCAAATGGTGA	0.522											OREG0013929	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000241704.7																			0				central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46						c.(3169-3171)tgC>tgT		coatomer protein complex, subunit alpha							191.0	193.0	192.0					1																	160261696		2203	4300	6503	SO:0001819	synonymous_variant	1314				COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity	g.chr1:160261696G>A	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"""WD repeat domain containing"", ""Endogenous ligands"""	2230	protein-coding gene	gene with protein product	"""proxenin"", ""xenin"""	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.3171C>T	1.37:g.160261696G>A			OREG0013929	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1807	COPA_ENST00000368069.3_Silent_p.C1066C	p.C1057C	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.111)		30	3400	-	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		1057					Q5T201|Q8IXZ9	Silent	SNP	ENST00000241704.7	37	c.3171C>T	CCDS1202.1																																																																																				0.522	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		5	266	0	0	0	1	0	5	266				
PLA2G15	23659	broad.mit.edu	37	16	68289778	68289778	+	Silent	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr16:68289778G>A	ENST00000219345.5	+	5	695	c.612G>A	c.(610-612)acG>acA	p.T204T	PLA2G15_ENST00000444212.2_Intron|RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000413021.2_Intron|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000566188.1_Intron	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	204					ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						ACATGTACACGCTCTACTTTC	0.637																																						ENST00000219345.5																			0				kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						c.(610-612)acG>acA		phospholipase A2, group XV							40.0	43.0	42.0					16																	68289778		2198	4300	6498	SO:0001819	synonymous_variant	23659				fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding	g.chr16:68289778G>A	AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066			17163	protein-coding gene	gene with protein product		609362	"""lysophospholipase 3 (lysosomal phospholipase A2)"""	LYPLA3		10092508, 16973413	Standard	XM_005255886		Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	ENST00000219345.5:c.612G>A	16.37:g.68289778G>A						PLA2G15_ENST00000566188.1_Intron|PLA2G15_ENST00000444212.2_Intron|PLA2G15_ENST00000413021.2_Intron	p.T204T	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN			5	695	+			204					B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Silent	SNP	ENST00000219345.5	37	c.612G>A	CCDS10864.1																																																																																				0.637	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320		30	36	0	0	0	1	0	30	36				
LRRC19	64922	broad.mit.edu	37	9	26999613	26999613	+	Splice_Site	SNP	C	C	G			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr9:26999613C>G	ENST00000380055.5	-	2	190	c.80G>C	c.(79-81)aGa>aCa	p.R27T	IFT74_ENST00000443698.1_Intron|LRRC19_ENST00000482770.1_5'Flank|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000433700.1_Intron|IFT74_ENST00000380062.5_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	27						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)	6		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		AAAACTTACTCTTTTAGAAGA	0.303																																						ENST00000380055.5																			0				breast(1)|endometrium(2)|kidney(1)|lung(2)	6						c.e2+1		leucine rich repeat containing 19							51.0	56.0	54.0					9																	26999613		2203	4300	6503	SO:0001630	splice_region_variant	64922					integral to membrane		g.chr9:26999613C>G	AK024955	CCDS6518.1	9p21.1	2008-02-05			ENSG00000184434	ENSG00000184434			23379	protein-coding gene	gene with protein product							Standard	NM_022901		Approved	FLJ21302	uc003zqh.3	Q9H756	OTTHUMG00000019710	ENST00000380055.5:c.81+1G>C	9.37:g.26999613C>G						IFT74_ENST00000380062.5_Intron|IFT74_ENST00000433700.1_Intron|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000443698.1_Intron	p.R27_splice	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)	2	190	-		all_neural(11;1.81e-09)	27					A0AV00|B9EG91	Splice_Site	SNP	ENST00000380055.5	37	c.81_splice	CCDS6518.1	.	.	.	.	.	.	.	.	.	.	C	6.093	0.385418	0.11524	.	.	ENSG00000184434	ENST00000380055	T	0.51817	0.69	4.78	-0.827	0.10802	.	0.741578	0.12725	N	0.444339	T	0.08714	0.0216	N	0.00119	-2.075	0.24539	N	0.994071	B	0.02656	0.0	B	0.01281	0.0	T	0.40720	-0.9548	10	0.02654	T	1	-0.3874	6.211	0.20630	0.1851:0.469:0.3459:0.0	.	27	Q9H756	LRC19_HUMAN	T	27	ENSP00000369395:R27T	ENSP00000369395:R27T	R	-	2	0	LRRC19	26989613	0.923000	0.31300	0.978000	0.43139	0.874000	0.50279	-0.108000	0.10857	0.025000	0.15241	-0.226000	0.12346	AGA		0.303	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2	NM_022901	Missense_Mutation	8	13	0	0	0	1	0	8	13				
RBP1	5947	broad.mit.edu	37	3	139258330	139258330	+	Silent	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr3:139258330C>T	ENST00000483943.2	-	1	231	c.231G>A	c.(229-231)gaG>gaA	p.E77E	RP11-319G6.1_ENST00000381790.3_RNA|RP11-319G6.1_ENST00000515247.1_RNA|RBP1_ENST00000232219.2_Silent_p.E77E|RBP1_ENST00000492918.1_Silent_p.E77E	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN	retinol binding protein 1, cellular	15					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	CCTCGAAATTCTCGTTGACCA	0.667																																						ENST00000483943.2																			0				endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5						c.(229-231)gaG>gaA		retinol binding protein 1, cellular	Vitamin A(DB00162)						42.0	30.0	34.0					3																	139258330		2203	4300	6503	SO:0001819	synonymous_variant	5947					cytoplasm	retinal binding|retinol binding|transporter activity	g.chr3:139258330C>T		CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"""Fatty acid binding protein family"""	9919	protein-coding gene	gene with protein product		180260	"""retinol-binding protein 1, cellular"""			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000483943.2:c.231G>A	3.37:g.139258330C>T						RBP1_ENST00000492918.1_Silent_p.E77E|RP11-319G6.1_ENST00000515247.1_RNA|RBP1_ENST00000232219.2_Silent_p.E77E	p.E77E	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN			1	231	-			15					A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Silent	SNP	ENST00000483943.2	37	c.231G>A	CCDS46925.1																																																																																				0.667	RBP1-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341497.2	NM_002899		10	19	0	0	0	1	0	10	19				
BRD3	8019	broad.mit.edu	37	9	136901310	136901310	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr9:136901310G>A	ENST00000303407.7	-	10	1965	c.1780C>T	c.(1780-1782)Cgg>Tgg	p.R594W	LINC00094_ENST00000605164.1_RNA|BRD3_ENST00000371834.2_3'UTR|BRD3_ENST00000473349.1_5'UTR	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	594	NET. {ECO:0000255|PROSITE- ProRule:PRU00857}.				chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)		BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		TGCACTACCCGGCCCAGCTTC	0.582			T	C15orf55	lethal midline carcinoma of young people																																	ENST00000303407.7				Dom	yes		9	9q34	8019	T	bromodomain containing 3			E	C15orf55		lethal midline carcinoma of young people	BRD3/C15orf55(3)	0				kidney(1)|skin(1)|stomach(4)	6						c.(1780-1782)Cgg>Tgg		bromodomain containing 3							71.0	69.0	69.0					9																	136901310		2203	4300	6503	SO:0001583	missense	8019					nucleus	protein binding	g.chr9:136901310G>A		CCDS6980.1	9q34	2010-12-23	2002-01-14		ENSG00000169925	ENSG00000169925			1104	protein-coding gene	gene with protein product	"""RING3-like"""	601541	"""bromodomain-containing 3"""			7584044, 8781126	Standard	NM_007371		Approved	RING3L, ORFX, KIAA0043	uc004cew.3	Q15059	OTTHUMG00000021004	ENST00000303407.7:c.1780C>T	9.37:g.136901310G>A	ENSP00000305918:p.Arg594Trp					BRD3_ENST00000473349.1_5'UTR|BRD3_ENST00000371834.2_3'UTR	p.R594W	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)	10	1965	-			594					B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Missense_Mutation	SNP	ENST00000303407.7	37	c.1780C>T	CCDS6980.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189403	0.78789	.	.	ENSG00000169925	ENST00000303407;ENST00000540795	T	0.27256	1.68	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000004	T	0.56558	0.1993	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	T	0.65138	-0.6241	10	0.87932	D	0	-8.8559	14.2026	0.65714	0.0:0.0:0.8503:0.1497	.	594	Q15059	BRD3_HUMAN	W	594;273	ENSP00000305918:R594W	ENSP00000305918:R594W	R	-	1	2	BRD3	135891131	1.000000	0.71417	0.999000	0.59377	0.873000	0.50193	3.400000	0.52594	2.403000	0.81681	0.491000	0.48974	CGG		0.582	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371		6	66	0	0	0	1	0	6	66				
MEFV	4210	broad.mit.edu	37	16	3293676	3293676	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr16:3293676G>A	ENST00000219596.1	-	10	1850	c.1811C>T	c.(1810-1812)gCa>gTa	p.A604V	MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000339854.4_Missense_Mutation_p.A424V|MEFV_ENST00000536379.1_Missense_Mutation_p.A393V	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	604	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						AGCGGTTTCTGCATCCAGAAT	0.488																																						ENST00000219596.1																			0				NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						c.(1810-1812)gCa>gTa		Mediterranean fever	Colchicine(DB01394)						147.0	161.0	156.0					16																	3293676		2197	4300	6497	SO:0001583	missense	4210				inflammatory response	cytoplasm|microtubule|microtubule associated complex|nucleus	actin binding|zinc ion binding	g.chr16:3293676G>A	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1811C>T	16.37:g.3293676G>A	ENSP00000219596:p.Ala604Val					MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000339854.4_Missense_Mutation_p.A424V|MEFV_ENST00000536379.1_Missense_Mutation_p.A393V	p.A604V	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN			10	1850	-			604			B30.2/SPRY.		D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	37	c.1811C>T	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.696442	0.48202	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000536379	T;T;T	0.10382	2.88;2.88;2.88	5.3	-3.79	0.04320	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	1.477610	0.04189	N	0.327958	T	0.07638	0.0192	L	0.31804	0.96	0.09310	N	1	B	0.20164	0.042	B	0.14578	0.011	T	0.36261	-0.9755	10	0.45353	T	0.12	-7.7931	4.3245	0.11034	0.3962:0.0:0.3666:0.2372	.	604	O15553	MEFV_HUMAN	V	604;604;424;393	ENSP00000219596:A604V;ENSP00000339639:A424V;ENSP00000445079:A393V	ENSP00000219596:A604V	A	-	2	0	MEFV	3233677	0.874000	0.30092	0.228000	0.23943	0.801000	0.45260	2.070000	0.41491	-0.950000	0.03659	-0.188000	0.12872	GCA		0.488	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		10	298	0	0	0	1	0	10	298				
RNF40	9810	broad.mit.edu	37	16	30780529	30780529	+	Missense_Mutation	SNP	A	A	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr16:30780529A>C	ENST00000324685.6	+	16	2705	c.2270A>C	c.(2269-2271)gAg>gCg	p.E757A	RNF40_ENST00000563683.1_Missense_Mutation_p.E717A|RNF40_ENST00000357890.5_Missense_Mutation_p.E657A|RNF40_ENST00000402121.3_Missense_Mutation_p.E449A	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	757					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			CTGCTCTCAGAGATGGATGTG	0.547																																						ENST00000324685.6																			0				central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30						c.(2269-2271)gAg>gCg		ring finger protein 40, E3 ubiquitin protein ligase							114.0	117.0	116.0					16																	30780529		2197	4300	6497	SO:0001583	missense	9810				histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding	g.chr16:30780529A>C	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"""RING-type (C3HC4) zinc fingers"""	16867	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"""	607700	"""ring finger protein 40"""			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.2270A>C	16.37:g.30780529A>C	ENSP00000325677:p.Glu757Ala					RNF40_ENST00000357890.5_Missense_Mutation_p.E657A|RNF40_ENST00000563683.1_Missense_Mutation_p.E717A|RNF40_ENST00000402121.3_Missense_Mutation_p.E449A	p.E757A	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586.1	O75150	BRE1B_HUMAN	Colorectal(24;0.198)		16	2705	+			757					Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	37	c.2270A>C	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.204931	0.79127	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121;ENST00000538323	T;T;T	0.62788	-0.0;0.03;0.11	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.80053	0.4553	M	0.81942	2.565	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.87578	0.994;0.998;0.986;0.997;0.997	T	0.83009	-0.0173	10	0.87932	D	0	-34.7099	14.8515	0.70300	1.0:0.0:0.0:0.0	.	89;449;657;757;757	F6SYU7;F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;.;BRE1B_HUMAN	A	757;657;449;89	ENSP00000325677:E757A;ENSP00000350563:E657A;ENSP00000384942:E449A	ENSP00000325677:E757A	E	+	2	0	RNF40	30688030	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	8.962000	0.93254	2.150000	0.67090	0.533000	0.62120	GAG		0.547	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		6	135	0	0	0	1	0	6	135				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382565.1_Intron			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000328354.6_Silent_p.S372S	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		4	69	0	0	0	1	0	4	69				
FGR	2268	broad.mit.edu	37	1	27943448	27943448	+	Missense_Mutation	SNP	C	C	T	rs376766171		TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:27943448C>T	ENST00000374005.3	-	7	890	c.602G>A	c.(601-603)cGc>cAc	p.R201H	FGR_ENST00000399173.1_Missense_Mutation_p.R201H|FGR_ENST00000545953.1_Missense_Mutation_p.R135H|FGR_ENST00000374004.1_Missense_Mutation_p.R201H	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	201	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GTCCAGTTTGCGGATCTTGTA	0.557																																						ENST00000374005.3																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16						c.(601-603)cGc>cAc		feline Gardner-Rasheed sarcoma viral oncogene homolog		C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	171.0	150.0	157.0		602,602,602	4.4	1.0	1		157	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	FGR	NM_001042729.1,NM_001042747.1,NM_005248.2	29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	201/530,201/530,201/530	27943448	1,13005	2203	4300	6503	SO:0001583	missense	2268				platelet activation|response to virus	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity	g.chr1:27943448C>T	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"""SH2 domain containing"""	3697	protein-coding gene	gene with protein product		164940	"""Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog"", ""v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog"", ""feline Gardner-Rasheed sarcoma viral oncogene homolog"""	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.602G>A	1.37:g.27943448C>T	ENSP00000363117:p.Arg201His					FGR_ENST00000374004.1_Missense_Mutation_p.R201H|FGR_ENST00000545953.1_Missense_Mutation_p.R135H|FGR_ENST00000399173.1_Missense_Mutation_p.R201H	p.R201H	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)	7	890	-		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)	201			SH2.		D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	37	c.602G>A	CCDS305.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031590	0.75504	0.0	1.16E-4	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003;ENST00000457296	D;D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42	4.38	4.38	0.52667	SH2 motif (5);	0.000000	0.56097	D	0.000040	D	0.89068	0.6610	M	0.85197	2.74	0.45541	D	0.998497	D	0.53619	0.961	B	0.37780	0.258	D	0.92007	0.5615	10	0.87932	D	0	.	16.3789	0.83431	0.0:1.0:0.0:0.0	.	201	P09769	FGR_HUMAN	H	201;135;201;201;201;201	ENSP00000363117:R201H;ENSP00000445302:R135H;ENSP00000382126:R201H;ENSP00000363116:R201H;ENSP00000363115:R201H;ENSP00000407670:R201H	ENSP00000363115:R201H	R	-	2	0	FGR	27816035	1.000000	0.71417	0.960000	0.40013	0.623000	0.37688	7.818000	0.86416	2.348000	0.79779	0.491000	0.48974	CGC		0.557	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		4	140	0	0	0	1	0	4	140				
DMXL1	1657	broad.mit.edu	37	5	118533558	118533558	+	Missense_Mutation	SNP	A	A	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr5:118533558A>C	ENST00000311085.8	+	32	7732	c.7652A>C	c.(7651-7653)tAt>tCt	p.Y2551S	DMXL1_ENST00000539542.1_Missense_Mutation_p.Y2551S	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2551										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CCTCAAAATTATATCGCAAGT	0.443																																						ENST00000311085.8																			0				breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86						c.(7651-7653)tAt>tCt		Dmx-like 1							124.0	123.0	124.0					5																	118533558		2202	4300	6502	SO:0001583	missense	1657							g.chr5:118533558A>C	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.7652A>C	5.37:g.118533558A>C	ENSP00000309690:p.Tyr2551Ser					DMXL1_ENST00000539542.1_Missense_Mutation_p.Y2551S	p.Y2551S	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)	32	7732	+		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)	2551						Missense_Mutation	SNP	ENST00000311085.8	37	c.7652A>C	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.533413	0.45073	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.16457	2.34;2.52	5.13	3.94	0.45596	.	0.170349	0.53938	D	0.000048	T	0.35508	0.0934	M	0.79123	2.44	0.51233	D	0.999911	P;P	0.52842	0.956;0.877	P;P	0.57720	0.826;0.739	T	0.12708	-1.0537	10	0.87932	D	0	-12.9877	10.118	0.42603	0.7333:0.0:0.0:0.2667	.	2551;2551	F5H269;Q9Y485	.;DMXL1_HUMAN	S	2551	ENSP00000309690:Y2551S;ENSP00000439479:Y2551S	ENSP00000309690:Y2551S	Y	+	2	0	DMXL1	118561457	1.000000	0.71417	0.989000	0.46669	0.384000	0.30261	2.636000	0.46545	0.876000	0.35872	0.379000	0.24179	TAT		0.443	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		4	161	0	0	0	1	0	4	161				
ANKRD35	148741	broad.mit.edu	37	1	145562072	145562072	+	Missense_Mutation	SNP	G	G	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:145562072G>C	ENST00000355594.4	+	10	1847	c.1760G>C	c.(1759-1761)aGg>aCg	p.R587T		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	587										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAGGAGAAAAGGGTTCCTGGG	0.582																																					Melanoma(9;127 754 22988 51047)	ENST00000355594.4																			0				NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47						c.(1759-1761)aGg>aCg		ankyrin repeat domain 35							42.0	54.0	50.0					1																	145562072		2201	4298	6499	SO:0001583	missense	148741							g.chr1:145562072G>C	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1760G>C	1.37:g.145562072G>C	ENSP00000347802:p.Arg587Thr						p.R587T	NM_144698.3	NP_653299.3	Q8N283	ANR35_HUMAN			10	1847	+	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		587					A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	c.1760G>C	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	1.868	-0.460894	0.04508	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.47177	0.85	4.87	1.75	0.24633	.	0.530505	0.17196	N	0.183332	T	0.19046	0.0457	L	0.60455	1.87	0.09310	N	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.24119	-1.0169	10	0.45353	T	0.12	-2.8407	4.6196	0.12444	0.2108:0.1779:0.6113:0.0	.	587	Q8N283	ANR35_HUMAN	T	496;587	ENSP00000347802:R587T	ENSP00000347802:R587T	R	+	2	0	ANKRD35	144273429	0.000000	0.05858	0.001000	0.08648	0.068000	0.16541	-0.170000	0.09897	0.184000	0.20083	0.655000	0.94253	AGG		0.582	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		39	50	0	0	0	1	0	39	50				
MSH5	4439	broad.mit.edu	37	6	31727947	31727947	+	Missense_Mutation	SNP	T	T	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr6:31727947T>A	ENST00000375755.3	+	19	2052	c.1766T>A	c.(1765-1767)gTc>gAc	p.V589D	MSH5_ENST00000375740.3_Missense_Mutation_p.V606D|MSH5_ENST00000375703.3_Missense_Mutation_p.V589D|SAPCD1_ENST00000415669.2_5'Flank|SAPCD1_ENST00000425424.1_5'Flank|MSH5_ENST00000431848.2_Missense_Mutation_p.V288D|MSH5_ENST00000534153.4_Missense_Mutation_p.V606D|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.V606D|MSH5_ENST00000395853.1_Missense_Mutation_p.V263D|MSH5_ENST00000375750.3_Missense_Mutation_p.V589D|MSH5_ENST00000375742.3_Missense_Mutation_p.V606D	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	589					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						AGGGTCAAAGTCATCACTGGA	0.567								Direct reversal of damage;Mismatch excision repair (MMR)																														ENST00000493662.2																			0											c.(1816-1818)gTc>gAc									112.0	106.0	108.0					6																	31727947		2203	4300	6503	SO:0001583	missense	0							g.chr6:31727947T>A	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.1766T>A	6.37:g.31727947T>A	ENSP00000364908:p.Val589Asp					MSH5_ENST00000431848.2_Missense_Mutation_p.V288D|MSH5_ENST00000375755.3_Missense_Mutation_p.V589D|MSH5_ENST00000375703.3_Missense_Mutation_p.V589D|MSH5_ENST00000534153.4_Missense_Mutation_p.V606D|MSH5_ENST00000375740.3_Missense_Mutation_p.V606D|MSH5_ENST00000375742.3_Missense_Mutation_p.V606D|MSH5_ENST00000375750.3_Missense_Mutation_p.V589D|MSH5_ENST00000395853.1_Missense_Mutation_p.V263D	p.V606D							19	1873	+								B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	37	c.1817T>A	CCDS4720.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.886614	0.91814	.	.	ENSG00000204410	ENST00000375755;ENST00000375742;ENST00000383401;ENST00000375750;ENST00000534153;ENST00000375703;ENST00000375740;ENST00000431848;ENST00000395853	D;D;D;D;D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3	6.06	6.06	0.98353	DNA mismatch repair protein MutS, C-terminal (2);	0.114093	0.56097	D	0.000033	D	0.92864	0.7730	M	0.89353	3.025	0.40186	D	0.977354	D;D;D;D;D	0.64830	0.994;0.992;0.989;0.992;0.992	P;D;P;P;P	0.63793	0.887;0.918;0.863;0.89;0.872	D	0.94233	0.7478	9	0.87932	D	0	4.1123	14.5614	0.68140	0.0:0.0:0.0:1.0	.	274;606;589;589;606	Q59EC5;O43196-4;O43196;O43196-2;O43196-3	.;.;MSH5_HUMAN;.;.	D	589;606;121;589;606;589;606;288;263	ENSP00000364908:V589D;ENSP00000364894:V606D;ENSP00000364903:V589D;ENSP00000431693:V606D;ENSP00000364855:V589D;ENSP00000364892:V606D;ENSP00000416784:V288D;ENSP00000379194:V263D	ENSP00000364855:V589D	V	+	2	0	MSH5	31835926	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.072000	0.76777	2.324000	0.78689	0.533000	0.62120	GTC		0.567	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4			51	75	0	0	0	1	0	51	75				
ADAMTSL1	92949	broad.mit.edu	37	9	18817126	18817126	+	Silent	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr9:18817126G>A	ENST00000380548.4	+	21	4164	c.3825G>A	c.(3823-3825)acG>acA	p.T1275T		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1275						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		TAGTGAAAACGTCACGAATGA	0.448																																						ENST00000380548.4																			0				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42						c.(3823-3825)acG>acA		ADAMTS-like 1																																				SO:0001819	synonymous_variant	92949					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding	g.chr9:18817126G>A	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3825G>A	9.37:g.18817126G>A							p.T1275T	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN		GBM - Glioblastoma multiforme(50;1.29e-17)	21	4164	+			1275					A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	c.3825G>A	CCDS47954.1																																																																																				0.448	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1			5	8	0	0	0	1	0	5	8				
KCNH1	3756	broad.mit.edu	37	1	210971076	210971076	+	Missense_Mutation	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr1:210971076C>T	ENST00000271751.4	-	9	1716	c.1689G>A	c.(1687-1689)atG>atA	p.M563I	KCNH1_ENST00000367007.4_Missense_Mutation_p.M536I			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	563					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TGTCGGCTCTCATGTCCTTGG	0.597																																						ENST00000367007.4																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68						c.(1606-1608)atG>atA		potassium voltage-gated channel, subfamily H (eag-related), member 1							57.0	53.0	55.0					1																	210971076		2203	4300	6503	SO:0001583	missense	3756				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity	g.chr1:210971076C>T	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1689G>A	1.37:g.210971076C>T	ENSP00000271751:p.Met563Ile					KCNH1_ENST00000271751.4_Missense_Mutation_p.M563I	p.M536I	NM_002238.3|NM_172362.2	NP_002229.1|NP_758872.1	O95259	KCNH1_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)	9	1777	-			563					B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	c.1608G>A	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885122	0.72410	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.96265	-3.96;-3.96	5.36	5.36	0.76844	Cyclic nucleotide-binding-like (1);	0.072927	0.85682	D	0.000000	D	0.94758	0.8308	L	0.46614	1.455	0.80722	D	1	B;B	0.17667	0.023;0.023	B;B	0.20184	0.028;0.028	D	0.91733	0.5398	10	0.66056	D	0.02	.	19.0956	0.93249	0.0:1.0:0.0:0.0	.	536;563	Q14CL3;O95259	.;KCNH1_HUMAN	I	563;536	ENSP00000271751:M563I;ENSP00000355974:M536I	ENSP00000271751:M563I	M	-	3	0	KCNH1	209037699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.538000	0.82048	2.506000	0.84524	0.655000	0.94253	ATG		0.597	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		17	36	0	0	0	1	0	17	36				
PLEKHH1	57475	broad.mit.edu	37	14	68053956	68053956	+	3'UTR	SNP	T	T	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr14:68053956T>C	ENST00000329153.5	+	0	4231				PLEKHH1_ENST00000417684.2_Missense_Mutation_p.I308T	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1							cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GCTGTGAATATTTCTCCTACC	0.517																																						ENST00000417684.2																			0				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19						c.(922-924)aTt>aCt		pleckstrin homology domain containing, family H (with MyTH4 domain) member 1							108.0	113.0	111.0					14																	68053956		1931	4125	6056	SO:0001624	3_prime_UTR_variant	57475					cytoskeleton	binding	g.chr14:68053956T>C	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.*4T>C	14.37:g.68053956T>C						PLEKHH1_ENST00000329153.5_3'UTR	p.I308T			Q9ULM0	PKHH1_HUMAN		all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)	12	1511	+			0					A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	c.923T>C	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.088823	0.36855	.	.	ENSG00000054690	ENST00000417684	.	.	.	5.34	4.21	0.49690	.	.	.	.	.	T	0.31827	0.0809	.	.	.	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.28267	-1.0049	7	0.87932	D	0	.	5.7233	0.17998	0.0:0.2383:0.0:0.7617	.	308	E7ESY2	.	T	308	.	ENSP00000397712:I308T	I	+	2	0	PLEKHH1	67123709	0.000000	0.05858	0.271000	0.24616	0.904000	0.53231	0.005000	0.13129	1.058000	0.40530	0.533000	0.62120	ATT		0.517	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		44	50	0	0	0	1	0	44	50				
TRIM26	7726	broad.mit.edu	37	6	30153814	30153814	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr6:30153814G>A	ENST00000454678.2	-	10	1895	c.1459C>T	c.(1459-1461)Cgg>Tgg	p.R487W	TRIM26_ENST00000437089.1_Missense_Mutation_p.R487W|TRIM26_ENST00000453195.1_Missense_Mutation_p.R487W	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	487	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						CCCACTCTCCGGGGCCGCAGT	0.642																																						ENST00000454678.2																			0				lung(1)|ovary(2)	3						c.(1459-1461)Cgg>Tgg		tripartite motif containing 26																																				SO:0001583	missense	7726						DNA binding|zinc ion binding	g.chr6:30153814G>A	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.1459C>T	6.37:g.30153814G>A	ENSP00000410446:p.Arg487Trp					TRIM26_ENST00000453195.1_Missense_Mutation_p.R487W|TRIM26_ENST00000437089.1_Missense_Mutation_p.R487W	p.R487W	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN			10	1895	-			487			B30.2/SPRY.		A6NG96|Q5SRL2	Missense_Mutation	SNP	ENST00000454678.2	37	c.1459C>T	CCDS4678.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.147009	0.37923	.	.	ENSG00000234127	ENST00000453195;ENST00000454678;ENST00000437089	T;T;T	0.71341	-0.56;-0.56;-0.56	5.53	2.39	0.29439	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.181709	0.26007	N	0.026912	T	0.74261	0.3693	M	0.87617	2.895	0.09310	N	1	D;D	0.76494	0.999;0.997	P;P	0.60609	0.877;0.828	T	0.67098	-0.5756	10	0.72032	D	0.01	.	9.307	0.37881	0.0:0.1199:0.4799:0.4002	.	487;487	Q5SRL2;Q12899	.;TRI26_HUMAN	W	487	ENSP00000391879:R487W;ENSP00000410446:R487W;ENSP00000395491:R487W	ENSP00000395491:R487W	R	-	1	2	TRIM26	30261793	0.760000	0.28428	0.067000	0.19924	0.880000	0.50808	0.929000	0.28844	0.674000	0.31244	0.446000	0.29264	CGG		0.642	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449		11	7	0	0	0	1	0	11	7				
ALLC	55821	broad.mit.edu	37	2	3749214	3749214	+	Silent	SNP	T	T	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr2:3749214T>A	ENST00000252505.3	+	11	1125	c.963T>A	c.(961-963)ctT>ctA	p.L321L	ALLC_ENST00000471711.1_3'UTR|AC010907.5_ENST00000441632.1_RNA	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	340					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		AACCACTGCTTCCAGTGACCA	0.488										HNSCC(21;0.051)																												ENST00000252505.3																			0				breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30						c.(961-963)ctT>ctA		allantoicase							65.0	64.0	64.0					2																	3749214		1948	4149	6097	SO:0001819	synonymous_variant	55821						allantoicase activity	g.chr2:3749214T>A	AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.963T>A	2.37:g.3749214T>A		HNSCC(21;0.051)				ALLC_ENST00000471711.1_3'UTR	p.L321L	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)	11	1125	+	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)	340					Q53T95|Q5RL81|Q96RE6|Q9NZA7	Silent	SNP	ENST00000252505.3	37	c.963T>A	CCDS46223.1																																																																																				0.488	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			9	13	0	0	0	1	0	9	13				
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382565.1_Intron			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			9	Substitution - Missense(9)	p.K373E(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(454-456)Aag>Gag	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2																																				SO:0001583	missense	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091840T>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu					CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E	p.K152E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1890	-			373			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.454A>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		4	70	0	0	0	1	0	4	70				
VPS53	55275	broad.mit.edu	37	17	556535	556535	+	Missense_Mutation	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr17:556535C>T	ENST00000571805.1	-	7	740	c.604G>A	c.(604-606)Gaa>Aaa	p.E202K	VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.E173K|VPS53_ENST00000437048.2_Missense_Mutation_p.E202K|VPS53_ENST00000401468.3_Intron|VPS53_ENST00000576149.1_Intron			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	202					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GTTTACCTTTCGGAAAGCTGC	0.483																																						ENST00000437048.2																			0				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19						c.(604-606)Gaa>Aaa		vacuolar protein sorting 53 homolog (S. cerevisiae)							80.0	80.0	80.0					17																	556535		2203	4299	6502	SO:0001583	missense	55275				protein transport	endosome membrane|Golgi apparatus		g.chr17:556535C>T		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.604G>A	17.37:g.556535C>T	ENSP00000459312:p.Glu202Lys					VPS53_ENST00000401468.3_Intron|VPS53_ENST00000576149.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.E173K|VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000571805.1_Missense_Mutation_p.E202K	p.E202K	NM_001128159.2	NP_001121631.1	Q5VIR6	VPS53_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)	7	750	-			202					A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37	c.604G>A		.	.	.	.	.	.	.	.	.	.	C	16.90	3.248797	0.59103	.	.	ENSG00000141252	ENST00000437048;ENST00000291074;ENST00000389040	T;T;T	0.31510	1.49;1.49;1.49	5.6	5.6	0.85130	Vps53-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.22244	0.0536	N	0.16201	0.385	0.80722	D	1	B;B;P	0.37038	0.209;0.211;0.579	B;B;B	0.35727	0.029;0.103;0.209	T	0.03695	-1.1012	10	0.40728	T	0.16	.	18.5315	0.90993	0.0:1.0:0.0:0.0	.	202;202;173	Q5VIR6-4;Q5VIR6;Q5VIR6-2	.;VPS53_HUMAN;.	K	202;173;202	ENSP00000401435:E202K;ENSP00000291074:E173K;ENSP00000373692:E202K	ENSP00000291074:E173K	E	-	1	0	VPS53	503285	1.000000	0.71417	0.997000	0.53966	0.261000	0.26267	7.176000	0.77643	2.800000	0.96347	0.543000	0.68304	GAA		0.483	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		5	185	0	0	0	1	0	5	185				
U2AF1	7307	broad.mit.edu	37	21	44513235	44513235	+	Missense_Mutation	SNP	G	G	A			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr21:44513235G>A	ENST00000291552.4	-	8	792	c.700C>T	c.(700-702)Cgt>Tgt	p.R234C	U2AF1_ENST00000380276.2_Missense_Mutation_p.R234C|U2AF1_ENST00000459639.1_Missense_Mutation_p.R161C|U2AF1_ENST00000398137.1_Missense_Mutation_p.R161C|U2AF1_ENST00000486519.1_5'Flank	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	234	Arg/Gly/Ser-rich (RS domain).				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						GATCTTTCACGATCTCTCGAC	0.552			Mis		"""CLL, MDS"""																																	ENST00000459639.1				Dom	yes		21	21q22.3	7307	Mis	U2 small nuclear RNA auxiliary factor 1			L			"""CLL, MDS"""		0				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						c.(481-483)Cgt>Tgt		U2 small nuclear RNA auxiliary factor 1							55.0	60.0	58.0					21																	44513235		2203	4300	6503	SO:0001583	missense	7307				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	Cajal body|catalytic step 2 spliceosome|nuclear speck	nucleotide binding|RNA binding|zinc ion binding	g.chr21:44513235G>A	BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"""RNA binding motif (RRM) containing"""	12453	protein-coding gene	gene with protein product		191317	"""U2(RNU2) small nuclear RNA auxiliary factor binding protein"", ""U2(RNU2) small nuclear RNA auxiliary factor 1"""	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.700C>T	21.37:g.44513235G>A	ENSP00000291552:p.Arg234Cys					U2AF1_ENST00000398137.1_Missense_Mutation_p.R161C|U2AF1_ENST00000291552.4_Missense_Mutation_p.R234C|U2AF1_ENST00000380276.2_Missense_Mutation_p.R234C	p.R161C			Q01081	U2AF1_HUMAN			7	1505	-			234					Q701P4|Q71RF1	Missense_Mutation	SNP	ENST00000291552.4	37	c.481C>T	CCDS13694.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.411142	0.42817	.	.	ENSG00000160201	ENST00000459639;ENST00000380276;ENST00000291552;ENST00000398137	T;T;T;T	0.13196	2.61;2.61;2.61;2.61	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.33556	0.0867	L	0.61218	1.895	0.80722	D	1	D;D	0.63046	0.992;0.992	D;D	0.63877	0.919;0.919	T	0.02244	-1.1189	10	0.39692	T	0.17	-13.3832	18.2435	0.89977	0.0:0.0:1.0:0.0	.	234;234	Q01081;Q701P4	U2AF1_HUMAN;.	C	161;234;234;161	ENSP00000418705:R161C;ENSP00000369629:R234C;ENSP00000291552:R234C;ENSP00000381205:R161C	ENSP00000291552:R234C	R	-	1	0	U2AF1	43386304	1.000000	0.71417	0.099000	0.21106	0.683000	0.39861	3.728000	0.54991	2.371000	0.80710	0.563000	0.77884	CGT		0.552	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195541.1	NM_006758		6	84	0	0	0	1	0	6	84				
USP9X	8239	broad.mit.edu	37	X	41043349	41043349	+	Missense_Mutation	SNP	C	C	G			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chrX:41043349C>G	ENST00000324545.8	+	22	3880	c.3247C>G	c.(3247-3249)Cct>Gct	p.P1083A	USP9X_ENST00000378308.2_Missense_Mutation_p.P1083A	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1083					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TTTCTTTGGTCCTTCAGCCTC	0.353																																					Ovarian(172;1807 2695 35459 49286)	ENST00000324545.7																			0				NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						c.(3247-3249)Cct>Gct		ubiquitin specific peptidase 9, X-linked							172.0	155.0	160.0					X																	41043349		1990	4189	6179	SO:0001583	missense	8239				BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity	g.chrX:41043349C>G	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3247C>G	X.37:g.41043349C>G	ENSP00000316357:p.Pro1083Ala					USP9X_ENST00000378308.2_Missense_Mutation_p.P1083A	p.P1083A	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN			22	3880	+			1083					O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	c.3247C>G	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.010086	0.54361	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.15718	2.4;2.4	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.08626	0.0214	N	0.03608	-0.345	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.10450	0.005;0.001	T	0.20405	-1.0276	10	0.08179	T	0.78	.	18.2822	0.90102	0.0:1.0:0.0:0.0	.	1083;1083	Q93008-1;Q93008	.;USP9X_HUMAN	A	1083	ENSP00000367558:P1083A;ENSP00000316357:P1083A	ENSP00000316357:P1083A	P	+	1	0	USP9X	40928293	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.398000	0.79919	2.255000	0.74692	0.513000	0.50165	CCT		0.353	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		9	70	0	0	0	1	0	9	70				
FBN3	84467	broad.mit.edu	37	19	8168496	8168496	+	Missense_Mutation	SNP	C	C	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr19:8168496C>T	ENST00000600128.1	-	39	5303	c.4889G>A	c.(4888-4890)tGt>tAt	p.C1630Y	FBN3_ENST00000270509.2_Missense_Mutation_p.C1630Y|FBN3_ENST00000601739.1_Missense_Mutation_p.C1630Y			Q75N90	FBN3_HUMAN	fibrillin 3	1630	EGF-like 25; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AGGGCAGACACAGGTGTAGTT	0.562																																						ENST00000600128.1																			0				NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						c.(4888-4890)tGt>tAt		fibrillin 3							147.0	120.0	129.0					19																	8168496		2203	4300	6503	SO:0001583	missense	84467					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent	g.chr19:8168496C>T		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4889G>A	19.37:g.8168496C>T	ENSP00000470498:p.Cys1630Tyr					FBN3_ENST00000601739.1_Missense_Mutation_p.C1630Y|FBN3_ENST00000270509.2_Missense_Mutation_p.C1630Y	p.C1630Y			Q75N90	FBN3_HUMAN			39	5303	-			1630			EGF-like 25; calcium-binding.		Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	c.4889G>A	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.056453	0.76074	.	.	ENSG00000142449	ENST00000270509	D	0.99445	-5.91	3.76	3.76	0.43208	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.99782	0.9909	H	0.99415	4.555	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.96501	0.9371	10	0.87932	D	0	.	15.9309	0.79659	0.0:1.0:0.0:0.0	.	1630	Q75N90	FBN3_HUMAN	Y	1630	ENSP00000270509:C1630Y	ENSP00000270509:C1630Y	C	-	2	0	FBN3	8074496	1.000000	0.71417	0.994000	0.49952	0.926000	0.56050	7.168000	0.77570	1.797000	0.52628	0.491000	0.48974	TGT		0.562	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		41	45	0	0	0	1	0	41	45				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		33	52	0	0	0	1	0	33	52				
PLCD1	5333	broad.mit.edu	37	3	38051629	38051629	+	Missense_Mutation	SNP	G	G	C			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr3:38051629G>C	ENST00000334661.4	-	7	1352	c.1130C>G	c.(1129-1131)gCc>gGc	p.A377G	PLCD1_ENST00000463876.1_Missense_Mutation_p.A398G|PLCD1_ENST00000479619.1_5'Flank	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	377	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CACCTTGAAGGCATAGTCCCG	0.607																																						ENST00000463876.1																			0				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24						c.(1192-1194)gCc>gGc		phospholipase C, delta 1							101.0	100.0	101.0					3																	38051629		2203	4300	6503	SO:0001583	missense	5333				intracellular signal transduction|lipid catabolic process|phospholipid metabolic process	cytoplasm	calcium ion binding|GTPase activating protein binding|phosphatidylinositol phospholipase C activity|signal transducer activity	g.chr3:38051629G>C		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"""EF-hand domain containing"""	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.1130C>G	3.37:g.38051629G>C	ENSP00000335600:p.Ala377Gly					PLCD1_ENST00000334661.4_Missense_Mutation_p.A377G	p.A398G	NM_001130964.1	NP_001124436.1	P51178	PLCD1_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)	7	1546	-			377			PI-PLC X-box.		B3KR14|Q86VN8	Missense_Mutation	SNP	ENST00000334661.4	37	c.1193C>G	CCDS2671.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301671	0.81136	.	.	ENSG00000187091	ENST00000463876;ENST00000334661	T;T	0.76968	-1.06;-1.06	4.98	4.98	0.66077	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.85682	D	0.000000	D	0.90137	0.6918	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.91773	0.5429	10	0.66056	D	0.02	.	18.6149	0.91299	0.0:0.0:1.0:0.0	.	377;398	P51178;B3KR14	PLCD1_HUMAN;.	G	398;377	ENSP00000430344:A398G;ENSP00000335600:A377G	ENSP00000335600:A377G	A	-	2	0	PLCD1	38026633	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	9.723000	0.98772	2.491000	0.84063	0.555000	0.69702	GCC		0.607	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			30	45	0	0	0	1	0	30	45				
BAGE2	85319	broad.mit.edu	37	21	11058168	11058168	+	RNA	SNP	A	A	T			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr21:11058168A>T	ENST00000470054.1	-	0	479							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TACATCTTTCAGGAGCTTGGT	0.388																																						ENST00000470054.1																			0													B melanoma antigen family, member 2							100.0	79.0	86.0					21																	11058168		692	1591	2283			85319							g.chr21:11058168A>T	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058168A>T												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	479	-								A8K925|Q08ER0	RNA	SNP	ENST00000470054.1	37																																																																																						0.388	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		5	88	0	0	0	1	0	5	88				
TAF1B	9014	broad.mit.edu	37	2	9989571	9989571	+	Frame_Shift_Del	DEL	A	A	-	rs528368939		TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr2:9989571delA	ENST00000263663.5	+	3	375	c.187delA	c.(187-189)aaafs	p.K65fs	TAF1B_ENST00000402170.1_3'UTR|TAF1B_ENST00000396242.3_5'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	65	B-reader.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCGGGGGCTTAAAAAAAAAAA	0.333																																						ENST00000263663.5																			0				breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14						c.(187-189)aafs		TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa				139,495,3606		1,2,135,2,489,1491	20.0	22.0	21.0			1.7	0.9	2		23	207,946,7081		0,0,207,0,946,2964	no	codingComplex	TAF1B	NM_005680.2		1,2,342,2,1435,4455	A1A1,A1A2,A1R,A2A2,A2R,RR		14.0029,14.9528,14.3258			9989571	346,1441,10687	2194	4292	6486	SO:0001589	frameshift_variant	9014				termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr2:9989571delA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.187delA	2.37:g.9989571delA	ENSP00000263663:p.Lys65fs					TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	p.K65fs	NM_005680.2	NP_005671.2	Q53T94	TAF1B_HUMAN			3	375	+	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)		65					B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Del	DEL	ENST00000263663.5	37	c.187delA	CCDS33143.1																																																																																				0.333	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		2	4						2	4	---	---	---	---
GPR123	84435	broad.mit.edu	37	10	134895345	134895345	+	Frame_Shift_Del	DEL	A	A	-	rs369146683	byFrequency	TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr10:134895345delA	ENST00000607359.1	+	5	988	c.988delA	c.(988-990)accfs	p.T330fs				Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	0					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CTCTGGCAGGACCCCCTGGAG	0.662																																						ENST00000607359.1																			0				endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14						c.(988-990)ccfs		G protein-coupled receptor 123							22.0	24.0	23.0					10																	134895345		1512	3505	5017	SO:0001589	frameshift_variant	84435					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr10:134895345delA	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000607359.1:c.988delA	10.37:g.134895345delA	ENSP00000475778:p.Thr330fs						p.T330fs			Q86SQ6	GP123_HUMAN		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)	5	988	+		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)	481					A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Frame_Shift_Del	DEL	ENST00000607359.1	37	c.988delA																																																																																					0.662	GPR123-004	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316904.2			2	4						2	4	---	---	---	---
HNRNPKP3	399881	broad.mit.edu	37	11	43283606	43283606	+	RNA	DEL	A	A	-	rs377012965		TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chr11:43283606delA	ENST00000511537.1	-	0	1329					NR_033868.1				heterogeneous nuclear ribonucleoprotein K pseudogene 3																		AAGCAAATGTAAAAAAAAAAA	0.388																																						ENST00000511537.1																			0																																																			0							g.chr11:43283606delA			11p12	2011-07-05				ENSG00000251557			42376	pseudogene	pseudogene							Standard	NR_033868		Approved		uc001mxe.2				11.37:g.43283606delA								NR_033868.1						0	1329	-									RNA	DEL	ENST00000511537.1	37																																																																																						0.388	HNRNPKP3-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000390385.1	NR_033868		4	6						4	6	---	---	---	---
TXLNGY	246126	broad.mit.edu	37	Y	21758004	21758005	+	RNA	DEL	AG	AG	-			TCGA-L6-A4EQ-01A-11D-A257-08	TCGA-L6-A4EQ-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	247b1c50-5882-4714-b26e-8059705de3f2	bef85d8f-bfee-493e-a438-2465d603b02a	g.chrY:21758004_21758005delAG	ENST00000253320.4	+	0	3085_3086																				haematopoietic_and_lymphoid_tissue(1)	1						GAAAGACATCAGAGAGAGAGAG	0.347																																						ENST00000253320.4																			0				haematopoietic_and_lymphoid_tissue(1)	1																																														0							g.chrY:21758004_21758005delAG																													Y.37:g.21758014_21758015delAG										Q9BZA5	CY15A_HUMAN			0	3085_3086	+									RNA	DEL	ENST00000253320.4	37																																																																																						0.347	TXLNG2P-012	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000088781.1			3	6						3	6	---	---	---	---
