#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
CYTH4	27128	broad.mit.edu	37	22	37688673	37688673	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr22:37688673C>A	ENST00000248901.6	+	2	218	c.31C>A	c.(31-33)Ctg>Atg	p.L11M	CYTH4_ENST00000439667.1_3'UTR|CYTH4_ENST00000402997.1_Missense_Mutation_p.L11M|CYTH4_ENST00000405206.3_Missense_Mutation_p.L11M	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	11					positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						GCCCGCGGAGCTGAGCAGCGG	0.612																																						ENST00000248901.6																			0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						c.(31-33)Ctg>Atg		cytohesin 4							143.0	125.0	131.0					22																	37688673		2203	4300	6503	SO:0001583	missense	27128				regulation of ARF protein signal transduction|regulation of cell adhesion	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity	g.chr22:37688673C>A	AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"""Pleckstrin homology (PH) domain containing"""	9505	protein-coding gene	gene with protein product		606514	"""pleckstrin homology, Sec7 and coiled/coil domains 4"", ""pleckstrin homology, Sec7 and coiled-coil domains 4"""	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.31C>A	22.37:g.37688673C>A	ENSP00000248901:p.Leu11Met					CYTH4_ENST00000402997.1_Missense_Mutation_p.L11M|CYTH4_ENST00000405206.3_Missense_Mutation_p.L11M|CYTH4_ENST00000439667.1_3'UTR	p.L11M	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN			2	218	+			11					Q5R3F9|Q9UGT6	Missense_Mutation	SNP	ENST00000248901.6	37	c.31C>A	CCDS13946.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.880178	0.51801	.	.	ENSG00000100055	ENST00000457992;ENST00000248901;ENST00000422721;ENST00000402997;ENST00000405206;ENST00000404204	T;T;T;T	0.57436	0.4;2.8;0.45;0.43	4.83	4.83	0.62350	.	1.012730	0.07907	N	0.973581	T	0.73273	0.3566	M	0.81802	2.56	0.22017	N	0.999412	D;D	0.89917	0.999;1.0	D;D	0.76071	0.98;0.987	T	0.58165	-0.7684	10	0.62326	D	0.03	.	9.188	0.37182	0.0:0.9001:0.0:0.0999	.	11;24	Q9UIA0;Q9H7Q0	CYH4_HUMAN;.	M	11;11;24;11;11;11	ENSP00000405442:L11M;ENSP00000248901:L11M;ENSP00000385997:L11M;ENSP00000384280:L11M	ENSP00000248901:L11M	L	+	1	2	CYTH4	36018619	1.000000	0.71417	0.997000	0.53966	0.314000	0.28054	2.572000	0.45999	2.236000	0.73375	0.561000	0.74099	CTG		0.612	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1			36	46	1	0	9.62906e-15	0.006230	1.69238e-14	36	46				
KIAA1755	85449	broad.mit.edu	37	20	36869357	36869357	+	Silent	SNP	T	T	C			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr20:36869357T>C	ENST00000279024.4	-	3	1447	c.1176A>G	c.(1174-1176)tcA>tcG	p.S392S		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	392										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CTGGCTCTTGTGAGACACCTG	0.587																																						ENST00000279024.4																			0				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54						c.(1174-1176)tcA>tcG		KIAA1755							85.0	88.0	87.0					20																	36869357		2203	4300	6503	SO:0001819	synonymous_variant	85449							g.chr20:36869357T>C	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1176A>G	20.37:g.36869357T>C							p.S392S	NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN			3	1447	-		Myeloproliferative disorder(115;0.00874)	392					Q9C0A8	Silent	SNP	ENST00000279024.4	37	c.1176A>G	CCDS33467.1																																																																																				0.587	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		71	158	0	0	0	0.003610	0	71	158				
MSH3	4437	broad.mit.edu	37	5	79950762	79950762	+	Silent	SNP	G	G	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr5:79950762G>A	ENST00000265081.6	+	1	296	c.216G>A	c.(214-216)ccG>ccA	p.P72P	DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	72					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CCGCCTTCCCGCCCCAGCTGC	0.761								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(214-216)ccG>ccA	Mismatch excision repair (MMR)	mutS homolog 3							3.0	3.0	3.0					5																	79950762		1506	3116	4622	SO:0001819	synonymous_variant	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79950762G>A	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.216G>A	5.37:g.79950762G>A						DHFR_ENST00000439211.2_5'UTR	p.P72P	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	1	296	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	72					A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	c.216G>A	CCDS34195.1																																																																																				0.761	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		4	9	0	0	0	0.000248	0	4	9				
ALDH1L1	10840	broad.mit.edu	37	3	125850235	125850235	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr3:125850235T>C	ENST00000393434.2	-	13	1964	c.1615A>G	c.(1615-1617)Aag>Gag	p.K539E	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.K539E|ALDH1L1_ENST00000393431.2_Intron|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.K438E|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.K549E	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	539	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	ACCTGGATCTTGTCACACCAG	0.607																																						ENST00000393434.2																			0				NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52						c.(1615-1617)Aag>Gag		aldehyde dehydrogenase 1 family, member L1	Tetrahydrofolic acid(DB00116)						141.0	136.0	138.0					3																	125850235		2203	4300	6503	SO:0001583	missense	10840				10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity	g.chr3:125850235T>C	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.1615A>G	3.37:g.125850235T>C	ENSP00000377083:p.Lys539Glu					ALDH1L1_ENST00000452905.2_Missense_Mutation_p.K438E|ALDH1L1_ENST00000393431.2_Intron|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.K539E|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.K549E	p.K539E	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN		GBM - Glioblastoma multiforme(114;0.0462)	13	1964	-			539			Aldehyde dehydrogenase.		B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	c.1615A>G	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.738676	0.69304	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	4.05	4.05	0.47172	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.86138	0.5861	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87440	0.2394	10	0.87932	D	0	.	11.2444	0.48987	0.0:0.0:0.0:1.0	.	438;539	E9PBX3;O75891	.;AL1L1_HUMAN	E	549;539;438;539	ENSP00000273450:K549E;ENSP00000420293:K539E;ENSP00000395881:K438E;ENSP00000377083:K539E	ENSP00000273450:K549E	K	-	1	0	ALDH1L1	127332925	1.000000	0.71417	1.000000	0.80357	0.533000	0.34776	7.277000	0.78572	1.815000	0.52974	0.383000	0.25322	AAG		0.607	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		86	224	0	0	0	0.003610	0	86	224				
STAT1	6772	broad.mit.edu	37	2	191862642	191862642	+	Missense_Mutation	SNP	C	C	G			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr2:191862642C>G	ENST00000361099.3	-	9	1112	c.725G>C	c.(724-726)aGa>aCa	p.R242T	STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000409465.1_Missense_Mutation_p.R242T|STAT1_ENST00000392323.2_Missense_Mutation_p.R244T|STAT1_ENST00000392322.3_Missense_Mutation_p.R242T	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	242					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			GCTCTGCTGTCTCCGCTTCCA	0.483																																						ENST00000361099.3																			0				autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						c.(724-726)aGa>aCa		signal transducer and activator of transcription 1, 91kDa	Fludarabine(DB01073)						79.0	75.0	77.0					2																	191862642		2203	4300	6503	SO:0001583	missense	6772				activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein	cytosol|nucleolus|nucleoplasm	calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr2:191862642C>G		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.725G>C	2.37:g.191862642C>G	ENSP00000354394:p.Arg242Thr					STAT1_ENST00000409465.1_Missense_Mutation_p.R242T|STAT1_ENST00000392323.2_Missense_Mutation_p.R244T|STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000392322.3_Missense_Mutation_p.R242T	p.R242T	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)		9	1112	-			242					A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	c.725G>C	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068218	0.76301	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323;ENST00000544783	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	5.28	5.28	0.74379	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.000000	0.85682	D	0.000000	D	0.82522	0.5055	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.99;0.991	D	0.85041	0.0923	10	0.72032	D	0.01	-27.766	19.1174	0.93346	0.0:1.0:0.0:0.0	.	242;242	P42224-2;P42224	.;STAT1_HUMAN	T	242;242;242;244;150	ENSP00000354394:R242T;ENSP00000386244:R242T;ENSP00000376136:R242T;ENSP00000376137:R244T	ENSP00000354394:R242T	R	-	2	0	STAT1	191570887	0.981000	0.34729	0.156000	0.22583	0.434000	0.31775	7.651000	0.83577	2.746000	0.94184	0.655000	0.94253	AGA		0.483	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		3	64	0	0	0	0.004672	0	3	64				
ZNF724P	440519	broad.mit.edu	37	19	23405748	23405748	+	Missense_Mutation	SNP	C	C	G			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr19:23405748C>G	ENST00000418100.1	-	4	1416	c.1299G>C	c.(1297-1299)caG>caC	p.Q433H				A8MTY0	ZN724_HUMAN	zinc finger protein 724, pseudogene	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|lung(2)|ovary(2)	8						GTTGTGAGAACTGGTTAAAGG	0.398																																						ENST00000418100.1																			0				endometrium(3)|kidney(1)|lung(2)|ovary(2)	8						c.(1297-1299)caG>caC																																						SO:0001583	missense	0							g.chr19:23405748C>G			19p12	2014-02-14	2010-08-03		ENSG00000196081	ENSG00000196081			32460	pseudogene	pseudogene			"""zinc finger protein 724 pseudogene"", ""zinc finger protein 724 (pseudogene)"""				Standard	NR_045525		Approved		uc021uru.1	A8MTY0	OTTHUMG00000183231	ENST00000418100.1:c.1299G>C	19.37:g.23405748C>G	ENSP00000413411:p.Gln433His						p.Q433H							4	1416	-									Missense_Mutation	SNP	ENST00000418100.1	37	c.1299G>C		.	.	.	.	.	.	.	.	.	.	C	0.001	-3.086005	0.00035	.	.	ENSG00000196081	ENST00000418100	T	0.36340	1.26	1.09	-0.0727	0.13738	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13586	0.0329	.	.	.	0.09310	N	1	B	0.20550	0.046	B	0.06405	0.002	T	0.25572	-1.0128	8	0.12430	T	0.62	.	0.2593	0.00216	0.2511:0.2826:0.2486:0.2178	.	433	A8MTY0	ZN724_HUMAN	H	433	ENSP00000413411:Q433H	ENSP00000413411:Q433H	Q	-	3	2	ZNF724P	23197588	0.000000	0.05858	0.438000	0.26821	0.394000	0.30568	-3.070000	0.00619	0.488000	0.27723	0.491000	0.48974	CAG		0.398	ZNF724P-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000465743.1			10	34	0	0	0	0.006214	0	10	34				
USP6	9098	broad.mit.edu	37	17	5076150	5076150	+	Nonsense_Mutation	SNP	T	T	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr17:5076150T>A	ENST00000574788.1	+	38	6328	c.4098T>A	c.(4096-4098)taT>taA	p.Y1366*	USP6_ENST00000332776.4_3'UTR|USP6_ENST00000250066.6_Nonsense_Mutation_p.Y1366*|USP6_ENST00000304328.5_Nonsense_Mutation_p.Y1049*			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1366	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TTCTTTTCTATGAGCAGCAGG	0.428			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts																																	ENST00000574788.1				Dom	yes		17	17p13	9098	T	ubiquitin specific peptidase 6 (Tre-2 oncogene)			M	"""COL1A1, CDH11, ZNF9, OMD"""		aneurysmal bone cysts		0				breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						c.(4096-4098)taT>taA		ubiquitin specific peptidase 6 (Tre-2 oncogene)							140.0	129.0	133.0					17																	5076150		2203	4297	6500	SO:0001587	stop_gained	9098				protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr17:5076150T>A	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.4098T>A	17.37:g.5076150T>A	ENSP00000460380:p.Tyr1366*					USP6_ENST00000332776.4_3'UTR|USP6_ENST00000304328.5_Nonsense_Mutation_p.Y1049*|USP6_ENST00000250066.6_Nonsense_Mutation_p.Y1366*	p.Y1366*			P35125	UBP6_HUMAN			38	6328	+			1366					Q15634|Q86WP6|Q8IWT4	Nonsense_Mutation	SNP	ENST00000574788.1	37	c.4098T>A	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	T	52	19.007308	0.99913	.	.	ENSG00000129204	ENST00000250066;ENST00000304328	.	.	.	2.35	1.25	0.21368	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.584	0.07963	0.0:0.355:0.0:0.645	.	.	.	.	X	1366;1049	.	ENSP00000250066:Y1366X	Y	+	3	2	USP6	5016874	0.994000	0.37717	1.000000	0.80357	0.491000	0.33493	0.327000	0.19663	1.080000	0.41073	0.155000	0.16302	TAT		0.428	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		44	115	0	0	0	0.003610	0	44	115				
UBP1	7342	broad.mit.edu	37	3	33451063	33451063	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr3:33451063G>A	ENST00000283629.3	-	6	1115	c.586C>T	c.(586-588)Cgg>Tgg	p.R196W	UBP1_ENST00000283628.5_Missense_Mutation_p.R196W|UBP1_ENST00000486388.1_5'Flank|UBP1_ENST00000447368.2_Missense_Mutation_p.R196W	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	196					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						CCGTGCTTCCGTGGAGTAAAT	0.418																																						ENST00000283629.3																			0				breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						c.(586-588)Cgg>Tgg		upstream binding protein 1 (LBP-1a)							110.0	106.0	107.0					3																	33451063		2203	4300	6503	SO:0001583	missense	7342				negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity	g.chr3:33451063G>A	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.586C>T	3.37:g.33451063G>A	ENSP00000283629:p.Arg196Trp					UBP1_ENST00000447368.2_Missense_Mutation_p.R196W|UBP1_ENST00000283628.5_Missense_Mutation_p.R196W	p.R196W	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN			6	1115	-			196					Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	c.586C>T	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.040841	0.55003	.	.	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628	T;T;T	0.18810	2.19;2.19;2.19	6.17	5.3	0.74995	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.85710	2.77	0.80722	D	1	B;P	0.43542	0.333;0.81	B;P	0.46299	0.061;0.511	T	0.49661	-0.8916	10	0.87932	D	0	-12.0005	17.0755	0.86585	0.0:0.0:0.872:0.1279	.	196;196	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	W	196	ENSP00000283629:R196W;ENSP00000395558:R196W;ENSP00000283628:R196W	ENSP00000283628:R196W	R	-	1	2	UBP1	33426067	0.999000	0.42202	0.997000	0.53966	0.992000	0.81027	2.631000	0.46502	1.609000	0.50190	0.655000	0.94253	CGG		0.418	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		22	86	0	0	0	0.002780	0	22	86				
DOCK3	1795	broad.mit.edu	37	3	51399384	51399384	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr3:51399384G>A	ENST00000266037.9	+	48	5124	c.5101G>A	c.(5101-5103)Ggc>Agc	p.G1701S		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1701					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		GCTGGGTGACGGCTCCATGGG	0.567																																						ENST00000266037.9																			0				breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45						c.(5101-5103)Ggc>Agc		dedicator of cytokinesis 3							88.0	92.0	90.0					3																	51399384		2151	4256	6407	SO:0001583	missense	1795					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding	g.chr3:51399384G>A	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.5101G>A	3.37:g.51399384G>A	ENSP00000266037:p.Gly1701Ser						p.G1701S	NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)	48	5124	+			1701					O15017	Missense_Mutation	SNP	ENST00000266037.9	37	c.5101G>A	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	1.698	-0.502187	0.04261	.	.	ENSG00000088538	ENST00000266037;ENST00000402669	T	0.04317	3.65	5.31	-0.0328	0.13903	.	0.409694	0.31847	N	0.006972	T	0.01800	0.0057	N	0.04018	-0.295	0.23089	N	0.998315	B	0.06786	0.001	B	0.04013	0.001	T	0.48647	-0.9017	10	0.02654	T	1	.	9.775	0.40614	0.6426:0.0:0.3574:0.0	.	1701	Q8IZD9	DOCK3_HUMAN	S	1701;497	ENSP00000266037:G1701S	ENSP00000266037:G1701S	G	+	1	0	DOCK3	51374424	1.000000	0.71417	0.925000	0.36789	0.419000	0.31324	2.190000	0.42630	0.107000	0.17824	-0.302000	0.09304	GGC		0.567	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		6	13	0	0	0	0.001168	0	6	13				
KRT18P55	284085	broad.mit.edu	37	17	26603792	26603792	+	RNA	SNP	T	T	C	rs138730739		TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr17:26603792T>C	ENST00000577198.1	-	0	1169				AC061975.8_ENST00000385109.1_RNA	NR_028334.1				keratin 18 pseudogene 55																		CCAAGTGACATTGGTGTCATC	0.502													T|||	1	0.000199681	0.0	0.0	5008	,	,		22443	0.001		0.0	False		,,,				2504	0.0					ENST00000577198.1																			0																				33.0	33.0	33.0					17																	26603792		2200	4300	6500			0							g.chr17:26603792T>C			17q11.2	2013-06-25			ENSG00000265480	ENSG00000265480			26874	pseudogene	pseudogene							Standard	NR_028334		Approved		uc002has.3		OTTHUMG00000179422		17.37:g.26603792T>C								NR_028334.1						0	1169	-									RNA	SNP	ENST00000577198.1	37																																																																																						0.502	KRT18P55-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000446194.1	NR_028334		23	45	0	0	0	0.003330	0	23	45				
NLRC4	58484	broad.mit.edu	37	2	32477651	32477651	+	Silent	SNP	C	C	G			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr2:32477651C>G	ENST00000404025.2	-	4	587	c.99G>C	c.(97-99)ctG>ctC	p.L33L	NLRC4_ENST00000342905.6_Silent_p.L33L|NLRC4_ENST00000360906.5_Silent_p.L33L|NLRC4_ENST00000402280.1_Silent_p.L33L			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	33	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CTTCGCGATTCAGAACATTCC	0.403																																						ENST00000404025.2																			0				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16						c.(97-99)ctG>ctC		NLR family, CARD domain containing 4							159.0	145.0	149.0					2																	32477651		2203	4300	6503	SO:0001819	synonymous_variant	58484				activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity	g.chr2:32477651C>G	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.99G>C	2.37:g.32477651C>G						NLRC4_ENST00000402280.1_Silent_p.L33L|NLRC4_ENST00000342905.6_Silent_p.L33L|NLRC4_ENST00000360906.5_Silent_p.L33L	p.L33L			Q9NPP4	NLRC4_HUMAN			4	587	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)		33			CARD.		A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Silent	SNP	ENST00000404025.2	37	c.99G>C	CCDS33174.1																																																																																				0.403	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		3	166	0	0	0	0.000248	0	3	166				
ACACB	32	broad.mit.edu	37	12	109650693	109650693	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr12:109650693G>A	ENST00000338432.7	+	22	3421	c.3302G>A	c.(3301-3303)cGa>cAa	p.R1101Q	ACACB_ENST00000377848.3_Missense_Mutation_p.R1101Q|ACACB_ENST00000377854.5_Missense_Mutation_p.R1101Q			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1101					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	AAGGCTGATCGAGAGGTCTTC	0.542																																						ENST00000338432.7																			0				NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95						c.(3301-3303)cGa>cAa		acetyl-CoA carboxylase beta	Biotin(DB00121)						204.0	179.0	187.0					12																	109650693		2203	4300	6503	SO:0001583	missense	32				acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding	g.chr12:109650693G>A	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3302G>A	12.37:g.109650693G>A	ENSP00000341044:p.Arg1101Gln					ACACB_ENST00000377848.3_Missense_Mutation_p.R1101Q|ACACB_ENST00000377854.5_Missense_Mutation_p.R1101Q	p.R1101Q			O00763	ACACB_HUMAN			22	3421	+			1101					A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	c.3302G>A	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.587522	0.86851	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.47177	0.85;0.85;0.85	5.48	5.48	0.80851	Acetyl-CoA carboxylase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.65770	0.2723	L	0.52206	1.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64685	-0.6349	10	0.54805	T	0.06	.	19.7462	0.96252	0.0:0.0:1.0:0.0	.	1101	O00763	ACACB_HUMAN	Q	1101;1101;1101;332	ENSP00000341044:R1101Q;ENSP00000367079:R1101Q;ENSP00000367085:R1101Q	ENSP00000341044:R1101Q	R	+	2	0	ACACB	108135076	1.000000	0.71417	0.973000	0.42090	0.927000	0.56198	9.756000	0.98918	2.736000	0.93811	0.655000	0.94253	CGA		0.542	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		50	121	0	0	0	0.003610	0	50	121				
CCDC54	84692	broad.mit.edu	37	3	107097052	107097052	+	Silent	SNP	C	C	T			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr3:107097052C>T	ENST00000261058.1	+	1	865	c.618C>T	c.(616-618)gaC>gaT	p.D206D		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	206										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						AGTCCACTGACCATCTTGAGA	0.393																																						ENST00000261058.1																			0				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						c.(616-618)gaC>gaT		coiled-coil domain containing 54							73.0	73.0	73.0					3																	107097052		2203	4300	6503	SO:0001819	synonymous_variant	84692							g.chr3:107097052C>T	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"""sperm protein 17"""					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.618C>T	3.37:g.107097052C>T							p.D206D	NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN			1	865	+			206					Q96A43	Silent	SNP	ENST00000261058.1	37	c.618C>T	CCDS2949.1																																																																																				0.393	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600		34	81	0	0	0	0.003271	0	34	81				
SYNE1	23345	broad.mit.edu	37	6	152765610	152765610	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr6:152765610T>C	ENST00000367255.5	-	30	4374	c.3773A>G	c.(3772-3774)cAa>cGa	p.Q1258R	SYNE1_ENST00000265368.4_Missense_Mutation_p.Q1258R|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q1265R|SYNE1_ENST00000367253.4_Missense_Mutation_p.Q1258R|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q1265R|SYNE1_ENST00000413186.2_Missense_Mutation_p.Q1258R|SYNE1_ENST00000341594.5_Missense_Mutation_p.Q1324R|SYNE1_ENST00000367248.3_Missense_Mutation_p.Q1248R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1258					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTTCTCAGCTTGTTCCTGGAC	0.368										HNSCC(10;0.0054)																												ENST00000367255.5																			0				NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.(3772-3774)cAa>cGa		spectrin repeat containing, nuclear envelope 1							122.0	120.0	121.0					6																	152765610		2203	4300	6503	SO:0001583	missense	23345				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152765610T>C	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3773A>G	6.37:g.152765610T>C	ENSP00000356224:p.Gln1258Arg	HNSCC(10;0.0054)				SYNE1_ENST00000265368.4_Missense_Mutation_p.Q1258R|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q1265R|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q1265R|SYNE1_ENST00000413186.2_Missense_Mutation_p.Q1258R|SYNE1_ENST00000341594.5_Missense_Mutation_p.Q1324R|SYNE1_ENST00000367253.4_Missense_Mutation_p.Q1258R|SYNE1_ENST00000367248.3_Missense_Mutation_p.Q1248R	p.Q1258R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	30	4374	-		Ovarian(120;0.0955)	1258					E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	c.3773A>G	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444066	0.63067	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;D;D;D	0.88975	0.45;0.45;0.36;0.45;0.52;-2.32;-2.44;-2.45	5.96	5.96	0.96718	.	0.570212	0.16882	N	0.195670	T	0.78457	0.4286	L	0.47716	1.5	0.80722	D	1	B;B;B;P;B;B	0.36282	0.22;0.006;0.004;0.546;0.006;0.01	B;B;B;B;B;B	0.32980	0.054;0.005;0.016;0.156;0.005;0.011	T	0.77384	-0.2608	10	0.16896	T	0.51	.	16.4277	0.83824	0.0:0.0:0.0:1.0	.	1241;1258;1248;1258;1258;1265	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	R	1258;1265;1258;1265;1324;1258;1248;1258	ENSP00000356224:Q1258R;ENSP00000396024:Q1265R;ENSP00000265368:Q1258R;ENSP00000390975:Q1265R;ENSP00000341887:Q1324R;ENSP00000356222:Q1258R;ENSP00000356217:Q1248R;ENSP00000414510:Q1258R	ENSP00000265368:Q1258R	Q	-	2	0	SYNE1	152807303	1.000000	0.71417	0.256000	0.24389	0.993000	0.82548	7.474000	0.81024	2.279000	0.76181	0.533000	0.62120	CAA		0.368	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		29	86	0	0	0	0.001786	0	29	86				
PCDHA3	56145	broad.mit.edu	37	5	140181378	140181378	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr5:140181378A>G	ENST00000522353.2	+	1	596	c.596A>G	c.(595-597)aAt>aGt	p.N199S	PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.N199S|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	199	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGAAAAAAAATTTAAATCGA	0.368																																						ENST00000522353.2																			0				NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95						c.(595-597)aAt>aGt									58.0	60.0	60.0					5																	140181378		2203	4300	6503	SO:0001583	missense	0							g.chr5:140181378A>G	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.596A>G	5.37:g.140181378A>G	ENSP00000429808:p.Asn199Ser					PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.N199S	p.N199S	NM_018906.2	NP_061729.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	596	+								O75286	Missense_Mutation	SNP	ENST00000522353.2	37	c.596A>G	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	a	0.001	-3.014999	0.00042	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.50813	0.73;0.73	4.86	-1.92	0.07618	Cadherin (4);Cadherin-like (1);	1.577750	0.04326	U	0.351602	T	0.12475	0.0303	N	0.00237	-1.79	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.26503	-1.0101	10	0.07990	T	0.79	.	6.2978	0.21095	0.1653:0.5433:0.0:0.2914	.	199;199	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	S	199	ENSP00000429808:N199S;ENSP00000434086:N199S	ENSP00000429808:N199S	N	+	2	0	PCDHA3	140161562	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-1.491000	0.02302	-0.250000	0.09555	-0.691000	0.03719	AAT		0.368	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		3	107	0	0	0	0.004672	0	3	107				
WSCD1	23302	broad.mit.edu	37	17	6014123	6014123	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr17:6014123A>C	ENST00000574946.1	+	7	1432	c.1042A>C	c.(1042-1044)Aac>Cac	p.N348H	WSCD1_ENST00000573634.1_Missense_Mutation_p.N232H|WSCD1_ENST00000574232.1_Missense_Mutation_p.N348H|WSCD1_ENST00000317744.5_Missense_Mutation_p.N348H|WSCD1_ENST00000539421.1_Missense_Mutation_p.N348H			Q658N2	WSCD1_HUMAN	WSC domain containing 1	348						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						GTTCCTGCCTAACAAATCCAA	0.493																																						ENST00000574946.1																			0				breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						c.(1042-1044)Aac>Cac		WSC domain containing 1							241.0	234.0	236.0					17																	6014123		2203	4300	6503	SO:0001583	missense	23302					integral to membrane	sulfotransferase activity	g.chr17:6014123A>C		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.1042A>C	17.37:g.6014123A>C	ENSP00000460825:p.Asn348His					WSCD1_ENST00000573634.1_Missense_Mutation_p.N232H|WSCD1_ENST00000539421.1_Missense_Mutation_p.N348H|WSCD1_ENST00000317744.5_Missense_Mutation_p.N348H|WSCD1_ENST00000574232.1_Missense_Mutation_p.N348H	p.N348H			Q658N2	WSCD1_HUMAN			7	1432	+			348					A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	c.1042A>C	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.951663	0.34471	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	T;T	0.31510	1.49;1.49	5.66	-1.23	0.09465	.	0.921371	0.09494	N	0.794513	T	0.17109	0.0411	L	0.27053	0.805	0.09310	N	1	B	0.24368	0.102	B	0.24541	0.054	T	0.28996	-1.0026	10	0.45353	T	0.12	-11.4931	1.9699	0.03404	0.5349:0.1237:0.2214:0.1201	.	348	Q658N2	WSCD1_HUMAN	H	348	ENSP00000323087:N348H;ENSP00000446032:N348H	ENSP00000323087:N348H	N	+	1	0	WSCD1	5954847	0.245000	0.23899	0.893000	0.35052	0.979000	0.70002	1.548000	0.36201	0.039000	0.15632	0.528000	0.53228	AAC		0.493	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		7	327	0	0	0	0.001984	0	7	327				
ZNF746	155061	broad.mit.edu	37	7	149171562	149171562	+	Silent	SNP	G	G	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr7:149171562G>A	ENST00000340622.3	-	7	2128	c.1848C>T	c.(1846-1848)tcC>tcT	p.S616S	ZNF746_ENST00000458143.2_Silent_p.S617S			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	616					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			AAGGTCCTTTGGAGGCGGGGC	0.687																																						ENST00000340622.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						c.(1846-1848)tcC>tcT		zinc finger protein 746							33.0	33.0	33.0					7																	149171562		2200	4298	6498	SO:0001819	synonymous_variant	155061				negative regulation of transcription, DNA-dependent|neuron death|regulation of cell death|transcription, DNA-dependent	cytoplasm|nucleus	transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding	g.chr7:149171562G>A	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.1848C>T	7.37:g.149171562G>A						ZNF746_ENST00000458143.2_Silent_p.S617S	p.S616S			Q6NUN9	ZN746_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00358)		7	2128	-	Melanoma(164;0.165)		616					A8K6Z9|Q6ZRF9	Silent	SNP	ENST00000340622.3	37	c.1848C>T	CCDS5897.1																																																																																				0.687	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557		13	15	0	0	0	0.004007	0	13	15				
AGGF1	55109	broad.mit.edu	37	5	76331518	76331518	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr5:76331518A>G	ENST00000312916.7	+	3	848	c.466A>G	c.(466-468)Aca>Gca	p.T156A	AGGF1_ENST00000506806.1_Missense_Mutation_p.T156A|AGGF1_ENST00000503538.1_3'UTR	NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	156					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		TACCGATAGAACAGAAAATGT	0.353																																						ENST00000312916.7																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20						c.(466-468)Aca>Gca		angiogenic factor with G patch and FHA domains 1							92.0	92.0	92.0					5																	76331518		2203	4300	6503	SO:0001583	missense	55109				angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding	g.chr5:76331518A>G	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.466A>G	5.37:g.76331518A>G	ENSP00000316109:p.Thr156Ala					AGGF1_ENST00000506806.1_Missense_Mutation_p.T156A|AGGF1_ENST00000503538.1_3'UTR	p.T156A	NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)	3	848	+		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)	156					O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	c.466A>G	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	A	8.141	0.785192	0.16189	.	.	ENSG00000164252	ENST00000312916;ENST00000506806	T;T	0.78816	1.2;-1.21	5.75	3.23	0.37069	.	0.797682	0.12034	N	0.505702	T	0.63402	0.2508	L	0.29908	0.895	0.09310	N	1	B;B	0.17268	0.005;0.021	B;B	0.23419	0.006;0.046	T	0.47169	-0.9138	10	0.12430	T	0.62	-4.8762	6.8657	0.24093	0.7952:0.0:0.0717:0.1331	.	156;156	Q8N302;Q8N302-3	AGGF1_HUMAN;.	A	156	ENSP00000316109:T156A;ENSP00000424733:T156A	ENSP00000316109:T156A	T	+	1	0	AGGF1	76367274	0.000000	0.05858	0.009000	0.14445	0.247000	0.25773	1.015000	0.29963	0.385000	0.24970	0.528000	0.53228	ACA		0.353	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		18	70	0	0	0	0.006122	0	18	70				
PCDH15	65217	broad.mit.edu	37	10	55782771	55782771	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr10:55782771G>C	ENST00000320301.6	-	19	2801	c.2407C>G	c.(2407-2409)Cta>Gta	p.L803V	PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373955.1_Missense_Mutation_p.L803V|PCDH15_ENST00000395430.1_Missense_Mutation_p.L803V|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Missense_Mutation_p.L732V|PCDH15_ENST00000395445.1_Missense_Mutation_p.L810V|PCDH15_ENST00000414778.1_Missense_Mutation_p.L808V|PCDH15_ENST00000395438.1_Missense_Mutation_p.L803V|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.L803V|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.L781V|PCDH15_ENST00000373965.2_Missense_Mutation_p.L810V|PCDH15_ENST00000395432.2_Missense_Mutation_p.L766V|PCDH15_ENST00000409834.1_Missense_Mutation_p.L414V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	803	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.L808I(1)|p.L803I(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GCCAAGGTTAGAGTTGAATGA	0.443										HNSCC(58;0.16)																												ENST00000373965.2																			2	Substitution - Missense(2)	p.L808I(1)|p.L803I(1)	pancreas(2)	NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237						c.(2428-2430)Cta>Gta		protocadherin-related 15							198.0	177.0	184.0					10																	55782771		2203	4300	6503	SO:0001583	missense	65217				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding	g.chr10:55782771G>C	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2407C>G	10.37:g.55782771G>C	ENSP00000322604:p.Leu803Val	HNSCC(58;0.16)				PCDH15_ENST00000437009.1_Missense_Mutation_p.L732V|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373955.1_Missense_Mutation_p.L803V|PCDH15_ENST00000414778.1_Missense_Mutation_p.L808V|PCDH15_ENST00000395445.1_Missense_Mutation_p.L810V|PCDH15_ENST00000395433.1_Missense_Mutation_p.L781V|PCDH15_ENST00000395430.1_Missense_Mutation_p.L803V|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.L803V|PCDH15_ENST00000409834.1_Missense_Mutation_p.L414V|PCDH15_ENST00000395432.2_Missense_Mutation_p.L766V|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.L803V|PCDH15_ENST00000320301.6_Missense_Mutation_p.L803V	p.L810V	NM_001142771.1|NM_001142772.1	NP_001136243.1|NP_001136244.1	Q96QU1	PCD15_HUMAN			20	2822	-		Melanoma(3;0.117)|Lung SC(717;0.238)	803			Cadherin 7.		A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	c.2428C>G	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	1.296	-0.606256	0.03717	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7	5.67	-0.106	0.13596	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.29945	0.0749	N	0.03294	-0.36	0.09310	N	0.999997	P;B;P;B;P;P;P;P;P;D;B;P;B;B	0.54601	0.484;0.09;0.694;0.022;0.479;0.484;0.484;0.935;0.943;0.967;0.418;0.89;0.3;0.09	P;B;P;B;B;P;P;P;P;P;B;P;B;B	0.58391	0.517;0.148;0.517;0.091;0.26;0.517;0.517;0.734;0.733;0.838;0.206;0.596;0.106;0.189	T	0.14615	-1.0466	9	0.14656	T	0.56	.	2.6737	0.05075	0.1747:0.1024:0.4131:0.3097	.	781;803;803;808;732;766;803;803;810;810;803;808;803;803	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	V	810;808;803;803;414;810;766;803;781;803;803;808;732;803	ENSP00000363076:L810V;ENSP00000410304:L808V;ENSP00000378826:L803V;ENSP00000386693:L414V;ENSP00000378832:L810V;ENSP00000378820:L766V;ENSP00000354950:L803V;ENSP00000378821:L781V;ENSP00000322604:L803V;ENSP00000378818:L803V;ENSP00000412628:L732V;ENSP00000363066:L803V	ENSP00000322604:L803V	L	-	1	2	PCDH15	55452777	0.017000	0.18338	0.287000	0.24848	0.401000	0.30781	0.226000	0.17776	-0.062000	0.13088	-2.724000	0.00131	CTA		0.443	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		28	88	0	0	0	0.005443	0	28	88				
PRSS3	5646	broad.mit.edu	37	9	33797869	33797869	+	Silent	SNP	G	G	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr9:33797869G>A	ENST00000361005.5	+	3	414	c.414G>A	c.(412-414)ctG>ctA	p.L138L	PRSS3_ENST00000429677.3_Silent_p.L74L|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000379405.3_Silent_p.L81L|PRSS3_ENST00000342836.4_Silent_p.L95L	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	138	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			TCAAAGTCCTGGAGGGGAATG	0.552																																						ENST00000361005.5																			0				large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13						c.(412-414)ctG>ctA		protease, serine, 3							177.0	150.0	159.0					9																	33797869		2203	4300	6503	SO:0001819	synonymous_variant	5646				digestion|endothelial cell migration|zymogen activation	extracellular space	calcium ion binding|protein binding|serine-type endopeptidase activity|serine-type peptidase activity	g.chr9:33797869G>A		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.414G>A	9.37:g.33797869G>A						PRSS3_ENST00000342836.4_Silent_p.L95L|PRSS3_ENST00000379405.3_Silent_p.L81L|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000429677.3_Silent_p.L74L	p.L138L	NM_007343.3	NP_031369.2	P35030	TRY3_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.0176)		3	414	+			138			Peptidase S1.		A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Silent	SNP	ENST00000361005.5	37	c.414G>A	CCDS47958.1																																																																																				0.552	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		4	74	0	0	0	0.003080	0	4	74				
SYNE1	23345	broad.mit.edu	37	6	152765611	152765611	+	Missense_Mutation	SNP	G	G	T			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr6:152765611G>T	ENST00000367255.5	-	30	4373	c.3772C>A	c.(3772-3774)Caa>Aaa	p.Q1258K	SYNE1_ENST00000265368.4_Missense_Mutation_p.Q1258K|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q1265K|SYNE1_ENST00000367253.4_Missense_Mutation_p.Q1258K|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q1265K|SYNE1_ENST00000413186.2_Missense_Mutation_p.Q1258K|SYNE1_ENST00000341594.5_Missense_Mutation_p.Q1324K|SYNE1_ENST00000367248.3_Missense_Mutation_p.Q1248K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1258					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCTCAGCTTGTTCCTGGACT	0.368										HNSCC(10;0.0054)																												ENST00000367255.5																			0				NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.(3772-3774)Caa>Aaa		spectrin repeat containing, nuclear envelope 1							120.0	118.0	119.0					6																	152765611		2203	4300	6503	SO:0001583	missense	23345				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152765611G>T	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3772C>A	6.37:g.152765611G>T	ENSP00000356224:p.Gln1258Lys	HNSCC(10;0.0054)				SYNE1_ENST00000265368.4_Missense_Mutation_p.Q1258K|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q1265K|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q1265K|SYNE1_ENST00000413186.2_Missense_Mutation_p.Q1258K|SYNE1_ENST00000341594.5_Missense_Mutation_p.Q1324K|SYNE1_ENST00000367253.4_Missense_Mutation_p.Q1258K|SYNE1_ENST00000367248.3_Missense_Mutation_p.Q1248K	p.Q1258K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	30	4373	-		Ovarian(120;0.0955)	1258					E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	c.3772C>A	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339778	0.41398	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;D;D;D	0.88586	0.49;0.5;0.4;0.49;0.56;-2.27;-2.39;-2.4	5.96	-0.386	0.12466	.	0.570212	0.16882	N	0.195670	T	0.74642	0.3743	L	0.47716	1.5	0.58432	D	0.999998	B;B;B;B;B;B	0.28055	0.055;0.031;0.052;0.199;0.031;0.052	B;B;B;B;B;B	0.29862	0.036;0.034;0.108;0.108;0.034;0.075	T	0.69566	-0.5111	10	0.06365	T	0.9	.	20.4109	0.99016	0.0:0.7567:0.1659:0.0775	.	1241;1258;1248;1258;1258;1265	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	K	1258;1265;1258;1265;1324;1258;1248;1258	ENSP00000356224:Q1258K;ENSP00000396024:Q1265K;ENSP00000265368:Q1258K;ENSP00000390975:Q1265K;ENSP00000341887:Q1324K;ENSP00000356222:Q1258K;ENSP00000356217:Q1248K;ENSP00000414510:Q1258K	ENSP00000265368:Q1258K	Q	-	1	0	SYNE1	152807304	0.326000	0.24669	0.015000	0.15790	0.992000	0.81027	0.812000	0.27211	-0.400000	0.07656	0.655000	0.94253	CAA		0.368	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		29	86	1	0	3.57733e-08	0.001786	6.1025e-08	29	86				
SUPT20H	55578	broad.mit.edu	37	13	37583813	37583813	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr13:37583813A>C	ENST00000350612.6	-	26	2556	c.2336T>G	c.(2335-2337)tTt>tGt	p.F779C	SUPT20H_ENST00000464744.1_3'UTR|SUPT20H_ENST00000356185.3_3'UTR|SUPT20H_ENST00000475892.1_3'UTR|SUPT20H_ENST00000360252.4_3'UTR	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	779					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										CAAGACTCAAAATTTTGGAGT	0.378																																						ENST00000350612.6																			0											c.(2335-2337)tTt>tGt		suppressor of Ty 20 homolog (S. cerevisiae)							155.0	155.0	155.0					13																	37583813		2203	4300	6503	SO:0001583	missense	55578							g.chr13:37583813A>C	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"""p38 interacting protein"", ""transcription factor (p38 interacting protein)"""	613417	"""chromosome 13 open reading frame 19"", ""family with sequence similarity 48, member A"""	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.2336T>G	13.37:g.37583813A>C	ENSP00000218894:p.Phe779Cys					SUPT20H_ENST00000356185.3_3'UTR|SUPT20H_ENST00000475892.1_3'UTR|SUPT20H_ENST00000464744.1_3'UTR|SUPT20H_ENST00000360252.4_3'UTR	p.F779C	NM_001014286.2	NP_001014308.2					26	2556	-								E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	c.2336T>G	CCDS31959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.602|9.602	1.128980|1.128980	0.21041|0.21041	.|.	.|.	ENSG00000102710|ENSG00000102710	ENST00000350612|ENST00000469488	T|.	0.36520|.	1.25|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.117949|0.117949	0.38837|0.38837	N|N	0.001554|0.001554	T|T	0.60715|0.60715	0.2290|0.2290	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	P|.	0.39576|.	0.679|.	B|.	0.40702|.	0.338|.	T|T	0.64449|0.64449	-0.6405|-0.6405	10|7	0.87932|0.87932	D|D	0|0	.|.	9.5838|9.5838	0.39504|0.39504	0.9159:0.0:0.0841:0.0|0.9159:0.0:0.0841:0.0	.|.	779|.	Q8NEM7|.	FA48A_HUMAN|.	C|V	779|322	ENSP00000218894:F779C|.	ENSP00000218894:F779C|ENSP00000419787:F322V	F|F	-|-	2|1	0|0	FAM48A|FAM48A	36481813|36481813	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.657000|0.657000	0.38888|0.38888	1.846000|1.846000	0.39289|0.39289	2.267000|2.267000	0.75376|0.75376	0.383000|0.383000	0.25322|0.25322	TTT|TTT		0.378	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569		58	111	0	0	0	0.003610	0	58	111				
OR2T27	403239	broad.mit.edu	37	1	248813367	248813367	+	Silent	SNP	A	A	T			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr1:248813367A>T	ENST00000344889.3	-	1	818	c.819T>A	c.(817-819)gcT>gcA	p.A273A		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	273						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AGGCAGATACAGCTTTGTCCT	0.522																																						ENST00000344889.3																			0				breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32						c.(817-819)gcT>gcA		olfactory receptor, family 2, subfamily T, member 27							72.0	65.0	67.0					1																	248813367		2180	4275	6455	SO:0001819	synonymous_variant	403239				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248813367A>T		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.819T>A	1.37:g.248813367A>T							p.A273A	NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	818	-	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	273						Silent	SNP	ENST00000344889.3	37	c.819T>A	CCDS31124.1																																																																																				0.522	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		38	33	0	0	0	0.005524	0	38	33				
KRTAP4-11	653240	broad.mit.edu	37	17	39274132	39274132	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr17:39274132G>A	ENST00000391413.2	-	1	474	c.436C>T	c.(436-438)Cgc>Tgc	p.R146C		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	146	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			caagaggggcggcagcagctg	0.657																																						ENST00000391413.2																			0				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(436-438)Cgc>Tgc		keratin associated protein 4-11																																				SO:0001583	missense	653240					keratin filament		g.chr17:39274132G>A	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.436C>T	17.37:g.39274132G>A	ENSP00000375232:p.Arg146Cys						p.R146C	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	474	-		Breast(137;0.000496)	146			27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.436C>T	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	13.24	2.179095	0.38511	.	.	ENSG00000212721	ENST00000391413	T	0.01538	4.79	4.57	-2.76	0.05896	.	0.000000	0.30714	U	0.009027	T	0.02929	0.0087	M	0.82132	2.575	0.09310	N	1	B	0.27997	0.197	B	0.23018	0.043	T	0.31558	-0.9939	10	0.56958	D	0.05	.	11.6836	0.51472	0.0:0.5692:0.3083:0.1226	.	146	Q9BYQ6	KR411_HUMAN	C	146	ENSP00000375232:R146C	ENSP00000375232:R146C	R	-	1	0	KRTAP4-11	36527658	.	.	0.005000	0.12908	0.303000	0.27691	.	.	-0.302000	0.08869	0.609000	0.83330	CGC		0.657	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			4	44	0	0	0	0.000248	0	4	44				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	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		24	74	0	0	0	0.006320	0	24	74				
NOS1	4842	broad.mit.edu	37	12	117725989	117725989	+	Missense_Mutation	SNP	G	G	T			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr12:117725989G>T	ENST00000344089.3	-	6	1758	c.1073C>A	c.(1072-1074)cCa>cAa	p.P358Q	NOS1_ENST00000317775.6_Silent_p.S339S|NOS1_ENST00000338101.4_Silent_p.S339S	NM_001204213.1|NM_001204214.1	NP_001191142.1|NP_001191143.1	Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GATGCATGATGGAGCCCATGC	0.483																																					Esophageal Squamous(162;1748 2599 51982 52956)	ENST00000344089.3																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						c.(1072-1074)cCa>cAa		nitric oxide synthase 1 (neuronal)	L-Citrulline(DB00155)						115.0	112.0	113.0					12																	117725989		1960	4164	6124	SO:0001583	missense	4842				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding	g.chr12:117725989G>T		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000344089.3:c.1073C>A	12.37:g.117725989G>T	ENSP00000339862:p.Pro358Gln					NOS1_ENST00000338101.4_Silent_p.S339S|NOS1_ENST00000317775.6_Silent_p.S339S	p.P358Q	NM_001204213.1|NM_001204214.1	NP_001191142.1|NP_001191143.1	P29475	NOS1_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.0561)	6	1758	-	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		0						Missense_Mutation	SNP	ENST00000344089.3	37	c.1073C>A		.	.	.	.	.	.	.	.	.	.	G	14.71	2.617219	0.46736	.	.	ENSG00000089250	ENST00000344089	T	0.09073	3.02	5.93	3.06	0.35304	.	.	.	.	.	T	0.09555	0.0235	.	.	.	0.25567	N	0.986938	.	.	.	.	.	.	T	0.31861	-0.9928	6	0.87932	D	0	-31.1613	3.2003	0.06647	0.1717:0.2277:0.4837:0.117	.	.	.	.	Q	358	ENSP00000339862:P358Q	ENSP00000339862:P358Q	P	-	2	0	NOS1	116210372	0.008000	0.16893	1.000000	0.80357	0.895000	0.52256	-0.287000	0.08388	0.380000	0.24823	0.563000	0.77884	CCA		0.483	NOS1-201	KNOWN	basic	protein_coding	protein_coding				25	50	1	0	0.000184323	0.007291	0.00030545	25	50				
ASXL1	171023	broad.mit.edu	37	20	31022741	31022741	+	Silent	SNP	G	G	C			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr20:31022741G>C	ENST00000375687.4	+	13	2650	c.2226G>C	c.(2224-2226)ggG>ggC	p.G742G	ASXL1_ENST00000306058.5_Silent_p.G737G	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	742					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TCACAGATGGGCTAGGAGATG	0.577			"""F, N, Mis"""		"""MDS, CMML"""																																	ENST00000375687.4				Rec	yes		20	20q11.1	171023	"""F, N, Mis"""	additional sex combs like 1			L			"""MDS, CMML"""		0				NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						c.(2224-2226)ggG>ggC		additional sex combs like 1 (Drosophila)							55.0	56.0	56.0					20																	31022741		2203	4300	6503	SO:0001819	synonymous_variant	171023				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding	g.chr20:31022741G>C	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.2226G>C	20.37:g.31022741G>C						ASXL1_ENST00000306058.5_Silent_p.G737G	p.G742G	NM_015338.5	NP_056153.2	Q8IXJ9	ASXL1_HUMAN			13	2650	+			742					B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	c.2226G>C	CCDS13201.1																																																																																				0.577	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		16	25	0	0	0	0.004007	0	16	25				
NCOA6	23054	broad.mit.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr20:33345744C>T	ENST00000374796.2	-	8	3377	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_ENST00000359003.2_Silent_p.Q269Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q269Q(15)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537																																						ENST00000374796.2																			15	Substitution - coding silent(15)	p.Q269Q(15)	lung(5)|prostate(4)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)	NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						c.(805-807)caG>caA		nuclear receptor coactivator 6							64.0	52.0	56.0					20																	33345744		2203	4300	6503	SO:0001819	synonymous_variant	23054				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	g.chr20:33345744C>T	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.807G>A	20.37:g.33345744C>T						NCOA6_ENST00000359003.2_Silent_p.Q269Q	p.Q269Q			Q14686	NCOA6_HUMAN			8	3377	-			269			CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.		A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	c.807G>A	CCDS13241.1																																																																																				0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		4	60	0	0	0	0.000248	0	4	60				
FAAH	2166	broad.mit.edu	37	1	46877297	46877298	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr1:46877297_46877298delCT	ENST00000243167.8	+	12	1414_1415	c.1330_1331delCT	c.(1330-1332)ctcfs	p.L444fs		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	444					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	GGCTGGAAAACTCTGGGAACTG	0.594																																						ENST00000243167.8																			0				breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22						c.(1330-1332)cfs		fatty acid amide hydrolase	Propofol(DB00818)|Thiopental(DB00599)																																			SO:0001589	frameshift_variant	2166				fatty acid catabolic process	cytoplasm|cytoskeleton|endomembrane system|integral to membrane|organelle membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|fatty acid amide hydrolase activity	g.chr1:46877297_46877298delCT	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1330_1331delCT	1.37:g.46877299_46877300delCT	ENSP00000243167:p.Leu444fs						p.L444fs	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN			12	1414_1415	+	Acute lymphoblastic leukemia(166;0.155)		444					D3DQ19|Q52M86|Q5TDF8	Frame_Shift_Del	DEL	ENST00000243167.8	37	c.1330_1331delCT	CCDS535.1																																																																																				0.594	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441		16	33						16	33	---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135888244	135888244	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr2:135888244delG	ENST00000264158.8	+	13	1232	c.1189delG	c.(1189-1191)gtafs	p.V397fs	RAB3GAP1_ENST00000442034.1_Frame_Shift_Del_p.V397fs|RAB3GAP1_ENST00000539493.1_Frame_Shift_Del_p.V353fs|RAB3GAP1_ENST00000487003.1_3'UTR	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	397					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		ACACAGAGGTGTAGAGGAGTC	0.338																																						ENST00000264158.8																			0				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32						c.(1189-1191)tafs		RAB3 GTPase activating protein subunit 1 (catalytic)							75.0	78.0	77.0					2																	135888244		2203	4300	6503	SO:0001589	frameshift_variant	22930					centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding	g.chr2:135888244delG	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.1189delG	2.37:g.135888244delG	ENSP00000264158:p.Val397fs					RAB3GAP1_ENST00000487003.1_3'UTR|RAB3GAP1_ENST00000442034.1_Frame_Shift_Del_p.V397fs|RAB3GAP1_ENST00000539493.1_Frame_Shift_Del_p.V353fs	p.V397fs	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.117)	13	1232	+			397					A6H8Z3|C9J837|Q659F5|Q8TBB4	Frame_Shift_Del	DEL	ENST00000264158.8	37	c.1189delG	CCDS33294.1																																																																																				0.338	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		20	57						20	57	---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149518533	149518533	+	RNA	DEL	C	C	-	rs11353848		TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr7:149518533delC	ENST00000378016.2	+	0	12602							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GAGGAGCAGTCCCAGAGCCAG	0.711																																						ENST00000378016.2																			0													SCO-spondin				326,3200		64,198,1501	4.0	5.0	5.0			3.0	1.0	7	dbSNP_120	5	1295,6157		261,773,2692	no	frameshift	SSPO	NM_198455.2		325,971,4193	A1A1,A1R,RR		17.3779,9.2456,14.7659			149518533	1621,9357	1809	3718	5527			23145				cell adhesion	extracellular space	peptidase inhibitor activity	g.chr7:149518533delC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149518533delC										A2VEC9	SSPO_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		0	12602	+	Melanoma(164;0.165)|Ovarian(565;0.177)							Q76B61	RNA	DEL	ENST00000378016.2	37																																																																																						0.711	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				3	3						3	3	---	---	---	---
TRAV9-2	28677	broad.mit.edu	37	14	22409533	22409539	+	RNA	DEL	CTCTCTC	CTCTCTC	-	rs374912343|rs371270332|rs2178778|rs587678559|rs201742006|rs367992314	byFrequency	TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr14:22409533_22409539delCTCTCTC	ENST00000390441.2	+	0	102									T cell receptor alpha variable 9-2																		ctctctctctctctctctTTTTTTTTT	0.415																																						ENST00000390441.2																			0																																																			0							g.chr14:22409533_22409539delCTCTCTC	AE000659		14q11.2	2012-02-07			ENSG00000211793	ENSG00000211793		"""T cell receptors / TRA locus"""	12154	other	T cell receptor gene						8188290	Standard	NG_001332		Approved				OTTHUMG00000170637		14.37:g.22409533_22409539delCTCTCTC														0	102	+									RNA	DEL	ENST00000390441.2	37																																																																																						0.415	TRAV9-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000409885.1	NG_001332		5	8						5	8	---	---	---	---
KRT17P4	339186	broad.mit.edu	37	17	16748911	16748913	+	RNA	DEL	GCT	GCT	-	rs374561720	byFrequency	TCGA-EL-A3GP-01A-11D-A202-08	TCGA-EL-A3GP-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c0897af2-30df-472e-b4d6-343c98c51231	028e9464-4ba4-4319-888b-583c4bbed034	g.chr17:16748911_16748913delGCT	ENST00000578037.1	-	0	593				KRT17P1_ENST00000580363.1_RNA																							CGCCCTCAAAGCTGCTGCTGCCA	0.65														2545	0.508187	0.5053	0.536	5008	,	,		12311	0.4067		0.5686	False		,,,				2504	0.5348					ENST00000580363.1																			0				lung(4)	4																																														0							g.chr17:16748911_16748913delGCT																													17.37:g.16748917_16748919delGCT														0	282_284	-									RNA	DEL	ENST00000578037.1	37																																																																																						0.650	AC022596.2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000444295.1			4	3						4	3	---	---	---	---
