#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
LIMD1	8994	broad.mit.edu	37	3	45636405	45636405	+	Missense_Mutation	SNP	A	A	T			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr3:45636405A>T	ENST00000273317.4	+	1	55	c.34A>T	c.(34-36)Agt>Tgt	p.S12C	LIMD1_ENST00000465039.1_Intron|AC099539.1_ENST00000516118.1_RNA|LIMD1_ENST00000440097.1_Missense_Mutation_p.S12C	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	12					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		CCTGGAGGCCAGTAAATTCAT	0.557																																						uc003coq.3																			0				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10						c.(34-36)Agt>Tgt		Homo sapiens LIM domains containing 1 (LIMD1), mRNA.							75.0	78.0	77.0					3																	45636405		2203	4300	6503	SO:0001583	missense	8994				cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	RNA-induced silencing complex|cytoplasmic mRNA processing body|nucleus	protein binding|zinc ion binding	g.chr3:45636405A>T	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.34A>T	3.37:g.45636405A>T	ENSP00000273317:p.Ser12Cys		Somatic					p.S12C	NM_014240	NP_055055	WXS	Illumina GAIIx	Phase_I	Q9UGP4	LIMD1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)	0	83	+			12					Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	37	c.34A>T	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.498507	0.85069	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.73575	-0.76;-0.52	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.77123	0.4084	N	0.24115	0.695	0.49582	D	0.999808	D	0.89917	1.0	D	0.85130	0.997	T	0.80348	-0.1420	10	0.87932	D	0	.	13.2074	0.59805	1.0:0.0:0.0:0.0	.	12	Q9UGP4	LIMD1_HUMAN	C	12	ENSP00000394537:S12C;ENSP00000273317:S12C	ENSP00000273317:S12C	S	+	1	0	LIMD1	45611409	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.875000	0.92372	1.520000	0.48965	0.379000	0.24179	AGT		0.557	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		11	30	0	0	0	1	0	11	30				
RPL36A	6173	broad.mit.edu	37	X	100650727	100650727	+	Silent	SNP	C	C	A			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chrX:100650727C>A	ENST00000553110.3	+	5	396	c.312C>A	c.(310-312)atC>atA	p.I104I	RPL36A-HNRNPH2_ENST00000409170.3_Intron|RPL36A_ENST00000427805.2_Silent_p.I140I|RPL36A_ENST00000471855.1_Silent_p.I23I			P83881	RL36A_HUMAN	ribosomal protein L36a	104					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			liver(4)|lung(1)|prostate(1)	6						GCCAAGTGATCCAGTTCTAAG	0.343																																						uc004ehk.3																			0											c.(310-312)atC>atA		Homo sapiens ribosomal protein L36a (RPL36A), transcript variant 1, mRNA.							157.0	138.0	144.0					X																	100650727		2203	4300	6503	SO:0001819	synonymous_variant	100529097							g.chrX:100650727C>A	BC001781	CCDS14483.1, CCDS14483.2	Xq22.1	2011-04-06	2002-01-15	2002-01-18	ENSG00000241343	ENSG00000241343		"""L ribosomal proteins"""	10359	protein-coding gene	gene with protein product		300902	"""ribosomal protein L44"""	RPL44		3461443	Standard	NM_021029		Approved	L36A		P83881	OTTHUMG00000022027	ENST00000553110.3:c.312C>A	X.37:g.100650727C>A			Somatic				RPL36A-HNRNPH2_uc022cag.1_Intron|RPL36A-HNRNPH2_uc022cah.1_Intron	p.I104I	NM_021029	NP_066357	WXS	Illumina GAIIx	Phase_I					4	466	+								P09896|P10661|Q08ES5|Q5J9I6	Silent	SNP	ENST00000553110.3	37	c.312C>A																																																																																					0.343	RPL36A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021029		8	22	0	0	0	1	0	8	22				
ZMYND8	23613	broad.mit.edu	37	20	45891129	45891129	+	Silent	SNP	G	G	A			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr20:45891129G>A	ENST00000311275.7	-	12	1717	c.1464C>T	c.(1462-1464)tcC>tcT	p.S488S	ZMYND8_ENST00000471951.2_Silent_p.S508S|ZMYND8_ENST00000372023.3_Silent_p.S483S|ZMYND8_ENST00000540497.1_Intron|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000536340.1_Silent_p.S515S|ZMYND8_ENST00000458360.2_Silent_p.S483S|ZMYND8_ENST00000262975.4_Silent_p.S488S|ZMYND8_ENST00000461685.1_Silent_p.S508S|ZMYND8_ENST00000396281.4_Silent_p.S488S|ZMYND8_ENST00000446994.2_Silent_p.S425S|ZMYND8_ENST00000360911.3_Silent_p.S483S|ZMYND8_ENST00000352431.2_Silent_p.S508S|ZMYND8_ENST00000355972.4_Silent_p.S488S	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	488					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			TTGGGCTGCCGGATAAACTCC	0.488																																						uc010zxy.1																			0				NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62						c.(1543-1545)tcC>tcT		Homo sapiens zinc finger, MYND-type containing 8 (ZMYND8), transcript variant 1, mRNA.							151.0	138.0	142.0					20																	45891129		2203	4300	6503	SO:0001819	synonymous_variant	23613						protein binding|zinc ion binding	g.chr20:45891129G>A	U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"""Zinc fingers, MYND-type"", ""Zinc fingers, PHD-type"""	9397	protein-coding gene	gene with protein product		615713	"""protein kinase C binding protein 1"""	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.1464C>T	20.37:g.45891129G>A			Somatic				ZMYND8_uc010ghq.1_Silent_p.S165S|ZMYND8_uc010ghr.1_Silent_p.S463S|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Silent_p.S488S|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Silent_p.S240S|ZMYND8_uc002xsx.1_Silent_p.S240S|ZMYND8_uc002xsy.1_Silent_p.S463S|ZMYND8_uc002xsz.1_Silent_p.S425S|ZMYND8_uc002xta.1_Silent_p.S488S|ZMYND8_uc002xtb.1_Silent_p.S508S|ZMYND8_uc002xss.2_Silent_p.S488S|ZMYND8_uc010zxz.1_Silent_p.S483S|ZMYND8_uc002xtc.1_Silent_p.S508S|ZMYND8_uc002xtd.1_Silent_p.S483S|ZMYND8_uc002xte.1_Silent_p.S488S|ZMYND8_uc010zya.1_Silent_p.S488S|ZMYND8_uc002xtf.1_Silent_p.S508S|ZMYND8_uc002xtg.3_Silent_p.S482S|ZMYND8_uc010ghs.2_Silent_p.S482S	p.S515S	NM_183047	NP_898868	WXS	Illumina GAIIx	Phase_I	Q9ULU4	PKCB1_HUMAN	Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)		11	1627	-			488					B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Silent	SNP	ENST00000311275.7	37	c.1545C>T		.	.	.	.	.	.	.	.	.	.	G	4.955	0.177490	0.09443	.	.	ENSG00000101040	ENST00000467200	.	.	.	5.34	-10.7	0.00240	.	.	.	.	.	T	0.57519	0.2059	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69146	-0.5222	4	.	.	.	-19.7031	13.7368	0.62821	0.7224:0.0:0.1564:0.1212	.	.	.	.	W	415	.	.	R	-	1	2	ZMYND8	45324536	0.000000	0.05858	0.272000	0.24630	0.564000	0.35744	-3.168000	0.00574	-2.275000	0.00679	-0.977000	0.02584	CGG		0.488	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		4	51	0	0	0	1	0	4	51				
PLEKHN1	84069	broad.mit.edu	37	1	907717	907717	+	Silent	SNP	C	C	T	rs371553226		TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr1:907717C>T	ENST00000379409.2	+	9	1101	c.1071C>T	c.(1069-1071)taC>taT	p.Y357Y	PLEKHN1_ENST00000379407.3_Silent_p.Y317Y|PLEKHN1_ENST00000379410.3_Silent_p.Y305Y			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	357	PH 2.									central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		ACGAGGACTACGGTCACTGGC	0.687																																						uc001ace.3																			0				central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9						c.(1069-1071)taC>taT		Homo sapiens pleckstrin homology domain containing, family N member 1 (PLEKHN1), transcript variant 1, mRNA.		C	,	1,4403	2.1+/-5.4	0,1,2201	30.0	29.0	30.0		951,915	0.2	0.4	1		30	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous	PLEKHN1	NM_001160184.1,NM_032129.2	,	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	,	317/577,305/612	907717	1,12993	2202	4295	6497	SO:0001819	synonymous_variant	84069							g.chr1:907717C>T	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"""Pleckstrin homology (PH) domain containing"""	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.1071C>T	1.37:g.907717C>T			Somatic				PLEKHN1_uc001acd.3_Silent_p.Y305Y|PLEKHN1_uc001acf.3_Silent_p.Y317Y	p.Y357Y	NM_032129	NP_115505	WXS	Illumina GAIIx	Phase_I	Q494U1	PKHN1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)	8	1106	+	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)	357			PH 2.		Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	37	c.1071C>T																																																																																					0.687	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129		3	47	0	0	0	1	0	3	47				
TSSK4	283629	broad.mit.edu	37	14	24676436	24676436	+	Silent	SNP	T	T	C			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr14:24676436T>C	ENST00000287913.6	+	3	693	c.525T>C	c.(523-525)tcT>tcC	p.S175S	CHMP4A_ENST00000542700.2_5'Flank|TSSK4_ENST00000556621.1_Silent_p.S99S|AL136419.6_ENST00000565988.1_RNA|TSSK4_ENST00000339917.5_Silent_p.S185S|TM9SF1_ENST00000530611.1_Intron|TSSK4_ENST00000428351.2_Intron|TM9SF1_ENST00000556387.1_Intron			Q6SA08	TSSK4_HUMAN	testis-specific serine kinase 4	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|positive regulation of CREB transcription factor activity (GO:0032793)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8				GBM - Glioblastoma multiforme(265;0.018)		TGGTGCCTTCTAACCAGCCTG	0.502																																						uc001wnh.3																			0				cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8						c.(553-555)tcT>tcC		Homo sapiens testis-specific serine kinase 4 (TSSK4), transcript variant 1, mRNA.							208.0	176.0	187.0					14																	24676436		2203	4300	6503	SO:0001819	synonymous_variant	283629				cell differentiation|multicellular organismal development|positive regulation of CREB transcription factor activity|spermatogenesis		ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity	g.chr14:24676436T>C	AF542390	CCDS9618.1, CCDS53890.1	14q11.2	2006-03-31	2005-03-10	2005-03-12	ENSG00000139908	ENSG00000139908			19825	protein-coding gene	gene with protein product	"""chromosome 14 open reading frame 20"""	610711	"""serine/threonine kinase 22E"""	C14orf20, STK22E			Standard	NM_174944		Approved		uc001wnh.3	Q6SA08	OTTHUMG00000029323	ENST00000287913.6:c.525T>C	14.37:g.24676436T>C			Somatic				TM9SF1_uc010tob.1_Intron|TSSK4_uc001wne.3_Silent_p.S99S|TSSK4_uc001wnf.3_Silent_p.S105S|TSSK4_uc001wng.3_Silent_p.S175S	p.S185S	NM_001184739	NP_001171668	WXS	Illumina GAIIx	Phase_I	Q6SA08	TSSK4_HUMAN		GBM - Glioblastoma multiforme(265;0.018)	2	759	+			175			Protein kinase.		Q2TA60|Q6ZNM2	Silent	SNP	ENST00000287913.6	37	c.555T>C	CCDS9618.1																																																																																				0.502	TSSK4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000073139.3	NM_174944		8	134	0	0	0	1	0	8	134				
FBXL20	84961	broad.mit.edu	37	17	37431233	37431233	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr17:37431233G>A	ENST00000264658.6	-	10	1077	c.817C>T	c.(817-819)Cca>Tca	p.P273S	FBXL20_ENST00000577399.1_Missense_Mutation_p.P275S|FBXL20_ENST00000394294.3_Missense_Mutation_p.P241S|FBXL20_ENST00000583610.1_Missense_Mutation_p.P273S	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	273					behavioral fear response (GO:0001662)	cytoplasm (GO:0005737)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22			LUAD - Lung adenocarcinoma(14;0.146)			CTAAGCCGTGGGCAGTTCTGA	0.408																																						uc002hrt.3																			0				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22						c.(817-819)Cca>Tca		Homo sapiens F-box and leucine-rich repeat protein 20 (FBXL20), transcript variant 1, mRNA.							122.0	113.0	116.0					17																	37431233		2203	4300	6503	SO:0001583	missense	84961					cytoplasm		g.chr17:37431233G>A	BC007557	CCDS32640.1, CCDS54116.1	17q21.2	2011-06-09				ENSG00000108306		"""F-boxes / Leucine-rich repeats"""	24679	protein-coding gene	gene with protein product		609086				12477932	Standard	NM_032875		Approved	MGC15482, Fbl2, Fbl20	uc002hrt.3	Q96IG2		ENST00000264658.6:c.817C>T	17.37:g.37431233G>A	ENSP00000264658:p.Pro273Ser		Somatic				FBXL20_uc010cvu.3_Missense_Mutation_p.P241S	p.P273S	NM_032875	NP_116264	WXS	Illumina GAIIx	Phase_I	Q96IG2	FXL20_HUMAN	LUAD - Lung adenocarcinoma(14;0.146)		9	1071	-			273					A8K729|Q38J52	Missense_Mutation	SNP	ENST00000264658.6	37	c.817C>T	CCDS32640.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413695	0.62511	.	.	ENSG00000108306	ENST00000264658;ENST00000394294	T;T	0.51817	0.69;0.69	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.48021	0.1477	L	0.52759	1.655	0.80722	D	1	B;B	0.26935	0.164;0.049	B;B	0.29077	0.098;0.04	T	0.30880	-0.9963	10	0.33141	T	0.24	.	19.9446	0.97177	0.0:0.0:1.0:0.0	.	241;273	Q96IG2-2;Q96IG2	.;FXL20_HUMAN	S	273;241	ENSP00000264658:P273S;ENSP00000377832:P241S	ENSP00000264658:P273S	P	-	1	0	FBXL20	34684759	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.431000	0.80335	2.814000	0.96858	0.591000	0.81541	CCA		0.408	FBXL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444315.2	NM_032875		20	49	0	0	0	1	0	20	49				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	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)	uc003vwc.4	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(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(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		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	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		Somatic					p.V600E	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	P15056	BRAF_HUMAN			14	1860	-	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		16	20	0	0	0	1	0	16	20				
TRAIP	10293	broad.mit.edu	37	3	49866894	49866894	+	Silent	SNP	C	C	T	rs146306196	byFrequency	TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr3:49866894C>T	ENST00000331456.2	-	14	1397	c.1284G>A	c.(1282-1284)caG>caA	p.Q428Q	TRAIP_ENST00000469027.1_Silent_p.Q273Q	NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	428	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGGATACAGGCTGGATGAATT	0.577																																						uc003cxs.1																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						c.(1282-1284)caG>caA		Homo sapiens TRAF interacting protein (TRAIP), mRNA.							61.0	63.0	63.0					3																	49866894		2203	4300	6503	SO:0001819	synonymous_variant	10293				cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding	g.chr3:49866894C>T	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"""RING-type (C3HC4) zinc fingers"""	30764	protein-coding gene	gene with protein product	"""ring finger protein 206"""	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1284G>A	3.37:g.49866894C>T			Somatic				TRAIP_uc010hla.1_Silent_p.Q329Q	p.Q428Q	NM_005879	NP_005870	WXS	Illumina GAIIx	Phase_I	Q9BWF2	TRAIP_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)	13	1390	-			428			Interaction with CYLD.		B5BU84|B5BUL3|O00467	Silent	SNP	ENST00000331456.2	37	c.1284G>A	CCDS2806.1																																																																																				0.577	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879		22	35	0	0	0	1	0	22	35				
TCF7L2	6934	broad.mit.edu	37	10	114911638	114911638	+	Silent	SNP	C	C	A			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr10:114911638C>A	ENST00000355995.4	+	10	1663	c.1156C>A	c.(1156-1158)Cgg>Agg	p.R386R	TCF7L2_ENST00000542695.1_Silent_p.R102R|TCF7L2_ENST00000369386.1_Silent_p.R29R|TCF7L2_ENST00000543371.1_Silent_p.R386R|TCF7L2_ENST00000536810.1_Silent_p.R386R|TCF7L2_ENST00000352065.5_Silent_p.R363R|TCF7L2_ENST00000545257.1_Silent_p.R386R|TCF7L2_ENST00000369397.4_Silent_p.R363R|TCF7L2_ENST00000534894.1_Silent_p.R386R|TCF7L2_ENST00000538897.1_Silent_p.R386R|TCF7L2_ENST00000355717.4_Silent_p.R410R|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000369389.1_Silent_p.R97R			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	386	Mediates interaction with MAD2L2.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GATCCTTGGGCGGAGGGTAGG	0.547			T	VTI1A	colorectal																																	uc021pyi.1				Dom	yes		10	10q25.3	6934	T	transcription factor 7-like 2			E	VTI1A		colorectal	VTI1A/TCF7L2(8)	0		p.L386L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41						c.(1156-1158)Cgg>Agg		Homo sapiens transcription factor 7-like 2 (T-cell specific, HMG-box) (TCF7L2), transcript variant 2, mRNA.							57.0	55.0	56.0					10																	114911638		2203	4300	6503	SO:0001819	synonymous_variant	6934				anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	PML body|beta-catenin-TCF7L2 complex|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding	g.chr10:114911638C>A	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1156C>A	10.37:g.114911638C>A			Somatic				TCF7L2_uc001lah.3_Silent_p.R368R|TCF7L2_uc010qro.2_Silent_p.R363R|TCF7L2_uc001lae.4_Silent_p.R386R|TCF7L2_uc010qrm.2_Silent_p.R386R|TCF7L2_uc010qrn.2_Silent_p.R329R|TCF7L2_uc021pyg.1_Silent_p.R102R|TCF7L2_uc021pyh.1_Silent_p.R368R|TCF7L2_uc021pyj.1_Silent_p.R386R|TCF7L2_uc021pyk.1_Silent_p.R368R|TCF7L2_uc021pyl.1_Silent_p.R368R|TCF7L2_uc010qrp.2_Silent_p.R363R|TCF7L2_uc021pym.1_Silent_p.R359R|TCF7L2_uc021pyn.1_Silent_p.R391R|TCF7L2_uc021pyo.1_Silent_p.R391R|TCF7L2_uc021pyp.1_Silent_p.R382R|TCF7L2_uc010qrq.2_Silent_p.R359R|TCF7L2_uc001lac.4_Silent_p.R363R|TCF7L2_uc010qrk.2_Silent_p.R363R|TCF7L2_uc001lad.4_Silent_p.R359R|TCF7L2_uc001lag.4_Silent_p.R410R|TCF7L2_uc001laf.4_Silent_p.R363R|TCF7L2_uc010qrl.2_Silent_p.R363R|TCF7L2_uc010qrr.2_Silent_p.R301R|TCF7L2_uc010qrs.2_Silent_p.R257R|TCF7L2_uc010qrt.2_Silent_p.R257R|TCF7L2_uc010qru.2_Silent_p.R285R|TCF7L2_uc010qrv.2_Silent_p.R203R|TCF7L2_uc010qrw.2_Silent_p.R90R|TCF7L2_uc010qrx.2_Silent_p.R243R|Mir_652_uc021pyq.1_5'Flank	p.R386R	NM_030756	NP_110383	WXS	Illumina GAIIx	Phase_I	Q9NQB0	TF7L2_HUMAN		Epithelial(162;0.00554)|all cancers(201;0.02)	9	1663	+		Breast(234;0.058)|Colorectal(252;0.0615)	386			Mediates interaction with MAD2L2.		B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Silent	SNP	ENST00000355995.4	37	c.1156C>A																																																																																					0.547	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		3	58	0	0	0	1	0	3	58				
COL11A2	1302	broad.mit.edu	37	6	33139342	33139342	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr6:33139342C>T	ENST00000374708.4	-	41	3160	c.2902G>A	c.(2902-2904)Ggc>Agc	p.G968S	COL11A2_ENST00000341947.2_Missense_Mutation_p.G1054S|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Missense_Mutation_p.G1007S|COL11A2_ENST00000374714.1_Missense_Mutation_p.G1028S|COL11A2_ENST00000395197.1_Missense_Mutation_p.G994S|COL11A2_ENST00000361917.1_Missense_Mutation_p.G947S|COL11A2_ENST00000374712.1_Missense_Mutation_p.G973S|COL11A2_ENST00000357486.1_Missense_Mutation_p.G1033S	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1054	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CCAATGGGGCCCTTCTCACCC	0.617																																					Melanoma(1;90 116 3946 5341 17093)	uc003ocx.1																			0				biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						c.(3160-3162)Ggc>Agc		Homo sapiens collagen, type XI, alpha 2 (COL11A2), transcript variant 1, mRNA.							28.0	30.0	30.0					6																	33139342		2203	4300	6503	SO:0001583	missense	1302				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging	g.chr6:33139342C>T	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.2902G>A	6.37:g.33139342C>T	ENSP00000363840:p.Gly968Ser		Somatic				COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Missense_Mutation_p.G968S|COL11A2_uc003ocz.1_Missense_Mutation_p.G947S	p.G1054S	NM_080680	NP_542411	WXS	Illumina GAIIx	Phase_I	P13942	COBA2_HUMAN			42	3388	-			1054			Triple-helical region.		A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	37	c.3160G>A	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.403879	0.42613	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.99607	-6.27;-4.82;-6.27;-6.27;-6.27;-6.27;-6.27;-6.27	3.79	3.79	0.43588	.	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.98314	4.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.96868	0.9637	10	0.87932	D	0	.	13.1962	0.59740	0.0:1.0:0.0:0.0	.	947;968;1054	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	S	968;1054;1033;1028;1007;994;973;947	ENSP00000363840:G968S;ENSP00000339915:G1054S;ENSP00000350079:G1033S;ENSP00000363846:G1028S;ENSP00000363845:G1007S;ENSP00000378623:G994S;ENSP00000363844:G973S;ENSP00000355123:G947S	ENSP00000339915:G1054S	G	-	1	0	COL11A2	33247320	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	7.597000	0.82733	1.945000	0.56424	0.297000	0.19635	GGC		0.617	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			7	14	0	0	0	1	0	7	14				
DNAH2	146754	broad.mit.edu	37	17	7722542	7722542	+	Missense_Mutation	SNP	G	G	A	rs373672740		TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr17:7722542G>A	ENST00000572933.1	+	72	12291	c.10831G>A	c.(10831-10833)Gcc>Acc	p.A3611T	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3611T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3611					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A3611T(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CCGCCCATGCGCCCAGCGGGC	0.607																																						uc002giu.1																			1	Substitution - Missense(1)	p.A3611T(2)	large_intestine(1)	NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189						c.(10831-10833)Gcc>Acc		Homo sapiens dynein, axonemal, heavy chain 2 (DNAH2), mRNA.		G	THR/ALA	0,4406		0,0,2203	71.0	58.0	63.0		10831	4.0	0.9	17		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH2	NM_020877.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	3611/4428	7722542	1,13005	2203	4300	6503	SO:0001583	missense	146754				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr17:7722542G>A	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10831G>A	17.37:g.7722542G>A	ENSP00000458355:p.Ala3611Thr		Somatic				DNAH2_uc010cnm.1_Missense_Mutation_p.A549T	p.A3611T	NM_020877	NP_065928	WXS	Illumina GAIIx	Phase_I	Q9P225	DYH2_HUMAN			70	10845	+		all_cancers(10;4.66e-07)|Prostate(122;0.081)	3611					A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	c.10831G>A	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591222	0.66219	0.0	1.16E-4	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.62232	0.04	4.02	4.02	0.46733	.	0.000000	0.64402	D	0.000001	D	0.87414	0.6171	H	0.99545	4.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.948	D	0.92179	0.5750	10	0.87932	D	0	.	13.5202	0.61563	0.0:0.0:1.0:0.0	.	3572;3611	Q9P225-2;Q9P225	.;DYH2_HUMAN	T	3572;3611	ENSP00000373825:A3611T	ENSP00000353818:A3572T	A	+	1	0	DNAH2	7663267	1.000000	0.71417	0.919000	0.36401	0.159000	0.22180	9.017000	0.93651	2.228000	0.72767	0.561000	0.74099	GCC		0.607	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		5	102	0	0	0	1	0	5	102				
PCLO	27445	broad.mit.edu	37	7	82584499	82584499	+	Missense_Mutation	SNP	T	T	C			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr7:82584499T>C	ENST00000333891.9	-	5	6107	c.5770A>G	c.(5770-5772)Aaa>Gaa	p.K1924E	PCLO_ENST00000423517.2_Missense_Mutation_p.K1924E	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGTGTGTTTTATGCATCATT	0.358																																						uc003uhx.2																			0				breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						c.(5770-5772)Aaa>Gaa		Homo sapiens piccolo (presynaptic cytomatrix protein) (PCLO), transcript variant 1, mRNA.							57.0	54.0	55.0					7																	82584499		1870	4096	5966	SO:0001583	missense	27445				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity	g.chr7:82584499T>C	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5770A>G	7.37:g.82584499T>C	ENSP00000334319:p.Lys1924Glu		Somatic				PCLO_uc003uhv.2_Missense_Mutation_p.K1924E	p.K1924E	NM_033026	NP_149015	WXS	Illumina GAIIx	Phase_I	Q9Y6V0	PCLO_HUMAN			4	6059	-			1855						Missense_Mutation	SNP	ENST00000333891.9	37	c.5770A>G	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	12.16	1.854446	0.32791	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.34275	1.37;1.39	5.38	5.38	0.77491	.	.	.	.	.	T	0.50154	0.1599	L	0.54323	1.7	0.80722	D	1	D;D	0.59767	0.972;0.986	P;P	0.56398	0.797;0.797	T	0.53585	-0.8418	9	0.87932	D	0	.	15.3967	0.74801	0.0:0.0:0.0:1.0	.	1924;1924	Q9Y6V0-5;Q9Y6V0-6	.;.	E	1855;1924;1924	ENSP00000334319:K1924E;ENSP00000388393:K1924E	ENSP00000334319:K1924E	K	-	1	0	PCLO	82422435	1.000000	0.71417	0.959000	0.39883	0.991000	0.79684	5.986000	0.70563	2.036000	0.60181	0.533000	0.62120	AAA		0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		4	4	0	0	0	1	0	4	4				
TULP4	56995	broad.mit.edu	37	6	158923511	158923511	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr6:158923511G>A	ENST00000367097.3	+	13	4173	c.2816G>A	c.(2815-2817)aGc>aAc	p.S939N	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	939					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CAGCCCTGCAGCAGTGCCACC	0.672																																						uc003qrf.3																			0				endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						c.(2815-2817)aGc>aAc		Homo sapiens tubby like protein 4 (TULP4), transcript variant 1, mRNA.							62.0	64.0	63.0					6																	158923511		2203	4300	6503	SO:0001583	missense	56995				intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity	g.chr6:158923511G>A		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.2816G>A	6.37:g.158923511G>A	ENSP00000356064:p.Ser939Asn		Somatic				TULP4_uc003qrg.3_Intron	p.S939N	NM_020245	NP_064630	WXS	Illumina GAIIx	Phase_I	Q9NRJ4	TULP4_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)	12	4173	+		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)	939					Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	c.2816G>A	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.180238	0.38511	.	.	ENSG00000130338	ENST00000367097	T	0.61742	0.08	4.49	3.61	0.41365	.	0.367408	0.31092	N	0.008266	T	0.34193	0.0889	L	0.38175	1.15	0.80722	D	1	B	0.19200	0.034	B	0.20577	0.03	T	0.37407	-0.9707	10	0.87932	D	0	-18.6353	14.7456	0.69488	0.0:0.8515:0.1484:0.0	.	939	Q9NRJ4	TULP4_HUMAN	N	939	ENSP00000356064:S939N	ENSP00000356064:S939N	S	+	2	0	TULP4	158843499	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.598000	0.46223	0.997000	0.38969	-0.270000	0.10280	AGC		0.672	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		4	128	0	0	0	1	0	4	128				
SPAG9	9043	broad.mit.edu	37	17	49067105	49067105	+	Nonsense_Mutation	SNP	C	C	A			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr17:49067105C>A	ENST00000262013.7	-	21	2954	c.2746G>T	c.(2746-2748)Gag>Tag	p.E916*	SPAG9_ENST00000357122.4_Nonsense_Mutation_p.E902*|SPAG9_ENST00000510283.1_Nonsense_Mutation_p.E759*|SPAG9_ENST00000505279.1_Nonsense_Mutation_p.E906*	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	916					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			AAGACATGCTCTGTGTAGACG	0.478																																						uc002itc.3																			0				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						c.(2746-2748)Gag>Tag		Homo sapiens sperm associated antigen 9 (SPAG9), transcript variant 1, mRNA.							158.0	128.0	138.0					17																	49067105		2203	4300	6503	SO:0001587	stop_gained	9043				positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm		g.chr17:49067105C>A	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2746G>T	17.37:g.49067105C>A	ENSP00000262013:p.Glu916*		Somatic				SPAG9_uc002itd.3_Nonsense_Mutation_p.E906*|SPAG9_uc002itb.3_Nonsense_Mutation_p.E902*|SPAG9_uc002itf.3_Nonsense_Mutation_p.E737*|SPAG9_uc002ita.3_Nonsense_Mutation_p.E759*|SPAG9_uc002ite.3_Nonsense_Mutation_p.E746*	p.E916*	NM_001130528	NP_001124000	WXS	Illumina GAIIx	Phase_I	O60271	JIP4_HUMAN	BRCA - Breast invasive adenocarcinoma(22;4.24e-07)		20	2955	-			916					A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Nonsense_Mutation	SNP	ENST00000262013.7	37	c.2746G>T	CCDS45740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	41|41	9.114315|9.114315	0.99069|0.99069	.|.	.|.	ENSG00000008294|ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000357791;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445|ENST00000513906	.|.	.|.	.|.	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	0.047130|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80053	.|0.4553	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77760	.|-0.2467	.|3	0.39692|.	T|.	0.17|.	-19.4506|-19.4506	19.9831|19.9831	0.97336|0.97336	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|H	916;673;663;453;759;906;902;514|159	.|.	ENSP00000262013:E916X|.	E|Q	-|-	1|3	0|2	SPAG9|SPAG9	46422104|46422104	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.131000|7.131000	0.77243|0.77243	2.728000|2.728000	0.93425|0.93425	0.650000|0.650000	0.86243|0.86243	GAG|CAG		0.478	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		4	36	0	0	0	1	0	4	36				
KIAA1211	57482	broad.mit.edu	37	4	57180750	57180752	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr4:57180750_57180752delAGG	ENST00000504228.1	+	6	1187_1189	c.1082_1084delAGG	c.(1081-1086)caggag>cag	p.E365del	KIAA1211_ENST00000541073.1_In_Frame_Del_p.E358del|KIAA1211_ENST00000264229.6_In_Frame_Del_p.E365del			Q6ZU35	K1211_HUMAN	KIAA1211	365	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					ctcaaaaggcaggaggaggagga	0.704																																						uc003hbk.2																			0				endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65						c.(1081-1086)caggag>cag		Homo sapiens KIAA1211 (KIAA1211), mRNA.				29,3525		9,11,1757						3.3	0.0			8	44,7146		13,18,3564	no	coding	KIAA1211	NM_020722.1		22,29,5321	A1A1,A1R,RR		0.612,0.816,0.6794				73,10671				SO:0001651	inframe_deletion	57482							g.chr4:57180750_57180752delAGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1082_1084delAGG	4.37:g.57180759_57180761delAGG	ENSP00000423366:p.Glu365del		Somatic				KIAA1211_uc010iha.2_In_Frame_Del_p.E358del|KIAA1211_uc011bzz.1_In_Frame_Del_p.E275del|KIAA1211_uc003hbm.1_In_Frame_Del_p.E251del	p.E365del	NM_020722	NP_065773	WXS	Illumina GAIIx	Phase_I	Q6ZU35	K1211_HUMAN			7	1473_1475	+	Glioma(25;0.08)|all_neural(26;0.101)		365			Glu-rich.		Q9NTE2|Q9NTP8|Q9ULK9	In_Frame_Del	DEL	ENST00000504228.1	37	c.1082_1084delAGG	CCDS43230.1																																																																																				0.704	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		2	4						2	4	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67257831	67257831	+	Frame_Shift_Del	DEL	A	A	-			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr17:67257831delA	ENST00000392676.3	-	25	3438	c.3374delT	c.(3373-3375)ttcfs	p.F1125fs	ABCA5_ENST00000588877.1_Frame_Shift_Del_p.F1125fs|ABCA5_ENST00000392677.2_Frame_Shift_Del_p.F1126fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	1125					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CTTAAAGGTGAAAGAAGCAAT	0.264																																						uc002jif.2																			0				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54						c.(3373-3375)ttcfs		Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 5 (ABCA5), transcript variant 1, mRNA.							19.0	19.0	19.0					17																	67257831		2192	4238	6430	SO:0001589	frameshift_variant	23461				cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity	g.chr17:67257831delA	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.3374delT	17.37:g.67257831delA	ENSP00000376443:p.Phe1125fs		Somatic				ABCA5_uc002jib.2_Frame_Shift_Del_p.F91fs|ABCA5_uc002jic.2_Frame_Shift_Del_p.F348fs|ABCA5_uc002jid.2_Frame_Shift_Del_p.F42fs|ABCA5_uc002jie.2_Non-coding_Transcript|ABCA5_uc002jig.2_Frame_Shift_Del_p.F1125fs	p.F1125fs	NM_018672	NP_758424	WXS	Illumina GAIIx	Phase_I	Q8WWZ7	ABCA5_HUMAN			23	4592	-	Breast(10;3.72e-11)		1125					Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	37	c.3374delT	CCDS11685.1																																																																																				0.264	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		2	4						2	4	---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79409285	79409285	+	Frame_Shift_Del	DEL	G	G	-			TCGA-ET-A3DP-01A-11D-A21A-08	TCGA-ET-A3DP-11A-22D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1d8a9ef-371b-4aff-a116-6e38a084f140	43940b7d-7b62-4832-9622-16fd0730a98e	g.chr17:79409285delG	ENST00000307745.7	+	9	910	c.910delG	c.(910-912)gggfs	p.G305fs																								CAGCTGTGCAGGGGGCATGCT	0.726																																						uc002kaf.2																			0				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(5)|urinary_tract(1)	26						c.(724-726)gggfs		Homo sapiens BAH domain and coiled-coil containing 1 (BAHCC1), mRNA.							3.0	4.0	3.0					17																	79409285		1715	3686	5401	SO:0001589	frameshift_variant	57597						DNA binding	g.chr17:79409285delG																												ENST00000307745.7:c.910delG	17.37:g.79409285delG	ENSP00000303486:p.Gly305fs		Somatic				BAHCC1_uc002kae.2_5'Flank	p.G242fs	NM_001080519	NP_001073988	WXS	Illumina GAIIx	Phase_I	Q9P281	BAHC1_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)		3	724	+	all_neural(118;0.0804)|Melanoma(429;0.242)		304						Frame_Shift_Del	DEL	ENST00000307745.7	37	c.724delG																																																																																					0.726	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				2	4						2	4	---	---	---	---
