#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_BAM_File	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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
LRRN2	10446	genome.wustl.edu	37	1	204588352	204588352	+	Silent	SNP	G	G	A			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr1:204588352G>A	ENST00000367175.1	-	1	2981	c.769C>T	c.(769-771)Ctg>Ttg	p.L257L	LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Silent_p.L257L|RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000367176.3_Silent_p.L257L			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	257					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.L257L(3)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			ACCTGTTCCAGTGCCCGCCTG	0.627																																						dbGAP											3	Substitution - coding silent(3)	haematopoietic_and_lymphoid_tissue(3)	1											32.0	37.0	35.0					1																	204588352		2203	4300	6503	202854975	SO:0001819	synonymous_variant	0			AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.769C>T	1.37:g.204588352G>A		Somatic	481	6.96324951644101	36		0	100.00	8	WXS	Illumina HiSeq	Phase_IV	202854975	324	44.3298969072165	258	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Silent	SNP	HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMSmart_SM00365,superfamily_Immunoglobulin,superfamily_L domain-like	p.L257	ENST00000367175.1	37	c.769	CCDS1448.1	1																																																																																			-	HMMSmart_SM00369,HMMSmart_SM00365,superfamily_L domain-like		0.627	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	LRRN2	protein_coding	OTTHUMT00000089894.1	G	NM_006338		202854975	-1	no_errors	NM_006338.2	genbank	human	reviewed	54_36p	silent	SNP	0.995	A
RN7SKP224	106480902	genome.wustl.edu	37	2	48444856	48444856	+	lincRNA	SNP	A	A	G	rs570916689		TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr2:48444856A>G	ENST00000447571.1	-	0	56				RN7SKP224_ENST00000364140.1_RNA														p.0?(2)									cgctcggtcaaaaagaatgac	0.527													A|||	1	0.000199681	0.0	0.0	5008	,	,		17135	0.0		0.001	False		,,,				2504	0.0					dbGAP											2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	2																																								48298360			0																															2.37:g.48444856A>G		Somatic	1276	13.66	202		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	48298360	560	45.21	462		RNA	SNP	-	NULL	ENST00000447571.1	37	NULL		2																																																																																			-	-		0.527	AC079807.4-001	KNOWN	basic	lincRNA	ENSG00000201010	lincRNA	OTTHUMT00000323780.4	A			48298360	+1	no_errors	ENST00000364140	ensembl	human	novel	54_36p	rna	SNP	1.000	G
KIF9	64147	genome.wustl.edu	37	3	47292039	47292039	+	Intron	SNP	G	G	A			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr3:47292039G>A	ENST00000265529.3	-	12	1740				KIF9_ENST00000487440.1_Intron|snoU13_ENST00000459492.1_RNA|KIF9_ENST00000452770.2_Intron|KIF9_ENST00000352910.4_Intron|KIF9_ENST00000444589.2_Intron|KIF9_ENST00000335044.2_Intron			Q9HAQ2	KIF9_HUMAN	kinesin family member 9						ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		tgccaatgtcgtaacaaggtt	0.368																																					Colon(44;962 1147 15977 24541)	dbGAP											0			3																																								47267043	SO:0001627	intron_variant	0			AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"""Kinesins"""	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1060-2463C>T	3.37:g.47292039G>A		Somatic	367	8.02005012531328	32		5	0.00	0	WXS	Illumina HiSeq	Phase_IV	47267043	284	45.5938697318008	238	Q86Z28|Q9H8A4	RNA	SNP	-	NULL	ENST00000265529.3	37	NULL	CCDS2752.1	3																																																																																			-	-		0.368	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SNORD13	protein_coding	OTTHUMT00000257475.2	G			47267043	-1	pseudogene	ENST00000387814	ensembl	human	known	54_36p	rna	SNP	0.210	A
SCUBE3	222663	genome.wustl.edu	37	6	35212479	35212479	+	Silent	SNP	C	C	T			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr6:35212479C>T	ENST00000274938.7	+	18	2292	c.2292C>T	c.(2290-2292)cgC>cgT	p.R764R	SCUBE3_ENST00000394681.1_Silent_p.R780R	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3									p.R764R(3)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						GCTGTATTCGCTGTGCCATGG	0.572																																						dbGAP											3	Substitution - coding silent(3)	haematopoietic_and_lymphoid_tissue(3)	6											175.0	158.0	164.0					6																	35212479		2203	4300	6503	35320457	SO:0001819	synonymous_variant	0			AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"""CUB domain and EGF-like repeat containing 3"""	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2292C>T	6.37:g.35212479C>T		Somatic	878	12.18	122		2	0.00	0	WXS	Illumina HiSeq	Phase_IV	35320457	381	46.11	326		Silent	SNP	PatternScan_ASX_HYDROXYL,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Growth factor receptor domain,HMMPfam_GCC2_GCC3,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin	p.R764	ENST00000274938.7	37	c.2292	CCDS4800.1	6																																																																																			-	HMMSmart_SM00181,superfamily_Growth factor receptor domain,HMMPfam_GCC2_GCC3		0.572	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCUBE3	protein_coding	OTTHUMT00000040275.1	C	NM_152753		35320457	+1	no_errors	NM_152753.2	genbank	human	provisional	54_36p	silent	SNP	1.000	T
BCLAF1	9774	genome.wustl.edu	37	6	136597378	136597378	+	Missense_Mutation	SNP	G	G	A	rs147977614	byFrequency	TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr6:136597378G>A	ENST00000531224.1	-	5	1537	c.1285C>T	c.(1285-1287)Cgg>Tgg	p.R429W	BCLAF1_ENST00000527759.1_Missense_Mutation_p.R427W|BCLAF1_ENST00000527536.1_Missense_Mutation_p.R429W|BCLAF1_ENST00000530767.1_Intron|BCLAF1_ENST00000353331.4_Missense_Mutation_p.R427W|BCLAF1_ENST00000392348.2_Missense_Mutation_p.R427W	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	429					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R429W(3)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TCAGTATTCCGGTGAGATGCA	0.403													G|||	2	0.000399361	0.0008	0.0	5008	,	,		20077	0.0		0.0	False		,,,				2504	0.001				Colon(142;1534 1789 5427 7063 28491)	dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	6						G	TRP/ARG,,TRP/ARG	9,4397	14.3+/-33.2	0,9,2194	216.0	211.0	213.0		1279,,1285	4.4	1.0	6	dbSNP_134	213	38,8562	16.0+/-53.3	0,38,4262	yes	missense,intron,missense	BCLAF1	NM_001077440.1,NM_001077441.1,NM_014739.2	101,,101	0,47,6456	AA,AG,GG		0.4419,0.2043,0.3614	benign,,benign	427/870,,429/921	136597378	47,12959	2203	4300	6503	136639071	SO:0001583	missense	0			AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.1285C>T	6.37:g.136597378G>A	ENSP00000435210:p.Arg429Trp	Somatic	1318	6.37	90		53	51.38	56	WXS	Illumina HiSeq	Phase_IV	136639071	623	19.87	155	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	NULL	p.R429W	ENST00000531224.1	37	c.1285	CCDS5177.1	6	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	14.60	2.583614	0.46006	0.002043	0.004419	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48;2.48	5.25	4.39	0.52855	.	0.000000	0.56097	D	0.000027	T	0.02727	0.0082	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.30031	-0.9992	10	0.42905	T	0.14	-4.7974	10.6261	0.45508	0.147:0.0:0.853:0.0	.	427;427;429	Q9NYF8-2;Q9NYF8-3;Q9NYF8	.;.;BCLF1_HUMAN	W	429;427;429;427;427;429	ENSP00000435210:R429W;ENSP00000229446:R427W;ENSP00000435441:R429W;ENSP00000434826:R427W;ENSP00000376159:R427W;ENSP00000431734:R429W	ENSP00000229446:R427W	R	-	1	2	BCLAF1	136639071	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.428000	0.52792	1.365000	0.46057	-0.128000	0.14901	CGG	-	NULL		0.403	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BCLAF1	protein_coding	OTTHUMT00000042375.2	G	NM_014739		136639071	-1	no_errors	NM_014739.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
MSR1	4481	genome.wustl.edu	37	8	15978072	15978072	+	Silent	SNP	G	G	A			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr8:15978072G>A	ENST00000262101.5	-	9	1198	c.1077C>T	c.(1075-1077)caC>caT	p.H359H	MSR1_ENST00000350896.3_Intron|MSR1_ENST00000445506.2_Silent_p.H377H|MSR1_ENST00000355282.2_Intron			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	359	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)	p.H359H(3)		haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		CCCTCCCCTCGTGAGGGCCGC	0.483																																						dbGAP											3	Substitution - coding silent(3)	haematopoietic_and_lymphoid_tissue(3)	8											75.0	77.0	76.0					8																	15978072		2203	4300	6503	16022443	SO:0001819	synonymous_variant	0			D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"""CD molecules"""	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.1077C>T	8.37:g.15978072G>A		Somatic	397	6.36792452830189	27		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	16022443	239	51.5212981744422	254	D3DSP3|O60505|P21759|Q45F10	Silent	SNP	HMMPfam_SRCR,PatternScan_SRCR_1,HMMPfam_Macscav_rec,HMMPfam_Collagen,HMMSmart_SM00202,superfamily_SRCR-like	p.H359	ENST00000262101.5	37	c.1077	CCDS5995.1	8																																																																																			-	HMMPfam_SRCR,PatternScan_SRCR_1,HMMSmart_SM00202,superfamily_SRCR-like		0.483	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MSR1	protein_coding	OTTHUMT00000211627.2	G			16022443	-1	no_errors	NM_138715.3	genbank	human	reviewed	54_36p	silent	SNP	0.042	A
EMX2OS	196047	genome.wustl.edu	37	10	119249126	119249126	+	RNA	SNP	T	T	C			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr10:119249126T>C	ENST00000551288.1	-	0	3848				EMX2OS_ENST00000423419.1_RNA|CTA-109P11.4_ENST00000549104.1_lincRNA|EMX2OS_ENST00000440007.1_RNA|EMX2OS_ENST00000450314.2_RNA	NR_002791.2				EMX2 opposite strand/antisense RNA																		aaccatataatgtgcttagca	0.368																																						dbGAP											0			10																																								119239116			0			AY117034		10q26.11	2012-10-19	2012-08-15	2011-11-14	ENSG00000229847	ENSG00000229847		"""Long non-coding RNAs"", ""-"""	18511	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 45"""	607637	"""empty spiracles homeobox 2 opposite strand"", ""EMX2 opposite strand (non-protein coding)"", ""EMX2 opposite strand/antisense RNA (non-protein coding)"""			12573261	Standard	NR_002791		Approved	NCRNA00045, EMX2-AS1	uc001ldg.3		OTTHUMG00000019125		10.37:g.119249126T>C		Somatic	685	5.12465373961219	37		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	119239116	497	47.5738396624473	451		RNA	SNP	-	NULL	ENST00000551288.1	37	NULL		10																																																																																			-	-		0.368	EMX2OS-006	KNOWN	basic	antisense	EMX2OS	antisense	OTTHUMT00000406746.1	T	NR_002791		119239116	-1	no_errors	NR_002791.2	genbank	human	provisional	54_36p	rna	SNP	0.001	C
WT1	7490	genome.wustl.edu	37	11	32413611	32413611	+	Splice_Site	SNP	C	C	T			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr11:32413611C>T	ENST00000379079.2	-	9	977		c.e9-1		WT1_ENST00000332351.3_Splice_Site|WT1_ENST00000530998.1_Splice_Site|WT1_ENST00000448076.3_Splice_Site	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1						adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.?(3)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			GGTTTCACACCTAAATGGACA	0.537			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													dbGAP	yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	3	Unknown(3)	haematopoietic_and_lymphoid_tissue(3)	11											133.0	124.0	127.0					11																	32413611		2202	4299	6501	32370187	SO:0001630	splice_region_variant	0	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.704-1G>A	11.37:g.32413611C>T		Somatic	1126	10.80	137		5	37.50	3	WXS	Illumina HiSeq	Phase_IV	32370187	311	43.38	239	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Splice_Site	SNP	-	e9-1	ENST00000379079.2	37	c.1340-1	CCDS55751.1	11	.	.	.	.	.	.	.	.	.	.	C	29.9	5.042933	0.93685	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076;ENST00000527882	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5792	0.99380	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WT1	32370187	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.794000	0.85869	2.873000	0.98535	0.561000	0.74099	.	-	-		0.537	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	WT1	protein_coding	OTTHUMT00000095434.1	C	NM_000378	Intron	32370187	-1	no_errors	NM_024426.3	genbank	human	reviewed	54_36p	splice_site	SNP	1.000	T
PLEKHH1	57475	genome.wustl.edu	37	14	68036718	68036718	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr14:68036718G>A	ENST00000329153.5	+	9	1555	c.1423G>A	c.(1423-1425)Gca>Aca	p.A475T		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	475						cytoskeleton (GO:0005856)		p.A475T(3)		endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		TGTCTACACAGCACTGAAGGG	0.567																																						dbGAP											3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	14											87.0	82.0	84.0					14																	68036718		1934	4150	6084	67106471	SO:0001583	missense	0			AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.1423G>A	14.37:g.68036718G>A	ENSP00000330278:p.Ala475Thr	Somatic	793	12.56	114		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	67106471	363	46.30	313	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	HMMPfam_MyTH4,HMMSmart_SM00139,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_FERM_M,superfamily_Second domain of FERM,HMMSmart_SM00295,superfamily_PH domain-like	p.A475T	ENST00000329153.5	37	c.1423	CCDS45128.1	14	.	.	.	.	.	.	.	.	.	.	g	5.676	0.309236	0.10733	.	.	ENSG00000054690	ENST00000329153	T	0.13089	2.62	4.74	1.53	0.23141	.	0.232821	0.43110	D	0.000602	T	0.04272	0.0118	N	0.11673	0.155	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.36504	-0.9745	10	0.02654	T	1	.	2.4409	0.04494	0.2103:0.0:0.291:0.4987	.	475	Q9ULM0	PKHH1_HUMAN	T	475	ENSP00000330278:A475T	ENSP00000330278:A475T	A	+	1	0	PLEKHH1	67106471	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.023000	0.49666	0.546000	0.28920	0.479000	0.44913	GCA	-	NULL		0.567	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLEKHH1	protein_coding	OTTHUMT00000412730.3	G	XM_031054		67106471	+1	no_errors	NM_020715.2	genbank	human	validated	54_36p	missense	SNP	0.998	A
RUNX1	861	genome.wustl.edu	37	21	36259153	36259153	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr21:36259153G>A	ENST00000344691.4	-	1	1834	c.257C>T	c.(256-258)cCc>cTc	p.P86L	RUNX1_ENST00000399240.1_Missense_Mutation_p.P86L|RUNX1_ENST00000437180.1_Missense_Mutation_p.P113L|RUNX1_ENST00000325074.5_Missense_Mutation_p.P101L|RUNX1_ENST00000358356.5_Missense_Mutation_p.P86L|RUNX1_ENST00000486278.2_Missense_Mutation_p.P89L|RUNX1_ENST00000300305.3_Missense_Mutation_p.P113L	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	86	Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P113L(4)|p.V90_K117del(1)|p.L112fs*24(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						GAAAGCGATGGGCAGGGTCTT	0.721			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																	dbGAP		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	6	Substitution - Missense(4)|Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(6)	21											54.0	52.0	53.0					21																	36259153		2203	4300	6503	35181023	SO:0001583	missense	0			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.257C>T	21.37:g.36259153G>A	ENSP00000340690:p.Pro86Leu	Somatic	312	10.3448275862069	36		6	97.90	280	WXS	Illumina HiSeq	Phase_IV	35181023	39	90.4176904176904	368	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI	p.P113L	ENST00000344691.4	37	c.338	CCDS42922.1	21	.	.	.	.	.	.	.	.	.	.	G	31	5.104392	0.94245	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278;ENST00000455571	D;D;D;D;D;D;D;D;D	0.99758	-6.65;-6.65;-6.65;-6.65;-6.65;-6.65;-6.65;-6.65;-6.65	4.45	4.45	0.53987	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	M	0.90870	3.155	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.997;1.0;0.999;1.0	D	0.96701	0.9518	10	0.87932	D	0	-22.778	17.2859	0.87141	0.0:0.0:1.0:0.0	.	113;86;113;101;86	Q2TAM6;Q01196-3;Q01196-8;Q01196-10;Q01196	.;.;.;.;RUNX1_HUMAN	L	86;113;113;101;86;89;86;101;89;100	ENSP00000340690:P86L;ENSP00000300305:P113L;ENSP00000409227:P113L;ENSP00000319459:P101L;ENSP00000382184:P86L;ENSP00000351123:P86L;ENSP00000382182:P101L;ENSP00000438019:P89L;ENSP00000388189:P100L	ENSP00000300305:P113L	P	-	2	0	RUNX1	35181023	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.078000	0.94023	2.296000	0.77279	0.563000	0.77884	CCC	-	superfamily_p53-like transcription factors,HMMPfam_Runt		0.721	RUNX1-001	KNOWN	basic|CCDS	protein_coding	RUNX1	protein_coding	OTTHUMT00000194230.1	G			35181023	-1	no_errors	NM_001754.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
BCOR	54880	genome.wustl.edu	37	X	39933858	39933858	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chrX:39933858delC	ENST00000378444.4	-	4	969	c.741delG	c.(739-741)ctgfs	p.L247fs	BCOR_ENST00000397354.3_Frame_Shift_Del_p.L247fs|BCOR_ENST00000378455.4_Frame_Shift_Del_p.L247fs|BCOR_ENST00000342274.4_Frame_Shift_Del_p.L247fs	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	247					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P248fs*18(3)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GAGGTGGCGGCAGGTAGAGAA	0.607			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																															dbGAP		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		3	Deletion - Frameshift(3)	haematopoietic_and_lymphoid_tissue(3)	X											67.0	45.0	52.0					X																	39933858		2202	4300	6502	39818802	SO:0001589	frameshift_variant	0			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.741delG	X.37:g.39933858delC	ENSP00000367705:p.Leu247fs	Somatic	999	10.01	113		2	82.61	57	WXS	Illumina HiSeq	Phase_IV	39818802	254	45.28	230	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Frame_Shift_Del	DEL	HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK	p.P248fs	ENST00000378444.4	37	c.741	CCDS48093.1	X																																																																																			-	NULL		0.607	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BCOR	protein_coding	OTTHUMT00000060666.2	C	NM_017745		39818802	-1	no_errors	NM_017745.1	genbank	human	reviewed	54_36p	frame_shift_del	DEL	1.000	-
FLT3	2322	genome.wustl.edu	37	13	28608258	28608259	+	In_Frame_Ins	INS	-	-	GGCGATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGG			TCGA-AB-2970-03A-01D-0739-09	TCGA-AB-2970-11A-01D-0739-09	-	-	-	GGCGATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGG	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8ace649f-6c0a-47a4-9ebb-081fd6f8a025	d0983a5d-cb05-4b25-8053-631d52627b28	g.chr13:28608258_28608259insGGCGATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGG	ENST00000241453.7	-	14	1878_1879	c.1797_1798insCCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATCGCC	c.(1795-1800)tatgat>tatCCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATCGCCgat	p.599_600YD>YPAPQIMSTSTLISENMNIAD	FLT3_ENST00000380982.4_In_Frame_Ins_p.599_600YD>YPAPQIMSTSTLISENMNIAD|FLT3_ENST00000537084.1_In_Frame_Ins_p.599_600YD>YPAPQIMSTSTLISENMNIAD	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	599					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.Y599_D600insPAPQIMSTSTLISENMNIA(2)|p.Y599_D600ins15(2)|p.D600_L601insVDFREYEY(1)|p.E598_Y599insWDFREYE(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CATTTGAGATCATATTCATATT	0.371			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	6	Insertion - In frame(6)	haematopoietic_and_lymphoid_tissue(6)	13																																								27506259	SO:0001652	inframe_insertion	0			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1797_1798insCCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATCGCC	13.37:g.28608258_28608259insGGCGATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGG	ENSP00000241453:p.Tyr599_Asp600insProAlaProGlnIleMetSerThrSerThrLeuIleSerGluAsnMetAsnIleAla	Somatic	228	14.6067415730337	39		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	27506258	145	60.9164420485175	226	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	In_Frame_Ins	INS	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.599in_frame_insPAPQIMSTSTLISENMNIA	ENST00000241453.7	37	c.1798_1797	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.371	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	-			27506259	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	1.000:1.000	GGCGATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGG
