#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
HK2P1	642546	genome.wustl.edu	37	X	79828118	79828118	+	IGR	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chrX:79828118C>T								FAM46D (127308 upstream) : BRWD3 (98234 downstream)																							AGCCACAGGTCATCATAGTTC	0.527																																						dbGAP											0			X																																								79714774	SO:0001628	intergenic_variant	0																															X.37:g.79828118C>T		Somatic	58	6.45	4		14	0.00	0	WXS	Illumina HiSeq	Phase_IV	79714774	21	75.58	65		RNA	SNP	-	NULL		37	NULL		X																																																																																			-	-	0	0.527					LOC642546			C			79714774	-1	pseudogene	XR_038841.1	genbank	human	model	54_36p	rna	SNP	1.000	T
RPS6KA6	27330	genome.wustl.edu	37	X	83320023	83320023	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chrX:83320023G>A	ENST00000262752.2	-	21	2075	c.2068C>T	c.(2068-2070)Cca>Tca	p.P690S	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.P690S	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	690					axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						TGATCATTTGGCAACTGGTCT	0.378																																						dbGAP											0			X											212.0	183.0	193.0					X																	83320023		2203	4300	6503	83206679	SO:0001583	missense	0			AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"""ribosomal protein S6 kinase, 90kD, polypeptide 6"""			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.2068C>T	X.37:g.83320023G>A	ENSP00000262752:p.Pro690Ser	Somatic	94	1.05	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	83206679	69	18.82	16	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	PatternScan_SERPIN,HMMSmart_SM00133,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,HMMPfam_Pkinase_C	p.P690S	ENST00000262752.2	37	c.2068	CCDS14451.1	X	.	.	.	.	.	.	.	.	.	.	G	8.092	0.774640	0.16051	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.39056	1.1;1.1	4.86	2.1	0.27182	Protein kinase-like domain (1);	0.161160	0.56097	N	0.000028	T	0.22244	0.0536	N	0.26042	0.785	0.51233	D	0.999916	B;B	0.15141	0.012;0.006	B;B	0.15052	0.012;0.006	T	0.13980	-1.0489	10	0.06236	T	0.91	.	6.8886	0.24216	0.1557:0.0:0.7025:0.1418	.	690;690	B7ZL90;Q9UK32	.;KS6A6_HUMAN	S	690	ENSP00000262752:P690S;ENSP00000440830:P690S	ENSP00000262752:P690S	P	-	1	0	RPS6KA6	83206679	1.000000	0.71417	0.003000	0.11579	0.982000	0.71751	5.905000	0.69893	0.079000	0.16929	-0.191000	0.12829	CCA	-	superfamily_Protein kinase-like (PK-like)		0.378	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPS6KA6	protein_coding	OTTHUMT00000057372.1	G	NM_014496		83206679	-1	no_errors	NM_014496.2	genbank	human	provisional	54_36p	missense	SNP	1.000	A
BCAN	63827	genome.wustl.edu	37	1	156617332	156617332	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr1:156617332C>T	ENST00000329117.5	+	4	835	c.499C>T	c.(499-501)Cgc>Tgc	p.R167C	RP11-284F21.10_ENST00000605886.1_RNA|RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.R167C	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	167	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGCTCTGCCCGCTATGCTTT	0.657																																						dbGAP											0			1											49.0	51.0	50.0					1																	156617332		2203	4300	6503	154883956	SO:0001583	missense	0			BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.499C>T	1.37:g.156617332C>T	ENSP00000331210:p.Arg167Cys	Somatic	121	1.63	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	154883956	146	43.63	113	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,PatternScan_IG_MHC,HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin	p.R167C	ENST00000329117.5	37	c.499	CCDS1149.1	1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.151304	0.78001	.	.	ENSG00000132692	ENST00000329117;ENST00000457777;ENST00000424639;ENST00000361588	T;T;T;T	0.15372	2.43;2.43;2.43;2.43	4.26	4.26	0.50523	C-type lectin fold (1);Link (4);C-type lectin-like (1);	0.000000	0.64402	D	0.000013	T	0.36963	0.0986	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.38845	-0.9642	10	0.87932	D	0	-17.5056	10.7581	0.46249	0.1901:0.8099:0.0:0.0	.	167;167	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	C	167;167;65;167	ENSP00000331210:R167C;ENSP00000389898:R167C;ENSP00000401709:R65C;ENSP00000354925:R167C	ENSP00000331210:R167C	R	+	1	0	BCAN	154883956	0.994000	0.37717	1.000000	0.80357	0.904000	0.53231	3.136000	0.50554	2.187000	0.69744	0.442000	0.29010	CGC	-	HMMPfam_Xlink,HMMSmart_SM00445,superfamily_C-type lectin-like		0.657	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BCAN	protein_coding	OTTHUMT00000081844.2	C	NM_021948		154883956	+1	no_errors	NM_021948.3	genbank	human	validated	54_36p	missense	SNP	1.000	T
ADSS	159	genome.wustl.edu	37	1	244580929	244580929	+	Splice_Site	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr1:244580929C>T	ENST00000366535.3	-	10	1387		c.e10+1		ADSS_ENST00000462358.1_5'Flank	NM_001126.3	NP_001117.2			adenylosuccinate synthase											endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)			AGAATACTCACGCAGTAAATC	0.363																																						dbGAP											0			1											86.0	85.0	85.0					1																	244580929		2203	4300	6503	242647552	SO:0001630	splice_region_variant	0			BC012356	CCDS1624.1	1q44	2008-02-05			ENSG00000035687	ENSG00000035687	6.3.4.4		292	protein-coding gene	gene with protein product		103060				2004783, 1592113	Standard	NM_001126		Approved		uc001iaj.3	P30520	OTTHUMG00000040102	ENST00000366535.3:c.1070+1G>A	1.37:g.244580929C>T		Somatic	92	0.00	0		8	27.27	3	WXS	Illumina HiSeq	Phase_IV	242647552	87	32.03	41		Splice_Site	SNP	-	e10+1	ENST00000366535.3	37	c.1070+1	CCDS1624.1	1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.730303	0.89390	.	.	ENSG00000035687	ENST00000366535;ENST00000449326	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7167	0.96124	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADSS	242647552	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.667000	0.90743	0.655000	0.94253	.	-	-		0.363	ADSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADSS	protein_coding	OTTHUMT00000096697.1	C	NM_001126	Intron	242647552	-1	no_errors	NM_001126.2	genbank	human	reviewed	54_36p	splice_site	SNP	1.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25463308	25463308	+	Missense_Mutation	SNP	G	G	A	rs200018028		TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr2:25463308G>A	ENST00000264709.3	-	19	2522	c.2185C>T	c.(2185-2187)Cgg>Tgg	p.R729W	DNMT3A_ENST00000380746.4_Missense_Mutation_p.R540W|DNMT3A_ENST00000402667.1_Missense_Mutation_p.R506W|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R729W	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	729	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.R729W(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGAAGAGCCGGCCAGTGCCC	0.612			"""Mis, F, N, S"""		AML								G|||	1	0.000199681	0.0	0.0	5008	,	,		18546	0.001		0.0	False		,,,				2504	0.0					dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	2											54.0	55.0	55.0					2																	25463308		2203	4300	6503	25316812	SO:0001583	missense	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2185C>T	2.37:g.25463308G>A	ENSP00000264709:p.Arg729Trp	Somatic	19	0.00	0		15	40.00	10	WXS	Illumina HiSeq	Phase_IV	25316812	27	49.06	26	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.R729W	ENST00000264709.3	37	c.2185	CCDS33157.1	2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	21.6	4.171186	0.78452	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.89462	0.6722	L	0.58354	1.805	0.80722	D	1	D;D	0.76494	0.999;0.997	P;D	0.65684	0.854;0.937	D	0.89215	0.3567	10	0.51188	T	0.08	-10.1334	12.7451	0.57278	0.0:0.0:0.8357:0.1643	.	729;540	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	W	540;729;729;506	ENSP00000370122:R540W;ENSP00000324375:R729W;ENSP00000264709:R729W;ENSP00000384237:R506W	ENSP00000264709:R729W	R	-	1	2	DNMT3A	25316812	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.075000	0.57584	2.540000	0.85666	0.561000	0.74099	CGG	-	HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.612	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552		25316812	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
ZNF638	27332	genome.wustl.edu	37	2	71654223	71654223	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr2:71654223G>A	ENST00000409544.1	+	24	5854	c.5224G>A	c.(5224-5226)Gac>Aac	p.D1742N	ZNF638_ENST00000264447.4_Missense_Mutation_p.D1742N|ZNF638_ENST00000409407.1_Missense_Mutation_p.D682N|ZNF638_ENST00000355812.3_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1742					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AATACAAGATGACAGCAGTGA	0.388																																						dbGAP											0			2											113.0	117.0	116.0					2																	71654223		2203	4300	6503	71507731	SO:0001583	missense	0			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5224G>A	2.37:g.71654223G>A	ENSP00000386433:p.Asp1742Asn	Somatic	192	0.52	1		41	50.00	41	WXS	Illumina HiSeq	Phase_IV	71507731	136	31.31	62	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00451,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_RNA-binding domain RBD	p.D1742N	ENST00000409544.1	37	c.5224	CCDS1917.1	2	.	.	.	.	.	.	.	.	.	.	G	28.2	4.900123	0.92035	.	.	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.50001	0.76;0.76;1.16	5.71	5.71	0.89125	.	0.114707	0.38959	N	0.001514	T	0.47911	0.1471	N	0.19112	0.55	0.80722	D	1	D;D	0.59357	0.985;0.974	P;P	0.54270	0.747;0.563	T	0.41088	-0.9528	10	0.38643	T	0.18	-2.2373	17.3445	0.87306	0.0:0.0:1.0:0.0	.	1742;1742	Q14966-3;Q14966	.;ZN638_HUMAN	N	1742;1742;682	ENSP00000264447:D1742N;ENSP00000386433:D1742N;ENSP00000386813:D682N	ENSP00000264447:D1742N	D	+	1	0	ZNF638	71507731	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.176000	0.77643	2.686000	0.91538	0.655000	0.94253	GAC	-	NULL		0.388	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	ZNF638	protein_coding	OTTHUMT00000327431.1	G	NM_014497		71507731	+1	no_errors	NM_001014972.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
SCN3A	6328	genome.wustl.edu	37	2	166003485	166003485	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr2:166003485C>G	ENST00000360093.3	-	12	1926	c.1435G>C	c.(1435-1437)Gga>Cga	p.G479R	SCN3A_ENST00000283254.7_Missense_Mutation_p.G479R|RN7SL455P_ENST00000580629.1_RNA|SCN3A_ENST00000409101.3_Missense_Mutation_p.G479R	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	479					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AACAGCTCTCCTAACCCACCT	0.443																																						dbGAP											0			2											114.0	116.0	115.0					2																	166003485		2203	4300	6503	165711731	SO:0001583	missense	0			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.1435G>C	2.37:g.166003485C>G	ENSP00000353206:p.Gly479Arg	Somatic	88	4.35	4		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	165711731	97	40.49	66	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Ion_trans,HMMPfam_Na_trans_assoc,superfamily_SSF81324	p.G479R	ENST00000360093.3	37	c.1435		2	.	.	.	.	.	.	.	.	.	.	C	20.0	3.931190	0.73327	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.96073	-3.9;-3.9;-3.87;-3.75	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000007	D	0.96558	0.8877	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.996;0.996;0.998;0.998;0.998	D	0.96983	0.9716	10	0.72032	D	0.01	.	19.922	0.97089	0.0:1.0:0.0:0.0	.	479;479;479;479;479	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	R	479	ENSP00000353206:G479R;ENSP00000283254:G479R;ENSP00000386726:G479R;ENSP00000403348:G479R	ENSP00000283254:G479R	G	-	1	0	SCN3A	165711731	0.931000	0.31567	0.976000	0.42696	0.870000	0.49936	1.830000	0.39131	2.780000	0.95670	0.655000	0.94253	GGA	-	NULL		0.443	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	SCN3A	protein_coding		C	NM_006922		165711731	-1	no_errors	NM_006922.1	genbank	human	reviewed	54_36p	missense	SNP	0.985	G
POC1A	25886	genome.wustl.edu	37	3	52172304	52172304	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr3:52172304C>T	ENST00000296484.2	-	7	733	c.694G>A	c.(694-696)Gtg>Atg	p.V232M	POC1A_ENST00000474012.1_Missense_Mutation_p.V194M|POC1A_ENST00000394970.2_Missense_Mutation_p.V232M	NM_015426.4	NP_056241.3	Q8NBT0	POC1A_HUMAN	POC1 centriolar protein A	232					cell projection organization (GO:0030030)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|large_intestine(4)|liver(1)|lung(4)|prostate(3)|skin(1)	14						AGCCCGTTCACTGCTGCACTG	0.597																																						dbGAP											0			3											70.0	58.0	62.0					3																	52172304		2203	4300	6503	52147344	SO:0001583	missense	0			AL117629	CCDS2846.1, CCDS54591.1, CCDS54592.1	3p21.2	2014-05-02	2013-08-21	2010-03-26	ENSG00000164087	ENSG00000164087		"""WD repeat domain containing"""	24488	protein-coding gene	gene with protein product		614783	"""WD repeat domain 51A"", ""POC1 centriolar protein homolog A (Chlamydomonas)"""	WDR51A		19109428, 22840364	Standard	NM_015426		Approved	DKFZP434C245	uc003dcu.3	Q8NBT0	OTTHUMG00000157817	ENST00000296484.2:c.694G>A	3.37:g.52172304C>T	ENSP00000296484:p.Val232Met	Somatic	121	1.63	2		13	48.00	12	WXS	Illumina HiSeq	Phase_IV	52147344	131	45.19	108	A4FUW4|E9PFC6|Q0VDF8|Q2TAK6|Q96IK6|Q9UFJ8	Missense_Mutation	SNP	HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40	p.V232M	ENST00000296484.2	37	c.694	CCDS2846.1	3	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150132	0.78001	.	.	ENSG00000164087	ENST00000296484;ENST00000394970;ENST00000474012	T;T;T	0.73897	-0.79;-0.79;-0.79	4.84	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.065827	0.64402	D	0.000012	D	0.88897	0.6562	M	0.91249	3.19	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79108	0.992;0.985	D	0.91406	0.5147	10	0.87932	D	0	.	16.8786	0.86058	0.0:1.0:0.0:0.0	.	232;232	Q8NBT0-2;Q8NBT0	.;POC1A_HUMAN	M	232;232;194	ENSP00000296484:V232M;ENSP00000378421:V232M;ENSP00000418968:V194M	ENSP00000296484:V232M	V	-	1	0	POC1A	52147344	1.000000	0.71417	0.746000	0.31095	0.626000	0.37791	5.525000	0.67110	2.517000	0.84864	0.655000	0.94253	GTG	-	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40		0.597	POC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WDR51A	protein_coding	OTTHUMT00000349685.1	C	NM_015426		52147344	-1	no_errors	NM_015426.3	genbank	human	provisional	54_36p	missense	SNP	0.999	T
ILDR1	286676	genome.wustl.edu	37	3	121725901	121725901	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr3:121725901C>T	ENST00000344209.5	-	2	292	c.166G>A	c.(166-168)Gtg>Atg	p.V56M	ILDR1_ENST00000462014.1_Missense_Mutation_p.V68M|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.V56M|ILDR1_ENST00000273691.3_Missense_Mutation_p.V56M	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	56	Ig-like V-type.				positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		GTCACCACCACGTCCTGGAGC	0.547																																						dbGAP											0			3											160.0	123.0	135.0					3																	121725901		2203	4300	6503	123208591	SO:0001583	missense	0			BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.166G>A	3.37:g.121725901C>T	ENSP00000345667:p.Val56Met	Somatic	122	1.61	2		0	100.00	1	WXS	Illumina HiSeq	Phase_IV	123208591	153	39.04	98	Q6ZP61|Q7Z578	Missense_Mutation	SNP	HMMSmart_IG,HMMPfam_LSR,superfamily_SSF48726	p.V56M	ENST00000344209.5	37	c.166	CCDS56271.1	3	.	.	.	.	.	.	.	.	.	.	C	22.1	4.248618	0.80024	.	.	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000383663;ENST00000393631;ENST00000462014	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72244	0.3436	M	0.70595	2.14	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.987;0.994;0.997	T	0.73811	-0.3865	10	0.59425	D	0.04	-18.9151	16.9785	0.86321	0.0:1.0:0.0:0.0	.	56;56;56;68	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	M	56;56;56;56;68	ENSP00000273691:V56M;ENSP00000345667:V56M;ENSP00000377251:V56M;ENSP00000419414:V68M	ENSP00000273691:V56M	V	-	1	0	ILDR1	123208591	1.000000	0.71417	0.973000	0.42090	0.984000	0.73092	4.675000	0.61619	2.598000	0.87819	0.650000	0.86243	GTG	-	HMMSmart_IG,superfamily_SSF48726		0.547	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ILDR1	protein_coding	OTTHUMT00000355666.1	C	NM_175924		123208591	-1	no_errors	NM_175924.2	genbank	human	provisional	54_36p	missense	SNP	0.997	T
KDR	3791	genome.wustl.edu	37	4	55964954	55964954	+	Silent	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr4:55964954C>T	ENST00000263923.4	-	16	2578	c.2283G>A	c.(2281-2283)acG>acA	p.T761T		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	761					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTTCCAAGTTCGTCTTTTCCT	0.393			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																												dbGAP		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	0			4											98.0	97.0	97.0					4																	55964954		2203	4300	6503	55659711	SO:0001819	synonymous_variant	0			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2283G>A	4.37:g.55964954C>T		Somatic	84	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	55659711	95	35.37	52	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.T761	ENST00000263923.4	37	c.2283	CCDS3497.1	4																																																																																			-	NULL		0.393	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KDR	protein_coding	OTTHUMT00000250645.1	C			55659711	-1	no_errors	NM_002253.2	genbank	human	validated	54_36p	silent	SNP	0.682	T
ENPP1	5167	genome.wustl.edu	37	6	132147334	132147334	+	Intron	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr6:132147334C>T	ENST00000360971.2	+	1	260					NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	AGCTACTTTTCCCCAAAGGTA	0.433																																					Colon(104;336 1535 5856 11019 33782)	dbGAP											0			6																																								132189027	SO:0001627	intron_variant	0			M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.240+17919C>T	6.37:g.132147334C>T		Somatic	49	2.00	1		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	132189027	57	44.66	46	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	RNA	SNP	-	NULL	ENST00000360971.2	37	NULL	CCDS5150.2	6																																																																																			-	-		0.433	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC100128322	protein_coding	OTTHUMT00000042238.2	C			132189027	-1	pseudogene	XR_039280.1	genbank	human	model	54_36p	rna	SNP	0.998	T
DUSP26	78986	genome.wustl.edu	37	8	33451143	33451143	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr8:33451143C>A	ENST00000256261.4	-	3	861	c.344G>T	c.(343-345)gGt>gTt	p.G115V	DUSP26_ENST00000523956.1_Missense_Mutation_p.G115V	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	115	Tyrosine-protein phosphatase.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		GGCCTCAACACCCAGGTAGCG	0.662																																						dbGAP											0			8											60.0	52.0	54.0					8																	33451143		2203	4300	6503	33570685	SO:0001583	missense	0			AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.344G>T	8.37:g.33451143C>A	ENSP00000256261:p.Gly115Val	Somatic	106	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	33570685	155	33.33	78	D3DSV8|Q9BTW0	Missense_Mutation	SNP	HMMPfam_DSPc,PatternScan_TYR_PHOSPHATASE_1,HMMSmart_SM00195,superfamily_(Phosphotyrosine protein) phosphatases II	p.G115V	ENST00000256261.4	37	c.344	CCDS6092.1	8	.	.	.	.	.	.	.	.	.	.	C	28.2	4.898842	0.91962	.	.	ENSG00000133878	ENST00000256261;ENST00000523956;ENST00000522982	T;T;T	0.59772	0.24;0.24;0.24	4.97	4.97	0.65823	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.050980	0.85682	D	0.000000	T	0.75867	0.3908	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78031	-0.2363	10	0.59425	D	0.04	-29.8557	18.1919	0.89809	0.0:1.0:0.0:0.0	.	115	Q9BV47	DUS26_HUMAN	V	115	ENSP00000256261:G115V;ENSP00000429176:G115V;ENSP00000430922:G115V	ENSP00000256261:G115V	G	-	2	0	DUSP26	33570685	1.000000	0.71417	0.978000	0.43139	0.918000	0.54935	7.667000	0.83888	2.470000	0.83445	0.563000	0.77884	GGT	-	HMMPfam_DSPc,HMMSmart_SM00195,superfamily_(Phosphotyrosine protein) phosphatases II		0.662	DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DUSP26	protein_coding	OTTHUMT00000376564.1	C	NM_024025		33570685	-1	no_errors	NM_024025.1	genbank	human	provisional	54_36p	missense	SNP	1.000	A
KCNU1	157855	genome.wustl.edu	37	8	36641947	36641947	+	Nonsense_Mutation	SNP	C	C	T	rs567477009		TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr8:36641947C>T	ENST00000399881.3	+	1	56	c.19C>T	c.(19-21)Cga>Tga	p.R7*		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	7					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GACTAAGCTACGAAATGAAAC	0.453																																						dbGAP											0			8											114.0	107.0	109.0					8																	36641947		1949	4146	6095	36761105	SO:0001587	stop_gained	0			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.19C>T	8.37:g.36641947C>T	ENSP00000382770:p.Arg7*	Somatic	112	0.88	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	36761105	157	31.74	73		Nonsense_Mutation	SNP	HMMPfam_BK_channel_a,HMMPfam_Ion_trans,superfamily_NAD(P)-bd,superfamily_SSF81324	p.R7*	ENST00000399881.3	37	c.19	CCDS55220.1	8	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153495	0.78114	.	.	ENSG00000215262	ENST00000523973;ENST00000399881	.	.	.	5.36	-1.52	0.08637	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	.	8.7258	0.34469	0.4875:0.2511:0.2613:0.0	.	.	.	.	X	7	.	ENSP00000382770:R7X	R	+	1	2	KCNU1	36761105	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.972000	0.03802	-0.177000	0.10690	-1.426000	0.01102	CGA	-	NULL		0.453	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	KCNU1	protein_coding	OTTHUMT00000376631.1	C	NM_001031836		36761105	+1	no_errors	NM_001031836.2	genbank	human	validated	54_36p	nonsense	SNP	0.000	T
KHDRBS3	10656	genome.wustl.edu	37	8	136554945	136554945	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr8:136554945C>T	ENST00000355849.5	+	3	666	c.256C>T	c.(256-258)Cgt>Tgt	p.R86C	KHDRBS3_ENST00000520981.1_Intron	NM_006558.1	NP_006549.1	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal transduction associated 3	86	KH.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R86C(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	26	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			TTCTCTGAAGCGTTTACAAGA	0.368																																						dbGAP											1	Substitution - Missense(1)	prostate(1)	8											122.0	128.0	126.0					8																	136554945		2203	4300	6503	136624127	SO:0001583	missense	0			AF069681	CCDS6374.1	8q24.23	2008-05-15			ENSG00000131773	ENSG00000131773			18117	protein-coding gene	gene with protein product		610421				10332027, 10564820	Standard	XR_242372		Approved	T-STAR, Etle, etoile, SALP, SLM2, SLM-2	uc003yuv.3	O75525	OTTHUMG00000164164	ENST00000355849.5:c.256C>T	8.37:g.136554945C>T	ENSP00000348108:p.Arg86Cys	Somatic	124	0.80	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	136624127	206	24.26	66	Q6NUL8|Q9UPA8	Missense_Mutation	SNP	HMMSmart_SM00322,superfamily_Eukaryotic type KH-domain (KH-domain type I)	p.R86C	ENST00000355849.5	37	c.256	CCDS6374.1	8	.	.	.	.	.	.	.	.	.	.	C	18.77	3.694485	0.68386	.	.	ENSG00000131773	ENST00000355849;ENST00000524199;ENST00000517394	T;T;T	0.22134	1.97;1.97;1.97	5.82	3.99	0.46301	K Homology (1);	0.044642	0.85682	D	0.000000	T	0.49830	0.1580	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	T	0.54302	-0.8314	10	0.87932	D	0	-10.2283	10.0747	0.42353	0.279:0.5864:0.1346:0.0	.	86;86	O75525-2;O75525	.;KHDR3_HUMAN	C	86;58;59	ENSP00000348108:R86C;ENSP00000431022:R58C;ENSP00000430284:R59C	ENSP00000348108:R86C	R	+	1	0	KHDRBS3	136624127	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.922000	0.48860	0.768000	0.33290	0.655000	0.94253	CGT	-	HMMSmart_SM00322,superfamily_Eukaryotic type KH-domain (KH-domain type I)		0.368	KHDRBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KHDRBS3	protein_coding	OTTHUMT00000377529.1	C			136624127	+1	no_errors	NM_006558.1	genbank	human	provisional	54_36p	missense	SNP	1.000	T
SMC3	9126	genome.wustl.edu	37	10	112343991	112343991	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr10:112343991G>A	ENST00000361804.4	+	13	1268	c.1142G>A	c.(1141-1143)cGa>cAa	p.R381Q		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	381					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)	p.R381L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		AAGCAGGGTCGAGGAAGCCAG	0.378																																						dbGAP											1	Substitution - Missense(1)	urinary_tract(1)	10											113.0	113.0	113.0					10																	112343991		2203	4300	6503	112333981	SO:0001583	missense	0			AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"""Structural maintenance of chromosomes proteins"", ""Proteoglycans / Extracellular Matrix : Other"""	2468	protein-coding gene	gene with protein product	"""bamacan proteoglycan"""	606062	"""chondroitin sulfate proteoglycan 6 (bamacan)"""	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.1142G>A	10.37:g.112343991G>A	ENSP00000354720:p.Arg381Gln	Somatic	102	1.92	2		51	40.00	34	WXS	Illumina HiSeq	Phase_IV	112333981	120	34.78	64	A8K156|O60464|Q5T482	Missense_Mutation	SNP	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain	p.R381Q	ENST00000361804.4	37	c.1142	CCDS31285.1	10	.	.	.	.	.	.	.	.	.	.	G	33	5.233286	0.95207	.	.	ENSG00000108055	ENST00000361804	T	0.76060	-0.99	5.76	5.76	0.90799	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.87047	0.6080	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85819	0.1384	10	0.44086	T	0.13	.	19.973	0.97292	0.0:0.0:1.0:0.0	.	381	Q9UQE7	SMC3_HUMAN	Q	381	ENSP00000354720:R381Q	ENSP00000354720:R381Q	R	+	2	0	SMC3	112333981	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.405000	0.97313	2.725000	0.93324	0.460000	0.39030	CGA	-	HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.378	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	SMC3	protein_coding	OTTHUMT00000050337.1	G	NM_005445		112333981	+1	no_errors	NM_005445.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
DOCK1	1793	genome.wustl.edu	37	10	128840889	128840889	+	Splice_Site	SNP	T	T	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr10:128840889T>A	ENST00000280333.6	+	20	2057	c.1948T>A	c.(1948-1950)Ttt>Att	p.F650I		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	650					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GTCTATGCAGTTTCTTCAGGA	0.468																																						dbGAP											0			10											170.0	167.0	168.0					10																	128840889		2066	4234	6300	128730879	SO:0001630	splice_region_variant	0			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.1948-1T>A	10.37:g.128840889T>A		Somatic	138	0.00	0		3	76.92	10	WXS	Illumina HiSeq	Phase_IV	128730879	107	39.89	71	A9Z1Z5	Missense_Mutation	SNP	HMMPfam_SH3_1,HMMSmart_SH3,superfamily_SH3,superfamily_Cytochrome_c	p.F650I	ENST00000280333.6	37	c.1948		10	.	.	.	.	.	.	.	.	.	.	T	21.8	4.196671	0.79015	.	.	ENSG00000150760	ENST00000280333	T	0.22743	1.94	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	M	0.93328	3.405	0.80722	D	1	P;P	0.45827	0.758;0.867	B;B	0.41412	0.356;0.356	T	0.57888	-0.7733	9	.	.	.	.	14.8377	0.70197	0.0:0.0:0.0:1.0	.	650;650	B2RUU3;Q14185	.;DOCK1_HUMAN	I	650	ENSP00000280333:F650I	.	F	+	1	0	DOCK1	128730879	1.000000	0.71417	1.000000	0.80357	0.507000	0.33981	7.768000	0.85345	2.145000	0.66743	0.533000	0.62120	TTT	-	NULL		0.468	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	DOCK1	protein_coding	OTTHUMT00000050979.2	T	NM_001380	Missense_Mutation	128730879	+1	no_errors	ENST00000398025	ensembl	human	known	54_36p	missense	SNP	1.000	A
PUS1	80324	genome.wustl.edu	37	12	132425864	132425864	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr12:132425864A>T	ENST00000376649.3	+	5	1072	c.572A>T	c.(571-573)aAc>aTc	p.N191I	PUS1_ENST00000542167.2_Missense_Mutation_p.N138I|PUS1_ENST00000440818.2_Missense_Mutation_p.N163I|PUS1_ENST00000443358.2_Missense_Mutation_p.N163I|PUS1_ENST00000535067.1_Intron	NM_025215.5	NP_079491.2	Q9Y606	TRUA_HUMAN	pseudouridylate synthase 1	191					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|tRNA pseudouridine synthesis (GO:0031119)	mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)|pseudouridylate synthase activity (GO:0004730)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	11	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.05e-08)|Epithelial(86;2.51e-07)|all cancers(50;2.94e-07)		GGCGGGTTTAACTCCAAGAAC	0.597																																					Esophageal Squamous(102;671 2009 17384 45666)	dbGAP											0			12											83.0	66.0	72.0					12																	132425864		2203	4300	6503	130991817	SO:0001583	missense	0			AF116238	CCDS9275.2, CCDS31928.1	12q24	2004-05-17			ENSG00000177192	ENSG00000177192			15508	protein-coding gene	gene with protein product		608109				10094309	Standard	NM_001002019		Approved		uc001ujf.3	Q9Y606	OTTHUMG00000128507	ENST00000376649.3:c.572A>T	12.37:g.132425864A>T	ENSP00000365837:p.Asn191Ile	Somatic	38	0.00	0		11	56.00	14	WXS	Illumina HiSeq	Phase_IV	130991817	54	45.45	45	A8K877|B3KQC1|Q8WYT2|Q9BU44	Missense_Mutation	SNP	HMMPfam_PseudoU_synth_1,superfamily_Pseudouridine synthase	p.N191I	ENST00000376649.3	37	c.572	CCDS9275.2	12	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178917	0.78564	.	.	ENSG00000177192	ENST00000443358;ENST00000376649;ENST00000322060;ENST00000440818;ENST00000542167;ENST00000537484	T;T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44;0.44	5.37	5.37	0.77165	Pseudouridine synthase I, TruA, N-terminal (1);Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase I, TruA, alpha/beta domain (1);	0.000000	0.85682	D	0.000000	T	0.74007	0.3660	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.78494	-0.2182	10	0.87932	D	0	-12.2595	15.3712	0.74568	1.0:0.0:0.0:0.0	.	138;191	F5H1S9;Q9Y606	.;TRUA_HUMAN	I	163;191;163;163;138;166	ENSP00000392451:N163I;ENSP00000365837:N191I;ENSP00000324726:N163I;ENSP00000400032:N163I;ENSP00000438948:N138I;ENSP00000440179:N166I	ENSP00000324726:N163I	N	+	2	0	PUS1	130991817	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	7.507000	0.81676	2.042000	0.60477	0.459000	0.35465	AAC	-	HMMPfam_PseudoU_synth_1,superfamily_Pseudouridine synthase		0.597	PUS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PUS1	protein_coding	OTTHUMT00000250313.2	A	NM_025215		130991817	+1	no_errors	NM_025215.1	genbank	human	validated	54_36p	missense	SNP	1.000	T
CCDC33	80125	genome.wustl.edu	37	15	74536466	74536466	+	Silent	SNP	C	C	T	rs368462763		TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr15:74536466C>T	ENST00000398814.3	+	2	593	c.162C>T	c.(160-162)tcC>tcT	p.S54S	CCDC33_ENST00000321288.5_Silent_p.S257S	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	257								p.S257S(1)|p.S54S(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						AGGATGGCTCCGAGCCGTGGC	0.587																																						dbGAP											2	Substitution - coding silent(2)	endometrium(2)	15						C		0,4058		0,0,2029	55.0	60.0	59.0		162	-8.3	0.0	15		59	1,8369		0,1,4184	no	coding-synonymous	CCDC33	NM_025055.3		0,1,6213	TT,TC,CC		0.0119,0.0,0.0080		54/756	74536466	1,12427	2029	4185	6214	72323519	SO:0001819	synonymous_variant	0			BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.162C>T	15.37:g.74536466C>T		Somatic	159	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	72323519	229	12.21	32	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Silent	SNP	HMMPfam_C2,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)	p.S54	ENST00000398814.3	37	c.162	CCDS42058.1	15																																																																																			-	HMMPfam_C2,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)		0.587	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CCDC33	protein_coding	OTTHUMT00000419491.2	C	NM_182791		72323519	+1	no_errors	NM_025055.3	genbank	human	validated	54_36p	silent	SNP	0.120	T
SLC25A35	399512	genome.wustl.edu	37	17	8198093	8198093	+	Silent	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr17:8198093G>A	ENST00000577745.1	-	1	543	c.33C>T	c.(31-33)tgC>tgT	p.C11C	SLC25A35_ENST00000380067.2_Silent_p.C11C|SLC25A35_ENST00000396278.1_Silent_p.C11C|SLC25A35_ENST00000580340.1_Silent_p.C11C|SLC25A35_ENST00000579192.1_Silent_p.C11C			Q3KQZ1	S2535_HUMAN	solute carrier family 25, member 35	11					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.C11C(1)		breast(2)|large_intestine(2)|lung(2)	6						CACAGGCCCCGCAGGCTGCCA	0.552																																						dbGAP											1	Substitution - coding silent(1)	large_intestine(1)	17											55.0	58.0	57.0					17																	8198093		2203	4300	6503	8138818	SO:0001819	synonymous_variant	0			AY498866	CCDS11138.1	17p13.1	2013-05-22			ENSG00000125434	ENSG00000125434		"""Solute carriers"""	31921	protein-coding gene	gene with protein product		610818					Standard	NM_201520		Approved	FLJ40217	uc002gku.1	Q3KQZ1		ENST00000577745.1:c.33C>T	17.37:g.8198093G>A		Somatic	68	0.00	0		0	100.00	4	WXS	Illumina HiSeq	Phase_IV	8138818	95	37.91	58	Q494X5|Q6RGS3|Q8N7Y5	Silent	SNP	superfamily_Mitoch_carrier,HMMPfam_Mito_carr	p.C11	ENST00000577745.1	37	c.33		17																																																																																			-	superfamily_Mitoch_carrier,HMMPfam_Mito_carr		0.552	SLC25A35-002	KNOWN	basic|appris_principal	protein_coding	SLC25A35	protein_coding	OTTHUMT00000442146.1	G	NM_201520		8138818	-1	no_errors	NM_201520.1	genbank	human	provisional	54_36p	silent	SNP	0.992	A
KRT19	3880	genome.wustl.edu	37	17	39680218	39680218	+	Missense_Mutation	SNP	G	G	C	rs149987744		TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr17:39680218G>C	ENST00000361566.3	-	6	1040	c.980C>G	c.(979-981)aCg>aGg	p.T327R	KRT15_ENST00000393976.2_5'Flank|KRT15_ENST00000254043.3_5'Flank|KRT15_ENST00000393974.3_5'Flank	NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	327	Coil 2.|Necessary for interaction with PNN.|Rod.	Stutter.			cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				GCGCGCCTCCGTTTCTGCCAG	0.607																																						dbGAP											0			17											38.0	40.0	39.0					17																	39680218		2203	4294	6497	36933744	SO:0001583	missense	0				CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6436	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 19"", ""keratin, type I, 40-kd"", ""cytokeratin 19"", ""40-kDa keratin intermediate filament"""	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.980C>G	17.37:g.39680218G>C	ENSP00000355124:p.Thr327Arg	Somatic	35	5.41	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	36933744	56	37.78	34	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Missense_Mutation	SNP	superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF	p.T327R	ENST00000361566.3	37	c.980	CCDS11399.1	17	.	.	.	.	.	.	.	.	.	.	G	14.58	2.576426	0.45902	.	.	ENSG00000171345	ENST00000361566	D	0.89552	-2.53	5.17	4.18	0.49190	Filament (1);	0.151167	0.30979	N	0.008497	D	0.95909	0.8668	H	0.95574	3.69	0.80722	D	1	P;D	0.76494	0.949;0.999	P;D	0.77557	0.872;0.99	D	0.96806	0.9593	10	0.87932	D	0	.	14.1268	0.65225	0.0738:0.0:0.9262:0.0	.	490;327	B4DE59;P08727	.;K1C19_HUMAN	R	327	ENSP00000355124:T327R	ENSP00000355124:T327R	T	-	2	0	KRT19	36933744	1.000000	0.71417	0.643000	0.29450	0.038000	0.13279	6.717000	0.74707	1.155000	0.42497	0.556000	0.70494	ACG	-	HMMPfam_Filament		0.607	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRT19	protein_coding	OTTHUMT00000257285.1	G	NM_002276		36933744	-1	no_errors	NM_002276.4	genbank	human	reviewed	54_36p	missense	SNP	0.990	C
UQCC1	55245	genome.wustl.edu	37	20	33962000	33962000	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr20:33962000C>A	ENST00000374385.5	-	5	570	c.393G>T	c.(391-393)gaG>gaT	p.E131D	UQCC1_ENST00000349714.5_Intron|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000374377.5_Intron|UQCC1_ENST00000397556.3_Missense_Mutation_p.E32D|UQCC1_ENST00000374384.2_Missense_Mutation_p.E131D|UQCC1_ENST00000542501.1_Intron|UQCC1_ENST00000359226.2_Intron|UQCC1_ENST00000397554.1_Missense_Mutation_p.E131D|UQCC1_ENST00000407996.2_Intron|UQCC1_ENST00000374380.2_Missense_Mutation_p.E63D|UQCC1_ENST00000491125.1_5'UTR	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	131						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											GAAAGAATTCCTCGAAGTCAG	0.343																																						dbGAP											0			20											78.0	77.0	78.0					20																	33962000		2203	4300	6503	33425414	SO:0001583	missense	0			AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.393G>T	20.37:g.33962000C>A	ENSP00000363506:p.Glu131Asp	Somatic	112	3.45	4		17	32.00	8	WXS	Illumina HiSeq	Phase_IV	33425414	99	40.36	67	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	HMMPfam_Ubiq_cyt_C_chap	p.E131D	ENST00000374385.5	37	c.393	CCDS13252.1	20	.	.	.	.	.	.	.	.	.	.	C	10.44	1.351587	0.24512	.	.	ENSG00000101019	ENST00000374384;ENST00000374380;ENST00000374385;ENST00000397556;ENST00000424405;ENST00000438533;ENST00000397554	T;T;T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13;-0.13;-0.13	4.61	4.61	0.57282	.	0.061380	0.64402	D	0.000005	T	0.61540	0.2355	L	0.39085	1.19	0.80722	D	1	B;D;D;D;P	0.67145	0.0;0.99;0.996;0.99;0.604	B;P;P;P;B	0.59115	0.001;0.852;0.754;0.852;0.277	T	0.53892	-0.8374	10	0.13108	T	0.6	-1.4588	10.7304	0.46093	0.0:0.9109:0.0:0.0891	.	63;123;131;131;131	B1AKV5;Q59FR0;B7ZBG3;B1AKV2;Q9NVA1	.;.;.;.;UQCC_HUMAN	D	131;63;131;32;99;145;131	ENSP00000363505:E131D;ENSP00000363501:E63D;ENSP00000363506:E131D;ENSP00000380688:E32D;ENSP00000399713:E99D;ENSP00000398531:E145D;ENSP00000380686:E131D	ENSP00000363501:E63D	E	-	3	2	UQCC	33425414	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.158000	0.42329	2.540000	0.85666	0.557000	0.71058	GAG	-	NULL		0.343	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	UQCC	protein_coding	OTTHUMT00000078866.1	C	NM_018244		33425414	-1	no_errors	NM_018244.3	genbank	human	validated	54_36p	missense	SNP	1.000	A
RUNX1	861	genome.wustl.edu	37	21	36252877	36252877	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr21:36252877C>T	ENST00000344691.4	-	2	1981	c.404G>A	c.(403-405)aGg>aAg	p.R135K	RUNX1_ENST00000486278.2_Missense_Mutation_p.R138K|RUNX1_ENST00000325074.5_Missense_Mutation_p.R150K|RUNX1_ENST00000437180.1_Missense_Mutation_p.R162K|RUNX1_ENST00000399240.1_Missense_Mutation_p.R135K|RUNX1_ENST00000358356.5_Missense_Mutation_p.R135K|RUNX1_ENST00000300305.3_Missense_Mutation_p.R162K	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	135	Interaction with DNA.|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.N159fs*49(1)|p.R162K(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						ACCGACAAACCTGAGGTCATT	0.438			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	2	Substitution - Missense(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	21											122.0	108.0	113.0					21																	36252877		2203	4300	6503	35174747	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.404G>A	21.37:g.36252877C>T	ENSP00000340690:p.Arg135Lys	Somatic	49	3.92	2		230	48.31	215	WXS	Illumina HiSeq	Phase_IV	35174747	36	37.93	22	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.R162K	ENST00000344691.4	37	c.485	CCDS42922.1	21	.	.	.	.	.	.	.	.	.	.	C	36	5.747782	0.96882	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278	D;D;D;D;D;D;D;D	0.99677	-6.37;-6.37;-6.37;-6.37;-6.37;-6.37;-6.37;-6.37	5.31	5.31	0.75309	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	0.99782	0.9909	M	0.91300	3.195	0.80722	D	1	D;P;P;P;D;D;D	0.76494	0.999;0.954;0.745;0.472;0.963;0.998;0.995	D;D;D;P;D;D;D	0.85130	0.997;0.975;0.942;0.901;0.983;0.992;0.989	D	0.97315	0.9940	10	0.87932	D	0	-23.5262	19.3355	0.94316	0.0:1.0:0.0:0.0	.	162;135;135;138;162;150;135	Q2TAM6;Q01196-5;Q01196-3;C9JK12;Q01196-8;Q01196-10;Q01196	.;.;.;.;.;.;RUNX1_HUMAN	K	135;162;162;150;135;138;135;150;138	ENSP00000340690:R135K;ENSP00000300305:R162K;ENSP00000409227:R162K;ENSP00000319459:R150K;ENSP00000382184:R135K;ENSP00000351123:R135K;ENSP00000382182:R150K;ENSP00000438019:R138K	ENSP00000300305:R162K	R	-	2	0	RUNX1	35174747	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.652000	0.90054	0.655000	0.94253	AGG	-	superfamily_p53-like transcription factors,HMMPfam_Runt		0.438	RUNX1-001	KNOWN	basic|CCDS	protein_coding	RUNX1	protein_coding	OTTHUMT00000194230.1	C			35174747	-1	no_errors	NM_001754.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
U2AF1	7307	genome.wustl.edu	37	21	44524456	44524456	+	Missense_Mutation	SNP	G	G	A	rs371769427		TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chr21:44524456G>A	ENST00000291552.4	-	2	193	c.101C>T	c.(100-102)tCt>tTt	p.S34F	U2AF1_ENST00000380276.2_Missense_Mutation_p.S34F|U2AF1_ENST00000459639.1_5'UTR|U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000398137.1_5'UTR	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	34					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S34F(45)|p.S34Y(12)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						GTGCAACCGAGAGCACCTGTC	0.358			Mis		"""CLL, MDS"""																																	dbGAP		Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	57	Substitution - Missense(57)	haematopoietic_and_lymphoid_tissue(43)|lung(12)|endometrium(2)	21						G	PHE/SER,PHE/SER,	1,4405		0,1,2202	67.0	64.0	65.0		101,101,	5.5	1.0	21		65	0,8600		0,0,4300	no	missense,missense,utr-5	U2AF1	NM_001025203.1,NM_006758.2,NM_001025204.1	155,155,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,	34/241,34/241,	44524456	1,13005	2203	4300	6503	43397525	SO:0001583	missense	0			BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"""RNA binding motif (RRM) containing"""	12453	protein-coding gene	gene with protein product		191317	"""U2(RNU2) small nuclear RNA auxiliary factor binding protein"", ""U2(RNU2) small nuclear RNA auxiliary factor 1"""	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.101C>T	21.37:g.44524456G>A	ENSP00000291552:p.Ser34Phe	Somatic	39	0.00	0		78	46.94	69	WXS	Illumina HiSeq	Phase_IV	43397525	55	36.05	31	Q701P4|Q71RF1	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	p.S34F	ENST00000291552.4	37	c.101	CCDS13694.1	21	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025187	0.93518	2.27E-4	0.0	ENSG00000160201	ENST00000380276;ENST00000291552	T;T	0.46063	0.88;0.88	5.47	5.47	0.80525	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	H	0.96430	3.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.997	D	0.84864	0.0821	10	0.87932	D	0	-15.7954	19.3169	0.94218	0.0:0.0:1.0:0.0	.	34;34;34	Q69YM7;Q01081;Q701P4	.;U2AF1_HUMAN;.	F	34	ENSP00000369629:S34F;ENSP00000291552:S34F	ENSP00000291552:S34F	S	-	2	0	U2AF1	43397525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.864000	0.92294	2.560000	0.86352	0.563000	0.77884	TCT	-	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1		0.358	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	U2AF1	protein_coding	OTTHUMT00000195541.1	G	NM_006758		43397525	-1	no_errors	NM_001025203.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
PHF6	84295	genome.wustl.edu	37	X	133511712	133511713	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	-	-	-	A	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	g.chrX:133511712_133511713insA	ENST00000332070.3	+	2	267_268	c.65_66insA	c.(64-69)tcaaatfs	p.N23fs	PHF6_ENST00000370803.3_Frame_Shift_Ins_p.N23fs|PHF6_ENST00000394292.1_Frame_Shift_Ins_p.N23fs|PHF6_ENST00000416404.2_Frame_Shift_Ins_p.N23fs|PHF6_ENST00000370800.4_Frame_Shift_Ins_p.N23fs|PHF6_ENST00000370799.1_Frame_Shift_Ins_p.N23fs	NM_032458.2	NP_115834.1	Q8IWS0	PHF6_HUMAN	PHD finger protein 6	23	Extended PHD1 domain (ePHD1).				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|scaffold protein binding (GO:0097110)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(88)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(1)|skin(1)|urinary_tract(1)	103	Acute lymphoblastic leukemia(192;0.000127)					TTTTGTAAGTCAAATAGAGACA	0.416			"""F, N, Splice, Mis"""		ETP ALL																																Colon(100;666 1493 6344 21231 35807)	dbGAP		Rec	yes		X	Xq26.3	84295	PHD finger protein 6		L	0			X																																								133339379	SO:0001589	frameshift_variant	0			AB058726	CCDS14639.1, CCDS14640.1	Xq26	2014-09-17			ENSG00000156531	ENSG00000156531		"""Zinc fingers, PHD-type"""	18145	protein-coding gene	gene with protein product	"""centromere protein 31"""	300414	"""Borjeson-Forssman-Lehmann syndrome"""	BFLS, BORJ		12415272, 15466013	Standard	NM_032335		Approved	KIAA1823, MGC14797, CENP-31	uc004exk.3	Q8IWS0	OTTHUMG00000022453	ENST00000332070.3:c.68dupA	X.37:g.133511715_133511715dupA	ENSP00000329097:p.Asn23fs	Somatic	24	0.00	0		4	66.67	8	WXS	Illumina HiSeq	Phase_IV	133339378	17	64.58	31	A8K230|B4E0G4|D3DTG3|E9PC97|Q5JRC7|Q5JRC8|Q96JK3|Q9BRU0	Frame_Shift_Ins	INS	HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger	p.N23fs	ENST00000332070.3	37	c.65_66	CCDS14639.1	X																																																																																			-	NULL		0.416	PHF6-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	PHF6	protein_coding	OTTHUMT00000058367.1	-	NM_032458		133339379	+1	no_errors	NM_001015877.1	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	A
