#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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	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
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	T	T	C			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	T	T	T	C	T	T	Verified	Invalid:failed_liftOver	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chrUnknown:0T>C								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								14767	SO:0001628	intergenic_variant	0																															Unknown.37:g.0T>C		2497	1.07	27		NA	NA	NA	14767	804	16.77	165		Missense_Mutation	SNP	HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome	p.I7T		37	c.20		MT																																																																																			-	superfamily_Transmembr_di-haem_cytochrome	0	0					MT-CYB			T			14767	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000361789	ensembl	human	known	54_36p	missense	SNP	NULL	C
TFDP3	51270	genome.wustl.edu	37	X	132351106	132351106	+	Silent	SNP	G	G	A			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chrX:132351106G>A	ENST00000310125.4	-	1	1270	c.1182C>T	c.(1180-1182)aaC>aaT	p.N394N		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	394	Asp/Glu-rich (acidic; NCB domain).				cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					GGTCGTCATCGTTGTTGTCCT	0.498																																						dbGAP											0			X											95.0	93.0	94.0					X																	132351106		2201	4299	6500	132178772	SO:0001819	synonymous_variant	0			AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.1182C>T	X.37:g.132351106G>A		71	0.00	0		NA	NA	NA	132178772	98	65.87	193	Q6DK49|Q9NZ54	Silent	SNP	"HMMPfam_E2F_TDP,HMMPfam_DP,superfamily_""Winged helix"" DNA-binding domain"	p.N334	ENST00000310125.4	37	c.1002	CCDS14636.2	X																																																																																			-	NULL		0.498	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TFDP3	protein_coding	OTTHUMT00000058337.1	G	NM_016521		132178772	-1	no_errors	NM_016521.2	genbank	human	validated	54_36p	silent	SNP	1.000	A
FAM212B	55924	genome.wustl.edu	37	1	112270297	112270297	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr1:112270297C>T	ENST00000357260.5	-	2	368	c.187G>A	c.(187-189)Gtg>Atg	p.V63M	FAM212B_ENST00000444059.2_Missense_Mutation_p.V48M|FAM212B_ENST00000534365.1_Missense_Mutation_p.V63M	NM_019099.4	NP_061972.1	Q9NTI7	F212B_HUMAN	family with sequence similarity 212, member B	63										cervix(1)|endometrium(1)	2						CTGCCTGGCACAGGACCCCCT	0.607																																						dbGAP											0			1											80.0	80.0	80.0					1																	112270297		2203	4300	6503	112071820	SO:0001583	missense	0			AK055667	CCDS841.1, CCDS44195.1	1p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000197852	ENSG00000197852			28045	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 183"""	C1orf183			Standard	NM_019099		Approved	FLJ31105	uc001ebo.2	Q9NTI7	OTTHUMG00000011953	ENST00000357260.5:c.187G>A	1.37:g.112270297C>T	ENSP00000349805:p.Val63Met	248	0.80	2		1	75.00	3	112071820	539	37.10	325	B3KP38|B4DF94|Q9NTI6	Missense_Mutation	SNP	NULL	p.V63M	ENST00000357260.5	37	c.187	CCDS841.1	1	.	.	.	.	.	.	.	.	.	.	C	2.462	-0.323961	0.05350	.	.	ENSG00000197852	ENST00000357260;ENST00000534365;ENST00000444059;ENST00000527621	.	.	.	5.03	3.13	0.36017	.	0.790668	0.12052	N	0.503974	T	0.07638	0.0192	N	0.08118	0	0.09310	N	1	B;B	0.28584	0.216;0.071	B;B	0.30572	0.117;0.117	T	0.31475	-0.9942	9	0.46703	T	0.11	-11.628	7.822	0.29292	0.0:0.7241:0.0:0.2759	.	48;63	Q9NTI7-2;Q9NTI7	.;CA183_HUMAN	M	63;63;48;72	.	ENSP00000349805:V63M	V	-	1	0	C1orf183	112071820	0.139000	0.22563	0.012000	0.15200	0.033000	0.12548	3.578000	0.53892	0.482000	0.27582	0.491000	0.48974	GTG	-	NULL		0.607	FAM212B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	C1orf183	protein_coding	OTTHUMT00000033060.2	C	NM_019099		112071820	-1	no_errors	NM_019099.3	genbank	human	validated	54_36p	missense	SNP	0.002	T
FAM58BP	339521	genome.wustl.edu	37	1	200183058	200183058	+	IGR	SNP	G	G	A			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr1:200183058G>A								NR5A2 (36506 upstream) : RP11-532L16.3 (101504 downstream)																							GGAGCTCCGGGACAGCATTGT	0.572																																						dbGAP											0			1											79.0	83.0	81.0					1																	200183058		2203	4300	6503	198449681	SO:0001628	intergenic_variant	0																															1.37:g.200183058G>A		108	0.00	0		NA	NA	NA	198449681	505	32.33	246		Missense_Mutation	SNP	HMMSmart_CYCLIN,PatternScan_CYCLINS,superfamily_Cyclin_like	p.D123N		37	c.367		1																																																																																			-	HMMSmart_CYCLIN,superfamily_Cyclin_like	0	0.572					FAM58B			G			198449681	+1	no_errors	NM_001105517.1	genbank	human	inferred	54_36p	missense	SNP	1.000	A
DNMT3A	1788	genome.wustl.edu	37	2	25457242	25457242	+	Missense_Mutation	SNP	C	C	T	rs147001633	byFrequency	TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr2:25457242C>T	ENST00000264709.3	-	23	2982	c.2645G>A	c.(2644-2646)cGc>cAc	p.R882H	DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000402667.1_Missense_Mutation_p.R659H|DNMT3A_ENST00000321117.5_Missense_Mutation_p.R882H|DNMT3A_ENST00000380746.4_Missense_Mutation_p.R693H	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	882	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.		R -> C (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> H (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.|R -> P (in a patient with chronic myelomonocytic leukemia; somatic mutation). {ECO:0000269|PubMed:21828135}.		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.R882H(209)|p.R882P(5)		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)					CCTCGCCAAGCGGCTCATGTT	0.592			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	214	Substitution - Missense(214)	haematopoietic_and_lymphoid_tissue(214)	2						C	HIS/ARG,HIS/ARG,HIS/ARG	4,4402	6.2+/-15.9	0,4,2199	56.0	51.0	53.0		2645,2078,2645	5.7	1.0	2	dbSNP_134	53	5,8595	3.0+/-9.4	0,5,4295	yes	missense,missense,missense	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	29,29,29	0,9,6494	TT,TC,CC		0.0581,0.0908,0.0692	possibly-damaging,possibly-damaging,possibly-damaging	882/913,693/724,882/913	25457242	9,12997	2203	4300	6503	25310746	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.2645G>A	2.37:g.25457242C>T	ENSP00000264709:p.Arg882His	121	2.42	3		33	50.75	34	25310746	169	35.61	94	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.R882H	ENST00000264709.3	37	c.2645	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380427	0.82682	9.08E-4	5.81E-4	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97186	-4.28;-4.28;-4.28;-4.28	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.95843	0.8647	M	0.80982	2.52	0.80722	D	1	P;B	0.38922	0.651;0.11	B;B	0.23018	0.043;0.003	D	0.95939	0.8945	10	0.62326	D	0.03	-8.768	18.4404	0.90665	0.0:1.0:0.0:0.0	.	882;693	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	H	693;882;882;659	ENSP00000370122:R693H;ENSP00000324375:R882H;ENSP00000264709:R882H;ENSP00000384237:R659H	ENSP00000264709:R882H	R	-	2	0	DNMT3A	25310746	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.698000	0.92095	0.561000	0.74099	CGC	-	superfamily_S-adenosyl-L-methionine-dependent methyltransferases		0.592	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552		25310746	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
PRDM9	56979	genome.wustl.edu	37	5	23526786	23526786	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr5:23526786G>A	ENST00000296682.3	+	11	1771	c.1589G>A	c.(1588-1590)gGa>gAa	p.G530E		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	530					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGAGAGTGTGGACAAGGTTTC	0.473										HNSCC(3;0.000094)																												dbGAP											0			5											106.0	109.0	108.0					5																	23526786		2106	4263	6369	23562543	SO:0001583	missense	0			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1589G>A	5.37:g.23526786G>A	ENSP00000296682:p.Gly530Glu	144	0.00	0		NA	NA	NA	23562543	369	33.87	191	B4DX22|Q27Q50	Missense_Mutation	SNP	HMMSmart_SET,HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,HMMPfam_SSXRD,superfamily_SSF57667,superfamily_SSF82199	p.G530E	ENST00000296682.3	37	c.1589	CCDS43307.1	5	.	.	.	.	.	.	.	.	.	.	G	14.45	2.539446	0.45176	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.34859	1.34	2.53	1.57	0.23409	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.893248	0.09267	N	0.825708	T	0.29749	0.0743	L	0.31752	0.955	0.37806	D	0.927886	D	0.55385	0.971	P	0.45428	0.48	T	0.21586	-1.0241	10	0.54805	T	0.06	-2.6514	8.2322	0.31605	0.0:0.0:0.7602:0.2398	.	530	Q9NQV7	PRDM9_HUMAN	E	530;324	ENSP00000296682:G530E	ENSP00000253473:G324E	G	+	2	0	PRDM9	23562543	0.198000	0.23374	0.002000	0.10522	0.029000	0.11900	0.874000	0.28065	0.529000	0.28599	0.400000	0.26472	GGA	-	HMMSmart_ZnF_C2H2		0.473	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRDM9	protein_coding	OTTHUMT00000366375.1	G	NM_020227		23562543	+1	no_errors	NM_020227.2	genbank	human	provisional	54_36p	missense	SNP	0.974	A
RREB1	6239	genome.wustl.edu	37	6	7230591	7230591	+	Silent	SNP	C	C	G			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr6:7230591C>G	ENST00000349384.6	+	10	2573	c.2259C>G	c.(2257-2259)acC>acG	p.T753T	RREB1_ENST00000379933.3_Silent_p.T753T|RREB1_ENST00000334984.6_Silent_p.T753T|RREB1_ENST00000379938.2_Silent_p.T753T	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	753					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCCCGGACACCGTGTGCCGGC	0.672																																						dbGAP											0			6											43.0	41.0	41.0					6																	7230591		2203	4299	6502	7175590	SO:0001819	synonymous_variant	0			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.2259C>G	6.37:g.7230591C>G		53	1.85	1		35	54.55	42	7175590	79	39.85	53	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	p.T753	ENST00000349384.6	37	c.2259	CCDS34336.1	6																																																																																			-	HMMPfam_zf-C2H2,HMMSmart_ZnF_C2H2		0.672	RREB1-002	KNOWN	basic|CCDS	protein_coding	RREB1	protein_coding	OTTHUMT00000352985.1	C			7175590	+1	no_errors	NM_001003699.2	genbank	human	validated	54_36p	silent	SNP	0.984	G
MTUS1	57509	genome.wustl.edu	37	8	17541960	17541960	+	Silent	SNP	C	C	T			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr8:17541960C>T	ENST00000262102.6	-	7	2939	c.2715G>A	c.(2713-2715)ttG>ttA	p.L905L	MTUS1_ENST00000297488.6_Silent_p.L71L|MTUS1_ENST00000519263.1_Silent_p.L851L|MTUS1_ENST00000381861.3_Silent_p.L152L|MTUS1_ENST00000544260.1_Silent_p.L50L|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000381869.3_Silent_p.L851L|MIR548V_ENST00000584165.1_RNA	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	905					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TATATTGCGTCAATTCAAGTG	0.443																																						dbGAP											0			8											263.0	255.0	258.0					8																	17541960		1939	4141	6080	17586240	SO:0001819	synonymous_variant	0			AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2715G>A	8.37:g.17541960C>T		214	0.46	1		2	0.00	0	17586240	603	26.17	218	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	NULL	p.L905	ENST00000262102.6	37	c.2715	CCDS43717.1	8																																																																																			-	NULL		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	MTUS1	protein_coding	OTTHUMT00000375247.1	C	XM_372031		17586240	-1	no_errors	NM_001001924.2	genbank	human	reviewed	54_36p	silent	SNP	0.954	T
OR51A7	119687	genome.wustl.edu	37	11	4929441	4929441	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr11:4929441T>G	ENST00000359350.4	+	1	842	c.842T>G	c.(841-843)tTg>tGg	p.L281W	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	281						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATGTTCTTGTTGGTGCCGCCC	0.463																																						dbGAP											0			11											169.0	162.0	164.0					11																	4929441		2201	4298	6499	4886017	SO:0001583	missense	0			AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.842T>G	11.37:g.4929441T>G	ENSP00000352305:p.Leu281Trp	205	1.91	4		NA	NA	NA	4886017	382	37.40	230	Q6IFH8	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.L281W	ENST00000359350.4	37	c.842	CCDS31364.1	11	.	.	.	.	.	.	.	.	.	.	T	13.73	2.324280	0.41197	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.73258	-0.73	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38272	N	0.001757	D	0.89259	0.6664	H	0.97440	4.005	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84365	0.0540	10	0.87932	D	0	.	13.7058	0.62639	0.0:0.0:0.0:1.0	.	281	Q8NH64	O51A7_HUMAN	W	281;281;270	ENSP00000352305:L281W	ENSP00000352305:L281W	L	+	2	0	OR51A7	4886017	0.405000	0.25336	0.988000	0.46212	0.468000	0.32798	4.099000	0.57755	2.098000	0.63641	0.533000	0.62120	TTG	-	HMMPfam_7tm_1,superfamily_SSF81321		0.463	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR51A7	protein_coding	OTTHUMT00000142175.1	T	NM_001004749		4886017	+1	no_errors	NM_001004749.1	genbank	human	provisional	54_36p	missense	SNP	0.120	G
VPS26B	112936	genome.wustl.edu	37	11	134095072	134095072	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr11:134095072C>G	ENST00000281187.5	+	1	534	c.56C>G	c.(55-57)gCa>gGa	p.A19G	NCAPD3_ENST00000534548.2_5'Flank|VPS26B_ENST00000525095.2_Missense_Mutation_p.A19G|NCAPD3_ENST00000526422.1_5'Flank	NM_052875.3	NP_443107.1	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B (S. pombe)	19					protein transport (GO:0015031)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)	14	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		CTGAACGATGCAGAGAGTAGG	0.617																																					Colon(171;1263 1952 15904 45703 47982)	dbGAP											0			11											67.0	71.0	70.0					11																	134095072		2201	4297	6498	133600282	SO:0001583	missense	0				CCDS8495.1	11q25	2008-02-05	2007-01-12		ENSG00000151502	ENSG00000151502			28119	protein-coding gene	gene with protein product		610027	"""vacuolar protein sorting 26 homolog B (yeast)"""			16190980	Standard	NM_052875		Approved	MGC10485, Pep8b	uc001qhe.3	Q4G0F5	OTTHUMG00000167175	ENST00000281187.5:c.56C>G	11.37:g.134095072C>G	ENSP00000281187:p.Ala19Gly	249	7.43	20		41	46.75	36	133600282	97	48.13	90	Q96A55	Missense_Mutation	SNP	HMMPfam_Vps26	p.A19G	ENST00000281187.5	37	c.56	CCDS8495.1	11	.	.	.	.	.	.	.	.	.	.	C	16.23	3.064089	0.55432	.	.	ENSG00000151502	ENST00000281187;ENST00000525095	.	.	.	4.82	4.82	0.62117	.	0.056183	0.64402	D	0.000001	T	0.50377	0.1612	L	0.36672	1.1	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43893	-0.9363	9	0.20046	T	0.44	-17.6543	13.6091	0.62065	0.0:0.8443:0.1557:0.0	.	19	Q4G0F5	VP26B_HUMAN	G	19	.	ENSP00000281187:A19G	A	+	2	0	VPS26B	133600282	0.975000	0.34042	1.000000	0.80357	0.987000	0.75469	2.448000	0.44926	2.194000	0.70268	0.563000	0.77884	GCA	-	HMMPfam_Vps26		0.617	VPS26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VPS26B	protein_coding	OTTHUMT00000393591.1	C	NM_052875		133600282	+1	no_errors	NM_052875.3	genbank	human	validated	54_36p	missense	SNP	0.999	G
KRTAP4-2	85291	genome.wustl.edu	37	17	39334314	39334314	+	Missense_Mutation	SNP	A	A	T	rs200720939		TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr17:39334314A>T	ENST00000377726.2	-	1	146	c.103T>A	c.(103-105)Tgc>Agc	p.C35S		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	35	20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament (GO:0045095)				kidney(2)|lung(4)|upper_aerodigestive_tract(1)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGGCGGCAGCAGGTGGTCCTG	0.657																																						dbGAP											0			17											48.0	52.0	50.0					17																	39334314		2199	4289	6488	36587840	SO:0001583	missense	0			AJ406934	CCDS11384.1	17q21.2	2013-06-25			ENSG00000244537	ENSG00000244537		"""Keratin associated proteins"""	18900	protein-coding gene	gene with protein product						11279113	Standard	NM_033062		Approved	KAP4.2	uc002hwd.3	Q9BYR5	OTTHUMG00000133437	ENST00000377726.2:c.103T>A	17.37:g.39334314A>T	ENSP00000366955:p.Cys35Ser	72	1.37	1		NA	NA	NA	36587840	213	19.55	52	A0JP64	Missense_Mutation	SNP	HMMPfam_Keratin_B2	p.C35S	ENST00000377726.2	37	c.103	CCDS11384.1	17	.	.	.	.	.	.	.	.	.	.	.	9.002	0.980423	0.18812	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.02085	4.46	4.24	4.24	0.50183	.	0.212644	0.23275	U	0.049980	T	0.10035	0.0246	H	0.95402	3.665	0.32423	N	0.54916	B	0.33883	0.43	B	0.40602	0.334	T	0.00912	-1.1517	10	0.49607	T	0.09	.	11.5905	0.50943	1.0:0.0:0.0:0.0	.	35	Q9BYR5	KRA42_HUMAN	S	35;152	ENSP00000366955:C35S	ENSP00000366955:C35S	C	-	1	0	KRTAP4-2	36587840	0.997000	0.39634	0.987000	0.45799	0.045000	0.14185	4.092000	0.57707	1.667000	0.50832	0.421000	0.28195	TGC	-	HMMPfam_Keratin_B2		0.657	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP4-2	protein_coding	OTTHUMT00000257305.1	A			36587840	-1	no_errors	NM_033062.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
KRT13	3860	genome.wustl.edu	37	17	39658952	39658952	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr17:39658952G>A	ENST00000246635.3	-	5	1056	c.1010C>T	c.(1009-1011)tCc>tTc	p.S337F	KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000587544.1_Missense_Mutation_p.S337F|KRT13_ENST00000336861.3_Missense_Mutation_p.S337F|AC019349.5_ENST00000411759.1_RNA	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	337	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				GCTCAGCTGGGACTGCAGCTC	0.587																																						dbGAP											0			17											138.0	123.0	128.0					17																	39658952		2203	4300	6503	36912478	SO:0001583	missense	0				CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6415	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 13"", ""cytokeratin 13"""	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.1010C>T	17.37:g.39658952G>A	ENSP00000246635:p.Ser337Phe	151	0.00	0		NA	NA	NA	36912478	188	32.63	93	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF	p.S337F	ENST00000246635.3	37	c.1010	CCDS11396.1	17	.	.	.	.	.	.	.	.	.	.	G	19.35	3.811282	0.70797	.	.	ENSG00000171401	ENST00000246635;ENST00000336861;ENST00000157775	D;D	0.89939	-2.59;-2.59	4.45	4.45	0.53987	Filament (1);	0.000000	0.45606	D	0.000355	D	0.94558	0.8247	M	0.93720	3.45	0.48395	D	0.999648	P;P;P;P	0.47962	0.903;0.828;0.794;0.828	P;P;P;P	0.53912	0.618;0.737;0.618;0.737	D	0.95923	0.8932	10	0.87932	D	0	.	15.7991	0.78436	0.0:0.0:1.0:0.0	.	325;337;337;337	P13646-2;A1A4E9;P13646-3;P13646	.;.;.;K1C13_HUMAN	F	337;337;325	ENSP00000246635:S337F;ENSP00000336604:S337F	ENSP00000157775:S325F	S	-	2	0	KRT13	36912478	1.000000	0.71417	0.995000	0.50966	0.773000	0.43773	7.753000	0.85153	2.460000	0.83146	0.478000	0.44815	TCC	-	superfamily_Prefoldin,HMMPfam_Filament		0.587	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KRT13	protein_coding	OTTHUMT00000257297.1	G	NM_153490		36912478	-1	no_errors	NM_153490.3	genbank	human	reviewed	54_36p	missense	SNP	0.999	A
COL18A1	80781	genome.wustl.edu	37	21	46841432	46841432	+	Intron	SNP	G	G	A			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr21:46841432G>A	ENST00000400337.2	+	2	200				COL18A1-AS1_ENST00000397787.1_RNA|COL18A1-AS1_ENST00000485206.1_RNA	NM_130445.2	NP_569712	P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		ACGCGGGTCAGCAGCCCATCC	0.562																																						dbGAP											0			21											85.0	77.0	80.0					21																	46841432		2203	4300	6503	45665860	SO:0001627	intron_variant	0				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000400337.2:c.106+16044G>A	21.37:g.46841432G>A		42	0.00	0		NA	NA	NA	45665860	35	31.37	16	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	NULL	p.L86	ENST00000400337.2	37	c.256	CCDS42971.1	21																																																																																			-	NULL		0.562	COL18A1-002	KNOWN	basic|CCDS	protein_coding	C21orf123	protein_coding	OTTHUMT00000206828.1	G			45665860	-1	no_errors	ENST00000330082	ensembl	human	known	54_36p	silent	SNP	0.023	A
NPM1	4869	genome.wustl.edu	37	5	170837545	170837546	+	Frame_Shift_Ins	INS	-	-	CTGC			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	-	-	-	CTGC	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr5:170837545_170837546insCTGC	ENST00000296930.5	+	11	1162_1163	c.861_862insCTGC	c.(862-864)tggfs	p.W288fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.W259fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.W288fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(12)|p.W288fs*>9(2)|p.W288fs*10(2)|p.L287F(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTCAAGATCTCTGGCAGTGGAG	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	17	Insertion - Frameshift(14)|Complex - frameshift(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(17)	5																																								170770151	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	Exception_encountered	5.37:g.170837545_170837546insCTGC	ENSP00000296930:p.Trp288fs	NA	NA	NA		NA	NA	NA	170770150	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W287fs	ENST00000296930.5	37	c.861_862	CCDS4376.1	5																																																																																			-	NULL		0.312	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770151	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	CTGC
HNRNPK	3190	genome.wustl.edu	37	9	86591919	86591920	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	GA	GA	GA	-	GA	GA	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr9:86591919_86591920delGA	ENST00000376264.2	-	5	461_462	c.203_204delTC	c.(202-204)ctcfs	p.L68fs	RP11-575L7.8_ENST00000448389.1_RNA|HNRNPK_ENST00000351839.3_Frame_Shift_Del_p.L68fs|HNRNPK_ENST00000376263.3_Frame_Shift_Del_p.L68fs|HNRNPK_ENST00000376281.4_Frame_Shift_Del_p.L68fs|HNRNPK_ENST00000360384.5_Frame_Shift_Del_p.L68fs	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	68	2 X 22 AA approximate repeats.|5 X 4 AA repeats of G-X-G-G.|Interaction with ASFV p30.|KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.|Necessary for interaction with DDX1.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|regulation of low-density lipoprotein particle clearance (GO:0010988)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|single-stranded DNA binding (GO:0003697)			endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						CGTCTGTACGGAGAGCCTTAAT	0.337																																						dbGAP											0			9																																								85781740	SO:0001589	frameshift_variant	0				CCDS6667.1, CCDS6668.1	9q21.32-q21.33	2011-10-24		2008-04-18	ENSG00000165119	ENSG00000165119			5044	protein-coding gene	gene with protein product	"""transformation upregulated nuclear protein"""	600712		HNRPK		8107114	Standard	NM_031263		Approved	CSBP, TUNP	uc004anf.4	P61978	OTTHUMG00000020107	ENST00000376264.2:c.203_204delTC	9.37:g.86591921_86591922delGA	ENSP00000365440:p.Leu68fs	0	0.00	0		0	23.08	3	85781739	0	29.32	73	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Frame_Shift_Del	DEL	HMMSmart_SM00322,HMMPfam_ROKNT,HMMPfam_KH_1,superfamily_Eukaryotic type KH-domain (KH-domain type I)	p.L68fs	ENST00000376264.2	37	c.204_203	CCDS6667.1	9																																																																																			-	HMMSmart_SM00322,HMMPfam_KH_1,superfamily_Eukaryotic type KH-domain (KH-domain type I)		0.337	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	HNRNPK	protein_coding	OTTHUMT00000052846.2	GA			85781740	-1	no_errors	NM_002140.3	genbank	human	reviewed	54_36p	frame_shift_del	DEL	0.999:1.000	-
USP10	9100	genome.wustl.edu	37	16	84779243	84779243	+	Frame_Shift_Del	DEL	C	C	-	rs199654727		TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr16:84779243delC	ENST00000219473.7	+	4	1269	c.1156delC	c.(1156-1158)ccgfs	p.P386fs	USP10_ENST00000570191.1_Frame_Shift_Del_p.P390fs	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	386					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						AGGGCTTGTTCCGGTTTCAGA	0.468																																						dbGAP											0			16											14.0	15.0	15.0					16																	84779243		1860	4111	5971	83336744	SO:0001589	frameshift_variant	0			D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.1156delC	16.37:g.84779243delC	ENSP00000219473:p.Pro386fs	36	0.00	0		16	15.00	3	83336744	215	27.00	81	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Frame_Shift_Del	DEL	HMMPfam_UCH,HMMPfam_PAM2,PatternScan_UCH_2_1,PatternScan_UCH_2_2,superfamily_SSF54001	p.P386fs	ENST00000219473.7	37	c.1156	CCDS45537.1	16																																																																																			-	NULL		0.468	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	USP10	protein_coding	OTTHUMT00000433660.1	C			83336744	+1	no_errors	NM_005153.2	genbank	human	reviewed	54_36p	frame_shift_del	DEL	1.000	-
MIR518A2	574491	genome.wustl.edu	37	19	54240182	54240183	+	RNA	DEL	TT	TT	-			TCGA-AB-2859-03B-01W-0728-08	TCGA-AB-2859-11B-01W-0729-08	TT	TT	TT	-	TT	TT	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b4f66f34-4aa4-413b-b4ca-21ec2c850d0c	db602e88-3b9e-4f38-9035-91bdcec0962f	g.chr19:54240182_54240183delTT	ENST00000384966.1	+	0	0				MIR516B1_ENST00000385211.1_RNA|MIR518D_ENST00000385014.1_RNA	NR_030213.1				microRNA 518a-2																		AGGGTTACTCTTTGAGAAAAGC	0.411																																						dbGAP											0			19																																								58931995			0					19q13.42	2011-09-12		2008-12-18	ENSG00000207699	ENSG00000207699		"""ncRNAs / Micro RNAs"""	32123	non-coding RNA	RNA, micro				MIRN518A-2, MIRN518A2			Standard	NR_030213		Approved	hsa-mir-518a-2	uc021vaq.1				19.37:g.54240182_54240183delTT		0	0.00	0		0	0.00	0	58931994	0	9.76	8		RNA	DEL	-	NULL	ENST00000384966.1	37	NULL		19																																																																																			-	-		0.411	MIR518A2-201	KNOWN	basic	miRNA	MIRN516B1	miRNA		TT	NR_030213		58931995	+1	no_errors	ENST00000385211	ensembl	human	known	54_36p	rna	DEL	0.000:0.000	-
