#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	G	G	A			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	G	G	G	A	G	G	Verified	Invalid:failed_liftOver	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chrUnknown:0G>A								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								3919	SO:0001628	intergenic_variant	0																															Unknown.37:g.0G>A		3558	0.44	16		NA	NA	NA	3919	1035	64.27	1880		Silent	SNP	HMMPfam_NADHdh,PatternScan_COMPLEX1_ND1_1,PatternScan_COMPLEX1_ND1_2	p.E204		37	c.612		MT																																																																																			-	HMMPfam_NADHdh,PatternScan_COMPLEX1_ND1_2	0	0					MT-ND1			G			3919	+1	no_errors	ENST00000361390	ensembl	human	known	54_36p	silent	SNP	NULL	A
PHIP	55023	genome.wustl.edu	37	6	79735852	79735852	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chr6:79735852C>A	ENST00000275034.4	-	8	797	c.630G>T	c.(628-630)tgG>tgT	p.W210C		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	210					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CATCTGTTGCCCATATTTTCA	0.348																																						dbGAP											0			6											235.0	227.0	230.0					6																	79735852		2203	4300	6503	79792571	SO:0001583	missense	0			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.630G>T	6.37:g.79735852C>A	ENSP00000275034:p.Trp210Cys	155	0.00	0		56	15.15	10	79792571	133	15.72	25	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain,HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,PatternScan_BROMODOMAIN_1,PatternScan_WD_REPEATS_1,HMMPfam_WD40	p.W210C	ENST00000275034.4	37	c.630	CCDS4987.1	6	.	.	.	.	.	.	.	.	.	.	C	23.4	4.413535	0.83449	.	.	ENSG00000146247	ENST00000275034	D	0.83506	-1.73	5.56	5.56	0.83823	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	D	0.94125	0.8116	H	0.96662	3.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95673	0.8725	9	.	.	.	-5.7854	18.5098	0.90911	0.0:1.0:0.0:0.0	.	210;210	A7J992;Q8WWQ0	.;PHIP_HUMAN	C	210	ENSP00000275034:W210C	.	W	-	3	0	PHIP	79792571	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.600000	0.87896	0.650000	0.86243	TGG	-	HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,HMMPfam_WD40		0.348	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHIP	protein_coding	OTTHUMT00000041297.2	C			79792571	-1	no_errors	NM_017934.5	genbank	human	validated	54_36p	missense	SNP	1.000	A
AK9	221264	genome.wustl.edu	37	6	109814625	109814625	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chr6:109814625G>A	ENST00000424296.2	-	41	5759	c.5683C>T	c.(5683-5685)Cat>Tat	p.H1895Y	RP5-919F19.5_ENST00000423747.2_RNA	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1895					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTTAACTTATGATCAAAGTCA	0.393																																						dbGAP											0			6											201.0	201.0	201.0					6																	109814625		2203	4300	6503	109921318	SO:0001583	missense	0			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.5683C>T	6.37:g.109814625G>A	ENSP00000410186:p.His1895Tyr	105	0.93	1		4	33.33	2	109921318	115	39.58	76	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	NULL	p.H294Y	ENST00000424296.2	37	c.880	CCDS55048.1	6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.25|11.25	1.582039|1.582039	0.28180|0.28180	.|.	.|.	ENSG00000155085|ENSG00000155085	ENST00000424296|ENST00000490722	T|.	0.65178|.	-0.14|.	5.58|5.58	3.79|3.79	0.43588|0.43588	.|.	0.527425|.	0.21983|.	N|.	0.066277|.	T|T	0.42086|0.42086	0.1187|0.1187	L|L	0.53249|0.53249	1.67|1.67	0.54753|0.54753	D|D	0.999982|0.999982	P;B|.	0.34977|.	0.478;0.003|.	B;B|.	0.33295|.	0.161;0.005|.	T|T	0.37197|0.37197	-0.9716|-0.9716	9|5	.|.	.|.	.|.	.|.	6.3624|6.3624	0.21435|0.21435	0.2146:0.1326:0.6529:0.0|0.2146:0.1326:0.6529:0.0	.|.	280;1895|.	B7ZL24;Q5TCS8|.	.;AKD1_HUMAN|.	Y|L	1895|295	ENSP00000410186:H1895Y|.	.|.	H|S	-|-	1|2	0|0	AKD1|AKD1	109921318|109921318	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.886000|0.886000	0.51366|0.51366	1.950000|1.950000	0.40323|0.40323	0.710000|0.710000	0.31997|0.31997	0.591000|0.591000	0.81541|0.81541	CAT|TCA	-	NULL		0.393	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	C6orf224	protein_coding		G	NM_001145128		109921318	-1	no_errors	NM_173559.1	genbank	human	predicted	54_36p	missense	SNP	0.975	A
MLLT4	4301	genome.wustl.edu	37	6	168352305	168352305	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chr6:168352305G>A	ENST00000447894.2	+	29	4250	c.4250G>A	c.(4249-4251)cGt>cAt	p.R1417H	MLLT4_ENST00000392112.1_Missense_Mutation_p.R1400H|MLLT4_ENST00000392108.3_Missense_Mutation_p.R1417H|MLLT4_ENST00000366806.2_Missense_Mutation_p.R1417H|MLLT4_ENST00000351017.4_Missense_Mutation_p.R1424H|MLLT4_ENST00000400822.3_Missense_Mutation_p.R1416H|MLLT4_ENST00000344191.4_Missense_Mutation_p.R1417H			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1417					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GAACATCAGCGTTGGTATGAG	0.592			T	MLL	AL																																	dbGAP		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	0			6											92.0	86.0	88.0					6																	168352305		2203	4300	6503	168095154	SO:0001583	missense	0			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.4250G>A	6.37:g.168352305G>A	ENSP00000404595:p.Arg1417His	43	2.27	1		NA	NA	NA	168095154	124	32.97	61	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	HMMPfam_RA,HMMSmart_RA,HMMPfam_FHA,HMMSmart_FHA,HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ,superfamily_SMAD_FHA,HMMPfam_DIL,superfamily_SSF54236	p.R1416H	ENST00000447894.2	37	c.4247		6	.	.	.	.	.	.	.	.	.	.	G	17.32	3.360765	0.61403	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.05996	3.58;3.44;3.58;3.54;3.36;3.45;3.44	5.52	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.15176	0.0366	M	0.72479	2.2	0.51482	D	0.999921	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.997;0.997	T	0.00790	-1.1565	10	0.72032	D	0.01	-8.0543	14.1994	0.65693	0.0714:0.0:0.9286:0.0	.	1417;1416;1417;1401	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	H	1417;1424;1417;1417;1400;1417;1416;1417	ENSP00000341118:R1417H;ENSP00000252692:R1424H;ENSP00000375956:R1417H;ENSP00000355771:R1417H;ENSP00000375960:R1400H;ENSP00000383623:R1416H;ENSP00000404595:R1417H	ENSP00000345834:R1417H	R	+	2	0	MLLT4	168095154	1.000000	0.71417	0.802000	0.32245	0.086000	0.17979	6.948000	0.75965	1.333000	0.45449	0.655000	0.94253	CGT	-	NULL		0.592	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	MLLT4	protein_coding	OTTHUMT00000372077.1	G	NM_005936		168095154	+1	no_errors	NM_001040001.1	genbank	human	validated	54_36p	missense	SNP	1.000	A
FAM155A	728215	genome.wustl.edu	37	13	107822902	107822902	+	Silent	SNP	G	G	A			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chr13:107822902G>A	ENST00000375915.2	-	3	1458	c.1320C>T	c.(1318-1320)gcC>gcT	p.A440A		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	440						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						AGCTCAGTCCGGCTGTGTTCT	0.532																																						dbGAP											0			13											145.0	113.0	124.0					13																	107822902		2203	4300	6503	106620903	SO:0001819	synonymous_variant	0			L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.1320C>T	13.37:g.107822902G>A		299	0.33	1		NA	NA	NA	106620903	243	30.57	107	B2RUV1|B7Z334	Silent	SNP	NULL	p.A440	ENST00000375915.2	37	c.1320	CCDS32006.1	13																																																																																			-	NULL		0.532	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM155A	protein_coding	OTTHUMT00000045736.2	G	NM_001080396		106620903	-1	no_errors	NM_001080396.1	genbank	human	provisional	54_36p	silent	SNP	0.272	A
OR11H12	440153	genome.wustl.edu	37	14	19378512	19378512	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chr14:19378512C>A	ENST00000550708.1	+	1	991	c.919C>A	c.(919-921)Ctc>Atc	p.L307I		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TATCTATAGCCTCCAGAATAA	0.428																																						dbGAP											0			14											10.0	12.0	11.0					14																	19378512		1699	3687	5386	18448512	SO:0001583	missense	0				CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"""GPCR / Class A : Olfactory receptors"""	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.919C>A	14.37:g.19378512C>A	ENSP00000449002:p.Leu307Ile	63	0.00	0		NA	NA	NA	18448512	32	41.82	23		Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.L307I	ENST00000550708.1	37	c.919	CCDS32017.1	14	.	.	.	.	.	.	.	.	.	.	c	10.56	1.384023	0.25031	.	.	ENSG00000257115	ENST00000550708	T	0.44881	0.91	0.585	0.585	0.17428	.	0.204155	0.23694	U	0.045482	T	0.62122	0.2402	M	0.91249	3.19	0.22066	N	0.999384	D	0.71674	0.998	D	0.72625	0.978	T	0.65463	-0.6162	9	0.87932	D	0	.	3.0137	0.06052	0.0:0.6523:0.0:0.3477	.	307	B2RN74	O11HC_HUMAN	I	307	ENSP00000449002:L307I	ENSP00000449002:L307I	L	+	1	0	CR383656.1	18448512	0.153000	0.22777	0.689000	0.30133	0.318000	0.28184	-0.103000	0.10940	0.619000	0.30197	0.064000	0.15345	CTC	-	superfamily_SSF81321		0.428	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR11H12	protein_coding	OTTHUMT00000408402.1	C	NM_001013354		18448512	+1	no_errors	NM_001013354.1	genbank	human	provisional	54_36p	missense	SNP	0.968	A
RPL3L	6123	genome.wustl.edu	37	16	1991314	1991314	+	IGR	SNP	T	T	C			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chr16:1991314T>C	ENST00000268661.7	-	0	2182				MSRB1_ENST00000399753.2_Missense_Mutation_p.I50V|MSRB1_ENST00000564908.1_Missense_Mutation_p.I50V|MSRB1_ENST00000489198.1_5'UTR|MSRB1_ENST00000361871.3_Missense_Mutation_p.I50V	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						TCGGCGTGAATGGTCTCGGTG	0.622																																						dbGAP											0			16											52.0	54.0	54.0					16																	1991314		2051	4186	6237	1931315	SO:0001628	intergenic_variant	0			U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685		16.37:g.1991314T>C		48	0.00	0		52	48.00	48	1931315	24	29.41	10		Missense_Mutation	SNP	HMMPfam_SelR,superfamily_Mss4_like	p.I50V	ENST00000268661.7	37	c.148	CCDS10450.1	16	.	.	.	.	.	.	.	.	.	.	T	8.648	0.897664	0.17686	.	.	ENSG00000198736	ENST00000361871;ENST00000399753	T;T	0.76578	-1.03;-1.03	4.74	4.74	0.60224	Mss4-like (1);Methionine sulphoxide reductase B (2);	0.053525	0.64402	D	0.000001	T	0.60366	0.2263	N	0.17594	0.5	0.37359	D	0.911159	B	0.09022	0.002	B	0.15870	0.014	T	0.59526	-0.7438	10	0.33940	T	0.23	-3.1815	7.9224	0.29854	0.0:0.0939:0.0:0.9061	.	50	Q9NZV6	MSRB1_HUMAN	V	50	ENSP00000355084:I50V;ENSP00000382657:I50V	ENSP00000355084:I50V	I	-	1	0	SEPX1	1931315	0.991000	0.36638	1.000000	0.80357	0.323000	0.28346	0.157000	0.16402	1.778000	0.52293	0.533000	0.62120	ATT	-	HMMPfam_SelR,superfamily_Mss4_like		0.622	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEPX1	protein_coding	OTTHUMT00000250582.2	T	NM_005061		1931315	-1	no_errors	ENST00000399753	ensembl	human	known	54_36p	missense	SNP	1.000	C
CALR	811	genome.wustl.edu	37	19	13050446	13050447	+	Splice_Site	INS	-	-	T			TCGA-AB-2897-03A-01W-0733-08	TCGA-AB-2897-11A-01W-0732-08	-	-	-	T	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	c5cf74cb-e85e-4c8e-867f-e31d71d24045	0ca12dcf-77b9-4ee1-9509-b7619271484c	g.chr19:13050446_13050447insT	ENST00000316448.5	+	3	470		c.e3+1			NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	ATCATGTTTGGTGAGGGCCTGC	0.475																																						dbGAP											0			19																																								12911447	SO:0001630	splice_region_variant	0			M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"""Sicca syndrome antigen A (autoantigen Ro; calreticulin)"", ""autoantigen Ro"""	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.397+1->T	19.37:g.13050447_13050447dupT		110	0.00	0		4965	0.62	31	12911446	102	11.30	13	Q6IAT4|Q9UDG2	Splice_Site	INS	-	e3+1	ENST00000316448.5	37	c.397+1_397+1	CCDS12288.1	19																																																																																			-	-		0.475	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CALR	protein_coding	OTTHUMT00000451952.1	-	NM_004343	Intron	12911447	+1	no_errors	NM_004343.3	genbank	human	reviewed	54_36p	splice_site_ins	INS	1.000:1.000	T
