#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
NADK	65220	hgsc.bcm.edu	37	1	1686870	1686870	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:1686870A>T	ENST00000341426.5	-	7	852	c.631T>A	c.(631-633)Ttc>Atc	p.F211I	NADK_ENST00000342348.5_Missense_Mutation_p.F179I|NADK_ENST00000341991.3_Missense_Mutation_p.F211I|NADK_ENST00000492768.1_5'Flank|NADK_ENST00000378625.1_Missense_Mutation_p.F356I|NADK_ENST00000344463.4_Missense_Mutation_p.F356I	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	211					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		GGGGTCAGGAAGCCCAGGGAG	0.607																																					p.F356I		Atlas-SNP	.											.	NADK	79	.	0			c.T1066A						PASS	.						156.0	158.0	157.0					1																	1686870		2203	4300	6503	SO:0001583	missense	65220	exon9			TCAGGAAGCCCAG	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.631T>A	chr1.hg19:g.1686870A>T	ENSP00000341679:p.Phe211Ile	259.0	0.0	.		268.0	48.0	.	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Missense_Mutation	SNP	ENST00000341426.5	hg19	CCDS30565.1	.	.	.	.	.	.	.	.	.	.	A	33	5.256937	0.95336	.	.	ENSG00000008130	ENST00000341426;ENST00000341991;ENST00000378625;ENST00000344463;ENST00000342348;ENST00000400922	T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13	5.25	5.25	0.73442	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	D	0.84502	0.5486	H	0.98199	4.17	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;0.997;0.995;0.994	D	0.90129	0.4205	10	0.87932	D	0	-34.481	14.2701	0.66147	1.0:0.0:0.0:0.0	.	179;356;356;211	F5GXR5;Q9H2P2;Q5QPS4;O95544	.;.;.;NADK_HUMAN	I	211;211;356;356;179;179	ENSP00000341679:F211I;ENSP00000344340:F211I;ENSP00000367890:F356I;ENSP00000340925:F356I;ENSP00000339727:F179I;ENSP00000383713:F179I	ENSP00000341679:F211I	F	-	1	0	NADK	1676730	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.884000	0.92432	2.119000	0.64992	0.379000	0.24179	TTC	.	.	.	none		0.607	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
RPL11	6135	hgsc.bcm.edu	37	1	24021204	24021204	+	Missense_Mutation	SNP	T	T	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:24021204T>G	ENST00000374550.3	+	4	364	c.319T>G	c.(319-321)Ttt>Gtt	p.F107V	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	107					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)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|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)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		AAACTTTGGTTTTGGGATCCA	0.403																																					p.F107V		Atlas-SNP	.											.	RPL11	21	.	0			c.T319G						PASS	.						146.0	143.0	144.0					1																	24021204		2203	4300	6503	SO:0001583	missense	6135	exon4			TTTGGTTTTGGGA	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"""L ribosomal proteins"""	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.319T>G	chr1.hg19:g.24021204T>G	ENSP00000363676:p.Phe107Val	127.0	0.0	.		131.0	43.0	.	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	hg19	CCDS238.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.400589	0.83120	.	.	ENSG00000142676	ENST00000374550;ENST00000443624;ENST00000458455	D;D;D	0.82344	-1.6;-1.6;-1.6	5.85	5.85	0.93711	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	D	0.94159	0.8126	H	0.96301	3.8	0.80722	D	1	P;P	0.52061	0.938;0.95	D;D	0.80764	0.974;0.994	D	0.95729	0.8773	10	0.87932	D	0	-9.5649	16.233	0.82357	0.0:0.0:0.0:1.0	.	106;107	P62913-2;P62913	.;RL11_HUMAN	V	107;105;105	ENSP00000363676:F107V;ENSP00000390839:F105V;ENSP00000398888:F105V	ENSP00000363676:F107V	F	+	1	0	RPL11	23893791	1.000000	0.71417	0.993000	0.49108	0.476000	0.33039	7.874000	0.87199	2.239000	0.73571	0.529000	0.55759	TTT	.	.	.	none		0.403	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975	
ZSCAN20	7579	hgsc.bcm.edu	37	1	33956714	33956714	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:33956714A>G	ENST00000361328.3	+	6	1009	c.856A>G	c.(856-858)Agc>Ggc	p.S286G	ZSCAN20_ENST00000373413.2_Missense_Mutation_p.S232G	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	286					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TGGGAAAAGGAGCACTGCAGA	0.468																																					p.S286G		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.A856G						PASS	.						55.0	55.0	55.0					1																	33956714		1886	4113	5999	SO:0001583	missense	7579	exon6			AAAAGGAGCACTG	X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"""-"", ""Zinc fingers, C2H2-type"""	13093	protein-coding gene	gene with protein product		611315	"""zinc finger protein 31 (KOX 29)"", ""zinc finger protein 31"""	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.856A>G	chr1.hg19:g.33956714A>G	ENSP00000355053:p.Ser286Gly	82.0	0.0	.		86.0	4.0	.	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	hg19	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	A	6.309	0.425166	0.11987	.	.	ENSG00000121903	ENST00000373411;ENST00000326544;ENST00000373413;ENST00000361328;ENST00000401072	T	0.02140	4.43	5.64	3.3	0.37823	.	1.076990	0.06981	N	0.819956	T	0.02267	0.0070	L	0.29908	0.895	0.09310	N	1	B;B;B	0.29988	0.0;0.264;0.0	B;B;B	0.28011	0.001;0.085;0.0	T	0.50583	-0.8811	10	0.26408	T	0.33	-4.0623	5.892	0.18919	0.7468:0.1676:0.0855:0.0	.	286;232;286	P17040-3;P17040-4;P17040	.;.;ZSC20_HUMAN	G	232;286;232;220;220	ENSP00000362512:S232G	ENSP00000324450:S286G	S	+	1	0	ZSCAN20	33729301	0.934000	0.31675	0.009000	0.14445	0.304000	0.27724	1.295000	0.33377	0.495000	0.27882	0.533000	0.62120	AGC	.	.	.	none		0.468	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238	
ZBTB37	84614	hgsc.bcm.edu	37	1	173839638	173839638	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:173839638T>C	ENST00000367701.5	+	2	466	c.275T>C	c.(274-276)aTa>aCa	p.I92T	ZBTB37_ENST00000432989.1_Missense_Mutation_p.I92T|GAS5_ENST00000364084.1_RNA|ZBTB37_ENST00000367702.1_Missense_Mutation_p.I92T|ZBTB37_ENST00000367704.1_Missense_Mutation_p.I92T|ZBTB37_ENST00000427304.1_Missense_Mutation_p.I92T			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	92	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						ACAGGGCGGATATGCCTGCAA	0.433																																					p.I92T		Atlas-SNP	.											.	ZBTB37	38	.	0			c.T275C						PASS	.						74.0	74.0	74.0					1																	173839638		2203	4300	6503	SO:0001583	missense	84614	exon3			GGCGGATATGCCT	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.275T>C	chr1.hg19:g.173839638T>C	ENSP00000356674:p.Ile92Thr	71.0	0.0	.		80.0	19.0	.	NM_032522	Q5TC80|Q96M87|Q9BQ88	Missense_Mutation	SNP	ENST00000367701.5	hg19	CCDS44278.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.123564	0.77436	.	.	ENSG00000185278	ENST00000367704;ENST00000427304;ENST00000432989;ENST00000367702;ENST00000367701	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.85	5.85	0.93711	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.044936	0.85682	D	0.000000	T	0.71358	0.3330	L	0.48174	1.505	0.58432	D	0.999993	D;P	0.63880	0.993;0.941	D;P	0.68039	0.955;0.736	T	0.75639	-0.3248	10	0.87932	D	0	.	16.2271	0.82306	0.0:0.0:0.0:1.0	.	92;92	Q5TC79;Q5TC79-2	ZBT37_HUMAN;.	T	92	ENSP00000356677:I92T;ENSP00000415293:I92T;ENSP00000409408:I92T;ENSP00000356675:I92T;ENSP00000356674:I92T	ENSP00000356674:I92T	I	+	2	0	ZBTB37	172106261	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.698000	0.84413	2.234000	0.73211	0.460000	0.39030	ATA	.	.	.	none		0.433	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522	
NFASC	23114	hgsc.bcm.edu	37	1	204923960	204923960	+	Missense_Mutation	SNP	C	C	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:204923960C>A	ENST00000401399.1	+	6	615	c.416C>A	c.(415-417)tCt>tAt	p.S139Y	NFASC_ENST00000367169.4_Missense_Mutation_p.S139Y|NFASC_ENST00000403080.1_Missense_Mutation_p.S139Y|NFASC_ENST00000404076.1_Missense_Mutation_p.S133Y|NFASC_ENST00000360049.4_Missense_Mutation_p.S133Y|NFASC_ENST00000339876.6_Missense_Mutation_p.S139Y|NFASC_ENST00000404907.1_Missense_Mutation_p.S133Y|NFASC_ENST00000513543.1_Missense_Mutation_p.S133Y|NFASC_ENST00000539706.1_Missense_Mutation_p.S133Y|NFASC_ENST00000367171.4_Missense_Mutation_p.S139Y|NFASC_ENST00000338515.6_Missense_Mutation_p.S139Y|NFASC_ENST00000367170.4_Missense_Mutation_p.S139Y|NFASC_ENST00000338586.6_Missense_Mutation_p.S139Y|NFASC_ENST00000367172.4_Missense_Mutation_p.S139Y			O94856	NFASC_HUMAN	neurofascin	139					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TCTCCAGAATCTCCTCTGTGG	0.597																																					p.S139Y		Atlas-SNP	.											.	NFASC	396	.	0			c.C416A						PASS	.						105.0	107.0	106.0					1																	204923960		2203	4300	6503	SO:0001583	missense	23114	exon7			CAGAATCTCCTCT	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.416C>A	chr1.hg19:g.204923960C>A	ENSP00000385637:p.Ser139Tyr	190.0	0.0	.		213.0	51.0	.	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.3|29.3	4.998077|4.998077	0.93227|0.93227	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367173|ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.72282	.|1.09;-0.64;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	.|0.000000	.|0.52532	.|D	.|0.000064	D|D	0.83069|0.83069	0.5174|0.5174	M|M	0.64260|0.64260	1.97|1.97	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.87578	.|0.998;0.977;0.992;0.977;0.99;0.976	D|D	0.84410|0.84410	0.0565|0.0565	5|10	.|0.72032	.|D	.|0.01	.|.	18.6966|18.6966	0.91603|0.91603	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|133;133;235;139;133;139	.|O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.|.;.;.;.;.;.	I|Y	109|139;139;139;139;139;139;133;133;133;139;139;139;133;139;133;133;109	.|ENSP00000356140:S139Y;ENSP00000356139:S139Y;ENSP00000356138:S139Y;ENSP00000342128:S139Y;ENSP00000344786:S139Y;ENSP00000343509:S139Y;ENSP00000438614:S133Y;ENSP00000353154:S133Y;ENSP00000356137:S139Y;ENSP00000412161:S139Y;ENSP00000384875:S139Y;ENSP00000385676:S133Y;ENSP00000385637:S139Y;ENSP00000384061:S133Y;ENSP00000425908:S133Y;ENSP00000415031:S109Y	.|ENSP00000295776:S133Y	L|S	+|+	1|2	0|0	NFASC|NFASC	203190583|203190583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	7.797000|7.797000	0.85911|0.85911	2.516000|2.516000	0.84829|0.84829	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.	.	none		0.597	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
ALPI	248	hgsc.bcm.edu	37	2	233322816	233322816	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr2:233322816C>T	ENST00000295463.3	+	8	1042	c.965C>T	c.(964-966)cCc>cTc	p.P322L		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	322					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		AGCAGGAACCCCCGCGGCTTC	0.662																																					p.P322L		Atlas-SNP	.											.	ALPI	64	.	0			c.C965T						PASS	.						58.0	65.0	63.0					2																	233322816		2203	4300	6503	SO:0001583	missense	248	exon8			GGAACCCCCGCGG	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.965C>T	chr2.hg19:g.233322816C>T	ENSP00000295463:p.Pro322Leu	105.0	0.0	.		108.0	26.0	.	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	hg19	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273284	0.40194	.	.	ENSG00000163295	ENST00000295463	D	0.96300	-3.97	4.46	4.46	0.54185	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.106561	0.64402	D	0.000003	D	0.97238	0.9097	M	0.93328	3.405	0.58432	D	0.999999	P	0.38223	0.623	B	0.40741	0.339	D	0.98720	1.0708	10	0.62326	D	0.03	.	16.2794	0.82664	0.0:1.0:0.0:0.0	.	322	P09923	PPBI_HUMAN	L	322	ENSP00000295463:P322L	ENSP00000295463:P322L	P	+	2	0	ALPI	233031060	1.000000	0.71417	0.784000	0.31847	0.009000	0.06853	7.289000	0.78701	2.318000	0.78349	0.561000	0.74099	CCC	.	.	.	none		0.662	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
PLXNB1	5364	hgsc.bcm.edu	37	3	48459373	48459373	+	Silent	SNP	C	C	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:48459373C>A	ENST00000358536.4	-	16	3590	c.3321G>T	c.(3319-3321)acG>acT	p.T1107T	PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Silent_p.T924T|PLXNB1_ENST00000456774.1_Silent_p.T924T|PLXNB1_ENST00000296440.6_Silent_p.T1107T	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1107	IPT/TIG 1.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTCCAGCCACCGTGACCATGC	0.662																																					p.T1107T		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G3321T						PASS	.						60.0	58.0	59.0					3																	48459373		2203	4300	6503	SO:0001819	synonymous_variant	5364	exon16			AGCCACCGTGACC	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.3321G>T	chr3.hg19:g.48459373C>A		87.0	0.0	.		94.0	20.0	.	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.	.	none		0.662	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
NDUFAF3	25915	hgsc.bcm.edu	37	3	49059877	49059877	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:49059877A>T	ENST00000326925.6	+	2	1310	c.176A>T	c.(175-177)tAc>tTc	p.Y59F	MIR191_ENST00000384873.1_RNA|NDUFAF3_ENST00000395458.2_Missense_Mutation_p.Y2F|NDUFAF3_ENST00000451378.2_Missense_Mutation_p.Y2F|DALRD3_ENST00000440857.1_5'Flank|MIR425_ENST00000362162.1_RNA|DALRD3_ENST00000496568.1_5'Flank|DALRD3_ENST00000313778.5_5'Flank|NDUFAF3_ENST00000326912.4_Missense_Mutation_p.Y2F	NM_199069.1	NP_951032.1	Q9BU61	NDUF3_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 3	59					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	8						CAGGCAATGTACATCGACAGC	0.652																																					p.Y59F		Atlas-SNP	.											.	NDUFAF3	9	.	0			c.A176T						PASS	.						23.0	24.0	23.0					3																	49059877		2200	4299	6499	SO:0001583	missense	25915	exon2			CAATGTACATCGA		CCDS2784.1, CCDS2785.1	3p21.31	2012-10-12	2012-05-08	2009-03-18	ENSG00000178057	ENSG00000178057		"""Mitochondrial respiratory chain complex assembly factors"""	29918	protein-coding gene	gene with protein product		612911	"""chromosome 3 open reading frame 60"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3"""	C3orf60		12653254, 9349717	Standard	NM_199069		Approved	MGC10527, DKFZP564J0123, E3-3, 2P1	uc003cvq.3	Q9BU61	OTTHUMG00000156773	ENST00000326925.6:c.176A>T	chr3.hg19:g.49059877A>T	ENSP00000323076:p.Tyr59Phe	66.0	0.0	.		106.0	23.0	.	NM_199069		Missense_Mutation	SNP	ENST00000326925.6	hg19	CCDS2784.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.970503	0.53614	.	.	ENSG00000178057	ENST00000326912;ENST00000326925;ENST00000395458;ENST00000451378	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.29	2.73	0.32206	.	0.264355	0.36665	N	0.002471	T	0.70885	0.3275	L	0.33485	1.01	0.31716	N	0.638898	B	0.02656	0.0	B	0.06405	0.002	T	0.58493	-0.7627	10	0.11182	T	0.66	-8.5232	4.4326	0.11535	0.598:0.0:0.09:0.312	.	59	Q9BU61	NDUF3_HUMAN	F	2;59;2;2	ENSP00000323003:Y2F;ENSP00000323076:Y59F;ENSP00000378843:Y2F;ENSP00000402465:Y2F	ENSP00000323003:Y2F	Y	+	2	0	NDUFAF3	49034881	1.000000	0.71417	0.997000	0.53966	0.638000	0.38207	4.002000	0.57053	0.833000	0.34828	0.533000	0.62120	TAC	.	.	.	none		0.652	NDUFAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345683.2	NM_199069	
DNAH1	25981	hgsc.bcm.edu	37	3	52432935	52432935	+	Silent	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:52432935A>G	ENST00000420323.2	+	76	12420	c.12159A>G	c.(12157-12159)gtA>gtG	p.V4053V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	4118					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGGGGCTGGTAGTGATGTCCT	0.552																																					p.V4053V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A12159G						PASS	.						48.0	54.0	52.0					3																	52432935		2092	4227	6319	SO:0001819	synonymous_variant	25981	exon76			GCTGGTAGTGATG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.12159A>G	chr3.hg19:g.52432935A>G		36.0	0.0	.		49.0	11.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.	.	none		0.552	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
ASCC3	10973	hgsc.bcm.edu	37	6	101296249	101296249	+	Silent	SNP	T	T	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr6:101296249T>A	ENST00000369162.2	-	4	920	c.576A>T	c.(574-576)atA>atT	p.I192I	ASCC3_ENST00000522650.1_Silent_p.I192I	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	192					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AATCTAGGCTTATAGTTTTCT	0.378																																					p.I192I		Atlas-SNP	.											.	ASCC3	205	.	0			c.A576T						PASS	.						59.0	58.0	58.0					6																	101296249		2203	4300	6503	SO:0001819	synonymous_variant	10973	exon4			TAGGCTTATAGTT	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.576A>T	chr6.hg19:g.101296249T>A		67.0	0.0	.		70.0	16.0	.	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.	.	none		0.378	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
TTI2	80185	hgsc.bcm.edu	37	8	33369560	33369560	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr8:33369560A>T	ENST00000431156.2	-	2	1190	c.572T>A	c.(571-573)tTc>tAc	p.F191Y	TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000360742.5_Missense_Mutation_p.F191Y|TTI2_ENST00000520636.1_Missense_Mutation_p.F191Y|SNORD13_ENST00000459299.1_RNA	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	191																	TCCATGTAGGAATCCTGCCAC	0.502																																					p.F191Y		Atlas-SNP	.											.	.	.	.	0			c.T572A						PASS	.						191.0	196.0	194.0					8																	33369560		2203	4300	6503	SO:0001583	missense	80185	exon2			TGTAGGAATCCTG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"""chromosome 8 open reading frame 41"", ""Tel2 interacting protein 2 homolog (S. pombe)"""	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.572T>A	chr8.hg19:g.33369560A>T	ENSP00000411169:p.Phe191Tyr	353.0	0.0	.		363.0	95.0	.	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592154	0.66219	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397	T;T;T	0.76709	-1.04;-1.04;-1.04	4.66	4.66	0.58398	.	0.101991	0.43579	D	0.000544	D	0.85102	0.5620	M	0.76838	2.35	0.25824	N	0.984245	D;D;D	0.63880	0.993;0.993;0.993	P;P;P	0.60012	0.867;0.867;0.867	T	0.79057	-0.1959	10	0.72032	D	0.01	-23.4405	11.5884	0.50931	1.0:0.0:0.0:0.0	.	191;191;191	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	Y	191	ENSP00000353971:F191Y;ENSP00000411169:F191Y;ENSP00000428401:F191Y	ENSP00000353971:F191Y	F	-	2	0	C8orf41	33489102	1.000000	0.71417	0.326000	0.25389	0.530000	0.34684	5.556000	0.67307	1.954000	0.56735	0.533000	0.62120	TTC	.	.	.	none		0.502	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
PSCA	8000	hgsc.bcm.edu	37	8	143762846	143762846	+	Missense_Mutation	SNP	C	C	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr8:143762846C>G	ENST00000301258.4	+	2	210	c.127C>G	c.(127-129)Cgc>Ggc	p.R43G	PSCA_ENST00000505305.1_3'UTR|PSCA_ENST00000513264.1_Missense_Mutation_p.R43G	NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	52	UPAR/Ly6.					anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CTGGACCGCGCGCATCCGTGA	0.607																																					p.R43G		Atlas-SNP	.											.	PSCA	9	.	0			c.C127G						PASS	.						12.0	16.0	15.0					8																	143762846		2125	4209	6334	SO:0001583	missense	8000	exon2			ACCGCGCGCATCC	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.127C>G	chr8.hg19:g.143762846C>G	ENSP00000301258:p.Arg43Gly	14.0	0.0	.		16.0	6.0	.	NM_005672	Q6UW92	Missense_Mutation	SNP	ENST00000301258.4	hg19	CCDS47925.2	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686883	0.29962	.	.	ENSG00000167653	ENST00000301258;ENST00000513264	T	0.70399	-0.48	2.97	2.09	0.27110	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.295300	0.05740	N	0.601212	T	0.75079	0.3801	M	0.72894	2.215	0.09310	N	1	P	0.43169	0.8	P	0.50162	0.633	T	0.57837	-0.7742	10	0.26408	T	0.33	.	6.0755	0.19913	0.0:0.8561:0.0:0.1439	.	52	O43653	PSCA_HUMAN	G	52	ENSP00000426508:R52G	ENSP00000301258:R52G	R	+	1	0	PSCA	143759848	0.001000	0.12720	0.001000	0.08648	0.176000	0.22953	1.247000	0.32815	0.837000	0.34925	0.456000	0.33151	CGC	.	.	.	none		0.607	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
TLN1	7094	hgsc.bcm.edu	37	9	35698169	35698169	+	Splice_Site	SNP	C	C	G	rs555751291		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr9:35698169C>G	ENST00000314888.9	-	56	7725	c.7372G>C	c.(7372-7374)Gct>Cct	p.A2458P	TLN1_ENST00000540444.1_Splice_Site_p.A2346P	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2458	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTGCCAGCAGCCTGGGCAGAG	0.512																																					p.A2458P		Atlas-SNP	.											.	TLN1	185	.	0			c.G7372C						PASS	.						74.0	68.0	70.0					9																	35698169		2203	4300	6503	SO:0001630	splice_region_variant	7094	exon56			CAGCAGCCTGGGC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.7372-1G>C	chr9.hg19:g.35698169C>G		70.0	0.0	.		83.0	14.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417660	0.83449	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.31769	1.48;1.48	4.83	4.83	0.62350	I/LWEQ (4);	0.053747	0.85682	D	0.000000	T	0.56441	0.1985	M	0.79258	2.445	0.80722	D	1	D	0.63880	0.993	D	0.65323	0.934	T	0.60747	-0.7202	10	0.56958	D	0.05	-4.1588	18.0913	0.89476	0.0:1.0:0.0:0.0	.	2458	Q9Y490	TLN1_HUMAN	P	2458;2346	ENSP00000316029:A2458P;ENSP00000442981:A2346P	ENSP00000316029:A2458P	A	-	1	0	TLN1	35688169	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.752000	0.62176	2.509000	0.84616	0.655000	0.94253	GCT	.	.	.	none		0.512	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation
IFIT5	24138	hgsc.bcm.edu	37	10	91177427	91177427	+	Silent	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr10:91177427A>G	ENST00000371795.4	+	2	684	c.471A>G	c.(469-471)caA>caG	p.Q157Q	IFIT5_ENST00000416601.1_Silent_p.Q157Q	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	157					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						AGTATTATCAAAAGGCTAAAG	0.443																																					p.Q157Q		Atlas-SNP	.											.	IFIT5	32	.	0			c.A471G						PASS	.						71.0	74.0	73.0					10																	91177427		2203	4300	6503	SO:0001819	synonymous_variant	24138	exon2			TTATCAAAAGGCT	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"""Tetratricopeptide (TTC) repeat domain containing"""	13328	protein-coding gene	gene with protein product	"""retinoic acid- and interferon-inducible protein (58kD)"""					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.471A>G	chr10.hg19:g.91177427A>G		94.0	0.0	.		102.0	24.0	.	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Silent	SNP	ENST00000371795.4	hg19	CCDS7403.1																																																																																			.	.	.	none		0.443	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420	
DMBT1	1755	hgsc.bcm.edu	37	10	124352013	124352013	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr10:124352013G>A	ENST00000338354.3	+	20	2508	c.2402G>A	c.(2401-2403)cGc>cAc	p.R801H	DMBT1_ENST00000368909.3_Missense_Mutation_p.R801H|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.R791H|DMBT1_ENST00000368955.3_Missense_Mutation_p.R791H|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000359586.6_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	801	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GATGATGTGCGCTGCTCAGGA	0.607																																					p.R801H	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	.	0			c.G2402A						PASS	.						155.0	114.0	127.0					10																	124352013		2023	4110	6133	SO:0001583	missense	1755	exon20			ATGTGCGCTGCTC		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2402G>A	chr10.hg19:g.124352013G>A	ENSP00000342210:p.Arg801His	254.0	1.0	.		321.0	21.0	.	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	G	0.015	-1.564805	0.00903	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	3.9	-0.752	0.11072	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.43233	0.1238	L	0.42008	1.315	0.09310	N	1	D;B;B;B	0.76494	0.999;0.098;0.098;0.119	D;B;B;B	0.63033	0.91;0.005;0.005;0.008	T	0.26224	-1.0109	9	0.33141	T	0.24	.	1.6023	0.02676	0.3222:0.1635:0.395:0.1192	.	562;801;791;801	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	H	801;801;801;801;801;801;791;801;791	ENSP00000342210:R801H;ENSP00000343175:R791H;ENSP00000357905:R801H;ENSP00000357951:R791H	ENSP00000342210:R801H	R	+	2	0	DMBT1	124342003	0.000000	0.05858	0.023000	0.16930	0.017000	0.09413	-1.614000	0.02057	-0.442000	0.07190	-0.219000	0.12488	CGC	.	.	.	none		0.607	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
MS4A8	83661	hgsc.bcm.edu	37	11	60482801	60482801	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:60482801A>G	ENST00000300226.2	+	7	870	c.667A>G	c.(667-669)Aac>Gac	p.N223D		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	223						integral component of membrane (GO:0016021)											CATCTATCCAAACATCTATGC	0.512																																					p.N223D		Atlas-SNP	.											.	.	.	.	0			c.A667G						PASS	.						139.0	119.0	126.0					11																	60482801		2203	4300	6503	SO:0001583	missense	83661	exon7			TATCCAAACATCT	AF237905	CCDS7990.1	11q12	2013-03-01	2013-03-01	2013-03-01	ENSG00000166959	ENSG00000166959			13380	protein-coding gene	gene with protein product		606549	"""membrane-spanning 4-domains, subfamily A, member 8B"""	MS4A8B		11245982, 11401424	Standard	NM_031457		Approved	MS4A4, CD20L5	uc001npv.3	Q9BY19	OTTHUMG00000167686	ENST00000300226.2:c.667A>G	chr11.hg19:g.60482801A>G	ENSP00000300226:p.Asn223Asp	79.0	0.0	.		75.0	6.0	.	NM_031457	Q8TCA5	Missense_Mutation	SNP	ENST00000300226.2	hg19	CCDS7990.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.374|5.374	0.254305|0.254305	0.10185|0.10185	.|.	.|.	ENSG00000166959|ENSG00000166959	ENST00000529752|ENST00000300226	T|T	0.18016|0.08008	2.24|3.14	4.21|4.21	1.87|1.87	0.25490|0.25490	.|.	.|.	.|.	.|.	.|.	T|T	0.05318|0.05318	0.0141|0.0141	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|P	.|0.37466	.|0.596	.|B	.|0.32864	.|0.154	T|T	0.39251|0.39251	-0.9623|-0.9623	7|9	0.15499|0.30078	T|T	0.54|0.28	-8.3887|-8.3887	5.7024|5.7024	0.17889|0.17889	0.7776:0.0:0.2223:0.0|0.7776:0.0:0.2223:0.0	.|.	.|223	.|Q9BY19	.|M4A8B_HUMAN	R|D	205|223	ENSP00000436857:K205R|ENSP00000300226:N223D	ENSP00000436857:K205R|ENSP00000300226:N223D	K|N	+|+	2|1	0|0	MS4A8B|MS4A8B	60239377|60239377	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	1.017000|1.017000	0.29989|0.29989	0.279000|0.279000	0.22186|0.22186	-0.290000|-0.290000	0.09829|0.09829	AAA|AAC	.	.	.	none		0.512	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1		
HNRNPUL2	221092	hgsc.bcm.edu	37	11	62489600	62489600	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:62489600C>A	ENST00000301785.5	-	7	1540	c.1348G>T	c.(1348-1350)Gag>Tag	p.E450*	HNRNPUL2-BSCL2_ENST00000403734.2_Nonsense_Mutation_p.E450*	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	450						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TCACATTCCTCTATGGTCTTG	0.517																																					p.E450X		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.G1348T						PASS	.						72.0	71.0	71.0					11																	62489600		2062	4209	6271	SO:0001587	stop_gained	221092	exon7			ATTCCTCTATGGT		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1348G>T	chr11.hg19:g.62489600C>A	ENSP00000301785:p.Glu450*	74.0	0.0	.		101.0	25.0	.	NM_001079559	Q8N3B3	Nonsense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	C	38	7.037044	0.98017	.	.	ENSG00000214753	ENST00000301785	.	.	.	5.55	5.55	0.83447	.	0.262799	0.38217	N	0.001774	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.715	17.0466	0.86505	0.0:1.0:0.0:0.0	.	.	.	.	X	450	.	ENSP00000301785:E450X	E	-	1	0	HNRNPUL2	62246176	0.998000	0.40836	0.996000	0.52242	0.992000	0.81027	1.869000	0.39519	2.894000	0.99253	0.655000	0.94253	GAG	.	.	.	none		0.517	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877	
RAD51AP1	10635	hgsc.bcm.edu	37	12	4657343	4657343	+	Splice_Site	SNP	A	A	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:4657343A>T	ENST00000544927.1	+	5	415	c.405A>T	c.(403-405)ttA>ttT	p.L135F	RAD51AP1_ENST00000321524.7_Splice_Site_p.L152F|RAD51AP1_ENST00000543041.1_Splice_Site_p.L17F|RAD51AP1_ENST00000352618.4_Splice_Site_p.L135F|RAD51AP1_ENST00000228843.9_Splice_Site_p.L152F					RAD51 associated protein 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			GTGATTATTTAGGTAAGtttt	0.289																																					p.L152F		Atlas-SNP	.											.	RAD51AP1	30	.	0			c.A456T						PASS	.						59.0	67.0	64.0					12																	4657343		2202	4298	6500	SO:0001630	splice_region_variant	10635	exon6			TTATTTAGGTAAG	AF006259	CCDS8529.1, CCDS44805.1	12p13.2-p13.1	2004-09-16			ENSG00000111247	ENSG00000111247			16956	protein-coding gene	gene with protein product		603070				9396801	Standard	NM_001130862		Approved	PIR51	uc001qmw.3	Q96B01	OTTHUMG00000168125	ENST00000544927.1:c.406+1A>T	chr12.hg19:g.4657343A>T		82.0	0.0	.		108.0	46.0	.	NM_001130862		Missense_Mutation	SNP	ENST00000544927.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.48|17.48	3.400705|3.400705	0.62177|0.62177	.|.	.|.	ENSG00000111247|ENSG00000111247	ENST00000321524;ENST00000543041;ENST00000228843;ENST00000352618;ENST00000544927|ENST00000536117	T;T;T;T;T|.	0.37058|.	1.22;1.22;1.22;1.22;1.22|.	4.97|4.97	3.82|3.82	0.43975|0.43975	.|.	0.645832|.	0.14584|.	N|.	0.310677|.	T|.	0.48223|.	0.1488|.	L|L	0.41710|0.41710	1.295|1.295	0.34395|0.34395	D|D	0.694667|0.694667	D;B;P;B|.	0.89917|.	1.0;0.185;0.492;0.047|.	D;B;B;B|.	0.85130|.	0.997;0.171;0.171;0.032|.	T|.	0.57306|.	-0.7834|.	10|.	0.46703|.	T|.	0.11|.	-1.5623|-1.5623	8.1351|8.1351	0.31050|0.31050	0.7774:0.2226:0.0:0.0|0.7774:0.2226:0.0:0.0	.|.	17;152;152;135|.	B4DUS5;Q96B01;A8K313;Q96B01-2|.	.;R51A1_HUMAN;.;.|.	F|X	152;17;152;135;135|130	ENSP00000323750:L152F;ENSP00000439960:L17F;ENSP00000228843:L152F;ENSP00000309479:L135F;ENSP00000446296:L135F|.	ENSP00000228843:L152F|.	L|R	+|+	3|1	2|2	RAD51AP1|RAD51AP1	4527604|4527604	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.882000|1.882000	0.39648|0.39648	2.085000|2.085000	0.62840|0.62840	0.482000|0.482000	0.46254|0.46254	TTA|AGA	.	.	.	none		0.289	RAD51AP1-012	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399208.1	NM_006479	Missense_Mutation
LMBR1L	55716	hgsc.bcm.edu	37	12	49500795	49500795	+	Missense_Mutation	SNP	G	G	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:49500795G>T	ENST00000267102.8	-	2	448	c.106C>A	c.(106-108)Ctc>Atc	p.L36I	LMBR1L_ENST00000547382.1_Missense_Mutation_p.L36I|LMBR1L_ENST00000553204.1_5'UTR|LMBR1L_ENST00000395141.4_5'Flank	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	36	LCN1-binding.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ATGTGGCAGAGGATGTACAGT	0.512																																					p.L36I		Atlas-SNP	.											.	LMBR1L	61	.	0			c.C106A						PASS	.						141.0	161.0	154.0					12																	49500795		2105	4230	6335	SO:0001583	missense	55716	exon2			GGCAGAGGATGTA	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"""limb region 1 homolog (mouse)-like"""			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.106C>A	chr12.hg19:g.49500795G>T	ENSP00000267102:p.Leu36Ile	219.0	0.0	.		317.0	136.0	.	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Missense_Mutation	SNP	ENST00000267102.8	hg19	CCDS8780.2	.	.	.	.	.	.	.	.	.	.	G	9.092	1.001902	0.19121	.	.	ENSG00000139636	ENST00000267102;ENST00000547382;ENST00000547675;ENST00000550137;ENST00000551854;ENST00000551782	T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36	5.25	3.45	0.39498	LMBR1-like membrane protein (1);	0.130135	0.52532	D	0.000077	T	0.19685	0.0473	N	0.16368	0.405	0.80722	D	1	P;P	0.36412	0.496;0.552	B;B	0.38428	0.126;0.273	T	0.06625	-1.0816	10	0.02654	T	1	-2.6499	10.8004	0.46485	0.1557:0.0:0.8443:0.0	.	36;36	Q6UX01-3;Q6UX01	.;LMBRL_HUMAN	I	36;36;36;36;41;36	ENSP00000267102:L36I;ENSP00000447329:L36I;ENSP00000447240:L36I;ENSP00000446641:L41I;ENSP00000449633:L36I	ENSP00000267102:L36I	L	-	1	0	LMBR1L	47787062	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	1.966000	0.40481	0.813000	0.34350	0.563000	0.77884	CTC	.	.	.	none		0.512	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113	
PAH	5053	hgsc.bcm.edu	37	12	103234258	103234258	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:103234258A>G	ENST00000553106.1	-	12	1707	c.1235T>C	c.(1234-1236)gTt>gCt	p.V412A	PAH_ENST00000307000.2_Missense_Mutation_p.V407A	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	412					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GTCGTAGCGAACTGAGAAGGG	0.448																																					p.V412A		Atlas-SNP	.											.	PAH	77	.	0			c.T1235C						PASS	.						168.0	151.0	157.0					12																	103234258		2203	4300	6503	SO:0001583	missense	5053	exon12			TAGCGAACTGAGA	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.1235T>C	chr12.hg19:g.103234258A>G	ENSP00000448059:p.Val412Ala	140.0	0.0	.		144.0	64.0	.	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	hg19	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.379312	0.82682	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	D;D	0.99755	-6.64;-6.64	5.63	5.63	0.86233	Aromatic amino acid hydroxylase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99405	0.9790	M	0.78637	2.42	0.80722	D	1	P	0.39748	0.686	B	0.42422	0.387	D	0.98750	1.0720	10	0.56958	D	0.05	-29.1046	14.8162	0.70036	1.0:0.0:0.0:0.0	.	412	P00439	PH4H_HUMAN	A	412;407	ENSP00000448059:V412A;ENSP00000303500:V407A	ENSP00000303500:V407A	V	-	2	0	PAH	101758388	1.000000	0.71417	0.993000	0.49108	0.729000	0.41735	8.471000	0.90403	2.152000	0.67230	0.459000	0.35465	GTT	.	.	.	none		0.448	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
HCAR2	338442	hgsc.bcm.edu	37	12	123187395	123187395	+	Missense_Mutation	SNP	T	T	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:123187395T>A	ENST00000328880.5	-	1	495	c.436A>T	c.(436-438)Atc>Ttc	p.I146F	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	146					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	CAAGAGATGATGGCTGCTGTC	0.557																																					p.I146F		Atlas-SNP	.											.	HCAR2	36	.	0			c.A436T						PASS	.						128.0	113.0	118.0					12																	123187395		2203	4300	6503	SO:0001583	missense	338442	exon1			AGATGATGGCTGC	AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	24827	protein-coding gene	gene with protein product	"""niacin receptor 1"""	609163	"""G protein-coupled receptor 109A"""	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.436A>T	chr12.hg19:g.123187395T>A	ENSP00000375066:p.Ile146Phe	139.0	0.0	.		167.0	36.0	.	NM_177551	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	hg19	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	T	7.211	0.595394	0.13875	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.72615	-0.67	5.55	-6.58	0.01836	GPCR, rhodopsin-like superfamily (1);	0.529882	0.18506	N	0.139204	T	0.47783	0.1464	L	0.33189	0.99	0.09310	N	1	B	0.14438	0.01	B	0.19946	0.027	T	0.45454	-0.9260	10	0.10902	T	0.67	-17.8896	9.0102	0.36137	0.0:0.4452:0.345:0.2098	.	146	Q8TDS4	HCAR2_HUMAN	F	146	ENSP00000375066:I146F	ENSP00000375066:I146F	I	-	1	0	HCAR2	121753348	0.001000	0.12720	0.001000	0.08648	0.954000	0.61252	-0.487000	0.06505	-0.941000	0.03700	0.533000	0.62120	ATC	.	.	.	none		0.557	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551	
CHRNA5	1138	hgsc.bcm.edu	37	15	78885562	78885562	+	Missense_Mutation	SNP	A	A	C	rs558115871		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr15:78885562A>C	ENST00000299565.5	+	6	1574	c.1374A>C	c.(1372-1374)ttA>ttC	p.L458F	CHRNA5_ENST00000559554.1_3'UTR|RP11-650L12.2_ENST00000567141.1_RNA|CHRNA3_ENST00000348639.3_Intron	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	458					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	CAAATATATTAATACCAGTTC	0.338																																					p.L458F		Atlas-SNP	.											.	CHRNA5	48	.	0			c.A1374C						PASS	.						104.0	94.0	97.0					15																	78885562		2196	4293	6489	SO:0001583	missense	1138	exon6			TATATTAATACCA		CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1959	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 5 (neuronal)"""	118505	"""cholinergic receptor, nicotinic, alpha polypeptide 5"""			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.1374A>C	chr15.hg19:g.78885562A>C	ENSP00000299565:p.Leu458Phe	57.0	0.0	.		59.0	13.0	.	NM_000745	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	hg19	CCDS10304.1	.	.	.	.	.	.	.	.	.	.	A	12.30	1.895619	0.33442	.	.	ENSG00000169684	ENST00000299565	T	0.78481	-1.18	5.23	-1.75	0.08031	.	0.287773	0.35870	N	0.002933	T	0.50188	0.1601	N	0.08118	0	0.47065	D	0.999304	B	0.18461	0.028	B	0.14023	0.01	T	0.08994	-1.0695	10	0.54805	T	0.06	.	3.7176	0.08444	0.5096:0.0946:0.0656:0.3301	.	458	P30532	ACHA5_HUMAN	F	458	ENSP00000299565:L458F	ENSP00000299565:L458F	L	+	3	2	CHRNA5	76672617	0.756000	0.28383	0.039000	0.18376	0.834000	0.47266	0.062000	0.14389	-0.290000	0.09025	-1.450000	0.01041	TTA	.	.	.	none		0.338	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1		
ADCY9	115	hgsc.bcm.edu	37	16	4029168	4029168	+	Silent	SNP	G	G	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr16:4029168G>A	ENST00000294016.3	-	8	3166	c.2628C>T	c.(2626-2628)ccC>ccT	p.P876P		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	876					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CGGCCAGTGCGGGAAGCGACA	0.582																																					p.P876P		Atlas-SNP	.											.	ADCY9	151	.	0			c.C2628T						PASS	.						128.0	121.0	124.0					16																	4029168		2197	4300	6497	SO:0001819	synonymous_variant	115	exon8			CAGTGCGGGAAGC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2628C>T	chr16.hg19:g.4029168G>A		140.0	0.0	.		157.0	30.0	.	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.	.	none		0.582	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
ACSM3	6296	hgsc.bcm.edu	37	16	20787239	20787239	+	Silent	SNP	C	C	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr16:20787239C>T	ENST00000289416.5	+	3	773	c.298C>T	c.(298-300)Ctg>Ttg	p.L100L	ACSM3_ENST00000450120.2_Silent_p.L55L|ACSM3_ENST00000440284.2_Silent_p.L100L	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	100			L -> P (in dbSNP:rs5713).		cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						TTTTGAGGAACTGGGATCTCT	0.458																																					p.L100L		Atlas-SNP	.											.	ACSM3	113	.	0			c.C298T						PASS	.						119.0	127.0	125.0					16																	20787239		2201	4300	6501	SO:0001819	synonymous_variant	6296	exon3			GAGGAACTGGGAT	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"""Acyl-CoA synthetase family"""	10522	protein-coding gene	gene with protein product		145505	"""SA (rat hypertension-associated) homolog"", ""SA hypertension-associated homolog (rat)"""	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.298C>T	chr16.hg19:g.20787239C>T		188.0	0.0	.		248.0	53.0	.	NM_005622	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Silent	SNP	ENST00000289416.5	hg19	CCDS10589.1																																																																																			.	.	.	none		0.458	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622	
WDR81	124997	hgsc.bcm.edu	37	17	1631524	1631524	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:1631524G>A	ENST00000409644.1	+	1	3271	c.3271G>A	c.(3271-3273)Gtg>Atg	p.V1091M	WDR81_ENST00000309182.5_Missense_Mutation_p.V40M|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000545662.1_5'Flank	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1091					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CGGGCTCTATGTGACTGAGTC	0.662																																					p.V1091M		Atlas-SNP	.											.	WDR81	180	.	0			c.G3271A						PASS	.						38.0	45.0	43.0					17																	1631524		2202	4299	6501	SO:0001583	missense	124997	exon1			CTCTATGTGACTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3271G>A	chr17.hg19:g.1631524G>A	ENSP00000386609:p.Val1091Met	102.0	0.0	.		152.0	25.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.473006	0.84640	.	.	ENSG00000167716	ENST00000309182;ENST00000409644;ENST00000354680	T;T	0.56103	2.09;0.48	5.65	5.65	0.86999	.	0.060024	0.64402	D	0.000003	T	0.65481	0.2695	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	T	0.67589	-0.5632	10	0.87932	D	0	.	19.7221	0.96147	0.0:0.0:1.0:0.0	.	218;40	Q8TEL1;Q562E7	.;WDR81_HUMAN	M	40;1091;40	ENSP00000312074:V40M;ENSP00000386609:V1091M	ENSP00000312074:V40M	V	+	1	0	WDR81	1578274	1.000000	0.71417	0.962000	0.40283	0.655000	0.38815	9.327000	0.96396	2.679000	0.91253	0.655000	0.94253	GTG	.	.	.	none		0.662	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
MYO19	80179	hgsc.bcm.edu	37	17	34871758	34871758	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:34871758T>C	ENST00000431794.3	-	7	1012	c.490A>G	c.(490-492)Att>Gtt	p.I164V	MYO19_ENST00000586007.1_Missense_Mutation_p.I164V|MYO19_ENST00000544606.1_Missense_Mutation_p.I30V|MYO19_ENST00000268852.9_Missense_Mutation_p.I164V	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	164	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CTCTCTGCAATCTTGTGGCTC	0.522																																					p.I164V		Atlas-SNP	.											.	MYO19	130	.	0			c.A490G						PASS	.						78.0	81.0	80.0					17																	34871758		1998	4151	6149	SO:0001583	missense	80179	exon8			CTGCAATCTTGTG	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.490A>G	chr17.hg19:g.34871758T>C	ENSP00000409936:p.Ile164Val	54.0	0.0	.		74.0	13.0	.	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	hg19	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	T	4.263	0.047870	0.08243	.	.	ENSG00000141140	ENST00000431794;ENST00000268852;ENST00000544606	D;D;D	0.87103	-2.21;-2.21;-2.21	5.72	1.64	0.23874	Myosin head, motor domain (2);	0.524811	0.15805	N	0.243761	T	0.68632	0.3022	N	0.02736	-0.51	0.24560	N	0.993978	B;B;B;B	0.15473	0.0;0.0;0.0;0.013	B;B;B;B	0.12837	0.003;0.002;0.0;0.008	T	0.56679	-0.7939	10	0.30078	T	0.28	.	9.161	0.37023	0.0:0.3696:0.0:0.6304	.	30;164;164;164	B4DSL5;Q96H55;Q96H55-2;Q96H55-4	.;MYO19_HUMAN;.;.	V	164;164;30	ENSP00000409936:I164V;ENSP00000268852:I164V;ENSP00000438365:I30V	ENSP00000268852:I164V	I	-	1	0	MYO19	31945871	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.767000	0.38501	0.098000	0.17522	0.383000	0.25322	ATT	.	.	.	none		0.522	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
DGKE	8526	hgsc.bcm.edu	37	17	54926211	54926211	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:54926211A>G	ENST00000284061.3	+	6	1223	c.1043A>G	c.(1042-1044)gAt>gGt	p.D348G		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	348	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					ATTAAACTAGATCGGTAAGTT	0.378																																					p.D348G		Atlas-SNP	.											.	DGKE	47	.	0			c.A1043G						PASS	.						118.0	114.0	115.0					17																	54926211		2203	4300	6503	SO:0001583	missense	8526	exon6			AACTAGATCGGTA	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"""diacylglycerol kinase, epsilon (64kD)"""			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.1043A>G	chr17.hg19:g.54926211A>G	ENSP00000284061:p.Asp348Gly	93.0	0.0	.		112.0	26.0	.	NM_003647	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	hg19	CCDS11590.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.750777	0.89753	.	.	ENSG00000153933	ENST00000284061	T	0.60672	0.17	5.59	5.59	0.84812	Diacylglycerol kinase, catalytic domain (3);	0.090430	0.85682	D	0.000000	T	0.81692	0.4876	M	0.92880	3.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86463	0.1780	10	0.87932	D	0	.	15.7661	0.78128	1.0:0.0:0.0:0.0	.	348;348	A1L4Q0;P52429	.;DGKE_HUMAN	G	348	ENSP00000284061:D348G	ENSP00000284061:D348G	D	+	2	0	DGKE	52281210	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	8.532000	0.90613	2.134000	0.65973	0.460000	0.39030	GAT	.	.	.	none		0.378	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647	
STAP2	55620	hgsc.bcm.edu	37	19	4328673	4328673	+	Splice_Site	SNP	C	C	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr19:4328673C>G	ENST00000594605.1	-	6	712	c.589G>C	c.(589-591)Ggg>Cgg	p.G197R	STAP2_ENST00000600324.1_Splice_Site_p.G197R|STAP2_ENST00000597593.1_5'Flank	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	197	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CATGCGCACCCGTTGTGCATC	0.726																																					p.G197R		Atlas-SNP	.											.	STAP2	38	.	0			c.G589C						PASS	.						12.0	13.0	12.0					19																	4328673		2187	4277	6464	SO:0001630	splice_region_variant	55620	exon6			CGCACCCGTTGTG	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.590+1G>C	chr19.hg19:g.4328673C>G		19.0	0.0	.		23.0	10.0	.	NM_001013841	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	hg19	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.017070	0.35606	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	4.47	3.42	0.39159	SH2 motif (3);	0.167039	0.37261	N	0.002172	T	0.62196	0.2408	M	0.77103	2.36	0.43160	D	0.99494	B;B	0.28258	0.205;0.119	B;B	0.29176	0.066;0.099	T	0.64605	-0.6368	9	0.87932	D	0	-9.4374	10.5452	0.45056	0.0:0.9014:0.0:0.0986	.	197;197	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	R	197	.	ENSP00000317912:G197R	G	-	1	0	STAP2	4279673	0.703000	0.27826	0.790000	0.31976	0.373000	0.29922	1.145000	0.31577	0.866000	0.35629	0.479000	0.44913	GGG	.	.	.	none		0.726	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	Missense_Mutation
PPP1R16B	26051	hgsc.bcm.edu	37	20	37536822	37536822	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr20:37536822G>T	ENST00000299824.1	+	10	1369	c.1180G>T	c.(1180-1182)Gag>Tag	p.E394*	PPP1R16B_ENST00000373331.2_Nonsense_Mutation_p.E352*	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	394					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				GACAGACCAAGAGAATAAGGA	0.607																																					p.E394X		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.G1180T						PASS	.						88.0	81.0	84.0					20																	37536822		2203	4300	6503	SO:0001587	stop_gained	26051	exon10			GACCAAGAGAATA	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1180G>T	chr20.hg19:g.37536822G>T	ENSP00000299824:p.Glu394*	49.0	0.0	.		84.0	14.0	.	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Nonsense_Mutation	SNP	ENST00000299824.1	hg19	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.556183|7.556183	0.98355|0.98355	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000299824;ENST00000373331|ENST00000438192	.|.	.|.	.|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.154659|.	0.56097|.	D|.	0.000027|.	.|T	.|0.71341	.|0.3328	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68953	.|-0.5273	.|4	0.34782|.	T|.	0.22|.	.|.	14.8843|14.8843	0.70555|0.70555	0.0:0.0:0.8566:0.1433|0.0:0.0:0.8566:0.1433	.|.	.|.	.|.	.|.	X|N	394;352|294	.|.	ENSP00000299824:E394X|.	E|K	+|+	1|3	0|2	PPP1R16B|PPP1R16B	36970236|36970236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.369000|6.369000	0.73109|0.73109	2.771000|2.771000	0.95319|0.95319	0.644000|0.644000	0.83932|0.83932	GAG|AAG	.	.	.	none		0.607	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
PPP1R16B	26051	hgsc.bcm.edu	37	20	37536828	37536828	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr20:37536828A>G	ENST00000299824.1	+	10	1375	c.1186A>G	c.(1186-1188)Aag>Gag	p.K396E	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.K354E	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	396					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				CCAAGAGAATAAGGACCCTGT	0.607																																					p.K396E		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.A1186G						PASS	.						82.0	77.0	79.0					20																	37536828		2203	4300	6503	SO:0001583	missense	26051	exon10			GAGAATAAGGACC	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1186A>G	chr20.hg19:g.37536828A>G	ENSP00000299824:p.Lys396Glu	43.0	0.0	.		73.0	12.0	.	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	hg19	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.38|13.38	2.219266|2.219266	0.39201|0.39201	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000438192|ENST00000299824;ENST00000373331	.|T;T	.|0.70869	.|-0.31;-0.52	5.79|5.79	4.7|4.7	0.59300|0.59300	.|.	.|0.210830	.|0.50627	.|D	.|0.000114	T|T	0.54806|0.54806	0.1881|0.1881	L|L	0.36672|0.36672	1.1|1.1	0.25150|0.25150	N|N	0.990439|0.990439	.|B;B	.|0.19445	.|0.017;0.036	.|B;B	.|0.20767	.|0.007;0.031	T|T	0.36163|0.36163	-0.9759|-0.9759	5|10	.|0.07990	.|T	.|0.79	.|.	9.383|9.383	0.38325|0.38325	0.8649:0.0:0.1351:0.0|0.8649:0.0:0.1351:0.0	.|.	.|354;396	.|E9PFS8;Q96T49	.|.;PP16B_HUMAN	M|E	296|396;354	.|ENSP00000299824:K396E;ENSP00000362428:K354E	.|ENSP00000299824:K396E	I|K	+|+	3|1	3|0	PPP1R16B|PPP1R16B	36970242|36970242	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	4.056000|4.056000	0.57448|0.57448	2.236000|2.236000	0.73375|0.73375	0.524000|0.524000	0.50904|0.50904	ATA|AAG	.	.	.	none		0.607	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
APOL6	80830	hgsc.bcm.edu	37	22	36055619	36055619	+	Silent	SNP	C	C	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr22:36055619C>G	ENST00000409652.4	+	3	1284	c.1008C>G	c.(1006-1008)gtC>gtG	p.V336V		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	336					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						gtctgtgtgtctgtgtgtatg	0.483																																					p.V336V		Atlas-SNP	.											APOL6,NS,carcinoma,0,1	APOL6	26	.	0			c.C1008G						PASS	.						94.0	61.0	72.0					22																	36055619		2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			GTGTGTCTGTGTG	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"""Apolipoproteins"""	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.1008C>G	chr22.hg19:g.36055619C>G		27.0	0.0	.		32.0	3.0	.	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	hg19	CCDS13919.1																																																																																			.	.	.	none		0.483	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641	
MICALL1	85377	hgsc.bcm.edu	37	22	38313744	38313744	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr22:38313744C>T	ENST00000215957.6	+	4	494	c.368C>T	c.(367-369)gCa>gTa	p.A123V		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	123					endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					AAGGGCCTTGCACCCTGTTCC	0.622																																					p.A123V		Atlas-SNP	.											.	MICALL1	53	.	0			c.C368T						PASS	.						80.0	66.0	71.0					22																	38313744		2203	4300	6503	SO:0001583	missense	85377	exon4			GCCTTGCACCCTG	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.368C>T	chr22.hg19:g.38313744C>T	ENSP00000215957:p.Ala123Val	110.0	0.0	.		117.0	28.0	.	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	hg19	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.105894	0.37145	.	.	ENSG00000100139	ENST00000445494;ENST00000215957	T;T	0.73363	-0.74;0.52	3.8	2.78	0.32641	.	0.408833	0.20490	N	0.091317	T	0.55986	0.1955	N	0.19112	0.55	0.19775	N	0.999952	B	0.06786	0.001	B	0.06405	0.002	T	0.48833	-0.9000	10	0.48119	T	0.1	.	7.2373	0.26077	0.0:0.8793:0.0:0.1207	.	123	Q8N3F8	MILK1_HUMAN	V	39;123	ENSP00000404543:A39V;ENSP00000215957:A123V	ENSP00000215957:A123V	A	+	2	0	MICALL1	36643690	0.000000	0.05858	0.005000	0.12908	0.609000	0.37215	0.091000	0.15046	1.176000	0.42840	0.455000	0.32223	GCA	.	.	.	none		0.622	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
MORC4	79710	hgsc.bcm.edu	37	X	106201626	106201626	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chrX:106201626A>G	ENST00000355610.4	-	11	1599	c.1325T>C	c.(1324-1326)aTt>aCt	p.I442T	MORC4_ENST00000255495.7_Missense_Mutation_p.I442T|MORC4_ENST00000535534.1_Missense_Mutation_p.I190T	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	442						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						GGATGGATCAATCTTCCCAGG	0.423																																					p.I442T		Atlas-SNP	.											.	MORC4	155	.	0			c.T1325C						PASS	.						132.0	111.0	118.0					X																	106201626		2203	4300	6503	SO:0001583	missense	79710	exon11			GGATCAATCTTCC	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.1325T>C	chrX.hg19:g.106201626A>G	ENSP00000347821:p.Ile442Thr	50.0	0.0	.		59.0	32.0	.	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	hg19	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	A	11.41	1.630627	0.28978	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.30981	2.76;1.51;2.75	5.93	5.93	0.95920	Zinc finger, CW-type (2);	0.519296	0.19062	N	0.123746	T	0.27278	0.0669	L	0.37466	1.105	0.24268	N	0.995258	B;B;B	0.26975	0.165;0.042;0.042	B;B;B	0.28385	0.089;0.055;0.055	T	0.26815	-1.0092	10	0.72032	D	0.01	-5.7895	11.5626	0.50785	1.0:0.0:0.0:0.0	.	190;442;442	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	T	442;190;442	ENSP00000347821:I442T;ENSP00000440359:I190T;ENSP00000255495:I442T	ENSP00000255495:I442T	I	-	2	0	MORC4	106088282	0.305000	0.24481	0.911000	0.35937	0.454000	0.32378	1.929000	0.40114	2.004000	0.58718	0.441000	0.28932	ATT	.	.	.	none		0.423	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
NOM1	64434	hgsc.bcm.edu	37	7	156752614	156752614	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr7:156752614delA	ENST00000275820.3	+	4	1393	c.1378delA	c.(1378-1380)aaafs	p.K460fs	NOM1_ENST00000460332.1_3'UTR	NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	460	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		AAGCGAAGGGAAAGAGTGTGA	0.443																																					p.G459fs		Atlas-INDEL	.											.	NOM1	73	.	0			c.1377delG						PASS	.						128.0	109.0	115.0					7																	156752614		2203	4300	6503	SO:0001589	frameshift_variant	64434	exon4			.	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1378delA	chr7.hg19:g.156752614delA	ENSP00000275820:p.Lys460fs	58.0	0.0	0		61.0	16.0	0.262295	NM_138400	Q96I08	Frame_Shift_Del	DEL	ENST00000275820.3	hg19	CCDS34787.1																																																																																			.	.	.	none		0.443	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
ZNF407	55628	hgsc.bcm.edu	37	18	72344119	72344120	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr18:72344119_72344120insTA	ENST00000299687.5	+	1	1144_1145	c.1144_1145insTA	c.(1144-1146)ctafs	p.L382fs	ZNF407_ENST00000309902.6_Frame_Shift_Ins_p.L382fs|ZNF407_ENST00000582337.1_Frame_Shift_Ins_p.L382fs|ZNF407_ENST00000577538.1_Frame_Shift_Ins_p.L382fs	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAGTAGAAAGCTAGACACCTTA	0.431																																					p.L382fs		Atlas-INDEL	.											.	ZNF407	231	.	0			c.1144_1145insTA						PASS	.																																			SO:0001589	frameshift_variant	55628	exon1			.	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1145_1146dupTA	chr18.hg19:g.72344120_72344121dupTA	ENSP00000299687:p.Leu382fs	75.0	0.0	0		94.0	26.0	0.276596	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Frame_Shift_Ins	INS	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.	.	none		0.431	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
AGBL2	79841	hgsc.bcm.edu	37	11	47726183	47726183	+	Frame_Shift_Del	DEL	G	G	-	rs373862581		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:47726183delG	ENST00000525123.1	-	7	783	c.498delC	c.(496-498)ctcfs	p.L166fs	AGBL2_ENST00000298861.4_Frame_Shift_Del_p.L166fs|AGBL2_ENST00000528244.1_Frame_Shift_Del_p.L128fs|AGBL2_ENST00000357610.3_Frame_Shift_Del_p.L166fs|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	166						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						AAATGGAAAAGAGCTCTTGGG	0.428																																					p.F167fs		Atlas-INDEL	.											.	AGBL2	73	.	0			c.499delT						PASS	.						141.0	132.0	135.0					11																	47726183		2201	4298	6499	SO:0001589	frameshift_variant	79841	exon7			.		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"""cytoplasmic carboxypeptidase 2"""					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.498delC	chr11.hg19:g.47726183delG	ENSP00000435582:p.Leu166fs	112.0	0.0	0		98.0	24.0	0.244898	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Frame_Shift_Del	DEL	ENST00000525123.1	hg19	CCDS7944.1																																																																																			.	.	.	none		0.428	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
LMO4	8543	hgsc.bcm.edu	37	1	87805263	87805263	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:87805263delT	ENST00000370544.5	+	3	1061	c.281delT	c.(280-282)attfs	p.I94fs	LMO4_ENST00000489303.1_3'UTR|LMO4_ENST00000370542.1_Frame_Shift_Del_p.I94fs	NM_006769.3	NP_006760.1	P61968	LMO4_HUMAN	LIM domain only 4	94	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of protein complex assembly (GO:0031333)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell activation (GO:0050865)|regulation of cell fate specification (GO:0042659)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron differentiation (GO:0021522)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)|ventral spinal cord interneuron differentiation (GO:0021514)|ventricular septum development (GO:0003281)	transcription factor complex (GO:0005667)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(1)	9		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GGACAGTCGATTCCTGCGAGT	0.388																																					p.I94fs		Atlas-INDEL	.											.	LMO4	21	.	0			c.280delA						PASS	.						95.0	95.0	95.0					1																	87805263		2203	4300	6503	SO:0001589	frameshift_variant	8543	exon3			.	U24576	CCDS713.1	1p22.3	2008-02-05			ENSG00000143013	ENSG00000143013			6644	protein-coding gene	gene with protein product		603129					Standard	NM_006769		Approved		uc001dmi.3	P61968	OTTHUMG00000010248	ENST00000370544.5:c.281delT	chr1.hg19:g.87805263delT	ENSP00000359575:p.Ile94fs	54.0	0.0	0		58.0	17.0	0.293103	NM_006769	D3DT23|O00158|O88894	Frame_Shift_Del	DEL	ENST00000370544.5	hg19	CCDS713.1																																																																																			.	.	.	none		0.388	LMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028264.2	NM_006769	
PDGFRB	5159	hgsc.bcm.edu	37	5	149515196	149515213	+	In_Frame_Del	DEL	CCGTGTCTAGCCCAGTGA	CCGTGTCTAGCCCAGTGA	-	rs141870925|rs188981582|rs556826386	byFrequency	TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	CCGTGTCTAGCCCAGTGA	CCGTGTCTAGCCCAGTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr5:149515196_149515213delCCGTGTCTAGCCCAGTGA	ENST00000261799.4	-	3	738_755	c.269_286delTCACTGGGCTAGACACGG	c.(268-288)ctcactgggctagacacggga>cga	p.90_96LTGLDTG>R		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	90	Ig-like C2-type 1.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAGTATTCTCCCGTGTCTAGCCCAGTGAGGTTGGTCAG	0.592			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""																																p.90_96del		Atlas-INDEL	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	PDGFRB	142	.	0			c.270_287del						PASS	.																																			SO:0001651	inframe_deletion	5159	exon3			.	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.269_286delTCACTGGGCTAGACACGG	chr5.hg19:g.149515196_149515213delCCGTGTCTAGCCCAGTGA	ENSP00000261799:p.Leu90_Gly96delinsArg	153.0	0.0	0		120.0	19.0	0.158333	NM_002609	B5A957|Q8N5L4	In_Frame_Del	DEL	ENST00000261799.4	hg19	CCDS4303.1																																																																																			.	.	.	none		0.592	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
