#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_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_ORegAnno_bin	i_TTotCov	i_TVarCov	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_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
GPN2	54707	hgsc.bcm.edu	37	1	27210697	27210697	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:27210697C>A	ENST00000374135.4	-	4	1014	c.814G>T	c.(814-816)Gaa>Taa	p.E272*	GPN2_ENST00000461282.1_5'Flank|GPN2_ENST00000374133.3_Nonsense_Mutation_p.E93*	NM_018066.3	NP_060536.3			GPN-loop GTPase 2											endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9						ATCATGGCTTCCAAGCTTCGC	0.547																																					p.E272X		Atlas-SNP	.											.	GPN2	18	.	0			c.G814T						.						89.0	74.0	79.0					1																	27210697		2203	4300	6503	SO:0001587	stop_gained	54707	exon4			TGGCTTCCAAGCT	AK001211	CCDS289.1	1p36.11	2008-04-30	2008-04-30	2008-04-30	ENSG00000142751	ENSG00000142751		"""GPN-loop GTPases"""	25513	protein-coding gene	gene with protein product			"""ATP binding domain 1 family, member B"""	ATPBD1B		12975309	Standard	NM_018066		Approved	FLJ10349	uc001bnd.1	Q9H9Y4	OTTHUMG00000004227	ENST00000374135.4:c.814G>T	chr1.hg19:g.27210697C>A	ENSP00000363250:p.Glu272*	137.0	0.0		127.0	17.0	NM_018066		Nonsense_Mutation	SNP	ENST00000374135.4	hg19	CCDS289.1	.	.	.	.	.	.	.	.	.	.	C	37	6.442196	0.97572	.	.	ENSG00000142751	ENST00000374135;ENST00000374133	.	.	.	5.41	5.41	0.78517	.	0.113746	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-26.9871	18.8009	0.92016	0.0:1.0:0.0:0.0	.	.	.	.	X	272;93	.	ENSP00000363248:E93X	E	-	1	0	GPN2	27083284	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	4.984000	0.63838	2.536000	0.85505	0.491000	0.48974	GAA	.	.		0.547	GPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012175.2	NM_018066	
IL12RB2	3595	hgsc.bcm.edu	37	1	67795378	67795378	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:67795378G>C	ENST00000262345.1	+	6	1413	c.773G>C	c.(772-774)aGa>aCa	p.R258T	IL12RB2_ENST00000544434.1_Missense_Mutation_p.R258T|IL12RB2_ENST00000371000.1_Missense_Mutation_p.R258T|IL12RB2_ENST00000541374.1_Missense_Mutation_p.R258T	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	258	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						AATCGACTCAGATATCGGCCC	0.428																																					p.R258T		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G773C						.						127.0	121.0	123.0					1																	67795378		2203	4300	6503	SO:0001583	missense	3595	exon6			GACTCAGATATCG	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.773G>C	chr1.hg19:g.67795378G>C	ENSP00000262345:p.Arg258Thr	150.0	0.0		142.0	23.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	hg19	CCDS638.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.31|14.31	2.495951|2.495951	0.44352|0.44352	.|.	.|.	ENSG00000081985|ENSG00000081985	ENST00000441640|ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	.|T;T;T;T	.|0.56444	.|0.46;0.46;0.46;0.46	5.2|5.2	2.04|2.04	0.26737|0.26737	.|Fibronectin, type III (3);Immunoglobulin-like fold (1);	.|0.213014	.|0.49916	.|D	.|0.000125	T|T	0.52208|0.52208	0.1720|0.1720	M|M	0.78637|0.78637	2.42|2.42	0.37417|0.37417	D|D	0.913466|0.913466	.|P;D;P;D	.|0.60575	.|0.547;0.988;0.946;0.961	.|B;P;P;P	.|0.58721	.|0.276;0.844;0.754;0.617	T|T	0.56226|0.56226	-0.8014|-0.8014	5|10	.|0.56958	.|D	.|0.05	-11.6493|-11.6493	7.2644|7.2644	0.26222|0.26222	0.3292:0.0:0.6708:0.0|0.3292:0.0:0.6708:0.0	.|.	.|258;258;258;258	.|B4DGA4;F5H7L6;Q99665-2;Q99665	.|.;.;.;I12R2_HUMAN	H|T	125|258	.|ENSP00000262345:R258T;ENSP00000360039:R258T;ENSP00000445276:R258T;ENSP00000442443:R258T	.|ENSP00000262345:R258T	Q|R	+|+	3|2	2|0	IL12RB2|IL12RB2	67567966|67567966	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.290000|0.290000	0.27261|0.27261	1.499000|1.499000	0.35671|0.35671	0.587000|0.587000	0.29643|0.29643	0.561000|0.561000	0.74099|0.74099	CAG|AGA	.	.		0.428	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859947	144859947	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:144859947T>C	ENST00000369354.3	-	38	6326	c.6137A>G	c.(6136-6138)cAc>cGc	p.H2046R	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.H2131R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.H1940R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.H2046R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.H2182R|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2046					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGCCACCAGGTGGCTCAGGTC	0.547			T	PDGFRB	MPD																																p.H2046R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6137G						.						102.0	97.0	98.0					1																	144859947		2203	4297	6500	SO:0001583	missense	9659	exon38			ACCAGGTGGCTCA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6137A>G	chr1.hg19:g.144859947T>C	ENSP00000358360:p.His2046Arg	242.0	0.0		305.0	29.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	3.859	-0.030327	0.07543	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01516	4.81;4.89;4.89;4.91;4.89	5.1	-1.38	0.09027	.	.	.	.	.	T	0.00666	0.0022	M	0.61703	1.905	0.18873	N	0.999982	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42531	-0.9446	9	0.22109	T	0.4	.	5.581	0.17250	0.0:0.3664:0.1494:0.4842	.	1940;2046	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	R	1940;2046;2046;2131;2182	ENSP00000327209:H1940R;ENSP00000358360:H2046R;ENSP00000358363:H2046R;ENSP00000435654:H2131R;ENSP00000358366:H2182R	ENSP00000327209:H1940R	H	-	2	0	PDE4DIP	143571304	0.963000	0.33076	0.914000	0.36105	0.085000	0.17905	0.421000	0.21280	0.067000	0.16545	0.528000	0.53228	CAC	.	.		0.547	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
RASSF5	83593	hgsc.bcm.edu	37	1	206730943	206730943	+	Intron	SNP	G	G	T			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr1:206730943G>T	ENST00000355294.4	+	2	636				RASSF5_ENST00000367117.3_Intron|RASSF5_ENST00000304534.8_Silent_p.L14L	NM_182663.2	NP_872604.1	Q8WWW0	RASF5_HUMAN	Ras association (RalGDS/AF-6) domain family member 5						apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein localization to nucleus (GO:1900180)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	8	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			ACTGCAGCCTGGACGAGGAAC	0.542																																					p.L14L	GBM(162;656 1984 11916 22872 31529)	Atlas-SNP	.											.	RASSF5	54	.	0			c.G42T						.						98.0	92.0	94.0					1																	206730943		2203	4300	6503	SO:0001627	intron_variant	83593	exon1			CAGCCTGGACGAG	BC004270	CCDS1463.1, CCDS1464.1, CCDS30998.1	1q31	2014-04-10	2008-02-22		ENSG00000136653	ENSG00000266094			17609	protein-coding gene	gene with protein product		607020				11978988, 11965544	Standard	NM_182663		Approved	Maxp1, NORE1, RAPL	uc001hed.3	Q8WWW0	OTTHUMG00000184616	ENST00000355294.4:c.579+19321G>T	chr1.hg19:g.206730943G>T		97.0	0.0		122.0	18.0	NM_182665	A8K1E6|Q5SY32|Q8WWV9|Q8WXF4|Q9BT99	Silent	SNP	ENST00000355294.4	hg19	CCDS30998.1																																																																																			.	.		0.542	RASSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088469.1	NM_031437	
BIRC6	57448	hgsc.bcm.edu	37	2	32692803	32692803	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr2:32692803T>C	ENST00000421745.2	+	27	5701	c.5567T>C	c.(5566-5568)aTg>aCg	p.M1856T		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1856					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGCAGATTCATGAAGGTAAAG	0.333																																					p.M1856T	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T5567C						.						53.0	49.0	50.0					2																	32692803		2203	4300	6503	SO:0001583	missense	57448	exon27			GATTCATGAAGGT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5567T>C	chr2.hg19:g.32692803T>C	ENSP00000393596:p.Met1856Thr	129.0	0.0		123.0	22.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	17.40	3.378901	0.61735	.	.	ENSG00000115760	ENST00000421745	T	0.75477	-0.94	5.61	5.61	0.85477	.	0.090659	0.64402	D	0.000001	T	0.69869	0.3159	L	0.50333	1.59	0.58432	D	0.999992	P	0.37864	0.61	B	0.34824	0.19	T	0.74250	-0.3726	10	0.87932	D	0	.	15.8638	0.79047	0.0:0.0:0.0:1.0	.	1856	Q9NR09	BIRC6_HUMAN	T	1856	ENSP00000393596:M1856T	ENSP00000393596:M1856T	M	+	2	0	BIRC6	32546307	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	7.717000	0.84732	2.162000	0.67917	0.456000	0.33151	ATG	.	.		0.333	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LONRF2	164832	hgsc.bcm.edu	37	2	100906810	100906810	+	Silent	SNP	G	G	A			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr2:100906810G>A	ENST00000393437.3	-	10	2469	c.1830C>T	c.(1828-1830)gaC>gaT	p.D610D	LONRF2_ENST00000409647.1_Silent_p.D367D	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	610	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						TGCCAATCGCGTCTACAACAG	0.458																																					p.D610D		Atlas-SNP	.											.	LONRF2	62	.	0			c.C1830T						.						146.0	131.0	136.0					2																	100906810		2203	4300	6503	SO:0001819	synonymous_variant	164832	exon10			AATCGCGTCTACA	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1830C>T	chr2.hg19:g.100906810G>A		170.0	0.0		165.0	29.0	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	hg19	CCDS2046.2																																																																																			.	.		0.458	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
FARSB	10056	hgsc.bcm.edu	37	2	223505623	223505623	+	Silent	SNP	T	T	A			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr2:223505623T>A	ENST00000281828.6	-	4	560	c.297A>T	c.(295-297)gtA>gtT	p.V99V	FARSB_ENST00000536361.1_5'UTR	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	99					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|RNA binding (GO:0003723)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	24		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	CATCAGGCATTACCCGTTTAT	0.254																																					p.V99V		Atlas-SNP	.											.	FARSB	49	.	0			c.A297T						.						37.0	39.0	39.0					2																	223505623		2201	4297	6498	SO:0001819	synonymous_variant	10056	exon4			AGGCATTACCCGT	AF042346	CCDS2454.1	2q36.2	2011-07-01	2007-02-23	2007-02-23	ENSG00000116120	ENSG00000116120	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	17800	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, beta, cytoplasmic"""	609690	"""phenylalanyl-tRNA synthetase-like, beta subunit"""	FARSLB		10049785	Standard	NM_005687		Approved	PheHB, FRSB	uc002vne.1	Q9NSD9	OTTHUMG00000133155	ENST00000281828.6:c.297A>T	chr2.hg19:g.223505623T>A		633.0	0.0		329.0	54.0	NM_005687	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	Silent	SNP	ENST00000281828.6	hg19	CCDS2454.1																																																																																			.	.		0.254	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687	
CADPS	8618	hgsc.bcm.edu	37	3	62484884	62484884	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr3:62484884C>T	ENST00000383710.4	-	18	3008	c.2659G>A	c.(2659-2661)Gaa>Aaa	p.E887K	CADPS_ENST00000283269.9_Missense_Mutation_p.E904K|CADPS_ENST00000357948.3_Missense_Mutation_p.E864K	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	887	Interaction with DRD2.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		ATGACTAGTTCAGCAAGACGT	0.448																																					p.E904K		Atlas-SNP	.											CADPS_ENST00000383710,NS,haematopoietic_neoplasm,0,4	CADPS	387	.	0			c.G2710A						.						162.0	138.0	146.0					3																	62484884		2203	4300	6503	SO:0001583	missense	8618	exon18			CTAGTTCAGCAAG	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2659G>A	chr3.hg19:g.62484884C>T	ENSP00000373215:p.Glu887Lys	272.0	1.0		294.0	75.0	NM_183394	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.992910	0.93167	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269	T;T;T	0.56611	0.48;0.47;0.45	5.89	5.89	0.94794	Calcium-dependent secretion activator (1);	0.000000	0.85682	D	0.000000	T	0.75982	0.3924	M	0.80616	2.505	0.80722	D	1	P;D;D;D	0.63880	0.911;0.99;0.969;0.993	P;D;P;P	0.72982	0.674;0.979;0.735;0.864	T	0.77566	-0.2540	10	0.87932	D	0	.	20.2562	0.98421	0.0:1.0:0.0:0.0	.	864;904;887;887	Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4	.;.;CAPS1_HUMAN;.	K	887;887;864;904	ENSP00000373215:E887K;ENSP00000350632:E864K;ENSP00000283269:E904K	ENSP00000283269:E904K	E	-	1	0	CADPS	62459924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.797000	0.96272	0.563000	0.77884	GAA	.	.		0.448	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
RAPGEF2	9693	hgsc.bcm.edu	37	4	160225597	160225597	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr4:160225597G>C	ENST00000264431.4	+	2	583	c.164G>C	c.(163-165)gGg>gCg	p.G55A	RAPGEF2_ENST00000504604.1_3'UTR	NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	55					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		AGTGATTCTGGGAGCAGCAGT	0.413																																					p.G55A		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.G164C						.						167.0	157.0	160.0					4																	160225597		1915	4127	6042	SO:0001583	missense	9693	exon2			ATTCTGGGAGCAG	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.164G>C	chr4.hg19:g.160225597G>C	ENSP00000264431:p.Gly55Ala	423.0	0.0		389.0	51.0	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	hg19	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781279	0.90282	.	.	ENSG00000109756	ENST00000505478;ENST00000510510;ENST00000264431;ENST00000514565	T	0.50548	0.74	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.70011	0.3175	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69658	-0.5086	10	0.52906	T	0.07	.	19.8097	0.96542	0.0:0.0:1.0:0.0	.	55	Q9Y4G8	RPGF2_HUMAN	A	211;53;55;36	ENSP00000264431:G55A	ENSP00000264431:G55A	G	+	2	0	RAPGEF2	160445047	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.476000	0.97823	2.685000	0.91497	0.484000	0.47621	GGG	.	.		0.413	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
FOXK1	221937	hgsc.bcm.edu	37	7	4799104	4799104	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr7:4799104T>G	ENST00000328914.4	+	7	1574	c.1574T>G	c.(1573-1575)gTc>gGc	p.V525G	FOXK1_ENST00000446823.1_Missense_Mutation_p.V362G	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GTCACCATGGTCAGGGTGGTC	0.697																																					p.V525G		Atlas-SNP	.											.	FOXK1	64	.	0			c.T1574G						.						37.0	29.0	32.0					7																	4799104		2192	4297	6489	SO:0001583	missense	221937	exon7			CCATGGTCAGGGT	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1574T>G	chr7.hg19:g.4799104T>G	ENSP00000328720:p.Val525Gly	29.0	0.0		74.0	10.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159664	0.78226	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.96136	-3.54;-3.92	5.65	5.65	0.86999	.	0.061247	0.64402	D	0.000004	D	0.94686	0.8286	L	0.46157	1.445	0.80722	D	1	D;B	0.54047	0.964;0.449	P;B	0.49140	0.601;0.329	D	0.94630	0.7821	10	0.51188	T	0.08	.	15.3584	0.74448	0.0:0.0:0.0:1.0	.	525;362	P85037;P85037-2	FOXK1_HUMAN;.	G	362;281;525;408	ENSP00000394442:V362G;ENSP00000328720:V525G	ENSP00000328720:V525G	V	+	2	0	FOXK1	4765630	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	7.556000	0.82233	2.279000	0.76181	0.533000	0.62120	GTC	.	.		0.697	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
SUPV3L1	6832	hgsc.bcm.edu	37	10	70951452	70951452	+	Silent	SNP	A	A	G			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr10:70951452A>G	ENST00000359655.4	+	6	843	c.783A>G	c.(781-783)acA>acG	p.T261T	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	261	Helicase ATP-binding.				ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGCGTGTGACAGTTCAGCCAA	0.378																																					p.T261T		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.A783G						.						219.0	181.0	194.0					10																	70951452		2203	4300	6503	SO:0001819	synonymous_variant	6832	exon6			TGTGACAGTTCAG	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"""suppressor of var1 (S.cerevisiae) 3-like 1"""			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.783A>G	chr10.hg19:g.70951452A>G		451.0	0.0		336.0	53.0	NM_003171	A8K301|O43630	Silent	SNP	ENST00000359655.4	hg19	CCDS7287.1																																																																																			.	.		0.378	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
CEP290	80184	hgsc.bcm.edu	37	12	88508195	88508195	+	Splice_Site	SNP	A	A	C			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr12:88508195A>C	ENST00000552810.1	-	20	2396		c.e20+1		CEP290_ENST00000309041.7_Splice_Site|CEP290_ENST00000397838.3_Splice_Site	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						aaaataacTTACATTAACTAG	0.318																																					.		Atlas-SNP	.											.	CEP290	195	.	0			c.2052+2T>G						.						146.0	129.0	134.0					12																	88508195		1475	3267	4742	SO:0001630	splice_region_variant	80184	exon21			TAACTTACATTAA	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2052+1T>G	chr12.hg19:g.88508195A>C		201.0	0.0		109.0	31.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Splice_Site	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.440396	0.83993	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CEP290	87032326	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.744000	0.85034	2.323000	0.78572	0.528000	0.53228	.	.	.		0.318	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	Intron
BRCA2	675	hgsc.bcm.edu	37	13	32912486	32912486	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr13:32912486C>T	ENST00000380152.3	+	11	4227	c.3994C>T	c.(3994-3996)Cat>Tat	p.H1332Y	BRCA2_ENST00000544455.1_Missense_Mutation_p.H1332Y			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1332					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAGAAATTCTCATAACTTAGA	0.308			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.H1332Y	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.C3994T						.						24.0	24.0	24.0					13																	32912486		2202	4289	6491	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AATTCTCATAACT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3994C>T	chr13.hg19:g.32912486C>T	ENSP00000369497:p.His1332Tyr	160.0	0.0		124.0	26.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.113434	0.00032	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00678	5.87;5.87	5.44	-0.395	0.12431	.	1.264310	0.05114	N	0.489382	T	0.00440	0.0014	N	0.10874	0.06	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	10	0.02654	T	1	.	0.2365	0.00187	0.2378:0.2012:0.1562:0.4049	.	1332	P51587	BRCA2_HUMAN	Y	1332	ENSP00000369497:H1332Y;ENSP00000439902:H1332Y	ENSP00000369497:H1332Y	H	+	1	0	BRCA2	31810486	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.239000	0.08965	0.374000	0.24650	-0.484000	0.04775	CAT	.	.		0.308	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
IPO5	3843	hgsc.bcm.edu	37	13	98670928	98670928	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr13:98670928G>A	ENST00000490680.1	+	23	2871	c.2806G>A	c.(2806-2808)Ggt>Agt	p.G936S	IPO5_ENST00000261574.5_Missense_Mutation_p.G954S|IPO5_ENST00000539640.1_Missense_Mutation_p.G811S			O00410	IPO5_HUMAN	importin 5	936					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						GGCACAGTACGGTGGAGATAA	0.443																																					p.G954S		Atlas-SNP	.											.	IPO5	90	.	0			c.G2860A						.						183.0	130.0	148.0					13																	98670928		2203	4300	6503	SO:0001583	missense	3843	exon26			CAGTACGGTGGAG	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"""Importins"""	6402	protein-coding gene	gene with protein product		602008	"""karyopherin (importin) beta 3"", ""RAN binding protein 5"""	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.2806G>A	chr13.hg19:g.98670928G>A	ENSP00000418393:p.Gly936Ser	151.0	0.0		184.0	38.0	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Missense_Mutation	SNP	ENST00000490680.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.481160	0.96307	.	.	ENSG00000065150	ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.82	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.78868	0.4351	M	0.77820	2.39	0.80722	D	1	D	0.76494	0.999	P	0.58331	0.837	T	0.81807	-0.0763	10	0.62326	D	0.03	-9.9941	14.6536	0.68817	0.0694:0.0:0.9306:0.0	.	954	O00410-3	.	S	954;936;936;811	ENSP00000261574:G954S;ENSP00000350219:G936S;ENSP00000418393:G936S;ENSP00000445126:G811S	ENSP00000261574:G954S	G	+	1	0	IPO5	97468929	1.000000	0.71417	0.805000	0.32314	0.995000	0.86356	9.581000	0.98210	1.469000	0.48083	0.650000	0.86243	GGT	.	.		0.443	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271	
ZNF267	10308	hgsc.bcm.edu	37	16	31925948	31925948	+	Silent	SNP	T	T	C			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr16:31925948T>C	ENST00000300870.10	+	4	587	c.378T>C	c.(376-378)aaT>aaC	p.N126N	ZNF267_ENST00000394846.3_3'UTR	NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	126					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AAGGGCACAATGGATGTTATG	0.363																																					p.N126N		Atlas-SNP	.											.	ZNF267	94	.	0			c.T378C						.						123.0	122.0	122.0					16																	31925948		2197	4300	6497	SO:0001819	synonymous_variant	10308	exon4			GCACAATGGATGT	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"""Zinc fingers, C2H2-type"", ""-"""	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.378T>C	chr16.hg19:g.31925948T>C		158.0	0.0		148.0	28.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Silent	SNP	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.363	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414	
SKAP1	8631	hgsc.bcm.edu	37	17	46262096	46262096	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr17:46262096G>A	ENST00000336915.6	-	7	625	c.556C>T	c.(556-558)Cgc>Tgc	p.R186C	RP11-456D7.1_ENST00000582246.1_RNA|SKAP1_ENST00000584924.1_Missense_Mutation_p.R186C	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	186	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						TCATAGCTGCGCCTATCCTGG	0.522																																					p.R186C		Atlas-SNP	.											.	SKAP1	41	.	0			c.C556T						.						210.0	193.0	199.0					17																	46262096		2203	4300	6503	SO:0001583	missense	8631	exon7			AGCTGCGCCTATC	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"""Pleckstrin homology (PH) domain containing"""	15605	protein-coding gene	gene with protein product		604969	"""src family associated phosphoprotein 1"""	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.556C>T	chr17.hg19:g.46262096G>A	ENSP00000338171:p.Arg186Cys	138.0	0.0		128.0	26.0	NM_003726	D3DTV1|O15268	Missense_Mutation	SNP	ENST00000336915.6	hg19	CCDS32674.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.326383	0.41197	.	.	ENSG00000141293	ENST00000336915	T	0.18502	2.21	5.55	5.55	0.83447	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.061153	0.64402	D	0.000002	T	0.54303	0.1850	M	0.93283	3.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.991	T	0.66416	-0.5929	10	0.87932	D	0	-54.9613	17.2809	0.87128	0.0:0.0:1.0:0.0	.	186;186	Q86WV1-2;Q86WV1	.;SKAP1_HUMAN	C	186	ENSP00000338171:R186C	ENSP00000338171:R186C	R	-	1	0	SKAP1	43617095	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.764000	0.74960	2.612000	0.88384	0.557000	0.71058	CGC	.	.		0.522	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726	
GPR142	350383	hgsc.bcm.edu	37	17	72367888	72367888	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr17:72367888G>A	ENST00000335666.4	+	4	586	c.538G>A	c.(538-540)Gcc>Acc	p.A180T		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	180						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A180T(1)		central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						GACCGCAGTGGCCCTGGCGCG	0.622																																					p.A180T		Atlas-SNP	.											GPR142,NS,carcinoma,0,1	GPR142	74	.	1	Substitution - Missense(1)	lung(1)	c.G538A						.						45.0	40.0	42.0					17																	72367888		2203	4300	6503	SO:0001583	missense	350383	exon4			GCAGTGGCCCTGG	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"""GPCR / Class A : Orphans"""	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.538G>A	chr17.hg19:g.72367888G>A	ENSP00000335158:p.Ala180Thr	44.0	0.0		47.0	10.0	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	hg19	CCDS11698.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.762461	0.31228	.	.	ENSG00000257008	ENST00000335666	T	0.38560	1.13	4.68	3.71	0.42584	GPCR, rhodopsin-like superfamily (1);	0.175229	0.49916	N	0.000129	T	0.44052	0.1275	L	0.50919	1.6	0.40575	D	0.981335	P;P	0.47484	0.896;0.476	P;B	0.47118	0.538;0.219	T	0.48614	-0.9020	10	0.56958	D	0.05	-3.3935	12.8413	0.57805	0.0831:0.0:0.9169:0.0	.	180;1142	Q7Z601;Q8NGB0	GP142_HUMAN;.	T	180	ENSP00000335158:A180T	ENSP00000335158:A180T	A	+	1	0	GPR142	69879483	1.000000	0.71417	0.892000	0.35008	0.219000	0.24729	3.189000	0.50965	1.283000	0.44513	0.558000	0.71614	GCC	.	.		0.622	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790	
FBF1	85302	hgsc.bcm.edu	37	17	73918105	73918105	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr17:73918105C>G	ENST00000586717.1	-	14	1678	c.1405G>C	c.(1405-1407)Ggg>Cgg	p.G469R	FBF1_ENST00000319129.5_Missense_Mutation_p.G468R|FBF1_ENST00000389570.4_Missense_Mutation_p.G469R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	469					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGCTCAAGCCCTTGTGTGCTG	0.622																																					p.G468R		Atlas-SNP	.											.	FBF1	48	.	0			c.G1402C						.						41.0	47.0	45.0					17																	73918105		2071	3986	6057	SO:0001583	missense	85302	exon14			CAAGCCCTTGTGT	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1405G>C	chr17.hg19:g.73918105C>G	ENSP00000465132:p.Gly469Arg	120.0	0.0		108.0	20.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.75	1.437176	0.25900	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.17370	2.28;2.28	5.45	3.43	0.39272	.	.	.	.	.	T	0.12817	0.0311	L	0.44542	1.39	0.09310	N	1	B;B;B	0.31548	0.328;0.029;0.102	B;B;B	0.29598	0.104;0.021;0.063	T	0.22626	-1.0211	9	0.11485	T	0.65	-8.5154	8.9107	0.35552	0.0:0.8223:0.0:0.1777	.	483;469;468	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	R	469;469;468;482	ENSP00000374221:G469R;ENSP00000324292:G468R	ENSP00000324292:G468R	G	-	1	0	FBF1	71429700	0.001000	0.12720	0.005000	0.12908	0.002000	0.02628	1.370000	0.34238	1.287000	0.44583	0.655000	0.94253	GGG	.	.		0.622	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
POLD1	5424	hgsc.bcm.edu	37	19	50912834	50912834	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr19:50912834C>T	ENST00000440232.2	+	17	2118	c.2065C>T	c.(2065-2067)Cgg>Tgg	p.R689W	POLD1_ENST00000595904.1_Missense_Mutation_p.R715W|POLD1_ENST00000599857.1_Missense_Mutation_p.R689W	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	689					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CCTGGATGGACGGCAGCTGGC	0.672								DNA polymerases (catalytic subunits)																													p.R689W		Atlas-SNP	.											POLD1_ENST00000440232,colon,carcinoma,0,2	POLD1	174	.	0			c.C2065T						.						58.0	65.0	62.0					19																	50912834		2203	4299	6502	SO:0001583	missense	5424	exon17			GATGGACGGCAGC		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2065C>T	chr19.hg19:g.50912834C>T	ENSP00000406046:p.Arg689Trp	138.0	0.0		154.0	27.0	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.471484	0.84533	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.19806	2.12	4.38	4.38	0.52667	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.000000	0.85682	D	0.000000	T	0.64659	0.2618	H	0.99156	4.45	0.80722	D	1	D;D	0.60160	0.987;0.987	P;D	0.66979	0.887;0.948	T	0.81986	-0.0681	10	0.87932	D	0	-33.0089	16.0916	0.81094	0.0:1.0:0.0:0.0	.	715;689	E7EVW0;P28340	.;DPOD1_HUMAN	W	689;690	ENSP00000406046:R689W	ENSP00000366129:R690W	R	+	1	2	POLD1	55604646	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.126000	0.64721	2.190000	0.69967	0.561000	0.74099	CGG	.	.		0.672	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
XKR7	343702	hgsc.bcm.edu	37	20	30585125	30585125	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr20:30585125G>A	ENST00000562532.2	+	3	1779	c.1605G>A	c.(1603-1605)tgG>tgA	p.W535*		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	535						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			ACCCGGCCTGGGATGCTCATT	0.632																																					p.W535X		Atlas-SNP	.											.	XKR7	62	.	0			c.G1605A						.						50.0	57.0	55.0					20																	30585125		2203	4300	6503	SO:0001587	stop_gained	343702	exon3			GGCCTGGGATGCT	AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 7"", ""chromosome 20 open reading frame 159"""	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.1605G>A	chr20.hg19:g.30585125G>A	ENSP00000477059:p.Trp535*	37.0	0.0		22.0	7.0	NM_001011718	Q9NUG5	Nonsense_Mutation	SNP	ENST00000562532.2	hg19	CCDS33459.1	.	.	.	.	.	.	.	.	.	.	G	37	6.445175	0.97572	.	.	ENSG00000101321	ENST00000217299	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5108	16.7017	0.85351	0.0:0.0:1.0:0.0	.	.	.	.	X	535	.	ENSP00000217299:W535X	W	+	3	0	XKR7	30048786	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.657000	0.98554	2.518000	0.84900	0.561000	0.74099	TGG	.	.		0.632	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3	NM_001011718	
TDRD9	122402	hgsc.bcm.edu	37	14	104473004	104473005	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DD-A1EC-01A-21D-A12Z-10	TCGA-DD-A1EC-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b9bbd66-c9e2-4d37-ba06-3137ad936c06	f5663abe-78b9-4a8e-925d-e5a08d29c2ff	g.chr14:104473004_104473005insT	ENST00000409874.4	+	17	1949_1950	c.1901_1902insT	c.(1900-1905)aattttfs	p.NF634fs	TDRD9_ENST00000339063.5_Frame_Shift_Ins_p.NF634fs	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	634					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TCTTTGAAGAATTTTTTTGCAA	0.332																																					p.N634fs		Pindel	.											.	TDRD9	175	.	0			c.1901_1902insT						.																																			SO:0001589	frameshift_variant	122402	exon17			.	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1908dupT	chr14.hg19:g.104473011_104473011dupT	ENSP00000387303:p.Asn634fs	299.0	0.0		235.0	14.0	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Frame_Shift_Ins	INS	ENST00000409874.4	hg19	CCDS9987.2																																																																																			.	.		0.332	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
