#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
KIF1B	23095	hgsc.bcm.edu	37	1	10435400	10435400	+	Missense_Mutation	SNP	G	G	C			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:10435400G>C	ENST00000377086.1	+	48	5579	c.5377G>C	c.(5377-5379)Gcc>Ccc	p.A1793P	KIF1B_ENST00000263934.6_Missense_Mutation_p.A1747P|KIF1B_ENST00000377081.1_Missense_Mutation_p.A1793P			O60333	KIF1B_HUMAN	kinesin family member 1B	1793	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CTGGTTGTATGCCTTCAACCC	0.448																																					p.A1747P		Atlas-SNP	.											.	KIF1B	242	.	0			c.G5239C						PASS	.						120.0	110.0	113.0					1																	10435400		2203	4300	6503	SO:0001583	missense	23095	exon46			TTGTATGCCTTCA	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.5377G>C	chr1.hg19:g.10435400G>C	ENSP00000366290:p.Ala1793Pro	178.0	0.0	.		150.0	34.0	.	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.472787	0.96274	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.79845	-1.31;-1.31;-1.31	5.38	5.38	0.77491	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.91925	0.7443	M	0.89534	3.04	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.999;0.991	D	0.93192	0.6584	10	0.72032	D	0.01	.	19.1601	0.93527	0.0:0.0:1.0:0.0	.	1779;1753;1793;1767;1793;1747	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	P	1793;1747;1793;1793	ENSP00000263934:A1747P;ENSP00000366290:A1793P;ENSP00000366284:A1793P	ENSP00000263934:A1747P	A	+	1	0	KIF1B	10357987	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	9.864000	0.99589	2.520000	0.84964	0.585000	0.79938	GCC	.	.	.	none		0.448	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
DHDDS	79947	hgsc.bcm.edu	37	1	26759444	26759444	+	Missense_Mutation	SNP	G	G	T			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:26759444G>T	ENST00000236342.7	+	2	101	c.8G>T	c.(7-9)tGg>tTg	p.W3L	DHDDS_ENST00000427245.2_Missense_Mutation_p.W3L|DHDDS_ENST00000374185.3_Missense_Mutation_p.W3L|DHDDS_ENST00000525682.2_Missense_Mutation_p.W3L|DHDDS_ENST00000531955.1_3'UTR|DHDDS_ENST00000526219.1_Missense_Mutation_p.W3L|DHDDS_ENST00000360009.2_Missense_Mutation_p.W3L			Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase	3					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)			breast(5)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	15		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		ACTATGTCATGGATCAAGGAA	0.468																																					p.W3L		Atlas-SNP	.											.	DHDDS	33	.	0			c.G8T						PASS	.						148.0	137.0	141.0					1																	26759444		2203	4300	6503	SO:0001583	missense	79947	exon2			TGTCATGGATCAA	AK023164	CCDS281.1, CCDS282.1, CCDS57984.1, CCDS57983.1	1p35.3	2014-01-28			ENSG00000117682	ENSG00000117682			20603	protein-coding gene	gene with protein product		608172				12591616	Standard	NM_024887		Approved	HDS, FLJ13102, DS, RP59	uc001bmk.3	Q86SQ9	OTTHUMG00000003554	ENST00000236342.7:c.8G>T	chr1.hg19:g.26759444G>T	ENSP00000236342:p.Trp3Leu	140.0	0.0	.		134.0	42.0	.	NM_001243564	B7Z4B9|B7ZB20|D3DPK7|D3DPK8|D3DPK9|E9KL43|Q5T0A4|Q8NE90|Q9BTG5|Q9BTK3|Q9H905	Missense_Mutation	SNP	ENST00000236342.7	hg19	CCDS282.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435781	0.83885	.	.	ENSG00000117682	ENST00000427245;ENST00000525682;ENST00000236342;ENST00000526219;ENST00000374185;ENST00000360009;ENST00000533087;ENST00000531312;ENST00000525165;ENST00000525326;ENST00000525546;ENST00000436153;ENST00000530781;ENST00000430232	T;T;T;T;T	0.56103	0.55;0.5;0.55;0.48;0.71	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.73345	0.3575	M	0.87900	2.915	0.80722	D	1	D;P;P;D	0.59357	0.985;0.944;0.928;0.957	P;P;P;P	0.55667	0.728;0.448;0.609;0.781	T	0.77800	-0.2452	10	0.87932	D	0	-13.9392	19.2865	0.94077	0.0:0.0:1.0:0.0	.	3;3;3;3	B7Z4B9;Q86SQ9-3;Q86SQ9;Q86SQ9-2	.;.;DHDDS_HUMAN;.	L	3	ENSP00000434984:W3L;ENSP00000236342:W3L;ENSP00000434219:W3L;ENSP00000353104:W3L;ENSP00000397584:W3L	ENSP00000236342:W3L	W	+	2	0	DHDDS	26632031	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.358000	0.90090	2.802000	0.96397	0.655000	0.94253	TGG	.	.	.	none		0.468	DHDDS-011	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392504.1	NM_024887	
GON4L	54856	hgsc.bcm.edu	37	1	155785662	155785662	+	Missense_Mutation	SNP	T	T	A			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:155785662T>A	ENST00000368331.1	-	8	1143	c.1095A>T	c.(1093-1095)gaA>gaT	p.E365D	GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000271883.5_Missense_Mutation_p.E365D|GON4L_ENST00000361040.5_Missense_Mutation_p.E365D|GON4L_ENST00000437809.1_Missense_Mutation_p.E365D	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	365					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					AATCATCTTCTTCAAGGTGGA	0.368																																					p.E365D		Atlas-SNP	.											.	GON4L	392	.	0			c.A1095T						PASS	.						92.0	84.0	87.0					1																	155785662		2203	4300	6503	SO:0001583	missense	54856	exon8			ATCTTCTTCAAGG	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"""gon-4 homolog (C.elegans)"""	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.1095A>T	chr1.hg19:g.155785662T>A	ENSP00000357315:p.Glu365Asp	171.0	0.0	.		205.0	51.0	.	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.44	3.828178	0.71143	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000539959;ENST00000361040	T;T;T;T	0.12774	2.87;2.85;2.87;2.65	5.28	2.78	0.32641	.	0.131508	0.51477	D	0.000095	T	0.11707	0.0285	L	0.49350	1.555	0.32400	N	0.552129	D;D;D;D;D	0.71674	0.986;0.998;0.998;0.997;0.998	P;D;D;D;D	0.77557	0.84;0.99;0.941;0.978;0.99	T	0.06250	-1.0837	10	0.28530	T	0.3	.	3.7085	0.08410	0.0:0.2293:0.1888:0.5819	.	59;365;365;365;365	Q9H5U2;A4PB68;Q3T8J9-2;Q3T8J9;Q3T8J9-3	.;.;.;GON4L_HUMAN;.	D	365	ENSP00000396117:E365D;ENSP00000357315:E365D;ENSP00000271883:E365D;ENSP00000354322:E365D	ENSP00000271883:E365D	E	-	3	2	GON4L	154052286	0.972000	0.33761	1.000000	0.80357	0.998000	0.95712	0.009000	0.13219	0.938000	0.37419	0.533000	0.62120	GAA	.	.	.	none		0.368	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292	
KDM3A	55818	hgsc.bcm.edu	37	2	86693629	86693629	+	Missense_Mutation	SNP	A	A	G			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr2:86693629A>G	ENST00000409556.1	+	11	1507	c.1142A>G	c.(1141-1143)aAa>aGa	p.K381R	KDM3A_ENST00000312912.5_Missense_Mutation_p.K381R|KDM3A_ENST00000409064.1_Missense_Mutation_p.K381R|KDM3A_ENST00000542128.1_Missense_Mutation_p.K329R			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	381					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						GGAGACTTGAAAATTCTGACT	0.448																																					p.K381R	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.A1142G						PASS	.						116.0	118.0	117.0					2																	86693629		2203	4300	6503	SO:0001583	missense	55818	exon10			ACTTGAAAATTCT	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1142A>G	chr2.hg19:g.86693629A>G	ENSP00000386660:p.Lys381Arg	81.0	0.0	.		129.0	40.0	.	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.675086	0.47781	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.71	4.54	0.55810	.	0.336240	0.28914	N	0.013724	T	0.38558	0.1045	N	0.14661	0.345	0.24510	N	0.994213	B;B	0.28933	0.228;0.146	B;B	0.25140	0.058;0.038	T	0.26155	-1.0111	10	0.44086	T	0.13	.	10.9773	0.47473	0.8434:0.1566:0.0:0.0	.	329;381	F5H070;Q9Y4C1	.;KDM3A_HUMAN	R	381;381;381;381;329	ENSP00000386660:K381R;ENSP00000323659:K381R;ENSP00000386516:K381R;ENSP00000438324:K329R	ENSP00000323659:K381R	K	+	2	0	KDM3A	86547140	0.046000	0.20272	0.980000	0.43619	0.993000	0.82548	2.137000	0.42130	0.963000	0.38082	0.533000	0.62120	AAA	.	.	.	none		0.448	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
ADAM23	8745	hgsc.bcm.edu	37	2	207457453	207457453	+	Missense_Mutation	SNP	G	G	C			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr2:207457453G>C	ENST00000264377.3	+	22	2399	c.2071G>C	c.(2071-2073)Gac>Cac	p.D691H	ADAM23_ENST00000374415.3_Missense_Mutation_p.D691H|ADAM23_ENST00000374416.1_Missense_Mutation_p.D691H	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	691					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		CCGGGTGATTGACTGCAGGTA	0.353																																					p.D691H	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.G2071C						PASS	.						117.0	102.0	107.0					2																	207457453		2203	4300	6503	SO:0001583	missense	8745	exon22			GTGATTGACTGCA	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"""ADAM metallopeptidase domain containing"""	202	protein-coding gene	gene with protein product		603710	"""a disintegrin and metalloproteinase domain 23"""			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.2071G>C	chr2.hg19:g.207457453G>C	ENSP00000264377:p.Asp691His	232.0	0.0	.		155.0	9.0	.	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	hg19	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.482645	0.44147	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.21932	1.98;1.98;1.98	5.52	5.52	0.82312	ADAM, cysteine-rich (2);	0.000000	0.64402	D	0.000006	T	0.24275	0.0588	L	0.46157	1.445	0.80722	D	1	P	0.48016	0.904	P	0.44673	0.457	T	0.00742	-1.1585	10	0.48119	T	0.1	.	13.7002	0.62604	0.0741:0.0:0.9259:0.0	.	691	O75077	ADA23_HUMAN	H	691;691;585;691	ENSP00000264377:D691H;ENSP00000363537:D691H;ENSP00000363536:D691H	ENSP00000264377:D691H	D	+	1	0	ADAM23	207165698	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	5.445000	0.66594	2.593000	0.87608	0.591000	0.81541	GAC	.	.	.	none		0.353	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	
ZPLD1	131368	hgsc.bcm.edu	37	3	102171980	102171980	+	Silent	SNP	G	G	A			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:102171980G>A	ENST00000491959.1	+	10	1206	c.324G>A	c.(322-324)ctG>ctA	p.L108L	ZPLD1_ENST00000466937.1_Silent_p.L108L|ZPLD1_ENST00000306176.1_Silent_p.L124L			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	108	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						GAAACAACCTGGTGGTAAGAT	0.433																																					p.L124L		Atlas-SNP	.											.	ZPLD1	82	.	0			c.G372A						PASS	.						63.0	55.0	58.0					3																	102171980		2203	4300	6503	SO:0001819	synonymous_variant	131368	exon3			CAACCTGGTGGTA	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.324G>A	chr3.hg19:g.102171980G>A		88.0	0.0	.		77.0	13.0	.	NM_175056	Q49AS1|Q8WU36	Silent	SNP	ENST00000491959.1	hg19																																																																																				.	.	.	none		0.433	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056	
TNFSF10	8743	hgsc.bcm.edu	37	3	172232753	172232753	+	Silent	SNP	A	A	G			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:172232753A>G	ENST00000241261.2	-	2	290	c.168T>C	c.(166-168)tgT>tgC	p.C56C	TNFSF10_ENST00000420541.2_Silent_p.C56C	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	56					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CTTTTAAGAAACAAGCAATGC	0.408																																					p.C56C		Atlas-SNP	.											.	TNFSF10	30	.	0			c.T168C						PASS	.						143.0	140.0	141.0					3																	172232753		2203	4300	6503	SO:0001819	synonymous_variant	8743	exon2			TAAGAAACAAGCA	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.168T>C	chr3.hg19:g.172232753A>G		110.0	0.0	.		109.0	27.0	.	NM_003810	A1Y9B3	Silent	SNP	ENST00000241261.2	hg19	CCDS3219.1																																																																																			.	.	.	none		0.408	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1		
CCDC39	339829	hgsc.bcm.edu	37	3	180379790	180379790	+	Silent	SNP	A	A	G			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:180379790A>G	ENST00000442201.2	-	3	335	c.216T>C	c.(214-216)ctT>ctC	p.L72L	CCDC39_ENST00000273654.4_Silent_p.L156L	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	72					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TTGCTTTGCAAAGAGACTACA	0.323																																					p.L72L		Atlas-SNP	.											.	CCDC39	242	.	0			c.T216C						PASS	.						56.0	45.0	49.0					3																	180379790		1776	4011	5787	SO:0001819	synonymous_variant	339829	exon3			TTTGCAAAGAGAC	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.216T>C	chr3.hg19:g.180379790A>G		207.0	0.0	.		269.0	59.0	.	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	hg19	CCDS46964.1																																																																																			.	.	.	none		0.323	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
CHRD	8646	hgsc.bcm.edu	37	3	184099117	184099117	+	Missense_Mutation	SNP	A	A	G			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:184099117A>G	ENST00000204604.1	+	3	593	c.347A>G	c.(346-348)cAg>cGg	p.Q116R	CHRD_ENST00000545352.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000348986.3_Missense_Mutation_p.Q116R|CHRD_ENST00000450923.1_Missense_Mutation_p.Q116R	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	116	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.			RQLP -> QVAA (in Ref. 4; AAC69835). {ECO:0000305}.	BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CAGCCGCGCCAGCTGCCGGGA	0.692																																					p.Q116R		Atlas-SNP	.											.	CHRD	149	.	0			c.A347G						PASS	.						8.0	11.0	10.0					3																	184099117		2170	4243	6413	SO:0001583	missense	8646	exon3			CGCGCCAGCTGCC	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.347A>G	chr3.hg19:g.184099117A>G	ENSP00000204604:p.Gln116Arg	176.0	0.0	.		154.0	40.0	.	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	hg19	CCDS3266.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.514869	0.64634	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.72282	-0.64;-0.64;-0.64	5.18	3.94	0.45596	von Willebrand factor, type C (3);	0.069374	0.64402	D	0.000016	T	0.37865	0.1019	N	0.02368	-0.58	0.80722	D	1	B;B	0.33318	0.101;0.408	B;B	0.31495	0.102;0.131	T	0.34925	-0.9809	10	0.11485	T	0.65	-21.1397	7.5131	0.27585	0.6909:0.0:0.0:0.3091	.	116;116	E7ESX1;Q9H2X0	.;CHRD_HUMAN	R	116	ENSP00000204604:Q116R;ENSP00000408972:Q116R;ENSP00000334036:Q116R	ENSP00000204604:Q116R	Q	+	2	0	CHRD	185581811	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	3.705000	0.54823	1.954000	0.56735	0.459000	0.35465	CAG	.	.	.	none		0.692	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
ZNF721	170960	hgsc.bcm.edu	37	4	436272	436272	+	Missense_Mutation	SNP	T	T	A			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr4:436272T>A	ENST00000338977.5	-	2	1996	c.1948A>T	c.(1948-1950)Att>Ttt	p.I650F	ZNF721_ENST00000511833.2_Missense_Mutation_p.I662F|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA			Q8TF20	ZN721_HUMAN	zinc finger protein 721	650					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(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						CCAGTAAGAATTTTCGTGTGT	0.408																																					p.L662L		Atlas-SNP	.											.	ZNF721	205	.	0			c.T1984T						PASS	.						151.0	158.0	156.0					4																	436272		2008	4191	6199	SO:0001583	missense	170960	exon3			TAAGAATTTTCGT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1948A>T	chr4.hg19:g.436272T>A	ENSP00000340524:p.Ile650Phe	271.0	0.0	.		339.0	94.0	.	NM_133474	Q69YG7	Silent	SNP	ENST00000338977.5	hg19		.	.	.	.	.	.	.	.	.	.	T	15.96	2.987248	0.53934	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.17370	2.28;2.28	1.02	1.02	0.19986	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22126	0.0533	M	0.75085	2.285	0.24841	N	0.992466	D;D;D	0.54601	0.967;0.967;0.96	P;P;B	0.45577	0.486;0.486;0.354	T	0.14448	-1.0472	9	0.66056	D	0.02	.	6.213	0.20640	0.0:0.0:0.0:1.0	.	650;662;662	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	F	650;662	ENSP00000340524:I650F;ENSP00000428878:I662F	ENSP00000340524:I650F	I	-	1	0	ZNF721	426272	0.100000	0.21855	0.009000	0.14445	0.110000	0.19582	1.945000	0.40273	0.733000	0.32492	0.155000	0.16302	ATT	.	.	.	none		0.408	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
TRIP13	9319	hgsc.bcm.edu	37	5	914652	914652	+	Missense_Mutation	SNP	A	A	T			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr5:914652A>T	ENST00000166345.3	+	11	1449	c.1093A>T	c.(1093-1095)Aac>Tac	p.N365Y		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	365					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CATTGAAAACAACGTGTCAAA	0.428																																					p.N365Y		Atlas-SNP	.											.	TRIP13	41	.	0			c.A1093T						PASS	.						196.0	201.0	199.0					5																	914652		2203	4300	6503	SO:0001583	missense	9319	exon11			GAAAACAACGTGT	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"""ATPases / AAA-type"""	12307	protein-coding gene	gene with protein product	"""thyroid receptor interacting protein 13"""	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.1093A>T	chr5.hg19:g.914652A>T	ENSP00000166345:p.Asn365Tyr	63.0	0.0	.		42.0	10.0	.	NM_004237	C9K0T3|D3DTC0|O15324	Missense_Mutation	SNP	ENST00000166345.3	hg19	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	15.36	2.811141	0.50527	.	.	ENSG00000071539	ENST00000166345	D	0.95307	-3.67	5.8	5.8	0.92144	.	0.218259	0.51477	D	0.000093	D	0.89856	0.6836	L	0.34521	1.04	0.51233	D	0.999919	B	0.33694	0.421	B	0.31337	0.128	D	0.88757	0.3254	10	0.51188	T	0.08	-5.4017	10.9531	0.47341	0.9266:0.0:0.0734:0.0	.	365	Q15645	PCH2_HUMAN	Y	365	ENSP00000166345:N365Y	ENSP00000166345:N365Y	N	+	1	0	TRIP13	967652	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	3.960000	0.56752	2.224000	0.72417	0.533000	0.62120	AAC	.	.	.	none		0.428	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237	
PGBD1	84547	hgsc.bcm.edu	37	6	28268788	28268788	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr6:28268788C>T	ENST00000405948.2	+	7	1577	c.1157C>T	c.(1156-1158)cCa>cTa	p.P386L	PGBD1_ENST00000259883.3_Missense_Mutation_p.P386L	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	386						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						TCATGTTTCCCAGAAAAGAGT	0.433																																					p.P386L		Atlas-SNP	.											.	PGBD1	106	.	0			c.C1157T						PASS	.						64.0	68.0	67.0					6																	28268788		2203	4300	6503	SO:0001583	missense	84547	exon7			GTTTCCCAGAAAA	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1157C>T	chr6.hg19:g.28268788C>T	ENSP00000385213:p.Pro386Leu	79.0	0.0	.		67.0	17.0	.	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	hg19	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396990	0.25205	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01347	4.99;4.99	4.54	3.65	0.41850	.	0.184961	0.26715	N	0.022869	T	0.00580	0.0019	L	0.34521	1.04	0.40026	D	0.97547	B	0.28378	0.209	B	0.21360	0.034	T	0.59026	-0.7531	10	0.42905	T	0.14	-10.7499	9.9021	0.41353	0.2033:0.7967:0.0:0.0	.	386	Q96JS3	PGBD1_HUMAN	L	386	ENSP00000385213:P386L;ENSP00000259883:P386L	ENSP00000259883:P386L	P	+	2	0	PGBD1	28376767	0.417000	0.25432	0.214000	0.23707	0.588000	0.36517	2.102000	0.41796	1.218000	0.43458	0.655000	0.94253	CCA	.	.	.	none		0.433	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
HOXA2	3199	hgsc.bcm.edu	37	7	27140420	27140420	+	Silent	SNP	T	T	A			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr7:27140420T>A	ENST00000222718.5	-	2	1366	c.1056A>T	c.(1054-1056)gtA>gtT	p.V352V	HOTAIRM1_ENST00000593300.1_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000428939.3_RNA|HOTAIRM1_ENST00000429611.3_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	352					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						CTGAAATATCTACGGGACTGT	0.443																																					p.V352V		Atlas-SNP	.											.	HOXA2	56	.	0			c.A1056T						PASS	.						87.0	87.0	87.0					7																	27140420		2203	4300	6503	SO:0001819	synonymous_variant	3199	exon2			AATATCTACGGGA		CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"""Homeoboxes / ANTP class : HOXL subclass"""	5103	protein-coding gene	gene with protein product		604685	"""homeo box A2"""	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.1056A>T	chr7.hg19:g.27140420T>A		174.0	0.0	.		201.0	52.0	.	NM_006735	A1L4K3|B2RMW3	Silent	SNP	ENST00000222718.5	hg19	CCDS5403.1																																																																																			.	.	.	none		0.443	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2		
DPY19L1	23333	hgsc.bcm.edu	37	7	35006553	35006553	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr7:35006553C>T	ENST00000310974.4	-	10	970	c.826G>A	c.(826-828)Ggg>Agg	p.G276R	DPY19L1_ENST00000462134.2_5'UTR	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	276						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						TCAATGTACCCGACAACATAT	0.249																																					p.G276R		Atlas-SNP	.											.	DPY19L1	56	.	0			c.G826A						PASS	.						43.0	40.0	41.0					7																	35006553		1783	4020	5803	SO:0001583	missense	23333	exon10			TGTACCCGACAAC	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.826G>A	chr7.hg19:g.35006553C>T	ENSP00000308695:p.Gly276Arg	216.0	0.0	.		209.0	11.0	.	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	hg19	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.649777	0.67358	.	.	ENSG00000173852	ENST00000310974;ENST00000446375	T;T	0.58358	0.34;0.34	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.68329	0.2989	L	0.60845	1.875	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.68221	-0.5466	10	0.44086	T	0.13	-13.2136	15.6504	0.77088	0.0:1.0:0.0:0.0	.	276	Q2PZI1	D19L1_HUMAN	R	276;75	ENSP00000308695:G276R;ENSP00000400510:G75R	ENSP00000308695:G276R	G	-	1	0	DPY19L1	34973078	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.342000	0.65970	2.365000	0.80145	0.555000	0.69702	GGG	.	.	.	none		0.249	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1		
TRAPPC9	83696	hgsc.bcm.edu	37	8	141468506	141468506	+	5'Flank	SNP	C	C	T	rs572038747	byFrequency	TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr8:141468506C>T	ENST00000438773.2	-	0	0				TRAPPC9_ENST00000389328.4_Missense_Mutation_p.G53E|TRAPPC9_ENST00000389327.3_5'Flank	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9						cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CCCGTGACTCCCACGGTCGTG	0.721													C|||	66	0.0131789	0.0484	0.0029	5008	,	,		12228	0.0		0.0	False		,,,				2504	0.0				p.G53E		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.G158A						PASS	.						13.0	13.0	13.0					8																	141468506		2190	4273	6463	SO:0001631	upstream_gene_variant	83696	exon1			TGACTCCCACGGT	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187		chr8.hg19:g.141468506C>T	Exception_encountered	66.0	0.0	.		83.0	17.0	.	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	C	9.074	0.997622	0.19043	.	.	ENSG00000167632	ENST00000389328	.	.	.	0.857	-0.237	0.13061	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.20505	-1.0273	8	0.87932	D	0	.	2.8882	0.05668	0.0:0.5548:0.0:0.4452	.	53	Q96Q05-2	.	E	53	.	ENSP00000373979:G53E	G	-	2	0	TRAPPC9	141537688	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.171000	0.16685	-0.127000	0.11661	0.498000	0.49722	GGG	.	.	.	none		0.721	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
OR52J3	119679	hgsc.bcm.edu	37	11	5067977	5067977	+	Silent	SNP	C	C	G			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr11:5067977C>G	ENST00000380370.1	+	1	222	c.222C>G	c.(220-222)gcC>gcG	p.A74A		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	74						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGATTTGGCCCTTTCTACAA	0.493																																					p.A74A		Atlas-SNP	.											.	OR52J3	77	.	0			c.C222G						PASS	.						131.0	111.0	118.0					11																	5067977		2201	4298	6499	SO:0001819	synonymous_variant	119679	exon1			TTTGGCCCTTTCT	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.222C>G	chr11.hg19:g.5067977C>G		186.0	0.0	.		191.0	29.0	.	NM_001001916	Q6IFE4	Silent	SNP	ENST00000380370.1	hg19	CCDS31370.1																																																																																			.	.	.	none		0.493	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
PLCB3	5331	hgsc.bcm.edu	37	11	64033788	64033788	+	Splice_Site	SNP	G	G	A			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr11:64033788G>A	ENST00000540288.1	+	28	3371	c.3268G>A	c.(3268-3270)Gag>Aag	p.E1090K	PLCB3_ENST00000325234.5_Splice_Site_p.E1023K|PLCB3_ENST00000279230.6_Splice_Site_p.E1090K	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	1090				REKKELQKILDRKRHNSISEAKMRDKHKKEA -> SWPSWP RSVRSSGRGSPRRSAGACWARCRRG (in Ref. 2; CAA85776). {ECO:0000305}.	inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						CTTCTCCAGGGAGAAGAAGGA	0.572																																					p.E1090K		Atlas-SNP	.											.	PLCB3	103	.	0			c.G3268A						PASS	.						54.0	60.0	58.0					11																	64033788		2201	4297	6498	SO:0001630	splice_region_variant	5331	exon28			TCCAGGGAGAAGA	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.3267-1G>A	chr11.hg19:g.64033788G>A		28.0	0.0	.		28.0	7.0	.	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	hg19	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.957261	0.92726	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.58652	0.32;0.32;0.32	5.17	5.17	0.71159	PLC-beta, C-terminal (1);	0.686476	0.15459	N	0.261221	T	0.75568	0.3867	M	0.65498	2.005	0.80722	D	1	D;P	0.76494	0.999;0.927	D;P	0.81914	0.995;0.842	T	0.76814	-0.2820	10	0.72032	D	0.01	.	17.4353	0.87550	0.0:0.0:1.0:0.0	.	1023;1090	G5E960;Q01970	.;PLCB3_HUMAN	K	1090;1090;1023	ENSP00000279230:E1090K;ENSP00000443631:E1090K;ENSP00000324660:E1023K	ENSP00000279230:E1090K	E	+	1	0	PLCB3	63790364	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	9.167000	0.94773	2.421000	0.82119	0.555000	0.69702	GAG	.	.	.	none		0.572	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		Missense_Mutation
MMP28	79148	hgsc.bcm.edu	37	17	34122300	34122300	+	Missense_Mutation	SNP	C	C	T	rs201598708	byFrequency	TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr17:34122300C>T	ENST00000250144.8	-	1	411	c.82G>A	c.(82-84)Gga>Aga	p.G28R		NM_001032278.1	NP_001027449.1	Q9H239	MMP28_HUMAN	matrix metallopeptidase 28	28					negative regulation of macrophage chemotaxis (GO:0010760)	cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|skin(5)	16		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)	Marimastat(DB00786)	TCCTGGCCTCCGCGCTCCGCG	0.716																																					p.G28R		Atlas-SNP	.											.	MMP28	41	.	0			c.G82A						PASS	.						7.0	9.0	9.0					17																	34122300		1771	3550	5321	SO:0001583	missense	79148	exon1			GGCCTCCGCGCTC	AF315683	CCDS45651.1, CCDS74036.1	17q12	2014-08-12	2005-08-08		ENSG00000271447	ENSG00000271447			14366	protein-coding gene	gene with protein product		608417	"""matrix metalloproteinase 28"""			11121398, 11255011	Standard	NM_024302		Approved	MMP-25, MM28, EPILYSIN, MMP-28	uc002hjy.1	Q9H239	OTTHUMG00000188387	ENST00000250144.8:c.82G>A	chr17.hg19:g.34122300C>T	ENSP00000250144:p.Gly28Arg	48.0	0.0	.		41.0	13.0	.	NM_001032278	Q96F04|Q96TE2	Missense_Mutation	SNP	ENST00000250144.8	hg19	CCDS45651.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.062543	0.36373	.	.	ENSG00000129270	ENST00000338839;ENST00000538544;ENST00000250144	T	0.67171	-0.25	4.41	3.42	0.39159	.	1.443060	0.04714	N	0.418131	T	0.58090	0.2098	.	.	.	0.09310	N	1	D;P	0.54047	0.964;0.898	P;B	0.46299	0.511;0.108	T	0.46119	-0.9214	9	0.12430	T	0.62	.	9.8502	0.41053	0.2041:0.7959:0.0:0.0	.	28;28	Q9H239-2;Q9H239	.;MMP28_HUMAN	R	28	ENSP00000250144:G28R	ENSP00000250144:G28R	G	-	1	0	MMP28	31146413	0.000000	0.05858	0.001000	0.08648	0.130000	0.20726	0.615000	0.24329	1.428000	0.47296	-0.188000	0.12872	GGA	.	.	.	alt		0.716	MMP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449269.1	NM_024302	
CBX4	8535	hgsc.bcm.edu	37	17	77807917	77807917	+	Silent	SNP	T	T	C			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr17:77807917T>C	ENST00000269397.4	-	5	1701	c.1524A>G	c.(1522-1524)gcA>gcG	p.A508A		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	508	Interaction with BMI1.|Poly-Ala.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TGGGTgccgctgccgccgcca	0.687																																					p.A508A		Atlas-SNP	.											.,1	CBX4	40	.	0			c.A1524G						PASS	.						16.0	24.0	21.0					17																	77807917		2078	4093	6171	SO:0001819	synonymous_variant	8535	exon5			TGCCGCTGCCGCC	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"""NS5ATP1-binding protein 16"", ""Pc class 2 homolog (Drosophila)"""	603079	"""chromobox homolog 4 (Drosophila Pc class)"""			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1524A>G	chr17.hg19:g.77807917T>C		96.0	1.0	.		49.0	4.0	.	NM_003655	B1PJR7|Q6TPI8|Q96C04	Silent	SNP	ENST00000269397.4	hg19	CCDS32758.1																																																																																			.	.	.	none		0.687	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655	
CBX4	8535	hgsc.bcm.edu	37	17	77807927	77807927	+	Missense_Mutation	SNP	A	A	G	rs200965379		TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr17:77807927A>G	ENST00000269397.4	-	5	1691	c.1514T>C	c.(1513-1515)gTg>gCg	p.V505A		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	505	Interaction with BMI1.|Poly-Ala.			V -> VAA (in Ref. 3; ACA49234). {ECO:0000305}.	chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			tgccgccgccaccgccaccgc	0.711																																					p.V505A		Atlas-SNP	.											CBX4,uveal_tract,malignant_melanoma,0,1	CBX4	40	.	0			c.T1514C						PASS	.						15.0	21.0	19.0					17																	77807927		1776	3704	5480	SO:0001583	missense	8535	exon5			GCCGCCACCGCCA	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"""NS5ATP1-binding protein 16"", ""Pc class 2 homolog (Drosophila)"""	603079	"""chromobox homolog 4 (Drosophila Pc class)"""			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1514T>C	chr17.hg19:g.77807927A>G	ENSP00000269397:p.Val505Ala	85.0	0.0	.		38.0	10.0	.	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	a	0.008	-1.872700	0.00542	.	.	ENSG00000141582	ENST00000269397;ENST00000343048	.	.	.	0.575	0.575	0.17374	.	2.519730	0.02140	N	0.057046	T	0.20333	0.0489	N	0.08118	0	0.19775	N	0.999955	B	0.13594	0.008	B	0.04013	0.001	T	0.16217	-1.0410	8	0.32370	T	0.25	.	.	.	.	.	505	O00257	CBX4_HUMAN	A	505;235	.	ENSP00000269397:V505A	V	-	2	0	CBX4	75422522	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	0.179000	0.16840	0.475000	0.27415	0.158000	0.16466	GTG	.	.	.	weak		0.711	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655	
PALM3	342979	hgsc.bcm.edu	37	19	14164996	14164997	+	Missense_Mutation	DNP	CT	CT	TA			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr19:14164996_14164997CT>TA	ENST00000340790.4	-	6	1441_1442	c.1442_1443AG>TA	c.(1441-1443)gAG>gTA	p.E481V		NM_001145028.1	NP_001138500.1	A6NDB9	PALM3_HUMAN	paralemmin 3	481	Glu-rich.				negative regulation of cytokine-mediated signaling pathway (GO:0001960)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)			endometrium(1)|kidney(2)|pancreas(1)|skin(1)	5						gttcttctacctcctcctcctc	0.535																																					p.E481E|p.E481V		Atlas-SNP	.											.	PALM3	26	.	0			c.G1443A|c.A1442T						PASS	.																																			SO:0001583	missense	342979	exon6			TTCTACCTCCTCC|TCTACCTCCTCCT		CCDS46001.1	19p13.12	2010-04-15			ENSG00000187867	ENSG00000187867			33274	protein-coding gene	gene with protein product							Standard	NM_001145028		Approved		uc010xnk.1	A6NDB9		ENST00000340790.4:c.1442_1443delinsTA	chr19.hg19:g.14164996_14164997delinsTA	ENSP00000344996:p.Glu481Val	170.0	0.0	.		186.0|190.0	11.0|13.0	.	NM_001145028		Silent|Missense_Mutation	SNP	ENST00000340790.4	hg19	CCDS46001.1																																																																																			.	.	.	none		0.535	PALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458540.1	NM_001145028	
ATF5	22809	hgsc.bcm.edu	37	19	50436034	50436034	+	Silent	SNP	G	G	T	rs367836750	byFrequency	TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr19:50436034G>T	ENST00000423777.2	+	3	911	c.534G>T	c.(532-534)ccG>ccT	p.P178P	ATF5_ENST00000595125.1_Silent_p.P178P|MIR4751_ENST00000578027.1_RNA|CTC-326K19.6_ENST00000451973.1_Intron	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	178	Interaction with PTP4A1. {ECO:0000250}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	TGGGGATGCCGCCTCTGCCCC	0.672																																					p.P178P	GBM(48;768 989 9196 9511 26329)	Atlas-SNP	.											.	ATF5	27	.	0			c.G534T						PASS	.						29.0	23.0	25.0					19																	50436034		2201	4293	6494	SO:0001819	synonymous_variant	22809	exon4			GATGCCGCCTCTG	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"""basic leucine zipper proteins"""	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.534G>T	chr19.hg19:g.50436034G>T		52.0	0.0	.		58.0	14.0	.	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Silent	SNP	ENST00000423777.2	hg19	CCDS12789.1																																																																																			.	.	.	alt		0.672	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2		
ZNF584	201514	hgsc.bcm.edu	37	19	58928550	58928550	+	Missense_Mutation	SNP	C	C	A			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr19:58928550C>A	ENST00000306910.4	+	4	1188	c.665C>A	c.(664-666)gCc>gAc	p.A222D	ZNF584_ENST00000599238.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA|ZNF584_ENST00000593920.1_Missense_Mutation_p.A177D	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	222					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)|kidney(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		TGTGGGAAGGCCTTCAGTTAC	0.453																																					p.A222D		Atlas-SNP	.											.	ZNF584	31	.	0			c.C665A						PASS	.						65.0	64.0	65.0					19																	58928550		2203	4300	6503	SO:0001583	missense	201514	exon4			GGAAGGCCTTCAG	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"""Zinc fingers, C2H2-type"", ""-"""	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.665C>A	chr19.hg19:g.58928550C>A	ENSP00000306756:p.Ala222Asp	114.0	0.0	.		113.0	19.0	.	NM_173548	A8K203	Missense_Mutation	SNP	ENST00000306910.4	hg19	CCDS12979.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.520116	0.44866	.	.	ENSG00000171574	ENST00000306910;ENST00000354635	T	0.20069	2.1	3.78	1.63	0.23807	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20861	0.0502	L	0.52011	1.625	0.09310	N	1	B	0.33413	0.411	B	0.39771	0.309	T	0.30387	-0.9980	9	0.87932	D	0	.	3.7	0.08379	0.0:0.5578:0.2082:0.2339	.	222	Q8IVC4	ZN584_HUMAN	D	222;81	ENSP00000306756:A222D	ENSP00000306756:A222D	A	+	2	0	ZNF584	63620362	0.000000	0.05858	0.653000	0.29593	0.797000	0.45037	0.033000	0.13754	0.935000	0.37341	0.555000	0.69702	GCC	.	.	.	none		0.453	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548	
SEC23B	10483	hgsc.bcm.edu	37	20	18529410	18529410	+	Missense_Mutation	SNP	C	C	T	rs372083109		TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr20:18529410C>T	ENST00000336714.3	+	16	2333	c.1901C>T	c.(1900-1902)cCa>cTa	p.P634L	SEC23B_ENST00000377465.1_Missense_Mutation_p.P634L|SEC23B_ENST00000377475.3_Missense_Mutation_p.P634L|AL121893.1_ENST00000578930.1_RNA|SEC23B_ENST00000262544.2_Missense_Mutation_p.P634L	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	634					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						CATGGGCCACCAGAGGTGAGG	0.433													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16828	0.0		0.0	False		,,,				2504	0.0				p.P634L		Atlas-SNP	.											.	SEC23B	70	.	0			c.C1901T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	0,4406		0,0,2203	105.0	89.0	95.0		1901,1901,1901,1847,1901	4.4	1.0	20		95	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	SEC23B	NM_032986.3,NM_032985.4,NM_006363.4,NM_001172746.1,NM_001172745.1	98,98,98,98,98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	634/768,634/768,634/768,616/750,634/768	18529410	1,13005	2203	4300	6503	SO:0001583	missense	10483	exon16			GGCCACCAGAGGT	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"""Sec23 (S. cerevisiae) homolog B"", ""congenital dyserythropoietic anemia, type II"""	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.1901C>T	chr20.hg19:g.18529410C>T	ENSP00000338844:p.Pro634Leu	125.0	0.0	.		126.0	33.0	.	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.171570	0.57584	0.0	1.16E-4	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465;ENST00000422877	T;T;T;T;D	0.93366	0.25;0.25;0.25;0.25;-3.21	4.44	4.44	0.53790	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	D	0.97142	0.9066	M	0.93720	3.45	0.80722	D	1	P;B	0.49862	0.929;0.291	P;B	0.59825	0.864;0.363	D	0.98225	1.0480	10	0.87932	D	0	-11.4968	16.5981	0.84802	0.0:1.0:0.0:0.0	.	616;634	B4DJW8;Q15437	.;SC23B_HUMAN	L	634;634;634;634;142	ENSP00000338844:P634L;ENSP00000262544:P634L;ENSP00000366695:P634L;ENSP00000366685:P634L;ENSP00000409882:P142L	ENSP00000262544:P634L	P	+	2	0	SEC23B	18477410	1.000000	0.71417	0.968000	0.41197	0.039000	0.13416	7.525000	0.81892	2.467000	0.83353	0.563000	0.77884	CCA	.	.	.	weak		0.433	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5		
ZMYND8	23613	hgsc.bcm.edu	37	20	45878117	45878117	+	Missense_Mutation	SNP	A	A	C			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr20:45878117A>C	ENST00000311275.7	-	13	1881	c.1628T>G	c.(1627-1629)gTt>gGt	p.V543G	ZMYND8_ENST00000352431.2_Missense_Mutation_p.V563G|ZMYND8_ENST00000446994.2_Missense_Mutation_p.V480G|ZMYND8_ENST00000536340.1_Missense_Mutation_p.V570G|ZMYND8_ENST00000372023.3_Missense_Mutation_p.V538G|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000360911.3_Missense_Mutation_p.V538G|ZMYND8_ENST00000262975.4_Missense_Mutation_p.V543G|ZMYND8_ENST00000355972.4_Missense_Mutation_p.V543G|ZMYND8_ENST00000471951.2_Missense_Mutation_p.V563G|ZMYND8_ENST00000396281.4_Missense_Mutation_p.V543G|ZMYND8_ENST00000540497.1_Missense_Mutation_p.V491G|ZMYND8_ENST00000458360.2_Missense_Mutation_p.V538G|ZMYND8_ENST00000461685.1_Missense_Mutation_p.V563G	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	543					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			GATGAGAGGAACAGGGGTGGA	0.488																																					p.V563G		Atlas-SNP	.											.	ZMYND8	166	.	0			c.T1688G						PASS	.						149.0	129.0	136.0					20																	45878117		2203	4300	6503	SO:0001583	missense	23613	exon13			AGAGGAACAGGGG	U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"""Zinc fingers, MYND-type"", ""Zinc fingers, PHD-type"""	9397	protein-coding gene	gene with protein product		615713	"""protein kinase C binding protein 1"""	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.1628T>G	chr20.hg19:g.45878117A>C	ENSP00000312237:p.Val543Gly	101.0	0.0	.		100.0	30.0	.	NM_183047	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.737|0.737	-0.777934|-0.777934	0.02929|0.02929	.|.	.|.	ENSG00000101040|ENSG00000101040	ENST00000467200|ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	.|D;D;D;D;D;D;D;D;D;D;D	.|0.90955	.|-1.91;-1.81;-1.94;-1.81;-1.92;-1.82;-1.82;-2.76;-1.81;-1.91;-1.88	5.7|5.7	3.47|3.47	0.39725|0.39725	.|.	.|0.203494	.|0.42294	.|D	.|0.000725	D|D	0.85270|0.85270	0.5658|0.5658	L|L	0.43152|0.43152	1.355|1.355	0.29997|0.29997	N|N	0.81633|0.81633	.|P;B;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B;B	.|0.47762	.|0.9;0.438;0.17;0.17;0.143;0.481;0.234;0.029;0.118;0.029;0.029;0.17;0.083;0.083;0.17;0.161;0.064;0.17	.|B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	.|0.40702	.|0.338;0.138;0.217;0.217;0.243;0.314;0.138;0.096;0.156;0.096;0.096;0.217;0.297;0.297;0.217;0.053;0.122;0.217	T|T	0.81543|0.81543	-0.0885|-0.0885	5|10	.|0.72032	.|D	.|0.01	-17.669|-17.669	8.2758|8.2758	0.31871|0.31871	0.789:0.0:0.211:0.0|0.789:0.0:0.211:0.0	.|.	.|538;570;538;538;518;537;563;543;538;563;563;543;480;538;491;563;491;543	.|B7ZM62;F5H0X3;Q2HXV7;Q2HXV3;Q5TH11;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8	.|.;.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.	W|G	470|538;543;538;544;564;563;543;570;543;480;563;538;491	.|ENSP00000354166:V538G;ENSP00000312237:V543G;ENSP00000392964:V538G;ENSP00000335537:V563G;ENSP00000379577:V543G;ENSP00000439800:V570G;ENSP00000348246:V543G;ENSP00000396725:V480G;ENSP00000418210:V563G;ENSP00000361093:V538G;ENSP00000443086:V491G	.|ENSP00000262975:V544G	C|V	-|-	3|2	2|0	ZMYND8|ZMYND8	45311524|45311524	0.955000|0.955000	0.32602|0.32602	0.029000|0.029000	0.17559|0.17559	0.067000|0.067000	0.16453|0.16453	3.510000|3.510000	0.53393|0.53393	0.451000|0.451000	0.26802|0.26802	0.528000|0.528000	0.53228|0.53228	TGT|GTT	.	.	.	none		0.488	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047	
HELZ2	85441	hgsc.bcm.edu	37	20	62196757	62196757	+	Missense_Mutation	SNP	C	C	T			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr20:62196757C>T	ENST00000467148.1	-	8	3487	c.3418G>A	c.(3418-3420)Gag>Aag	p.E1140K	HELZ2_ENST00000427522.2_Missense_Mutation_p.E571K	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1140					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GACGCCCGCTCGAAGGTCTCT	0.701																																					p.E1140K		Atlas-SNP	.											.	.	.	.	0			c.G3418A						PASS	.						12.0	13.0	13.0					20																	62196757		2172	4262	6434	SO:0001583	missense	85441	exon9			CCCGCTCGAAGGT	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.3418G>A	chr20.hg19:g.62196757C>T	ENSP00000417401:p.Glu1140Lys	59.0	0.0	.		41.0	16.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.502154	0.26949	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.21361	2.01;2.01	4.81	3.85	0.44370	.	0.563900	0.18326	N	0.144647	T	0.18800	0.0451	L	0.50333	1.59	0.09310	N	0.999995	B;P	0.39352	0.336;0.669	B;B	0.30316	0.022;0.114	T	0.05209	-1.0899	10	0.44086	T	0.13	-17.4384	14.9232	0.70856	0.0:0.8558:0.1442:0.0	.	1140;571	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	K	571;1140	ENSP00000393257:E571K;ENSP00000417401:E1140K	ENSP00000393257:E571K	E	-	1	0	RP4-697K14.7	61667201	0.009000	0.17119	0.030000	0.17652	0.014000	0.08584	1.911000	0.39937	1.001000	0.39076	0.491000	0.48974	GAG	.	.	.	none		0.701	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
EFCAB6	64800	hgsc.bcm.edu	37	22	44064754	44064754	+	Missense_Mutation	SNP	C	C	G			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr22:44064754C>G	ENST00000262726.7	-	16	2065	c.1812G>C	c.(1810-1812)gaG>gaC	p.E604D	EFCAB6_ENST00000396231.2_Missense_Mutation_p.E452D	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AATTTTACCTCTCAGAAAGAT	0.368																																					p.E604D		Atlas-SNP	.											.	EFCAB6	177	.	0			c.G1812C						PASS	.						93.0	86.0	89.0					22																	44064754		2203	4300	6503	SO:0001583	missense	64800	exon16			TTACCTCTCAGAA	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1812G>C	chr22.hg19:g.44064754C>G	ENSP00000262726:p.Glu604Asp	303.0	0.0	.		299.0	70.0	.	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	hg19	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	8.514	0.867300	0.17250	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.16324	2.35;2.39	4.97	3.95	0.45737	.	0.983709	0.08286	N	0.969105	T	0.19327	0.0464	M	0.62723	1.935	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05099	-1.0906	10	0.19590	T	0.45	-6.1905	9.2837	0.37744	0.0:0.9026:0.0:0.0974	.	604	Q5THR3	EFCB6_HUMAN	D	452;604	ENSP00000379533:E452D;ENSP00000262726:E604D	ENSP00000262726:E604D	E	-	3	2	EFCAB6	42396087	0.936000	0.31750	0.917000	0.36280	0.560000	0.35617	0.544000	0.23253	1.327000	0.45338	0.555000	0.69702	GAG	.	.	.	none		0.368	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
SEPT6	23157	hgsc.bcm.edu	37	X	118809562	118809562	+	Missense_Mutation	SNP	T	T	C			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chrX:118809562T>C	ENST00000343984.5	-	2	364	c.100A>G	c.(100-102)Aat>Gat	p.N34D	SEPT6_ENST00000394616.4_5'UTR|SEPT6_ENST00000489216.1_Missense_Mutation_p.N34D|SEPT6_ENST00000360156.7_Missense_Mutation_p.N34D|SEPT6_ENST00000354416.3_Missense_Mutation_p.N34D|SEPT6_ENST00000394610.1_Missense_Mutation_p.N34D|SEPT6_ENST00000354228.4_Missense_Mutation_p.N34D|SEPT6_ENST00000394617.2_Missense_Mutation_p.N64D	NM_015129.5	NP_055944.2	Q14141	SEPT6_HUMAN	septin 6	34					cytokinesis (GO:0000910)|viral process (GO:0016032)	axon terminus (GO:0043679)|kinetochore (GO:0000776)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(3)	17						ACGGACTTATTCACCAGCTGG	0.493			T	MLL	AML																																p.N34D		Atlas-SNP	.		Dom	yes		X	Xq24	23157	septin 6		L	.	SEPT6	53	.	0			c.A100G						PASS	.						70.0	46.0	54.0					X																	118809562		2203	4300	6503	SO:0001583	missense	23157	exon2			ACTTATTCACCAG	D50918	CCDS14583.1, CCDS14584.1, CCDS14585.1	Xq24	2013-01-21			ENSG00000125354	ENSG00000125354		"""Septins"""	15848	protein-coding gene	gene with protein product		300683				8590280, 10744683	Standard	NM_015129		Approved	KIAA0128, SEP2, SEPT2, MGC16619, MGC20339	uc004erv.3	Q14141	OTTHUMG00000022280	ENST00000343984.5:c.100A>G	chrX.hg19:g.118809562T>C	ENSP00000341524:p.Asn34Asp	158.0	0.0	.		187.0	53.0	.	NM_145802	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	Missense_Mutation	SNP	ENST00000343984.5	hg19	CCDS14584.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.685597	0.68157	.	.	ENSG00000125354	ENST00000360156;ENST00000354228;ENST00000489216;ENST00000354416;ENST00000394610;ENST00000343984;ENST00000394617;ENST00000520510	T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.82	5.82	0.92795	.	0.042909	0.85682	D	0.000000	T	0.45458	0.1343	L	0.56396	1.775	0.80722	D	1	P;B;B	0.48640	0.913;0.143;0.003	P;B;B	0.54544	0.755;0.173;0.005	T	0.33979	-0.9847	10	0.45353	T	0.12	.	14.1936	0.65654	0.0:0.0:0.0:1.0	.	64;34;34	F5H1J5;Q14141;Q548C9	.;SEPT6_HUMAN;.	D	34;34;34;34;34;34;64;34	ENSP00000353278:N34D;ENSP00000346169:N34D;ENSP00000418715:N34D;ENSP00000346397:N34D;ENSP00000378108:N34D;ENSP00000341524:N34D;ENSP00000378115:N64D	ENSP00000341524:N34D	N	-	1	0	SEPT6	118693590	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	1.950000	0.56595	0.417000	0.27973	AAT	.	.	.	none		0.493	SEPT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058059.1	NM_145802	
MT-CO1	4512	hgsc.bcm.edu	37	M	6575	6575	+	Silent	SNP	A	A	G			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chrM:6575A>G	ENST00000361624.2	+	1	672	c.672A>G	c.(670-672)ggA>ggG	p.G224G	MT-TN_ENST00000387400.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-CO2_ENST00000361739.1_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TW_ENST00000387382.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	224			G -> A. {ECO:0000269|PubMed:1757091}.		aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						GACCCCGCCGGAGGAGGAGAC	0.478																																					p.G224G		Atlas-SNP	.											.	.	.	.	0			c.A672G						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			CGCCGGAGGAGGA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.672A>G	chrM.hg19:g.6575A>G		10.0	0.0	.		64.0	55.0	.	ENST00000361624	Q34770	Silent	SNP	ENST00000361624.2	hg19																																																																																				.	.	.	none		0.478	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
TRIM13	10206	hgsc.bcm.edu	37	13	50588496	50588497	+	3'UTR	INS	-	-	ATACAC	rs199807501|rs35381218|rs377384125		TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr13:50588496_50588497insATACAC	ENST00000378182.3	+	0	3158_3159				TRIM13_ENST00000478111.1_Intron|KCNRG_ENST00000312942.1_5'Flank|KCNRG_ENST00000360473.4_5'Flank	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13						anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		tatatatatatacacacacaca	0.292																																					.		Atlas-INDEL	.											.	TRIM13	30	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	10206	.			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.*1197->ATACAC	chr13.hg19:g.50588496_50588497insATACAC		44.0	0.0	0		50.0	13.0	0.26	.	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	RNA	INS	ENST00000378182.3	hg19	CCDS9423.1																																																																																			.	.	.	alt		0.292	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
TRIM13	10206	hgsc.bcm.edu	37	13	50589227	50589252	+	3'UTR	DEL	AAAAATATATATATATATATATATAT	AAAAATATATATATATATATATATAT	-	rs9535412|rs59009716|rs12875615|rs60457674|rs71082132		TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	AAAAATATATATATATATATATATAT	AAAAATATATATATATATATATATAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr13:50589227_50589252delAAAAATATATATATATATATATATAT	ENST00000378182.3	+	0	3889_3914				TRIM13_ENST00000478111.1_Intron|KCNRG_ENST00000312942.1_5'Flank|KCNRG_ENST00000360473.4_5'Flank	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13						anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		aaaaaaaaaaaaaaatatatatatatatatatatatatatatatat	0.252																																					.		Atlas-INDEL	.											.	TRIM13	30	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	10206	.			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.*1952AAAAATATATATATATATATATATAT>-	chr13.hg19:g.50589227_50589252delAAAAATATATATATATATATATATAT		41.0	0.0	0		72.0	21.0	0.291667	.	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	RNA	DEL	ENST00000378182.3	hg19	CCDS9423.1																																																																																			.	.	.	none		0.252	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
CDK11B	984	hgsc.bcm.edu	37	1	1577073	1577078	+	In_Frame_Del	DEL	TCCTCT	TCCTCT	-			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	TCCTCT	TCCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:1577073_1577078delTCCTCT	ENST00000407249.3	-	10	962_967	c.963_968delAGAGGA	c.(961-969)gaagaggag>gag	p.321_323EEE>E	CDK11B_ENST00000341832.6_In_Frame_Del_p.274_276EEE>E|CDK11B_ENST00000340677.5_In_Frame_Del_p.308_310EEE>E|CDK11B_ENST00000317673.7_In_Frame_Del_p.319_321EEE>E			P21127	CD11B_HUMAN	cyclin-dependent kinase 11B	331	Glu-rich.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(3)|lung(4)|skin(1)|stomach(2)	12						ctcctcctcctcctcttcctcttcct	0.563																																					p.317_318del		Pindel	.											.	CDK11B	37	.	0			c.949_954del						PASS	.																																			SO:0001651	inframe_deletion	984	exon9			.	AK000081	CCDS72682.1, CCDS72683.1, CCDS72684.1	1p36.33	2013-09-24	2009-12-16	2009-12-16	ENSG00000248333	ENSG00000248333		"""Cyclin-dependent kinases"""	1729	protein-coding gene	gene with protein product		176873	"""cell division cycle 2-like 1 (PITSLRE proteins)"""	CDC2L1		1774066, 14511641, 19884882	Standard	XM_006711061		Approved	CDK11-p110, CDK11-p58, CDK11-p46	uc001agv.1	P21127	OTTHUMG00000078638	ENST00000407249.3:c.963_968delAGAGGA	chr1.hg19:g.1577079_1577084delTCCTCT	ENSP00000464036:p.Glu325_Glu326del	87.0	0.0	.		108.0	10.0	0.093	NM_033486	O95265|Q12817|Q12818|Q12819|Q12820|Q12822|Q8N530|Q9NZS5|Q9UBJ0|Q9UBQ1|Q9UBR0|Q9UNY2|Q9UP57|Q9UP58|Q9UP59	In_Frame_Del	DEL	ENST00000407249.3	hg19																																																																																				.	.	.	none		0.563	CDK11B-204	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001787	
CDK11A	728642	hgsc.bcm.edu	37	1	1640283	1640288	+	In_Frame_Del	DEL	TCCTCT	TCCTCT	-			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	TCCTCT	TCCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:1640283_1640288delTCCTCT	ENST00000378633.1	-	9	1036_1041	c.957_962delAGAGGA	c.(955-963)gaagaggag>gag	p.319_321EEE>E	CDK11A_ENST00000356200.3_In_Frame_Del_p.282_284EEE>E|CDK11A_ENST00000358779.5_In_Frame_Del_p.306_308EEE>E|CDK11A_ENST00000378638.2_In_Frame_Del_p.282_284EEE>E|CDK11A_ENST00000404249.3_In_Frame_Del_p.316_318EEE>E|CDK11A_ENST00000378635.3_3'UTR|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000357760.2_In_Frame_Del_p.315_317EEE>E			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	319	Glu-rich.				apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						ctcctcctcctcctcttcctcttcct	0.563																																					p.317_318del	Pancreas(186;965 2119 30274 40311 50569)	Pindel	.											.	CDK11A	38	.	0			c.949_954del						PASS	.																																			SO:0001651	inframe_deletion	728642	exon9			.	AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"""Cyclin-dependent kinases"""	1730	protein-coding gene	gene with protein product		116951	"""cell division cycle 2-like 2"", ""cell division cycle 2-like 2 (PITSLRE proteins)"""	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.957_962delAGAGGA	chr1.hg19:g.1640289_1640294delTCCTCT	ENSP00000367900:p.Glu323_Glu324del	114.0	0.0	.		85.0	12.0	0.141	NM_024011	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	In_Frame_Del	DEL	ENST00000378633.1	hg19																																																																																				.	.	.	none		0.563	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011	
CNTLN	54875	hgsc.bcm.edu	37	9	17298345	17298346	+	Frame_Shift_Ins	INS	-	-	A	rs190561659		TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr9:17298345_17298346insA	ENST00000380647.3	+	7	1225_1226	c.1141_1142insA	c.(1141-1143)caafs	p.Q381fs	CNTLN_ENST00000262360.5_Frame_Shift_Ins_p.Q381fs|CNTLN_ENST00000425824.1_Frame_Shift_Ins_p.Q381fs|CNTLN_ENST00000380641.4_Frame_Shift_Ins_p.Q381fs			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	381					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		TATATCATATCAAAAAGTATGC	0.307																																					p.Q381fs		Pindel	.											.	CNTLN	128	.	0			c.1141_1142insA						PASS	.																																			SO:0001589	frameshift_variant	54875	exon7			.	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1146dupA	chr9.hg19:g.17298350_17298350dupA	ENSP00000370021:p.Gln381fs	252.0	0.0	.		225.0	49.0	0.218	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Frame_Shift_Ins	INS	ENST00000380647.3	hg19	CCDS43789.1																																																																																			.	.	.	none		0.307	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
