#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
MTOR	2475	hgsc.bcm.edu	37	1	11273603	11273603	+	Silent	SNP	G	G	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:11273603G>C	ENST00000361445.4	-	21	3214	c.3138C>G	c.(3136-3138)acC>acG	p.T1046T		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1046					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCTGAATTGAGGTGTTCATGA	0.458																																					p.T1046T		Atlas-SNP	.											.	MTOR	327	.	0			c.C3138G						PASS	.						97.0	98.0	98.0					1																	11273603		2203	4300	6503	SO:0001819	synonymous_variant	2475	exon21			AATTGAGGTGTTC	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.3138C>G	chr1.hg19:g.11273603G>C		129.0	0.0	.		187.0	71.0	.	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	hg19	CCDS127.1																																																																																			.	.	.	none		0.458	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
UBR4	23352	hgsc.bcm.edu	37	1	19490300	19490300	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:19490300C>G	ENST00000375254.3	-	34	4749	c.4722G>C	c.(4720-4722)aaG>aaC	p.K1574N	UBR4_ENST00000375226.2_Missense_Mutation_p.K1574N|UBR4_ENST00000375267.2_Missense_Mutation_p.K1574N|UBR4_ENST00000375217.2_Missense_Mutation_p.K1574N	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1574					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAACTACATTCTTCTGTGACA	0.403																																					p.K1574N		Atlas-SNP	.											.	UBR4	415	.	0			c.G4722C						PASS	.						191.0	172.0	178.0					1																	19490300		2203	4300	6503	SO:0001583	missense	23352	exon34			TACATTCTTCTGT	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.4722G>C	chr1.hg19:g.19490300C>G	ENSP00000364403:p.Lys1574Asn	214.0	0.0	.		175.0	70.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698108	0.68386	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.15	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.73273	0.3566	L	0.39898	1.24	0.80722	D	1	D	0.57899	0.981	D	0.67231	0.95	T	0.73040	-0.4108	10	0.49607	T	0.09	.	12.9635	0.58472	0.0:0.9263:0.0:0.0737	.	1574	Q5T4S7	UBR4_HUMAN	N	1574;1574;1574;1574;284;790	ENSP00000364403:K1574N;ENSP00000364416:K1574N;ENSP00000364365:K1574N;ENSP00000364374:K1574N;ENSP00000404897:K284N	ENSP00000364365:K1574N	K	-	3	2	UBR4	19362887	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.411000	0.59781	2.674000	0.91012	0.655000	0.94253	AAG	.	.	.	none		0.403	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
EPHA8	2046	hgsc.bcm.edu	37	1	22927186	22927186	+	Silent	SNP	A	A	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:22927186A>T	ENST00000166244.3	+	14	2493	c.2421A>T	c.(2419-2421)ccA>ccT	p.P807P		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	807	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGACGGCCCCAGAGGCCATCG	0.682																																					p.P807P		Atlas-SNP	.											.	EPHA8	221	.	0			c.A2421T						PASS	.						58.0	61.0	60.0					1																	22927186		2203	4299	6502	SO:0001819	synonymous_variant	2046	exon14			GGCCCCAGAGGCC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2421A>T	chr1.hg19:g.22927186A>T		249.0	0.0	.		225.0	82.0	.	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.	.	none		0.682	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
MCOLN3	55283	hgsc.bcm.edu	37	1	85487988	85487988	+	Missense_Mutation	SNP	C	C	A	rs375444573		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:85487988C>A	ENST00000370589.2	-	10	1243	c.1191G>T	c.(1189-1191)aaG>aaT	p.K397N	MCOLN3_ENST00000474447.1_5'UTR|MCOLN3_ENST00000341115.4_Missense_Mutation_p.K341N|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	397					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		TTACGTTGTACTTTGCAAAGA	0.433																																					p.K397N		Atlas-SNP	.											.	MCOLN3	74	.	0			c.G1191T						PASS	.						85.0	78.0	81.0					1																	85487988		2203	4300	6503	SO:0001583	missense	55283	exon10			GTTGTACTTTGCA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1191G>T	chr1.hg19:g.85487988C>A	ENSP00000359621:p.Lys397Asn	27.0	0.0	.		52.0	19.0	.	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	hg19	CCDS701.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319843	0.41096	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115	T;T	0.69926	-0.44;-0.44	5.74	4.78	0.61160	Polycystin cation channel, PKD1/PKD2 (1);	0.088648	0.85682	D	0.000000	T	0.40645	0.1125	L	0.41710	1.295	0.48830	D	0.999718	B;B	0.27625	0.076;0.183	B;B	0.29077	0.043;0.098	T	0.42949	-0.9421	10	0.41790	T	0.15	-17.9811	9.0071	0.36117	0.0:0.7676:0.0:0.2324	.	341;397	Q8TDD5-2;Q8TDD5	.;MCLN3_HUMAN	N	397;397;341;341	ENSP00000359621:K397N;ENSP00000342698:K341N	ENSP00000304843:K397N	K	-	3	2	MCOLN3	85260576	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	1.405000	0.34635	1.307000	0.44944	0.655000	0.94253	AAG	.	.	.	none		0.433	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298	
CD46	4179	hgsc.bcm.edu	37	1	207940508	207940508	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:207940508C>A	ENST00000358170.2	+	6	980	c.824C>A	c.(823-825)aCt>aAt	p.T275N	CD46_ENST00000361067.1_Missense_Mutation_p.T275N|CD46_ENST00000354848.1_Missense_Mutation_p.T275N|CD46_ENST00000322875.4_Missense_Mutation_p.T275N|CD46_ENST00000322918.5_Missense_Mutation_p.T275N|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000367042.1_Missense_Mutation_p.T275N|CD46_ENST00000441839.2_Missense_Mutation_p.T275N|CD46_ENST00000480003.1_Missense_Mutation_p.T275N|CD46_ENST00000367047.1_Missense_Mutation_p.T212N|CD46_ENST00000360212.2_Missense_Mutation_p.T275N|CD46_ENST00000367041.1_Missense_Mutation_p.T275N|CD46_ENST00000357714.1_Missense_Mutation_p.T275N	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	275	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						AGTAACAGTACTTGGGATCCC	0.358																																					p.T275N		Atlas-SNP	.											.	CD46	34	.	0			c.C824A						PASS	.						110.0	105.0	107.0					1																	207940508		2203	4300	6503	SO:0001583	missense	4179	exon6			ACAGTACTTGGGA	BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"""CD molecules"", ""Complement system"""	6953	protein-coding gene	gene with protein product		120920	"""antigen identified by monoclonal antibody TRA-2-10"", ""membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)"", ""CD46 antigen, complement regulatory protein"""	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.824C>A	chr1.hg19:g.207940508C>A	ENSP00000350893:p.Thr275Asn	80.0	0.0	.		60.0	23.0	.	NM_172352	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Missense_Mutation	SNP	ENST00000358170.2	hg19	CCDS1485.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142222	0.57044	.	.	ENSG00000117335	ENST00000358170;ENST00000354848;ENST00000322918;ENST00000367042;ENST00000367041;ENST00000357714;ENST00000322875;ENST00000367047;ENST00000441839;ENST00000361067;ENST00000360212;ENST00000480003	T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.05	-4.14	0.03892	Complement control module (2);Sushi/SCR/CCP (3);	1.003600	0.08033	N	0.993895	T	0.68815	0.3042	M	0.69463	2.115	0.09310	N	1	P;B;D;P;B;D;B;D;P;P;P;D;D;D	0.63880	0.582;0.253;0.993;0.582;0.253;0.969;0.395;0.979;0.582;0.836;0.582;0.961;0.961;0.975	B;B;P;B;B;D;B;P;B;B;B;D;D;D	0.75020	0.2;0.141;0.869;0.2;0.141;0.974;0.227;0.831;0.2;0.32;0.2;0.961;0.961;0.985	T	0.60647	-0.7222	10	0.72032	D	0.01	.	1.9531	0.03370	0.4968:0.2102:0.1229:0.1701	.	275;275;275;275;275;275;275;275;275;275;275;275;275;275	P15529-4;P15529-5;P15529-14;P15529-3;P15529-12;P15529-13;P15529-2;P15529-11;P15529-7;P15529-9;P15529-15;P15529-6;P15529-8;P15529	.;.;.;.;.;.;.;.;.;.;.;.;.;MCP_HUMAN	N	275;275;275;275;275;275;275;212;275;275;275;275	ENSP00000350893:T275N;ENSP00000346912:T275N;ENSP00000314664:T275N;ENSP00000356009:T275N;ENSP00000356008:T275N;ENSP00000350346:T275N;ENSP00000313875:T275N;ENSP00000356014:T212N;ENSP00000413543:T275N;ENSP00000354358:T275N;ENSP00000353342:T275N;ENSP00000418471:T275N	ENSP00000313875:T275N	T	+	2	0	CD46	206007131	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-0.614000	0.05604	-0.469000	0.06911	0.655000	0.94253	ACT	.	.	.	none		0.358	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361	
RBM34	23029	hgsc.bcm.edu	37	1	235318245	235318245	+	Missense_Mutation	SNP	T	T	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:235318245T>A	ENST00000408888.3	-	4	778	c.548A>T	c.(547-549)aAt>aTt	p.N183I	RBM34_ENST00000366606.3_Missense_Mutation_p.N178I			P42696	RBM34_HUMAN	RNA binding motif protein 34	183						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			AGTTCTCTCATTCTTTAATCT	0.328																																					p.N183I		Atlas-SNP	.											.	RBM34	41	.	0			c.A548T						PASS	.						159.0	139.0	145.0					1																	235318245		1826	4086	5912	SO:0001583	missense	23029	exon4			CTCTCATTCTTTA		CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"""RNA binding motif (RRM) containing"""	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.548A>T	chr1.hg19:g.235318245T>A	ENSP00000386226:p.Asn183Ile	288.0	0.0	.		266.0	90.0	.	NM_001161533	A8K8J7|Q8N2Z8|Q9H5A1	Missense_Mutation	SNP	ENST00000408888.3	hg19	CCDS41477.2	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643590	0.67244	.	.	ENSG00000188739	ENST00000408888;ENST00000366606;ENST00000447801	T;T;T	0.75154	-0.91;-0.91;0.96	5.87	5.87	0.94306	Nucleotide-binding, alpha-beta plait (1);	0.236119	0.48767	D	0.000162	D	0.85225	0.5648	M	0.76328	2.33	0.80722	D	1	D;B	0.89917	1.0;0.431	D;B	0.81914	0.995;0.186	D	0.85305	0.1075	10	0.45353	T	0.12	-17.2719	14.8054	0.69952	0.0:0.0:0.0:1.0	.	183;183	P42696-2;P42696	.;RBM34_HUMAN	I	183;178;181	ENSP00000386226:N183I;ENSP00000355565:N178I;ENSP00000400000:N181I	ENSP00000355565:N178I	N	-	2	0	RBM34	233384868	0.999000	0.42202	0.998000	0.56505	0.918000	0.54935	4.345000	0.59360	2.371000	0.80710	0.533000	0.62120	AAT	.	.	.	none		0.328	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014	
HADHA	3030	hgsc.bcm.edu	37	2	26459821	26459821	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:26459821G>C	ENST00000380649.3	-	4	345	c.216C>G	c.(214-216)ttC>ttG	p.F72L	HADHA_ENST00000461025.1_5'Flank|HADHA_ENST00000457468.2_Intron	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	72					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAACTTCTGAGAACTCTGAAT	0.403																																					p.F72L		Atlas-SNP	.											.	HADHA	87	.	0			c.C216G						PASS	.						102.0	99.0	100.0					2																	26459821		2203	4300	6503	SO:0001583	missense	3030	exon4			TTCTGAGAACTCT	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"""gastrin-binding protein"", ""long-chain-3-hydroxyacyl-CoA dehydrogenase"", ""long-chain 2-enoyl-CoA hydratase"", ""mitochondrial trifunctional protein, alpha subunit"""	600890	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"""			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.216C>G	chr2.hg19:g.26459821G>C	ENSP00000370023:p.Phe72Leu	180.0	0.0	.		246.0	82.0	.	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	hg19	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	G	5.697	0.313101	0.10789	.	.	ENSG00000084754	ENST00000380649	T	0.57907	0.37	5.78	1.36	0.22044	Crotonase, core (1);	0.277100	0.45126	N	0.000390	T	0.26011	0.0634	N	0.12831	0.26	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.07790	-1.0754	10	0.07990	T	0.79	-24.6945	7.1425	0.25564	0.2509:0.1413:0.6078:0.0	.	72	P40939	ECHA_HUMAN	L	72	ENSP00000370023:F72L	ENSP00000370023:F72L	F	-	3	2	HADHA	26313325	0.026000	0.19158	0.266000	0.24541	0.047000	0.14425	0.239000	0.18023	0.351000	0.24027	0.591000	0.81541	TTC	.	.	.	none		0.403	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182	
GTF3C2	2976	hgsc.bcm.edu	37	2	27565920	27565920	+	Silent	SNP	G	G	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565920G>T	ENST00000359541.2	-	3	771	c.342C>A	c.(340-342)ccC>ccA	p.P114P	GTF3C2_ENST00000264720.3_Silent_p.P114P|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000589853.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	114					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAGGCTGTTGGGGCCTTTTGG	0.537																																					p.V114V		Atlas-SNP	.											.	GTF3C2	73	.	0			c.T342A						PASS	.						94.0	89.0	91.0					2																	27565920		2203	4300	6503	SO:0001819	synonymous_variant	2976	exon4			CTGTTGGGGCCTT	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.342C>A	chr2.hg19:g.27565920G>T		331.0	1.0	.		227.0	78.0	.	NM_001521	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	hg19	CCDS1749.1																																																																																			.	.	.	none		0.537	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		
HAAO	23498	hgsc.bcm.edu	37	2	42994588	42994588	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:42994588G>C	ENST00000294973.6	-	10	905	c.850C>G	c.(850-852)Ccc>Gcc	p.P284A		NM_012205.2	NP_036337.2			3-hydroxyanthranilate 3,4-dioxygenase											breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2)	11						CACCCCAGGGGCTTCTTGCAG	0.617																																					p.P284A		Atlas-SNP	.											.	HAAO	26	.	0			c.C850G						PASS	.						38.0	38.0	38.0					2																	42994588		2203	4300	6503	SO:0001583	missense	23498	exon10			CCAGGGGCTTCTT	Z29481	CCDS33187.1	2p	2008-02-05			ENSG00000162882	ENSG00000162882	1.13.11.6		4796	protein-coding gene	gene with protein product		604521				7514594	Standard	NM_012205		Approved		uc002rst.4	P46952	OTTHUMG00000152348	ENST00000294973.6:c.850C>G	chr2.hg19:g.42994588G>C	ENSP00000294973:p.Pro284Ala	61.0	0.0	.		67.0	11.0	.	NM_012205		Missense_Mutation	SNP	ENST00000294973.6	hg19	CCDS33187.1	.	.	.	.	.	.	.	.	.	.	g	10.57	1.385999	0.25031	.	.	ENSG00000162882	ENST00000294973	T	0.30182	1.54	4.83	1.94	0.25998	.	0.156970	0.42682	N	0.000678	T	0.24275	0.0588	L	0.55743	1.74	0.45791	D	0.998671	B	0.06786	0.001	B	0.01281	0.0	T	0.06320	-1.0833	10	0.44086	T	0.13	.	5.3274	0.15915	0.1974:0.1834:0.6193:0.0	.	284	P46952	3HAO_HUMAN	A	284	ENSP00000294973:P284A	ENSP00000294973:P284A	P	-	1	0	HAAO	42848092	0.924000	0.31332	0.996000	0.52242	0.700000	0.40528	1.053000	0.30442	0.449000	0.26747	0.550000	0.68814	CCC	.	.	.	none		0.617	HAAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325948.2		
BIN1	274	hgsc.bcm.edu	37	2	127818193	127818193	+	Intron	SNP	C	C	G	rs117721706	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:127818193C>G	ENST00000316724.5	-	11	1269				BIN1_ENST00000466111.1_Intron|BIN1_ENST00000346226.3_Intron|BIN1_ENST00000348750.4_Intron|BIN1_ENST00000393041.3_Intron|BIN1_ENST00000259238.4_Missense_Mutation_p.R263P|BIN1_ENST00000357970.3_Intron|BIN1_ENST00000352848.3_Missense_Mutation_p.R263P|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000376113.2_Missense_Mutation_p.R263P|BIN1_ENST00000351659.3_Intron|BIN1_ENST00000409400.1_Intron	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1						cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		TCTGCGCAGCCGCGAAAACAG	0.632																																					p.R263P		Atlas-SNP	.											.	BIN1	85	.	0			c.G788C						PASS	.						120.0	112.0	114.0					2																	127818193		2203	4300	6503	SO:0001627	intron_variant	274	exon10			CGCAGCCGCGAAA	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.858-1462G>C	chr2.hg19:g.127818193C>G		183.0	0.0	.		143.0	47.0	.	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	hg19	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387780	0.61956	.	.	ENSG00000136717	ENST00000376113;ENST00000259238;ENST00000352848	T;T;T	0.56611	0.45;0.47;0.53	4.72	4.72	0.59763	.	.	.	.	.	T	0.68559	0.3014	.	.	.	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.75484	0.986;0.986;0.986	T	0.66031	-0.6024	8	0.29301	T	0.29	.	14.976	0.71273	0.0:1.0:0.0:0.0	.	263;263;263	O00499-8;O00499-11;O00499-10	.;.;.	P	263	ENSP00000365281:R263P;ENSP00000259238:R263P;ENSP00000315284:R263P	ENSP00000259238:R263P	R	-	2	0	BIN1	127534663	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.415000	0.52700	2.337000	0.79520	0.561000	0.74099	CGG	.	C|0.992;T|0.008	.	alt		0.632	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
TRNT1	51095	hgsc.bcm.edu	37	3	3189651	3189651	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:3189651G>C	ENST00000251607.6	+	8	1220	c.1118G>C	c.(1117-1119)tGt>tCt	p.C373S	TRNT1_ENST00000280591.6_Missense_Mutation_p.C353S	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	373					protein targeting to mitochondrion (GO:0006626)|tRNA 3'-end processing (GO:0042780)|tRNA 3'-terminal CCA addition (GO:0001680)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity (GO:0052929)|CTP:3'-cytidine-tRNA cytidylyltransferase activity (GO:0052928)|CTP:tRNA cytidylyltransferase activity (GO:0052927)|tRNA adenylyltransferase activity (GO:0004810)|tRNA binding (GO:0000049)			breast(2)|endometrium(3)|large_intestine(4)|lung(2)|urinary_tract(1)	12				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)		GGAGAGCACTGTCTCCTAAAG	0.438																																					p.C373S		Atlas-SNP	.											.	TRNT1	34	.	0			c.G1118C						PASS	.						118.0	110.0	113.0					3																	3189651		2203	4300	6503	SO:0001583	missense	51095	exon8			AGCACTGTCTCCT	AF151805	CCDS2561.2	3p25.1	2002-05-30			ENSG00000072756	ENSG00000072756	2.7.7.25		17341	protein-coding gene	gene with protein product		612907				10810093, 11504732	Standard	NM_182916		Approved	MtCCA, CGI-47, CCA1	uc003bpp.4	Q96Q11	OTTHUMG00000090259	ENST00000251607.6:c.1118G>C	chr3.hg19:g.3189651G>C	ENSP00000251607:p.Cys373Ser	38.0	0.0	.		20.0	8.0	.	NM_182916	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Missense_Mutation	SNP	ENST00000251607.6	hg19	CCDS2561.2	.	.	.	.	.	.	.	.	.	.	G	9.399	1.077394	0.20227	.	.	ENSG00000072756	ENST00000251607;ENST00000280591	T;T	0.39229	1.09;1.11	5.24	2.0	0.26442	.	1.262890	0.05220	N	0.508422	T	0.22085	0.0532	N	0.08118	0	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19910	-1.0291	10	0.17832	T	0.49	-3.7877	5.7122	0.17941	0.1687:0.3466:0.4847:0.0	.	353;373	Q96Q11-2;Q96Q11	.;TRNT1_HUMAN	S	373;353	ENSP00000251607:C373S;ENSP00000280591:C353S	ENSP00000251607:C373S	C	+	2	0	TRNT1	3164651	0.026000	0.19158	0.010000	0.14722	0.971000	0.66376	2.269000	0.43346	1.168000	0.42723	0.655000	0.94253	TGT	.	.	.	none		0.438	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1		
OSBPL10	114884	hgsc.bcm.edu	37	3	31774841	31774841	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:31774841G>A	ENST00000396556.2	-	6	1125	c.1003C>T	c.(1003-1005)Ctt>Ttt	p.L335F	OSBPL10_ENST00000467647.1_5'UTR|OSBPL10_ENST00000438237.2_Missense_Mutation_p.L271F	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	335					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		AAAGAGCCAAGTGTCCCATTT	0.473																																					p.L335F		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C1003T						PASS	.						166.0	156.0	159.0					3																	31774841		2203	4300	6503	SO:0001583	missense	114884	exon6			AGCCAAGTGTCCC	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1003C>T	chr3.hg19:g.31774841G>A	ENSP00000379804:p.Leu335Phe	318.0	0.0	.		285.0	80.0	.	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	hg19	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.285363	0.40394	.	.	ENSG00000144645	ENST00000396556;ENST00000438237;ENST00000428241	T;T;T	0.52983	1.87;2.22;0.64	5.66	2.21	0.28008	.	0.326770	0.33075	N	0.005319	T	0.41328	0.1154	M	0.68952	2.095	0.45076	D	0.998091	B;B;B	0.19445	0.036;0.005;0.001	B;B;B	0.15870	0.014;0.005;0.005	T	0.30621	-0.9972	10	0.52906	T	0.07	-1.9596	6.3688	0.21469	0.2078:0.138:0.6542:0.0	.	271;335;103	B4E212;Q9BXB5;Q59ED9	.;OSB10_HUMAN;.	F	335;271;143	ENSP00000379804:L335F;ENSP00000406124:L271F;ENSP00000399200:L143F	ENSP00000379804:L335F	L	-	1	0	OSBPL10	31749845	0.602000	0.26916	0.675000	0.29917	0.982000	0.71751	0.776000	0.26704	0.470000	0.27294	0.555000	0.69702	CTT	.	.	.	none		0.473	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
ATR	545	hgsc.bcm.edu	37	3	142274792	142274792	+	Silent	SNP	A	A	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:142274792A>T	ENST00000350721.4	-	10	2389	c.2268T>A	c.(2266-2268)tcT>tcA	p.S756S	ATR_ENST00000383101.3_Silent_p.S692S	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	756					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTTTTAGTTGAGAAGATGAAC	0.368								Other conserved DNA damage response genes																													p.S756S		Atlas-SNP	.											.	ATR	285	.	0			c.T2268A						PASS	.						118.0	119.0	119.0					3																	142274792		2203	4300	6503	SO:0001819	synonymous_variant	545	exon10			TAGTTGAGAAGAT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2268T>A	chr3.hg19:g.142274792A>T		178.0	0.0	.		128.0	42.0	.	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.	.	none		0.368	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
SLC26A1	10861	hgsc.bcm.edu	37	4	985220	985220	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:985220G>A	ENST00000361661.2	-	3	649	c.272C>T	c.(271-273)tCa>tTa	p.S91L	SLC26A1_ENST00000513138.1_5'Flank|SLC26A1_ENST00000398520.2_Missense_Mutation_p.S91L|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398516.2_Missense_Mutation_p.S91L|IDUA_ENST00000453894.1_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	91					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCCAGCAATGAGTAGGCGAT	0.632																																					p.S91L		Atlas-SNP	.											.	SLC26A1	44	.	0			c.C272T						PASS	.						105.0	99.0	101.0					4																	985220		2203	4300	6503	SO:0001583	missense	10861	exon2			AGCAATGAGTAGG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"""Solute carriers"""	10993	protein-coding gene	gene with protein product		610130	"""solute carrier family 26 (sulfate transporter), member 1"""				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.272C>T	chr4.hg19:g.985220G>A	ENSP00000354721:p.Ser91Leu	257.0	0.0	.		228.0	82.0	.	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	hg19	CCDS33934.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559905	0.65538	.	.	ENSG00000145217	ENST00000398520;ENST00000361661;ENST00000398516	D;D;D	0.92495	-3.05;-3.05;-3.05	5.18	5.18	0.71444	.	0.226096	0.46758	D	0.000276	D	0.96993	0.9018	M	0.93763	3.455	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.72338	0.977;0.969	D	0.98001	1.0360	10	0.87932	D	0	.	16.1549	0.81657	0.0:0.0:1.0:0.0	.	91;91	Q9H2B4;Q96BK0	S26A1_HUMAN;.	L	91	ENSP00000381532:S91L;ENSP00000354721:S91L;ENSP00000381528:S91L	ENSP00000354721:S91L	S	-	2	0	SLC26A1	975220	0.998000	0.40836	0.985000	0.45067	0.336000	0.28762	2.673000	0.46858	2.402000	0.81655	0.313000	0.20887	TCA	.	.	.	none		0.632	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425	
ACOX3	8310	hgsc.bcm.edu	37	4	8417674	8417674	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:8417674C>T	ENST00000356406.5	-	3	274	c.197G>A	c.(196-198)gGa>gAa	p.G66E	ACOX3_ENST00000413009.2_Missense_Mutation_p.G66E|ACOX3_ENST00000503233.1_Missense_Mutation_p.G66E	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	66					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						CAGATCGGCTCCAGGGGAACG	0.483																																					p.G66E		Atlas-SNP	.											.	ACOX3	70	.	0			c.G197A						PASS	.						71.0	67.0	68.0					4																	8417674		2203	4300	6503	SO:0001583	missense	8310	exon3			TCGGCTCCAGGGG	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"""acyl-Coenzyme A oxidase 3, pristanoyl"""			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.197G>A	chr4.hg19:g.8417674C>T	ENSP00000348775:p.Gly66Glu	231.0	0.0	.		197.0	74.0	.	NM_001101667	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	hg19	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	C	9.453	1.091143	0.20471	.	.	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	T;T;T	0.41758	0.99;0.99;0.99	5.39	-0.535	0.11879	Acyl-CoA dehydrogenase/oxidase (1);	0.611319	0.16430	N	0.214753	T	0.21509	0.0518	L	0.31664	0.95	0.38700	D	0.952962	B;B	0.16166	0.016;0.01	B;B	0.17433	0.018;0.005	T	0.33007	-0.9885	10	0.02654	T	1	-6.3195	6.2369	0.20768	0.0:0.5193:0.1203:0.3604	.	66;66	O15254-2;O15254	.;ACOX3_HUMAN	E	66	ENSP00000413994:G66E;ENSP00000348775:G66E;ENSP00000421625:G66E	ENSP00000348775:G66E	G	-	2	0	ACOX3	8468574	0.730000	0.28100	0.000000	0.03702	0.001000	0.01503	1.878000	0.39608	-0.212000	0.10109	-0.145000	0.13849	GGA	.	.	.	none		0.483	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4		
AASDH	132949	hgsc.bcm.edu	37	4	57248668	57248668	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:57248668A>T	ENST00000205214.6	-	3	506	c.326T>A	c.(325-327)aTc>aAc	p.I109N	AASDH_ENST00000451613.1_Missense_Mutation_p.I109N|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000513376.1_Missense_Mutation_p.I9N|AASDH_ENST00000502617.1_Missense_Mutation_p.I109N|AASDH_ENST00000510762.1_Intron|AASDH_ENST00000602986.1_Intron	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	109					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TTCAACAAGGATATACTTTAG	0.323																																					p.I109N		Atlas-SNP	.											.	AASDH	101	.	0			c.T326A						PASS	.						47.0	48.0	48.0					4																	57248668		2203	4300	6503	SO:0001583	missense	132949	exon3			ACAAGGATATACT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.326T>A	chr4.hg19:g.57248668A>T	ENSP00000205214:p.Ile109Asn	72.0	0.0	.		45.0	16.0	.	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.611899	0.87258	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000502617	T;T;T;T	0.66638	0.83;-0.22;0.83;0.83	5.88	5.88	0.94601	AMP-dependent synthetase/ligase (1);	0.289492	0.43919	D	0.000514	T	0.81093	0.4751	M	0.78049	2.395	0.25673	N	0.985874	D;D;D;D	0.65815	0.989;0.991;0.995;0.991	P;D;P;P	0.63957	0.87;0.92;0.902;0.873	T	0.76408	-0.2970	10	0.87932	D	0	-4.2072	15.9439	0.79779	1.0:0.0:0.0:0.0	.	109;109;109;109	Q4L235-4;B4E2K0;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	N	109;9;109;109	ENSP00000205214:I109N;ENSP00000423760:I9N;ENSP00000409656:I109N;ENSP00000421171:I109N	ENSP00000205214:I109N	I	-	2	0	AASDH	56943425	1.000000	0.71417	0.864000	0.33941	0.979000	0.70002	6.594000	0.74104	2.250000	0.74265	0.533000	0.62120	ATC	.	.	.	none		0.323	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
ABCG2	9429	hgsc.bcm.edu	37	4	89039327	89039327	+	Silent	SNP	A	A	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:89039327A>G	ENST00000237612.3	-	7	1320	c.775T>C	c.(775-777)Ttg>Ctg	p.L259L	ABCG2_ENST00000515655.1_Silent_p.L259L	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	259	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	CCTGAGGCCAATAAGGTGAGG	0.433																																					p.L259L		Atlas-SNP	.											.	ABCG2	151	.	0			c.T775C						PASS	.						127.0	115.0	119.0					4																	89039327		2203	4300	6503	SO:0001819	synonymous_variant	9429	exon7			AGGCCAATAAGGT	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"""CD molecules"", ""ATP binding cassette transporters / subfamily G"""	74	protein-coding gene	gene with protein product		603756	"""ATP-binding cassette, sub-family G (WHITE), member 2"""			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.775T>C	chr4.hg19:g.89039327A>G		99.0	0.0	.		86.0	32.0	.	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Silent	SNP	ENST00000237612.3	hg19	CCDS3628.1																																																																																			.	.	.	none		0.433	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	
NDST4	64579	hgsc.bcm.edu	37	4	115767018	115767018	+	Silent	SNP	G	G	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:115767018G>A	ENST00000264363.2	-	10	2754	c.2076C>T	c.(2074-2076)atC>atT	p.I692I		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	692	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GGTCAATGAGGATGGTGATGA	0.433																																					p.I692I		Atlas-SNP	.											.	NDST4	193	.	0			c.C2076T						PASS	.						135.0	126.0	129.0					4																	115767018		2203	4300	6503	SO:0001819	synonymous_variant	64579	exon10			AATGAGGATGGTG	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"""Sulfotransferases, membrane-bound"""	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2076C>T	chr4.hg19:g.115767018G>A		135.0	0.0	.		128.0	51.0	.	NM_022569	Q2KHM8	Silent	SNP	ENST00000264363.2	hg19	CCDS3706.1																																																																																			.	.	.	none		0.433	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569	
ASB5	140458	hgsc.bcm.edu	37	4	177136796	177136796	+	Silent	SNP	T	T	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:177136796T>C	ENST00000296525.3	-	7	1058	c.945A>G	c.(943-945)caA>caG	p.Q315Q	ASB5_ENST00000512254.1_Silent_p.Q262Q	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	315	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GCAGCTGGAGTTGTGGGATAA	0.368																																					p.Q315Q		Atlas-SNP	.											.	ASB5	88	.	0			c.A945G						PASS	.						119.0	109.0	113.0					4																	177136796		2203	4300	6503	SO:0001819	synonymous_variant	140458	exon7			CTGGAGTTGTGGG	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"""Ankyrin repeat domain containing"""	17180	protein-coding gene	gene with protein product		615050	"""ankyrin repeat and SOCS box-containing 5"""				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.945A>G	chr4.hg19:g.177136796T>C		68.0	0.0	.		56.0	16.0	.	NM_080874	Q8N7B5	Silent	SNP	ENST00000296525.3	hg19	CCDS3827.1																																																																																			.	.	.	none		0.368	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1		
FAM149A	25854	hgsc.bcm.edu	37	4	187077186	187077186	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:187077186A>G	ENST00000356371.5	+	7	1289	c.1289A>G	c.(1288-1290)cAg>cGg	p.Q430R	FAM149A_ENST00000503432.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000502970.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000227065.4_Missense_Mutation_p.Q139R|FAM149A_ENST00000514153.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000389354.5_Missense_Mutation_p.Q139R			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	430										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		AAACCAGCTCAGCCCGGTAGG	0.433																																					p.Q139R		Atlas-SNP	.											.	FAM149A	52	.	0			c.A416G						PASS	.						103.0	96.0	98.0					4																	187077186		2203	4300	6503	SO:0001583	missense	25854	exon6			CAGCTCAGCCCGG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1289A>G	chr4.hg19:g.187077186A>G	ENSP00000348732:p.Gln430Arg	132.0	0.0	.		114.0	41.0	.	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	hg19		.	.	.	.	.	.	.	.	.	.	A	8.579	0.881917	0.17467	.	.	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.11169	2.81;2.8;2.81;2.81;2.81;2.81	5.46	-10.9	0.00192	.	1.583490	0.03252	N	0.182041	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.08055	0.002;0.003;0.001	T	0.34004	-0.9846	10	0.12766	T	0.61	0.1667	2.1131	0.03708	0.3:0.2092:0.3344:0.1565	.	430;430;139	A5PLN7-3;A5PLN7;B4DHZ9	.;F149A_HUMAN;.	R	139;430;139;139;139;139	ENSP00000426835:Q139R;ENSP00000348732:Q430R;ENSP00000227065:Q139R;ENSP00000427155:Q139R;ENSP00000424380:Q139R;ENSP00000374005:Q139R	ENSP00000227065:Q139R	Q	+	2	0	FAM149A	187314180	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.206000	0.03011	-1.534000	0.01743	-0.343000	0.07986	CAG	.	.	.	none		0.433	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
LIFR	3977	hgsc.bcm.edu	37	5	38504185	38504185	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:38504185T>C	ENST00000263409.4	-	10	1492	c.1330A>G	c.(1330-1332)Att>Gtt	p.I444V	LIFR_ENST00000453190.2_Missense_Mutation_p.I444V|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	444	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GTTGAATTAATATCCTTCACT	0.269			T	PLAG1	salivary adenoma																																p.I444V	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A1330G						PASS	.						54.0	59.0	58.0					5																	38504185		2201	4295	6496	SO:0001583	missense	3977	exon10			AATTAATATCCTT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.1330A>G	chr5.hg19:g.38504185T>C	ENSP00000263409:p.Ile444Val	66.0	0.0	.		57.0	18.0	.	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	T	3.712	-0.059335	0.07317	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.56103	0.48;0.48	5.65	-2.44	0.06502	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.807977	0.11218	N	0.587055	T	0.34164	0.0888	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30534	-0.9975	10	0.11794	T	0.64	-5.8891	11.1796	0.48620	0.0:0.4564:0.0:0.5436	.	444	P42702	LIFR_HUMAN	V	444	ENSP00000263409:I444V;ENSP00000398368:I444V	ENSP00000263409:I444V	I	-	1	0	LIFR	38539942	0.638000	0.27225	0.525000	0.27900	0.996000	0.88848	0.083000	0.14871	-0.426000	0.07360	0.528000	0.53228	ATT	.	.	.	none		0.269	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
SLC36A3	285641	hgsc.bcm.edu	37	5	150660717	150660717	+	Nonsense_Mutation	SNP	G	G	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:150660717G>T	ENST00000335230.3	-	9	1413	c.1002C>A	c.(1000-1002)taC>taA	p.Y334*	SLC36A3_ENST00000377713.3_Nonsense_Mutation_p.Y375*	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	334						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCCGATAGAGTACATCAGCT	0.522																																					p.Y375X		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C1125A						PASS	.						222.0	171.0	188.0					5																	150660717		2203	4300	6503	SO:0001587	stop_gained	285641	exon10			GATAGAGTACATC	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"""Solute carriers"""	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.1002C>A	chr5.hg19:g.150660717G>T	ENSP00000334750:p.Tyr334*	186.0	0.0	.		198.0	75.0	.	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Nonsense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	G	39	7.569738	0.98365	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	.	.	.	4.06	1.12	0.20585	.	0.196500	0.45361	D	0.000367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.071	7.6369	0.28272	0.4739:0.0:0.5261:0.0	.	.	.	.	X	334;375	.	ENSP00000334750:Y334X	Y	-	3	2	SLC36A3	150640910	1.000000	0.71417	0.967000	0.41034	0.964000	0.63967	1.720000	0.38022	0.092000	0.17331	0.561000	0.74099	TAC	.	.	.	none		0.522	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
RGS14	10636	hgsc.bcm.edu	37	5	176797996	176797996	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:176797996G>T	ENST00000408923.3	+	11	1406	c.1218G>T	c.(1216-1218)aaG>aaT	p.K406N		NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	406	Necessary for interaction with RABGEF1. {ECO:0000250}.|RBD 2. {ECO:0000255|PROSITE- ProRule:PRU00262}.				cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCTGGAGAAGCACGGCTTGA	0.751																																					p.K406N	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.G1218T						PASS	.						10.0	12.0	11.0					5																	176797996		1750	3841	5591	SO:0001583	missense	10636	exon11			GGAGAAGCACGGC	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"""Regulators of G-protein signaling"""	9996	protein-coding gene	gene with protein product		602513	"""regulator of G-protein signalling 14"""				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.1218G>T	chr5.hg19:g.176797996G>T	ENSP00000386229:p.Lys406Asn	72.0	0.0	.		49.0	16.0	.	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	hg19	CCDS43405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.43|13.43	2.234827|2.234827	0.39498|0.39498	.|.	.|.	ENSG00000169220|ENSG00000169220	ENST00000408923;ENST00000336477|ENST00000511890	T|.	0.63417|.	-0.04|.	4.96|4.96	2.0|2.0	0.26442|0.26442	Raf-like Ras-binding (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61060|0.61060	0.2317|0.2317	M|M	0.71206|0.71206	2.165|2.165	0.42256|0.42256	D|D	0.991993|0.991993	D;D;D|.	0.89917|.	1.0;1.0;0.995|.	D;D;D|.	0.97110|.	1.0;0.999;0.951|.	T|T	0.57940|0.57940	-0.7724|-0.7724	10|5	0.87932|.	D|.	0|.	-28.6256|-28.6256	5.8726|5.8726	0.18812|0.18812	0.3015:0.0:0.5635:0.135|0.3015:0.0:0.5635:0.135	.|.	177;254;406|.	B3KUX0;O43566-5;O43566|.	.;.;RGS14_HUMAN|.	N|I	406;187|277	ENSP00000386229:K406N|.	ENSP00000336864:K187N|.	K|S	+|+	3|2	2|0	RGS14|RGS14	176730602|176730602	1.000000|1.000000	0.71417|0.71417	0.972000|0.972000	0.41901|0.41901	0.033000|0.033000	0.12548|0.12548	1.059000|1.059000	0.30517|0.30517	0.704000|0.704000	0.31869|0.31869	-0.225000|-0.225000	0.12378|0.12378	AAG|AGC	.	.	.	none		0.751	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480	
OR11A1	26531	hgsc.bcm.edu	37	6	29395381	29395381	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr6:29395381T>G	ENST00000377149.1	-	5	510	c.38A>C	c.(37-39)gAa>gCa	p.E13A	OR11A1_ENST00000377148.1_Missense_Mutation_p.E13A|OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Missense_Mutation_p.E13A			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						GAGGACAAATTCAGTAATAGT	0.398																																					p.E13A		Atlas-SNP	.											.	OR11A1	30	.	0			c.A38C						PASS	.						67.0	65.0	66.0					6																	29395381		1509	2709	4218	SO:0001583	missense	26531	exon1			ACAAATTCAGTAA		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"""GPCR / Class A : Olfactory receptors"""	8176	protein-coding gene	gene with protein product			"""olfactory receptor, family 11, subfamily A, member 2"""	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.38A>C	chr6.hg19:g.29395381T>G	ENSP00000366354:p.Glu13Ala	130.0	0.0	.		98.0	34.0	.	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	hg19	CCDS34363.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.118839	0.56505	.	.	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.01119	5.31;5.31;5.31	3.66	2.48	0.30137	.	0.000000	0.33290	U	0.005076	T	0.00998	0.0033	M	0.88512	2.96	0.09310	N	1	P	0.34977	0.478	B	0.38327	0.271	T	0.41928	-0.9481	10	0.54805	T	0.06	-0.4728	5.5487	0.17079	0.0:0.2499:0.0:0.7501	.	13	Q9GZK7	O11A1_HUMAN	A	13	ENSP00000366353:E13A;ENSP00000366354:E13A;ENSP00000366352:E13A	ENSP00000366352:E13A	E	-	2	0	OR11A1	29503360	0.004000	0.15560	0.093000	0.20910	0.716000	0.41182	0.571000	0.23669	0.465000	0.27167	0.327000	0.21459	GAA	.	.	.	none		0.398	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1		
SEPT7	989	hgsc.bcm.edu	37	7	35912377	35912377	+	Splice_Site	SNP	G	G	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:35912377G>A	ENST00000435235.1	+	4	650		c.e4+1		SEPT7_ENST00000475109.1_Splice_Site|SEPT7_ENST00000399035.3_Splice_Site|SEPT7_ENST00000494488.2_Splice_Site|SEPT7_ENST00000469679.2_Splice_Site|SEPT7_ENST00000350320.6_Splice_Site|SEPT7_ENST00000399034.2_Splice_Site			Q16181	SEPT7_HUMAN	septin 7						cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						ATAGTAATTGGTAAGAAGGGT	0.388																																					.		Atlas-SNP	.											.	SEPT7	24	.	0			c.374+1G>A						PASS	.						134.0	127.0	129.0					7																	35912377		1851	4091	5942	SO:0001630	splice_region_variant	989	exon4			TAATTGGTAAGAA	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"""Septins"""	1717	protein-coding gene	gene with protein product		603151	"""CDC10 cell division cycle 10 homolog (S. cerevisiae)"""	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.218+1G>A	chr7.hg19:g.35912377G>A		34.0	0.0	.		35.0	13.0	.	NM_001011553	Q52M76|Q6NX50	Splice_Site	SNP	ENST00000435235.1	hg19		.	.	.	.	.	.	.	.	.	.	g	24.0	4.477060	0.84640	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000469679;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0851	0.89455	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEPT7	35878902	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.695000	0.98691	2.338000	0.79540	0.574000	0.79327	.	.	.	.	none		0.388	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788	Intron
PRKRIP1	79706	hgsc.bcm.edu	37	7	102040095	102040096	+	Splice_Site	DNP	GG	GG	AA			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:102040095_102040096GG>AA	ENST00000496391.1	+	7	1616	c.306_306GG>AA	c.(304-306)aaGG>aaAAg	p.K102K	PRKRIP1_ENST00000482465.1_3'UTR|PRKRIP1_ENST00000354783.4_Splice_Site_p.K64K|PRKRIP1_ENST00000462601.1_Splice_Site_p.K45K|PRKRIP1_ENST00000397912.3_Splice_Site_p.K102K			Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)	102	Required for RNA-binding. {ECO:0000250}.				negative regulation of phosphorylation (GO:0042326)|negative regulation of protein kinase activity (GO:0006469)|renal system process (GO:0003014)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|lung(4)|ovary(1)	6						TGGCTGAGAAGGTCAGTGAGCC	0.554																																					p.K102K|.		Atlas-SNP	.											.	PRKRIP1	25	.	0			c.G306A|c.306+1G>A						PASS	.																																			SO:0001630	splice_region_variant	79706	exon3			TGAGAAGGTCAGT|GAGAAGGTCAGTG	AK023964	CCDS34714.1	7q22.1	2013-01-09			ENSG00000128563	ENSG00000128563		"""Zinc fingers, C2H2-type"", ""-"""	21894	protein-coding gene	gene with protein product	"""likely ortholog of mouse C114 dsRNA-binding protein"", ""KRAB box domain containing 3"""					12679338	Standard	NM_024653		Approved	C114, FLJ13902, KRBOX3	uc003uzh.2	Q9H875	OTTHUMG00000157717	Exception_encountered	chr7.hg19:g.102040095_102040096delinsAA		224.0|223.0	0.0	.		366.0|360.0	147.0	.	NM_024653	B4DGM2|Q8NDM6|Q96CF8	Silent|Splice_Site	SNP	ENST00000496391.1	hg19	CCDS34714.1																																																																																			.	.	.	none		0.554	PRKRIP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349489.1	NM_024653	Silent
ZNF777	27153	hgsc.bcm.edu	37	7	149129443	149129443	+	Silent	SNP	C	C	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:149129443C>T	ENST00000247930.4	-	6	2243	c.1920G>A	c.(1918-1920)gaG>gaA	p.E640E		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	640					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			TGCTGTCGCACTCGGGGCACT	0.652																																					p.E640E		Atlas-SNP	.											.	ZNF777	63	.	0			c.G1920A						PASS	.						90.0	106.0	100.0					7																	149129443		2182	4272	6454	SO:0001819	synonymous_variant	27153	exon6			GTCGCACTCGGGG	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1920G>A	chr7.hg19:g.149129443C>T		366.0	1.0	.		515.0	202.0	.	NM_015694	Q8N2R2|Q8N659	Silent	SNP	ENST00000247930.4	hg19	CCDS43675.1																																																																																			.	.	.	none		0.652	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
ZFHX4	79776	hgsc.bcm.edu	37	8	77776650	77776650	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr8:77776650C>A	ENST00000521891.2	+	11	11148	c.10700C>A	c.(10699-10701)tCa>tAa	p.S3567*	ZFHX4_ENST00000050961.6_Nonsense_Mutation_p.S3518*|ZFHX4_ENST00000518282.1_Nonsense_Mutation_p.S3541*|ZFHX4_ENST00000455469.2_Nonsense_Mutation_p.S3522*	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTTCAAACCTCACTACCCACA	0.493										HNSCC(33;0.089)																											p.S3567X		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C10700A						PASS	.						85.0	86.0	86.0					8																	77776650		2128	4274	6402	SO:0001587	stop_gained	79776	exon11			AAACCTCACTACC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.10700C>A	chr8.hg19:g.77776650C>A	ENSP00000430497:p.Ser3567*	51.0	0.0	.		106.0	5.0	.	NM_024721	G3V138|Q18PS0|Q6ZN20	Nonsense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	52	19.301884	0.99917	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	.	.	.	4.36	4.36	0.52297	.	0.000000	0.36628	U	0.002492	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.448	0.87584	0.0:1.0:0.0:0.0	.	.	.	.	X	3567;3551;3522;3518;3541	.	ENSP00000050961:S3518X	S	+	2	0	ZFHX4	77939205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.563000	0.82314	2.435000	0.82474	0.650000	0.86243	TCA	.	.	.	none		0.493	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
CA9	768	hgsc.bcm.edu	37	9	35674197	35674197	+	Nonsense_Mutation	SNP	G	G	T	rs201260414	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr9:35674197G>T	ENST00000378357.4	+	1	345	c.241G>T	c.(241-243)Gag>Tag	p.E81*	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	81	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.G79_P84delGEEDLP(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	ACCCGGAGAGGAGGATCTACC	0.557																																					p.E81X		Atlas-SNP	.											.	CA9	48	.	1	Deletion - In frame(1)	urinary_tract(1)	c.G241T						PASS	.						56.0	54.0	55.0					9																	35674197		2203	4300	6503	SO:0001587	stop_gained	768	exon1			GGAGAGGAGGATC	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.241G>T	chr9.hg19:g.35674197G>T	ENSP00000367608:p.Glu81*	112.0	0.0	.		84.0	23.0	.	NM_001216	Q5T4R1	Nonsense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.325846	0.41197	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	.	.	.	1.05	1.05	0.20165	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	3.3335	0.07093	0.3182:0.0:0.6818:0.0	.	.	.	.	X	81	.	ENSP00000367608:E81X	E	+	1	0	CA9	35664197	0.004000	0.15560	0.010000	0.14722	0.014000	0.08584	1.197000	0.32211	0.121000	0.18284	0.123000	0.15791	GAG	.	.	.	none		0.557	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
ECD	11319	hgsc.bcm.edu	37	10	74896486	74896486	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr10:74896486T>G	ENST00000372979.4	-	13	1886	c.1680A>C	c.(1678-1680)aaA>aaC	p.K560N	ECD_ENST00000454759.2_Missense_Mutation_p.K517N|ECD_ENST00000430082.2_Missense_Mutation_p.K593N	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	560					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					TGGTGAAACTTTTGCTGATGC	0.418																																					p.K593N		Atlas-SNP	.											.	ECD	50	.	0			c.A1779C						PASS	.						221.0	194.0	203.0					10																	74896486		2203	4300	6503	SO:0001583	missense	11319	exon14			GAAACTTTTGCTG	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1680A>C	chr10.hg19:g.74896486T>G	ENSP00000362070:p.Lys560Asn	225.0	0.0	.		179.0	75.0	.	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	hg19	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.034517	0.75617	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.19669	2.13;2.13;2.13	5.66	3.37	0.38596	.	0.091325	0.85682	D	0.000000	T	0.34048	0.0884	M	0.64997	1.995	0.47037	D	0.999297	D;D;P	0.60575	0.978;0.988;0.51	P;P;P	0.60286	0.872;0.872;0.493	T	0.03597	-1.1021	10	0.40728	T	0.16	-2.9522	7.962	0.30076	0.0:0.1669:0.0:0.8331	.	517;593;560	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	N	560;593;517	ENSP00000362070:K560N;ENSP00000401566:K593N;ENSP00000395786:K517N	ENSP00000362070:K560N	K	-	3	2	ECD	74566492	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.537000	0.36083	0.981000	0.38548	0.533000	0.62120	AAA	.	.	.	none		0.418	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
COX15	1355	hgsc.bcm.edu	37	10	101491791	101491791	+	Missense_Mutation	SNP	A	A	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr10:101491791A>C	ENST00000016171.5	-	1	66	c.16T>G	c.(16-18)Ttt>Gtt	p.F6V	CUTC_ENST00000493385.1_Intron|CUTC_ENST00000370476.5_5'Flank|COX15_ENST00000370483.5_Missense_Mutation_p.F6V			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	6					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		AACGGCGGAAAGAGCAATCGC	0.607																																					p.F6V		Atlas-SNP	.											.	COX15	25	.	0			c.T16G						PASS	.						48.0	36.0	40.0					10																	101491791		2203	4300	6503	SO:0001583	missense	1355	exon1			GCGGAAAGAGCAA	AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"""Mitochondrial respiratory chain complex assembly factors"""	2263	protein-coding gene	gene with protein product		603646	"""COX15 (yeast) homolog, cytochrome c oxidase assembly protein"", ""COX15 homolog, cytochrome c oxidase assembly protein (yeast)"""			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.16T>G	chr10.hg19:g.101491791A>C	ENSP00000016171:p.Phe6Val	56.0	0.0	.		56.0	18.0	.	NM_078470	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Missense_Mutation	SNP	ENST00000016171.5	hg19	CCDS7482.1	.	.	.	.	.	.	.	.	.	.	A	6.792	0.515219	0.12944	.	.	ENSG00000014919	ENST00000370483;ENST00000016171	.	.	.	4.58	0.265	0.15612	.	0.865040	0.09787	N	0.755882	T	0.23054	0.0557	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21621	-1.0240	9	0.27785	T	0.31	1.4857	3.7279	0.08481	0.4456:0.2267:0.3277:0.0	.	6;6	Q7KZN9-2;Q7KZN9	.;COX15_HUMAN	V	6	.	ENSP00000016171:F6V	F	-	1	0	COX15	101481781	0.005000	0.15991	0.002000	0.10522	0.186000	0.23388	-0.083000	0.11286	-0.100000	0.12241	0.454000	0.30748	TTT	.	.	.	none		0.607	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870	
E2F8	79733	hgsc.bcm.edu	37	11	19251275	19251275	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:19251275A>T	ENST00000527884.1	-	10	1851	c.1619T>A	c.(1618-1620)cTg>cAg	p.L540Q	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Missense_Mutation_p.L540Q	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	540					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CGTTGGGCTCAGGCCTTGGGG	0.582																																					p.L540Q		Atlas-SNP	.											.	E2F8	84	.	0			c.T1619A						PASS	.						116.0	110.0	112.0					11																	19251275		2199	4293	6492	SO:0001583	missense	79733	exon10			GGGCTCAGGCCTT		CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1619T>A	chr11.hg19:g.19251275A>T	ENSP00000434199:p.Leu540Gln	448.0	0.0	.		410.0	146.0	.	NM_001256372	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Missense_Mutation	SNP	ENST00000527884.1	hg19	CCDS7849.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.208327	0.39003	.	.	ENSG00000129173	ENST00000527884;ENST00000396159;ENST00000250024	T;T	0.19669	2.13;2.13	5.63	3.22	0.36961	.	0.443233	0.22737	N	0.056245	T	0.17323	0.0416	M	0.62723	1.935	0.38602	D	0.950684	P	0.37955	0.612	B	0.34722	0.188	T	0.13737	-1.0498	10	0.66056	D	0.02	-1.4647	1.4873	0.02450	0.4262:0.2981:0.1324:0.1433	.	540	A0AVK6	E2F8_HUMAN	Q	540	ENSP00000434199:L540Q;ENSP00000250024:L540Q	ENSP00000250024:L540Q	L	-	2	0	E2F8	19207851	0.981000	0.34729	1.000000	0.80357	0.949000	0.60115	1.281000	0.33214	0.376000	0.24707	0.533000	0.62120	CTG	.	.	.	none		0.582	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680	
QSER1	79832	hgsc.bcm.edu	37	11	32954930	32954930	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:32954930C>A	ENST00000399302.2	+	4	2074	c.1739C>A	c.(1738-1740)tCa>tAa	p.S580*	QSER1_ENST00000527788.1_Nonsense_Mutation_p.S341*	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	580										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TCTCTTGAGTCATCAACCCAA	0.398																																					p.S580X		Atlas-SNP	.											.	QSER1	153	.	0			c.C1739A						PASS	.						82.0	77.0	79.0					11																	32954930		1869	4115	5984	SO:0001587	stop_gained	79832	exon4			TTGAGTCATCAAC	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.1739C>A	chr11.hg19:g.32954930C>A	ENSP00000382241:p.Ser580*	47.0	0.0	.		48.0	14.0	.	NM_001076786	Q6ZU30|Q6ZUR5	Nonsense_Mutation	SNP	ENST00000399302.2	hg19	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.281137	0.80692	.	.	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	.	.	.	5.01	5.01	0.66863	.	0.480260	0.19152	N	0.121422	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6645	0.91485	0.0:1.0:0.0:0.0	.	.	.	.	X	580;341;341	.	ENSP00000078652:S341X	S	+	2	0	QSER1	32911506	0.999000	0.42202	0.049000	0.19019	0.007000	0.05969	5.597000	0.67577	2.496000	0.84212	0.591000	0.81541	TCA	.	.	.	none		0.398	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
MADD	8567	hgsc.bcm.edu	37	11	47304129	47304129	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:47304129T>G	ENST00000311027.5	+	9	1832	c.1667T>G	c.(1666-1668)cTt>cGt	p.L556R	MADD_ENST00000407859.3_Missense_Mutation_p.L556R|MADD_ENST00000402192.2_Missense_Mutation_p.L556R|MADD_ENST00000395336.3_Missense_Mutation_p.L556R|MADD_ENST00000402799.1_Missense_Mutation_p.L556R|MADD_ENST00000406482.1_Missense_Mutation_p.L556R|MADD_ENST00000342922.4_Missense_Mutation_p.L556R|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000349238.3_Missense_Mutation_p.L556R|MADD_ENST00000395344.3_Missense_Mutation_p.L556R	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GAATGGATCCTTAACCCCACC	0.537																																					p.L556R		Atlas-SNP	.											.	MADD	172	.	0			c.T1667G						PASS	.						69.0	53.0	58.0					11																	47304129		2201	4298	6499	SO:0001583	missense	8567	exon9			GGATCCTTAACCC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1667T>G	chr11.hg19:g.47304129T>G	ENSP00000310933:p.Leu556Arg	138.0	0.0	.		137.0	50.0	.	NM_130474		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.010292	0.93346	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.08896	3.16;3.05;3.05;3.14;3.15;3.04;3.06;3.15;3.16	5.77	5.77	0.91146	dDENN (1);	0.000000	0.85682	D	0.000000	T	0.28797	0.0714	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.91635	0.995;0.997;0.998;0.991;0.991;0.991;0.997;0.999;0.999;0.999	T	0.00686	-1.1610	10	0.87932	D	0	-13.2301	16.383	0.83481	0.0:0.0:0.0:1.0	.	556;556;556;556;556;556;556;556;556;556	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	R	556	ENSP00000343902:L556R;ENSP00000385585:L556R;ENSP00000384435:L556R;ENSP00000304505:L556R;ENSP00000310933:L556R;ENSP00000384204:L556R;ENSP00000378753:L556R;ENSP00000378745:L556R;ENSP00000384287:L556R	ENSP00000310933:L556R	L	+	2	0	MADD	47260705	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	7.628000	0.83189	2.326000	0.78906	0.533000	0.62120	CTT	.	.	.	none		0.537	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
HSPA8	3312	hgsc.bcm.edu	37	11	122931912	122931912	+	Missense_Mutation	SNP	A	A	G	rs75739900		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:122931912A>G	ENST00000532636.1	-	2	240	c.121T>C	c.(121-123)Tat>Cat	p.Y41H	SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Missense_Mutation_p.Y41H|HSPA8_ENST00000534319.1_5'Flank|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.Y41H|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Missense_Mutation_p.Y41H|HSPA8_ENST00000533540.1_Missense_Mutation_p.Y41H|HSPA8_ENST00000534624.1_Missense_Mutation_p.Y41H			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	41					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AAGGCGACATAGCTTGGAGTG	0.463																																					p.Y41H	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.T121C						PASS	.						99.0	82.0	87.0					11																	122931912		2202	4299	6501	SO:0001583	missense	3312	exon2			CGACATAGCTTGG	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.121T>C	chr11.hg19:g.122931912A>G	ENSP00000437125:p.Tyr41His	204.0	0.0	.		150.0	6.0	.	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	hg19	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.483750	0.84854	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000526110;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182;ENST00000524590;ENST00000530391	T;T;T;T;T;T;T;T;T;T;T;T;T	0.03951	5.39;5.39;5.39;5.39;5.39;5.39;3.75;5.39;5.39;5.39;5.39;5.39;5.39	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.35335	0.0928	H	0.98218	4.175	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0	D;D;D;D;D	0.91635	0.993;0.999;0.997;0.995;0.998	T	0.58831	-0.7567	10	0.87932	D	0	-22.5338	13.9807	0.64304	1.0:0.0:0.0:0.0	.	41;41;41;41;41	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	H	41	ENSP00000437125:Y41H;ENSP00000437189:Y41H;ENSP00000432083:Y41H;ENSP00000404372:Y41H;ENSP00000227378:Y41H;ENSP00000433584:Y41H;ENSP00000436762:Y41H;ENSP00000435154:Y41H;ENSP00000431641:Y41H;ENSP00000436183:Y41H;ENSP00000434415:Y41H;ENSP00000434565:Y41H;ENSP00000434851:Y41H	ENSP00000227378:Y41H	Y	-	1	0	HSPA8	122437122	1.000000	0.71417	0.995000	0.50966	0.781000	0.44180	9.337000	0.96545	1.748000	0.51833	0.397000	0.26171	TAT	.	.	.	weak		0.463	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
PIK3C2G	5288	hgsc.bcm.edu	37	12	18658292	18658292	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:18658292G>A	ENST00000266497.5	+	22	3135	c.3097G>A	c.(3097-3099)Gac>Aac	p.D1033N	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.D1033N|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.D1074N			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1033	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				GGGAGTATGTGACCGTCACAA	0.393																																					p.D1033N		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.G3097A						PASS	.						129.0	112.0	117.0					12																	18658292		1934	4151	6085	SO:0001583	missense	5288	exon23			GTATGTGACCGTC	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3097G>A	chr12.hg19:g.18658292G>A	ENSP00000266497:p.Asp1033Asn	16.0	0.0	.		11.0	7.0	.	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018323	0.93404	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	D;D;D	0.94897	-3.55;-3.55;-3.55	4.47	4.47	0.54385	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.127925	0.51477	D	0.000089	D	0.98105	0.9375	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98863	1.0763	10	0.87932	D	0	-20.5375	17.403	0.87465	0.0:0.0:1.0:0.0	.	1073;1074;1033	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	N	1033;1033;1074	ENSP00000404845:D1033N;ENSP00000266497:D1033N;ENSP00000445381:D1074N	ENSP00000266497:D1033N	D	+	1	0	PIK3C2G	18549559	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.524000	0.98036	2.771000	0.95319	0.650000	0.86243	GAC	.	.	.	none		0.393	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
PDZRN4	29951	hgsc.bcm.edu	37	12	41585335	41585335	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:41585335C>T	ENST00000402685.2	+	2	732	c.724C>T	c.(724-726)Cga>Tga	p.R242*		NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	242	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TATAGGAGGTCGACCAAATCA	0.303																																					p.R242X		Atlas-SNP	.											.	PDZRN4	346	.	0			c.C724T						PASS	.						97.0	90.0	92.0					12																	41585335		1568	3576	5144	SO:0001587	stop_gained	29951	exon2			GGAGGTCGACCAA	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.724C>T	chr12.hg19:g.41585335C>T	ENSP00000384197:p.Arg242*	56.0	0.0	.		105.0	34.0	.	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Nonsense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	C	37	6.538183	0.97646	.	.	ENSG00000165966	ENST00000402685	.	.	.	4.48	2.64	0.31445	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.2118	0.37322	0.0:0.8273:0.0:0.1727	.	.	.	.	X	242	.	ENSP00000384197:R242X	R	+	1	2	PDZRN4	39871602	0.791000	0.28800	0.992000	0.48379	0.995000	0.86356	1.196000	0.32198	0.591000	0.29711	0.563000	0.77884	CGA	.	.	.	none		0.303	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
ACAD10	80724	hgsc.bcm.edu	37	12	112184083	112184083	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:112184083C>A	ENST00000313698.4	+	14	2406	c.2251C>A	c.(2251-2253)Ccc>Acc	p.P751T	ACAD10_ENST00000392636.2_Missense_Mutation_p.P353T|ACAD10_ENST00000455480.2_Missense_Mutation_p.P782T|ACAD10_ENST00000413681.3_3'UTR	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	751						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						CCTGTATGCCCCCGAGGTACC	0.473																																					p.P782T		Atlas-SNP	.											.	ACAD10	93	.	0			c.C2344A						PASS	.						106.0	103.0	104.0					12																	112184083		2203	4300	6503	SO:0001583	missense	80724	exon15			TATGCCCCCGAGG	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"""acyl-Coenzyme A dehydrogenase family, member 10"""			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.2251C>A	chr12.hg19:g.112184083C>A	ENSP00000325137:p.Pro751Thr	265.0	0.0	.		339.0	89.0	.	NM_001136538	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	hg19	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.408994	0.62399	.	.	ENSG00000111271	ENST00000392636;ENST00000413681;ENST00000455480;ENST00000515283;ENST00000313698	D;D;D	0.99660	-6.32;-6.32;-6.32	5.29	3.43	0.39272	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.378699	0.25436	N	0.030684	D	0.99629	0.9864	H	0.97732	4.065	0.80722	D	1	D;B;B	0.53462	0.96;0.209;0.298	P;B;B	0.57057	0.812;0.396;0.141	D	0.98657	1.0682	10	0.87932	D	0	.	9.228	0.37418	0.1463:0.776:0.0:0.0777	.	782;751;751	G3XAJ0;Q6JQN1;Q6JQN1-2	.;ACD10_HUMAN;.	T	353;751;782;144;751	ENSP00000376411:P353T;ENSP00000389813:P782T;ENSP00000325137:P751T	ENSP00000325137:P751T	P	+	1	0	ACAD10	110668466	0.071000	0.21146	0.012000	0.15200	0.965000	0.64279	1.166000	0.31834	0.708000	0.31955	0.561000	0.74099	CCC	.	.	.	none		0.473	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247	
TMEM132D	121256	hgsc.bcm.edu	37	12	130184819	130184819	+	Silent	SNP	C	C	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:130184819C>G	ENST00000422113.2	-	2	830	c.504G>C	c.(502-504)ctG>ctC	p.L168L	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	168					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CAAAGACCCTCAGGCACGGCA	0.662																																					p.L168L		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G504C						PASS	.						18.0	20.0	20.0					12																	130184819		2203	4299	6502	SO:0001819	synonymous_variant	121256	exon2			GACCCTCAGGCAC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.504G>C	chr12.hg19:g.130184819C>G		96.0	0.0	.		103.0	57.0	.	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	hg19	CCDS9266.1																																																																																			.	.	.	none		0.662	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
SLC46A3	283537	hgsc.bcm.edu	37	13	29287510	29287510	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:29287510A>G	ENST00000266943.6	-	3	736	c.367T>C	c.(367-369)Tat>Cat	p.Y123H	SLC46A3_ENST00000380814.4_Missense_Mutation_p.Y123H	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	123					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		AAGGCAAAATAGCAAAGCAAA	0.408																																					p.Y123H		Atlas-SNP	.											.	SLC46A3	86	.	0			c.T367C						PASS	.						74.0	67.0	69.0					13																	29287510		2203	4300	6503	SO:0001583	missense	283537	exon3			CAAAATAGCAAAG		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"""Solute carriers"""	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.367T>C	chr13.hg19:g.29287510A>G	ENSP00000266943:p.Tyr123His	68.0	0.0	.		54.0	13.0	.	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	hg19	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.182467	0.78677	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.80994	-1.44;-1.44	6.17	5.0	0.66597	Major facilitator superfamily domain, general substrate transporter (1);	0.059964	0.64402	D	0.000002	D	0.88123	0.6352	M	0.74881	2.28	0.42496	D	0.992918	D;B;B	0.89917	1.0;0.36;0.413	D;B;B	0.79784	0.993;0.139;0.219	D	0.87590	0.2490	10	0.42905	T	0.14	-22.8055	12.1889	0.54257	0.9341:0.0:0.0659:0.0	.	48;123;123	B5MEH0;Q7Z3Q1-2;Q7Z3Q1	.;.;S46A3_HUMAN	H	123	ENSP00000266943:Y123H;ENSP00000370192:Y123H	ENSP00000266943:Y123H	Y	-	1	0	SLC46A3	28185510	1.000000	0.71417	0.981000	0.43875	0.958000	0.62258	6.725000	0.74752	1.160000	0.42584	0.533000	0.62120	TAT	.	.	.	none		0.408	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785	
ATP7B	540	hgsc.bcm.edu	37	13	52548108	52548108	+	Silent	SNP	A	A	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:52548108A>T	ENST00000242839.4	-	2	1404	c.1248T>A	c.(1246-1248)gcT>gcA	p.A416A	ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000542656.1_Silent_p.A384A|ATP7B_ENST00000448424.2_Silent_p.A416A|ATP7B_ENST00000344297.5_Silent_p.A416A|ATP7B_ENST00000400370.3_Silent_p.A416A|ATP7B_ENST00000400366.3_Silent_p.A305A|ATP7B_ENST00000418097.2_Silent_p.A416A	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	416	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGTCTTCTATAGCAGCTCTGA	0.458									Wilson disease																												p.A416A		Atlas-SNP	.											.	ATP7B	123	.	0			c.T1248A						PASS	.						100.0	98.0	98.0					13																	52548108		1934	4142	6076	SO:0001819	synonymous_variant	540	exon2	Familial Cancer Database		TTCTATAGCAGCT	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1248T>A	chr13.hg19:g.52548108A>T		201.0	0.0	.		245.0	90.0	.	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	hg19	CCDS41892.1																																																																																			.	.	.	none		0.458	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
RNF219	79596	hgsc.bcm.edu	37	13	79190506	79190506	+	Missense_Mutation	SNP	T	T	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:79190506T>A	ENST00000282003.6	-	6	1448	c.1390A>T	c.(1390-1392)Aca>Tca	p.T464S	RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000560584.2_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	464	Ser-rich.						zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		CAAAATCCTGTCTTTGGGGAA	0.333																																					p.T464S		Atlas-SNP	.											.	RNF219	94	.	0			c.A1390T						PASS	.						38.0	40.0	39.0					13																	79190506		2203	4298	6501	SO:0001583	missense	79596	exon6			ATCCTGTCTTTGG	BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"""RING-type (C3HC4) zinc fingers"""	20308	protein-coding gene	gene with protein product		615906	"""chromosome 13 open reading frame 7"""	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.1390A>T	chr13.hg19:g.79190506T>A	ENSP00000282003:p.Thr464Ser	34.0	0.0	.		58.0	25.0	.	NM_024546	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	hg19	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813748	0.32053	.	.	ENSG00000152193	ENST00000282003	T	0.13778	2.56	5.86	3.32	0.38043	.	0.182284	0.39475	N	0.001352	T	0.03959	0.0111	N	0.03608	-0.345	0.26073	N	0.9812	B	0.10296	0.003	B	0.08055	0.003	T	0.36841	-0.9731	10	0.10902	T	0.67	-12.2367	1.5693	0.02612	0.3186:0.0903:0.1164:0.4747	.	464	Q5W0B1	RN219_HUMAN	S	464	ENSP00000282003:T464S	ENSP00000282003:T464S	T	-	1	0	RNF219	78088507	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	1.424000	0.34848	1.050000	0.40346	0.533000	0.62120	ACA	.	.	.	none		0.333	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546	
KHNYN	23351	hgsc.bcm.edu	37	14	24910963	24910963	+	IGR	SNP	C	C	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr14:24910963C>G	ENST00000251343.5	+	0	6225				SDR39U1_ENST00000399390.1_5'Flank|SDR39U1_ENST00000555365.1_5'UTR|SDR39U1_ENST00000554698.1_Intron|SDR39U1_ENST00000538105.2_Intron|SDR39U1_ENST00000399395.3_Missense_Mutation_p.R82P|SDR39U1_ENST00000555561.1_5'Flank|SDR39U1_ENST00000553930.1_5'UTR			O15037	KHNYN_HUMAN	KH and NYN domain containing								RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GGTCTCTAGGCGGCTGCCGAT	0.498																																					p.R82P		Atlas-SNP	.											SDR39U1,colon,carcinoma,0,1	SDR39U1	19	.	0			c.G245C						PASS	.						48.0	39.0	42.0					14																	24910963		1856	4091	5947	SO:0001628	intergenic_variant	56948	exon4			TCTAGGCGGCTGC	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037			chr14.hg19:g.24910963C>G		84.0	0.0	.		74.0	6.0	.	NM_020195	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	hg19	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.024548	0.93518	.	.	ENSG00000100445	ENST00000399395;ENST00000336353	D	0.93426	-3.22	5.46	5.46	0.80206	NAD(P)-binding domain (1);	0.222455	0.46145	D	0.000301	D	0.96972	0.9011	M	0.84585	2.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97373	0.9977	10	0.87932	D	0	-11.9991	17.1594	0.86800	0.0:1.0:0.0:0.0	.	82;108	Q9NRG7-2;Q9NRG7	.;D39U1_HUMAN	P	82;108	ENSP00000382327:R82P	ENSP00000336854:R108P	R	-	2	0	SDR39U1	23980803	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.215000	0.77966	2.714000	0.92807	0.655000	0.94253	CGC	.	.	.	none		0.498	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
SPINT1	6692	hgsc.bcm.edu	37	15	41146021	41146021	+	Silent	SNP	C	C	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:41146021C>T	ENST00000344051.4	+	5	1089	c.855C>T	c.(853-855)ggC>ggT	p.G285G	SPINT1_ENST00000562057.1_Silent_p.G285G|SPINT1_ENST00000431806.1_Silent_p.G285G			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	285	BPTI/Kunitz inhibitor 1. {ECO:0000255|PROSITE-ProRule:PRU00031}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCTGCTTGGGCAACAAGAACA	0.572																																					p.G285G		Atlas-SNP	.											.	SPINT1	28	.	0			c.C855T						PASS	.						120.0	128.0	125.0					15																	41146021		2203	4300	6503	SO:0001819	synonymous_variant	6692	exon5			CTTGGGCAACAAG		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"""serine protease inhibitor, Kunitz type 1"""				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.855C>T	chr15.hg19:g.41146021C>T		391.0	0.0	.		317.0	106.0	.	NM_181642	Q7Z7D2	Silent	SNP	ENST00000344051.4	hg19	CCDS10067.1																																																																																			.	.	.	none		0.572	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710	
TP53BP1	7158	hgsc.bcm.edu	37	15	43724401	43724401	+	Silent	SNP	G	G	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:43724401G>A	ENST00000263801.3	-	17	3903	c.3651C>T	c.(3649-3651)ctC>ctT	p.L1217L	TP53BP1_ENST00000450115.2_Silent_p.L1222L|TP53BP1_ENST00000382039.3_Silent_p.L1222L|TP53BP1_ENST00000382044.4_Silent_p.L1222L	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1217					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CCTGGCTATGGAGCGACTCTG	0.483								Other conserved DNA damage response genes																													p.L1222L		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C3666T						PASS	.						137.0	112.0	121.0					15																	43724401		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon17			GCTATGGAGCGAC	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3651C>T	chr15.hg19:g.43724401G>A		48.0	0.0	.		37.0	13.0	.	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	hg19	CCDS10096.1																																																																																			.	.	.	none		0.483	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
CGNL1	84952	hgsc.bcm.edu	37	15	57730838	57730838	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:57730838C>G	ENST00000281282.5	+	2	719	c.641C>G	c.(640-642)aCa>aGa	p.T214R		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	214	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TCTGGTGTGACAGCTATTCGT	0.517																																					p.T214R		Atlas-SNP	.											.	CGNL1	125	.	0			c.C641G						PASS	.						132.0	132.0	132.0					15																	57730838		2192	4292	6484	SO:0001583	missense	84952	exon3			GTGTGACAGCTAT	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.641C>G	chr15.hg19:g.57730838C>G	ENSP00000281282:p.Thr214Arg	625.0	1.0	.		467.0	169.0	.	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	C	5.347	0.249277	0.10130	.	.	ENSG00000128849	ENST00000281282	T	0.76968	-1.06	4.98	4.04	0.47022	.	0.178508	0.26851	N	0.022178	T	0.70124	0.3188	L	0.51422	1.61	0.30026	N	0.813928	B	0.27625	0.183	B	0.19666	0.026	T	0.69495	-0.5130	10	0.56958	D	0.05	-12.3608	10.9213	0.47167	0.4244:0.5756:0.0:0.0	.	214	Q0VF96	CGNL1_HUMAN	R	214	ENSP00000281282:T214R	ENSP00000281282:T214R	T	+	2	0	CGNL1	55518130	0.432000	0.25554	0.389000	0.26208	0.182000	0.23217	1.535000	0.36061	1.275000	0.44379	0.650000	0.86243	ACA	.	.	.	none		0.517	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
MCTP2	55784	hgsc.bcm.edu	37	15	94841734	94841734	+	Silent	SNP	C	C	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:94841734C>T	ENST00000357742.4	+	1	240	c.240C>T	c.(238-240)agC>agT	p.S80S	MCTP2_ENST00000543482.1_Silent_p.S80S|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Silent_p.S80S	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	80					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CGGTGCCCAGCAGTCTGTCCA	0.587																																					p.S80S		Atlas-SNP	.											.	MCTP2	122	.	0			c.C240T						PASS	.						60.0	62.0	62.0					15																	94841734		2197	4298	6495	SO:0001819	synonymous_variant	55784	exon1			GCCCAGCAGTCTG	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.240C>T	chr15.hg19:g.94841734C>T		359.0	0.0	.		261.0	80.0	.	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	hg19	CCDS32338.1																																																																																			.	.	.	none		0.587	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
ATAD5	79915	hgsc.bcm.edu	37	17	29220728	29220728	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:29220728T>G	ENST00000321990.4	+	21	5235	c.4857T>G	c.(4855-4857)aaT>aaG	p.N1619K		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1619					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AAGGAAACAATCCAGAGACAA	0.393																																					p.N1619K		Atlas-SNP	.											.	ATAD5	150	.	0			c.T4857G						PASS	.						82.0	91.0	88.0					17																	29220728		2203	4300	6503	SO:0001583	missense	79915	exon21			AAACAATCCAGAG		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4857T>G	chr17.hg19:g.29220728T>G	ENSP00000313171:p.Asn1619Lys	120.0	0.0	.		126.0	28.0	.	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.522716	0.00149	.	.	ENSG00000176208	ENST00000321990	T	0.06218	3.33	4.7	-1.39	0.08997	.	7.549810	0.00481	N	0.000125	T	0.04998	0.0134	L	0.39898	1.24	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.32025	-0.9922	10	0.07325	T	0.83	.	2.0379	0.03544	0.2113:0.3553:0.099:0.3344	.	1619	Q96QE3	ATAD5_HUMAN	K	1619	ENSP00000313171:N1619K	ENSP00000313171:N1619K	N	+	3	2	ATAD5	26244854	0.000000	0.05858	0.027000	0.17364	0.126000	0.20510	-1.140000	0.03210	-0.300000	0.08895	-0.326000	0.08463	AAT	.	.	.	none		0.393	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
TANC2	26115	hgsc.bcm.edu	37	17	61466867	61466867	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:61466867C>A	ENST00000424789.2	+	15	2795	c.2791C>A	c.(2791-2793)Ctg>Atg	p.L931M	RP11-269G24.3_ENST00000583552.1_RNA|AC015923.1_ENST00000431604.1_RNA|TANC2_ENST00000389520.4_Missense_Mutation_p.L931M	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	931					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						AGCAGGGTACCTGAGCATTGT	0.537																																					p.L931M		Atlas-SNP	.											.	TANC2	266	.	0			c.C2791A						PASS	.						31.0	31.0	31.0					17																	61466867		2010	4178	6188	SO:0001583	missense	26115	exon15			GGGTACCTGAGCA	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30212	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.2791C>A	chr17.hg19:g.61466867C>A	ENSP00000387593:p.Leu931Met	29.0	0.0	.		57.0	28.0	.	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	hg19	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	C	8.463	0.855695	0.17106	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.68765	-0.35;-0.35	5.17	5.17	0.71159	Ankyrin repeat-containing domain (4);	0.063998	0.64402	D	0.000005	T	0.62998	0.2474	L	0.50333	1.59	0.51767	D	0.999933	B;B;B	0.28128	0.082;0.118;0.201	B;B;B	0.31390	0.036;0.091;0.129	T	0.58989	-0.7538	10	0.14656	T	0.56	.	18.698	0.91610	0.0:1.0:0.0:0.0	.	931;841;931	Q9HCD6-2;D3DU10;Q9HCD6	.;.;TANC2_HUMAN	M	931	ENSP00000374171:L931M;ENSP00000387593:L931M	ENSP00000374171:L931M	L	+	1	2	TANC2	58820599	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.060000	0.57477	2.401000	0.81631	0.555000	0.69702	CTG	.	.	.	none		0.537	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1		
SALL3	27164	hgsc.bcm.edu	37	18	76754972	76754972	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:76754972T>C	ENST00000537592.2	+	2	2981	c.2981T>C	c.(2980-2982)aTc>aCc	p.I994T	SALL3_ENST00000536229.3_Intron|SALL3_ENST00000575389.2_Intron	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	994					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		GCGTTGGAAATCCACTACCGC	0.562																																					p.I994T		Atlas-SNP	.											.	SALL3	162	.	0			c.T2981C						PASS	.						61.0	61.0	61.0					18																	76754972		2203	4300	6503	SO:0001583	missense	27164	exon2			TGGAAATCCACTA	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2981T>C	chr18.hg19:g.76754972T>C	ENSP00000441823:p.Ile994Thr	148.0	0.0	.		86.0	33.0	.	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890593	0.33348	.	.	ENSG00000256463	ENST00000537592	T	0.07114	3.22	5.15	5.15	0.70609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000142	T	0.10809	0.0264	N	0.12637	0.245	0.80722	D	1	P	0.50819	0.939	P	0.53988	0.739	T	0.22695	-1.0209	10	0.56958	D	0.05	-22.1664	14.9958	0.71431	0.0:0.0:0.0:1.0	.	994	Q9BXA9	SALL3_HUMAN	T	994	ENSP00000441823:I994T	ENSP00000299466:I994T	I	+	2	0	SALL3	74855960	1.000000	0.71417	0.961000	0.40146	0.689000	0.40095	4.390000	0.59646	1.943000	0.56356	0.379000	0.24179	ATC	.	.	.	none		0.562	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
DOT1L	84444	hgsc.bcm.edu	37	19	2191111	2191111	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:2191111C>G	ENST00000398665.3	+	5	401	c.365C>G	c.(364-366)cCc>cGc	p.P122R		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	122	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGACCGACCCCGAGAAGCTC	0.602																																					p.P122R		Atlas-SNP	.											.	DOT1L	205	.	0			c.C365G						PASS	.						70.0	80.0	77.0					19																	2191111		2112	4210	6322	SO:0001583	missense	84444	exon5			CCGACCCCGAGAA	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.365C>G	chr19.hg19:g.2191111C>G	ENSP00000381657:p.Pro122Arg	122.0	0.0	.		116.0	41.0	.	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.003702	0.93287	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	T;T	0.23754	1.89;1.89	4.75	4.75	0.60458	.	0.053872	0.85682	D	0.000000	T	0.58552	0.2130	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.68800	-0.5313	10	0.87932	D	0	-14.6108	16.8009	0.85614	0.0:1.0:0.0:0.0	.	122	Q8TEK3-2	.	R	122;122;98	ENSP00000381657:P122R;ENSP00000404284:P98R	ENSP00000221482:P122R	P	+	2	0	DOT1L	2142111	1.000000	0.71417	0.943000	0.38184	0.962000	0.63368	7.246000	0.78247	2.193000	0.70182	0.555000	0.69702	CCC	.	.	.	none		0.602	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
CASP14	23581	hgsc.bcm.edu	37	19	15164633	15164633	+	Silent	SNP	C	C	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:15164633C>T	ENST00000427043.3	+	4	575	c.267C>T	c.(265-267)caC>caT	p.H89H	CASP14_ENST00000221740.1_Silent_p.H89H|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	89					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						TCATGGCTCACGGGAGGGAAG	0.552																																					p.H89H		Atlas-SNP	.											.	CASP14	44	.	0			c.C267T						PASS	.						95.0	83.0	87.0					19																	15164633		2203	4300	6503	SO:0001819	synonymous_variant	23581	exon4			GGCTCACGGGAGG		CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"""apoptosis-related cysteine protease"""	605848	"""caspase 14, apoptosis-related cysteine protease"""			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.267C>T	chr19.hg19:g.15164633C>T		281.0	0.0	.		244.0	35.0	.	NM_012114	O95823|Q3SYC9	Silent	SNP	ENST00000427043.3	hg19	CCDS12323.1																																																																																			.	.	.	none		0.552	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114	
NWD1	284434	hgsc.bcm.edu	37	19	16918705	16918705	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:16918705G>A	ENST00000552788.1	+	16	4045	c.4045G>A	c.(4045-4047)Gag>Aag	p.E1349K	NWD1_ENST00000549814.1_Missense_Mutation_p.E1307K|NWD1_ENST00000523826.1_Missense_Mutation_p.E1143K|NWD1_ENST00000379808.3_Missense_Mutation_p.E1349K|NWD1_ENST00000524140.2_Missense_Mutation_p.E1349K|NWD1_ENST00000339803.6_Missense_Mutation_p.E1214K			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1349							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TCAGCTGCCCGAGACCCTCTC	0.567																																					p.E1349K		Atlas-SNP	.											.	NWD1	303	.	0			c.G4045A						PASS	.						152.0	131.0	138.0					19																	16918705		2203	4300	6503	SO:0001583	missense	284434	exon18			CTGCCCGAGACCC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.4045G>A	chr19.hg19:g.16918705G>A	ENSP00000447224:p.Glu1349Lys	475.0	0.0	.		404.0	153.0	.	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.61	1.989439	0.35131	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.57907	0.45;0.44;0.45;0.37;0.43;0.44	4.95	3.91	0.45181	WD40 repeat-like-containing domain (1);	0.427481	0.20913	N	0.083440	T	0.24509	0.0594	L	0.27053	0.805	0.09310	N	1	P;B;B	0.45078	0.85;0.145;0.089	B;B;B	0.25140	0.058;0.039;0.017	T	0.14952	-1.0454	10	0.09843	T	0.71	-19.7004	6.6582	0.22998	0.1992:0.0:0.8008:0.0	.	1349;1349;1214	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	K	1214;1349;1307;1349;1143;1349;1214	ENSP00000428579:E1349K;ENSP00000447548:E1307K;ENSP00000369136:E1349K;ENSP00000428955:E1143K;ENSP00000447224:E1349K;ENSP00000340159:E1214K	ENSP00000340159:E1214K	E	+	1	0	NWD1	16779705	0.274000	0.24191	0.991000	0.47740	0.505000	0.33919	1.839000	0.39220	2.282000	0.76494	0.655000	0.94253	GAG	.	.	.	none		0.567	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
ZNF285	26974	hgsc.bcm.edu	37	19	44896570	44896570	+	Missense_Mutation	SNP	C	C	G	rs144077949	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:44896570C>G	ENST00000330997.4	-	3	140	c.76G>C	c.(76-78)Gat>Cat	p.D26H	ZNF285_ENST00000591679.1_Missense_Mutation_p.D33H|CTC-512J12.4_ENST00000588655.1_RNA|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.D26H	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	26	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TGGGCTTTATCCAATAGTGCC	0.453																																					p.D26H		Atlas-SNP	.											.	ZNF285	86	.	0			c.G76C						PASS	.						149.0	132.0	138.0					19																	44896570		2203	4300	6503	SO:0001583	missense	26974	exon3			CTTTATCCAATAG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.76G>C	chr19.hg19:g.44896570C>G	ENSP00000333595:p.Asp26His	67.0	0.0	.		74.0	33.0	.	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	hg19	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405340	0.62288	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T;T	0.06142	3.34;4.17	3.07	1.89	0.25635	Krueppel-associated box (4);	.	.	.	.	T	0.23054	0.0557	M	0.88310	2.945	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	T	0.09640	-1.0665	9	0.87932	D	0	.	3.2985	0.06974	0.2577:0.5999:0.0:0.1424	.	50;26	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	H	49;26	ENSP00000439431:D49H;ENSP00000333595:D26H	ENSP00000333595:D26H	D	-	1	0	ZNF285	49588410	0.829000	0.29322	0.154000	0.22540	0.897000	0.52465	1.205000	0.32308	1.738000	0.51689	0.449000	0.29647	GAT	.	C|0.997;T|0.003	.	alt		0.453	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
ZNF665	79788	hgsc.bcm.edu	37	19	53669370	53669370	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:53669370C>G	ENST00000600412.1	-	2	293	c.178G>C	c.(178-180)Gct>Cct	p.A60P	ZNF665_ENST00000396424.3_Missense_Mutation_p.A125P|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	60					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCACGTTGAGCTCTTCTACCA	0.388																																					p.A125P		Atlas-SNP	.											.	ZNF665	136	.	0			c.G373C						PASS	.						118.0	124.0	122.0					19																	53669370		2073	4226	6299	SO:0001583	missense	79788	exon4			GTTGAGCTCTTCT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.178G>C	chr19.hg19:g.53669370C>G	ENSP00000469154:p.Ala60Pro	271.0	0.0	.		196.0	64.0	.	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.108	0.575466	0.13623	.	.	ENSG00000197497	ENST00000396424	T	0.08370	3.1	2.4	-0.298	0.12814	.	.	.	.	.	T	0.04588	0.0125	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44267	-0.9339	9	0.24483	T	0.36	.	6.4255	0.21768	0.1793:0.4658:0.3549:0.0	.	125	Q9H7R5-2	.	P	125	ENSP00000379702:A125P	ENSP00000379702:A125P	A	-	1	0	ZNF665	58361182	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	0.042000	0.13949	0.315000	0.23110	0.543000	0.68304	GCT	.	.	.	none		0.388	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
HELZ2	85441	hgsc.bcm.edu	37	20	62193087	62193087	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr20:62193087T>C	ENST00000467148.1	-	12	6772	c.6703A>G	c.(6703-6705)Aga>Gga	p.R2235G	HELZ2_ENST00000427522.2_Missense_Mutation_p.R1666G	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2235	Interaction with THRAP3.				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)										TCCATCCTTCTCAGGAGCAGT	0.667																																					p.R2235G		Atlas-SNP	.											.	.	.	.	0			c.A6703G						PASS	.						28.0	28.0	28.0					20																	62193087		2195	4295	6490	SO:0001583	missense	85441	exon13			TCCTTCTCAGGAG	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.6703A>G	chr20.hg19:g.62193087T>C	ENSP00000417401:p.Arg2235Gly	88.0	0.0	.		63.0	23.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	T	8.870	0.949007	0.18356	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.81821	-1.54;-1.54	2.96	1.78	0.24846	ATPase, AAA+ type, core (1);	1.202560	0.05584	N	0.573417	T	0.76772	0.4034	L	0.41124	1.26	0.29383	N	0.863141	B;B	0.29270	0.24;0.122	B;B	0.39027	0.288;0.19	T	0.68161	-0.5482	10	0.66056	D	0.02	-9.3242	4.3793	0.11286	0.0:0.1118:0.2045:0.6837	.	2235;1666	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	G	1666;2235	ENSP00000393257:R1666G;ENSP00000417401:R2235G	ENSP00000393257:R1666G	R	-	1	2	RP4-697K14.7	61663531	0.466000	0.25823	0.958000	0.39756	0.288000	0.27193	0.564000	0.23563	0.497000	0.27926	0.402000	0.26972	AGA	.	.	.	none		0.667	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
LSS	4047	hgsc.bcm.edu	37	21	47626684	47626684	+	Splice_Site	SNP	T	T	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr21:47626684T>G	ENST00000397728.3	-	16	1546		c.e16-2		LSS_ENST00000522411.1_Splice_Site|LSS_ENST00000356396.4_Splice_Site|LSS_ENST00000457828.2_Splice_Site	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)						cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					GTTCAGCAGCTGAAATCACAG	0.582																																					.	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.1468-2A>C						PASS	.						71.0	60.0	64.0					21																	47626684		2203	4300	6503	SO:0001630	splice_region_variant	4047	exon17			AGCAGCTGAAATC	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1468-2A>C	chr21.hg19:g.47626684T>G		175.0	0.0	.		154.0	59.0	.	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Splice_Site	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674567	0.47781	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4665	0.75406	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LSS	46451112	1.000000	0.71417	0.974000	0.42286	0.221000	0.24807	7.752000	0.85141	2.206000	0.71126	0.533000	0.62120	.	.	.	.	none		0.582	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		Intron
LONRF3	79836	hgsc.bcm.edu	37	X	118109101	118109101	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chrX:118109101G>T	ENST00000371628.3	+	1	389	c.358G>T	c.(358-360)Gcg>Tcg	p.A120S	LONRF3_ENST00000422289.2_5'Flank|LONRF3_ENST00000304778.7_Missense_Mutation_p.A120S	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	120							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GCAAGGCGAGGCGCTGGCGCC	0.731																																					p.A120S		Atlas-SNP	.											.	LONRF3	138	.	0			c.G358T						PASS	.						2.0	3.0	3.0					X																	118109101		1637	3395	5032	SO:0001583	missense	79836	exon1			GGCGAGGCGCTGG	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.358G>T	chrX.hg19:g.118109101G>T	ENSP00000360690:p.Ala120Ser	7.0	0.0	.		8.0	7.0	.	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	hg19	CCDS35374.1	.	.	.	.	.	.	.	.	.	.	G	3.593	-0.083174	0.07141	.	.	ENSG00000175556	ENST00000365713;ENST00000304778;ENST00000371628	T;T;T	0.80738	-1.41;-1.41;-1.17	4.27	3.38	0.38709	.	1.631660	0.03606	N	0.234137	T	0.65544	0.2701	N	0.08118	0	0.80722	D	1	B;B	0.23249	0.082;0.062	B;B	0.24394	0.053;0.024	T	0.41052	-0.9530	10	0.09590	T	0.72	-3.3969	10.5187	0.44905	0.0:0.1987:0.8013:0.0	.	120;120	Q496Y0-2;Q496Y0	.;LONF3_HUMAN	S	120	ENSP00000360691:A120S;ENSP00000307732:A120S;ENSP00000360690:A120S	ENSP00000307732:A120S	A	+	1	0	LONRF3	117993129	0.999000	0.42202	0.063000	0.19743	0.011000	0.07611	1.162000	0.31786	0.786000	0.33708	0.529000	0.55759	GCG	.	.	.	none		0.731	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
A2ML1	144568	hgsc.bcm.edu	37	12	9006738	9006738	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:9006738delA	ENST00000299698.7	+	21	2785	c.2605delA	c.(2605-2607)actfs	p.T869fs	A2ML1_ENST00000539547.1_Frame_Shift_Del_p.T378fs	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CATTAACTTTACTATTAGTAC	0.468																																					p.F868fs		Atlas-INDEL	.											.	A2ML1	199	.	0			c.2604delT						PASS	.						55.0	56.0	56.0					12																	9006738		1864	4095	5959	SO:0001589	frameshift_variant	144568	exon21			.	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.2605delA	chr12.hg19:g.9006738delA	ENSP00000299698:p.Thr869fs	75.0	0.0	0		134.0	72.0	0.537313	NM_144670		Frame_Shift_Del	DEL	ENST00000299698.7	hg19	CCDS8596.2																																																																																			.	.	.	none		0.468	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
PTPRM	5797	hgsc.bcm.edu	37	18	7567846	7567846	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:7567846delT	ENST00000332175.8	+	1	1067	c.30delT	c.(28-30)actfs	p.T10fs	PTPRM_ENST00000580170.1_Frame_Shift_Del_p.T10fs|PTPRM_ENST00000400060.4_Frame_Shift_Del_p.T10fs	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	10					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GCCTGGCGACTTTGGCCGGAC	0.766																																					p.T10fs		Atlas-INDEL	.											.	PTPRM	185	.	0			c.29delC						PASS	.						56.0	56.0	56.0					18																	7567846		2203	4300	6503	SO:0001589	frameshift_variant	5797	exon1			.	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.30delT	chr18.hg19:g.7567846delT	ENSP00000331418:p.Thr10fs	172.0	0.0	0		129.0	46.0	0.356589	NM_001105244	A7MBN1|D3DUH8|J3QL11	Frame_Shift_Del	DEL	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.	.	none		0.766	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
TOP3B	8940	hgsc.bcm.edu	37	22	22319734	22319735	+	In_Frame_Ins	INS	-	-	TTG			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr22:22319734_22319735insTTG	ENST00000398793.2	-	9	1299_1300	c.865_866insCAA	c.(865-867)agc>aCAAgc	p.288_289insT	TOP3B_ENST00000413067.2_In_Frame_Ins_p.17_18insT|TOP3B_ENST00000357179.5_In_Frame_Ins_p.288_289insT	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	288					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		TTCTTTCCTGCTTGTGGCCTCC	0.535																																					p.S289delinsTS		Atlas-INDEL	.											.	TOP3B	107	.	0			c.866_867insCAA						PASS	.																																			SO:0001652	inframe_insertion	8940	exon9			.	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.863_865dupCAA	chr22.hg19:g.22319735_22319737dupTTG	ENSP00000381773:p.Thr288_Thr288dup	68.0	0.0	0		55.0	14.0	0.254545	NM_003935	A0M8Q3|Q9BUP5	In_Frame_Ins	INS	ENST00000398793.2	hg19	CCDS13797.1																																																																																			.	.	.	none		0.535	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
XRCC5	7520	hgsc.bcm.edu	37	2	216981563	216981564	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:216981563_216981564insC	ENST00000392133.3	+	5	778_779	c.317_318insC	c.(316-321)gacttcfs	p.F107fs	XRCC5_ENST00000392132.2_Frame_Shift_Ins_p.F107fs			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	107					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		CAACAGGCTGACTGTATCCTTT	0.421								Non-homologous end-joining																													p.D106fs		Atlas-INDEL	.											.	XRCC5	64	.	0			c.317_318insC						PASS	.																																			SO:0001589	frameshift_variant	7520	exon3			.	AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"""Ku autoantigen, 80kDa"""	194364	"""X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"""			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.318dupC	chr2.hg19:g.216981564_216981564dupC	ENSP00000375978:p.Phe107fs	96.0	0.0	0		75.0	24.0	0.32	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Frame_Shift_Ins	INS	ENST00000392133.3	hg19	CCDS2402.1																																																																																			.	.	.	none		0.421	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735217	140735218	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:140735217_140735218insG	ENST00000571252.1	+	1	450_451	c.450_451insG	c.(451-453)agafs	p.R151fs	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	151	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCTGGGGCAAGATTTCCTCT	0.45																																					p.A150fs		Atlas-INDEL	.											.	PCDHGA4	150	.	0			c.450_451insG						PASS	.																																			SO:0001589	frameshift_variant	56111	exon1			.	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		Exception_encountered	chr5.hg19:g.140735217_140735218insG	ENSP00000458570:p.Arg151fs	110.0	0.0	0		77.0	22.0	0.285714	NM_032053	Q9Y5D3	Frame_Shift_Ins	INS	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.	.	none		0.450	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
GTF3C2	2976	hgsc.bcm.edu	37	2	27565919	27565920	+	Frame_Shift_Ins	INS	-	-	TGGCCTTT			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565919_27565920insTGGCCTTT	ENST00000359541.2	-	3	771_772	c.342_343insAAAGGCCA	c.(340-345)ccccaafs	p.Q115fs	GTF3C2_ENST00000264720.3_Frame_Shift_Ins_p.Q115fs|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000589853.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	115					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTAGGCTGTTGGGGCCTTTTGG	0.535																																					p.P115fs		Atlas-INDEL	.											GTF3C2,NS,malignant_melanoma,0,1	GTF3C2	73	.	0			c.343_344insAAAGGCCA						PASS	.																																			SO:0001589	frameshift_variant	2976	exon3			.	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.342_343insAAAGGCCA	chr2.hg19:g.27565919_27565920insTGGCCTTT	ENSP00000352536:p.Gln115fs	332.0	0.0	0		225.0	28.0	0.124444	NM_001035521	D6W557|Q16632|Q9BWI7	Frame_Shift_Ins	INS	ENST00000359541.2	hg19	CCDS1749.1																																																																																			.	.	.	none		0.535	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		
COL5A1	1289	hgsc.bcm.edu	37	9	137593045	137593045	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr9:137593045delA	ENST00000371817.3	+	4	934	c.520delA	c.(520-522)aagfs	p.K175fs	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	175	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CAGCGTCCACAAGAAAAATGT	0.478																																					p.H173fs		Atlas-INDEL	.											.	COL5A1	323	.	0			c.519delC						PASS	.						132.0	100.0	111.0					9																	137593045		2203	4298	6501	SO:0001589	frameshift_variant	1289	exon4			.	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.520delA	chr9.hg19:g.137593045delA	ENSP00000360882:p.Lys175fs	89.0	0.0	0		78.0	28.0	0.358974	NM_000093	Q15094|Q5SUX4	Frame_Shift_Del	DEL	ENST00000371817.3	hg19	CCDS6982.1																																																																																			.	.	.	none		0.478	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
HECA	51696	hgsc.bcm.edu	37	6	139495590	139495590	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr6:139495590delA	ENST00000367658.2	+	3	1666	c.1381delA	c.(1381-1383)aagfs	p.K461fs	RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000585447.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000590219.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	461					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		CATCTGCATCAAGTGTAAGTC	0.547																																					p.I460fs		Atlas-INDEL	.											.	HECA	45	.	0			c.1380delC						PASS	.						234.0	198.0	210.0					6																	139495590		2203	4300	6503	SO:0001589	frameshift_variant	51696	exon3			.	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.1381delA	chr6.hg19:g.139495590delA	ENSP00000356630:p.Lys461fs	156.0	0.0	0		180.0	59.0	0.327778	NM_016217		Frame_Shift_Del	DEL	ENST00000367658.2	hg19	CCDS5194.1																																																																																			.	.	.	none		0.547	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523507	42523516	+	Frame_Shift_Del	DEL	AGGGGGACGA	AGGGGGACGA	-	rs149686350|rs61745683	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	AGGGGGACGA	AGGGGGACGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr22:42523507_42523516delAGGGGGACGA	ENST00000360608.5	-	7	1220_1229	c.1106_1115delTCGTCCCCCT	c.(1105-1116)atcgtccccctgfs	p.IVPL369fs	CYP2D6_ENST00000389970.3_Frame_Shift_Del_p.IVPL369fs|CYP2D6_ENST00000359033.4_Frame_Shift_Del_p.IVPL318fs|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	369			I -> T (in allele CYP2D6*26).		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)	p.I318I(1)|p.I369I(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGTCACACCCAGGGGGACGATGTCCCCAAA	0.624																																					p.369_372del		Atlas-INDEL	.											.	CYP2D6	104	.	2	Substitution - coding silent(2)	urinary_tract(2)	c.1107_1116del						PASS	.																																			SO:0001589	frameshift_variant	1565	exon7			.	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1106_1115delTCGTCCCCCT	chr22.hg19:g.42523507_42523516delAGGGGGACGA	ENSP00000353820:p.Ile369fs	205.0	0.0	0		147.0	14.0	0.0952381	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Frame_Shift_Del	DEL	ENST00000360608.5	hg19	CCDS46721.1																																																																																			.	.	.	none		0.624	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
GTF3C2	2976	hgsc.bcm.edu	37	2	27565929	27565930	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565929_27565930delGG	ENST00000359541.2	-	3	761_762	c.332_333delCC	c.(331-333)cccfs	p.P111fs	GTF3C2_ENST00000264720.3_Frame_Shift_Del_p.P111fs|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000589853.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	111					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGGCCTTTTGGGGCCTTTTCG	0.525																																					p.111_112del		Atlas-INDEL	.											GTF3C2,NS,carcinoma,0,1	GTF3C2	73	.	0			c.333_334del						PASS	.																																			SO:0001589	frameshift_variant	2976	exon3			.	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.332_333delCC	chr2.hg19:g.27565931_27565932delGG	ENSP00000352536:p.Pro111fs	316.0	0.0	0		232.0	15.0	0.0646552	NM_001035521	D6W557|Q16632|Q9BWI7	Frame_Shift_Del	DEL	ENST00000359541.2	hg19	CCDS1749.1																																																																																			.	.	.	none		0.525	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		
ZMYM6	9204	hgsc.bcm.edu	37	1	35457962	35457962	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:35457962delT	ENST00000357182.4	-	15	2246	c.2019delA	c.(2017-2019)aaafs	p.K673fs	ZMYM6_ENST00000487874.1_Frame_Shift_Del_p.K673fs|ZMYM6_ENST00000373340.2_Frame_Shift_Del_p.K673fs|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	673					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				AAGATGGAAATTTCATAGCAT	0.383																																					p.F674fs		Atlas-INDEL	.											.	ZMYM6	110	.	0			c.2020delT						PASS	.						150.0	142.0	145.0					1																	35457962		2203	4300	6503	SO:0001589	frameshift_variant	9204	exon15			.	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.2019delA	chr1.hg19:g.35457962delT	ENSP00000349708:p.Lys673fs	196.0	0.0	0		165.0	54.0	0.327273	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Frame_Shift_Del	DEL	ENST00000357182.4	hg19	CCDS387.2																																																																																			.	.	.	none		0.383	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	
