#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
DRAXIN	374946	hgsc.bcm.edu	37	1	11771928	11771928	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:11771928C>A	ENST00000294485.5	+	4	798	c.663C>A	c.(661-663)gaC>gaA	p.D221E		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		CCAGGTCTGACGGGGAGGTGA	0.547																																					p.D221E		Atlas-SNP	.											.	.	.	.	0			c.C663A						.						67.0	49.0	55.0					1																	11771928		2203	4300	6503	SO:0001583	missense	374946	exon4			GTCTGACGGGGAG	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"""dorsal repulsive axon guidance protein"", ""neural tissue-specific cysteine-rich protein"""	612682	"""chromosome 1 open reading frame 187"""	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.663C>A	chr1.hg19:g.11771928C>A	ENSP00000294485:p.Asp221Glu	109.0	0.0		126.0	19.0	NM_198545		Missense_Mutation	SNP	ENST00000294485.5	hg19	CCDS135.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.798461	0.31777	.	.	ENSG00000162490	ENST00000294485	T	0.44881	0.91	5.7	-9.64	0.00541	.	0.259259	0.38436	N	0.001683	T	0.26011	0.0634	M	0.67953	2.075	0.28339	N	0.921429	P	0.40970	0.734	B	0.34779	0.189	T	0.12578	-1.0542	10	0.23891	T	0.37	-20.7068	8.5413	0.33395	0.0779:0.2014:0.0775:0.6432	.	221	Q8NBI3	DRAXI_HUMAN	E	221	ENSP00000294485:D221E	ENSP00000294485:D221E	D	+	3	2	C1orf187	11694515	0.000000	0.05858	0.095000	0.20976	0.643000	0.38383	-3.031000	0.00637	-2.447000	0.00545	-2.939000	0.00087	GAC	.	.		0.547	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545	
FHAD1	114827	hgsc.bcm.edu	37	1	15639652	15639652	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:15639652A>G	ENST00000375998.4	+	7	1139	c.1139A>G	c.(1138-1140)aAg>aGg	p.K380R	FHAD1_ENST00000417793.1_Missense_Mutation_p.K380R|FHAD1_ENST00000358897.4_Missense_Mutation_p.K380R|FHAD1_ENST00000375995.3_Missense_Mutation_p.K86R|FHAD1_ENST00000401090.2_Missense_Mutation_p.K86R|FHAD1_ENST00000375999.3_Missense_Mutation_p.K380R			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	380										skin(1)|stomach(1)	2						AACAAGGACAAGGACCACCAG	0.458																																					p.K380R		Atlas-SNP	.											.	FHAD1	78	.	0			c.A1139G						.						116.0	102.0	106.0					1																	15639652		692	1591	2283	SO:0001583	missense	114827	exon8			AGGACAAGGACCA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.1139A>G	chr1.hg19:g.15639652A>G	ENSP00000365166:p.Lys380Arg	344.0	0.0		396.0	56.0	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.96	2.392620	0.42410	.	.	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998;ENST00000375995;ENST00000401090	T;T;T;T;D;D	0.84370	0.75;0.74;0.72;0.75;-1.79;-1.84	4.98	4.98	0.66077	.	0.097484	0.39615	N	0.001310	D	0.88621	0.6486	L	0.58669	1.825	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.991;0.996	D	0.85212	0.1021	10	0.11794	T	0.64	-38.8874	11.3994	0.49862	1.0:0.0:0.0:0.0	.	380;107	B1AJZ9;B1AJZ8	FHAD1_HUMAN;.	R	380;380;380;380;86;86	ENSP00000351770:K380R;ENSP00000407615:K380R;ENSP00000365167:K380R;ENSP00000365166:K380R;ENSP00000365163:K86R;ENSP00000383868:K86R	ENSP00000351770:K380R	K	+	2	0	FHAD1	15512239	1.000000	0.71417	0.117000	0.21633	0.342000	0.28953	4.442000	0.59988	2.006000	0.58801	0.455000	0.32223	AAG	.	.		0.458	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
GDAP2	54834	hgsc.bcm.edu	37	1	118455267	118455268	+	Missense_Mutation	DNP	TG	TG	AT			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:118455267_118455268TG>AT	ENST00000369443.5	-	4	603_604	c.354_355CA>AT	c.(352-357)ttCAat>ttATat	p.118_119FN>LY	GDAP2_ENST00000369442.3_Missense_Mutation_p.118_119FN>LY	NM_017686.3	NP_060156.1	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated protein 2	118	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				response to retinoic acid (GO:0032526)	lysosomal membrane (GO:0005765)				kidney(2)|large_intestine(3)|lung(9)|ovary(2)	16		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		GCAGCTAGATTGAATCCTTTTG	0.416																																					p.N119Y|p.F118L		Atlas-SNP	.											.	GDAP2	37	.	0			c.A355T|c.C354A						.																																			SO:0001583	missense	54834	exon4			CTAGATTGAATCC|TAGATTGAATCCT	AK000149	CCDS897.1, CCDS44201.1	1q11	2011-10-20			ENSG00000196505	ENSG00000196505			18010	protein-coding gene	gene with protein product						1021725	Standard	NM_017686		Approved	FLJ20142, dJ776P7.1, MACROD3	uc001ehf.3	Q9NXN4	OTTHUMG00000012199	ENST00000369443.5:c.354_355delinsAT	chr1.hg19:g.118455267_118455268delinsAT	ENSP00000358451:p.F118_N119delinsLY	97.0|95.0	0.0		129.0|130.0	63.0	NM_017686	Q96DZ0	Missense_Mutation	SNP	ENST00000369443.5	hg19	CCDS897.1																																																																																			.	.		0.416	GDAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033732.2	NM_017686	
OR6N2	81442	hgsc.bcm.edu	37	1	158747387	158747387	+	Silent	SNP	C	C	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:158747387C>A	ENST00000339258.1	-	1	38	c.39G>T	c.(37-39)gtG>gtT	p.V13V		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					AGCCAAGGAACACAAATTCAG	0.463																																					p.V13V		Atlas-SNP	.											.	OR6N2	78	.	0			c.G39T						.						63.0	66.0	65.0					1																	158747387		2203	4300	6503	SO:0001819	synonymous_variant	81442	exon1			AAGGAACACAAAT	BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"""GPCR / Class A : Olfactory receptors"""	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.39G>T	chr1.hg19:g.158747387C>A		292.0	0.0		468.0	134.0	NM_001005278	Q6IFR2	Silent	SNP	ENST00000339258.1	hg19	CCDS30906.1																																																																																			.	.		0.463	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1		
ATP2B4	493	hgsc.bcm.edu	37	1	203702358	203702358	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:203702358T>C	ENST00000341360.2	+	20	3714	c.3317T>C	c.(3316-3318)gTa>gCa	p.V1106A	ATP2B4_ENST00000357681.5_Intron|ATP2B4_ENST00000391954.2_Missense_Mutation_p.V1070A|ATP2B4_ENST00000367218.3_Missense_Mutation_p.V1106A|ATP2B4_ENST00000367219.3_Missense_Mutation_p.V1094A			P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	1106	Calmodulin-binding subdomain B. {ECO:0000250}.				blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CAGATCGACGTAATTAACACA	0.473																																					p.V1106A		Atlas-SNP	.											.	ATP2B4	226	.	0			c.T3317C						.						110.0	107.0	108.0					1																	203702358		2203	4300	6503	SO:0001583	missense	493	exon21			TCGACGTAATTAA	M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"""ATPases / P-type"""	817	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 4"""	108732	"""matrix-remodelling associated 1"""	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000341360.2:c.3317T>C	chr1.hg19:g.203702358T>C	ENSP00000340930:p.Val1106Ala	70.0	0.0		140.0	23.0	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Missense_Mutation	SNP	ENST00000341360.2	hg19	CCDS30977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.689658|4.689658	0.88735|0.88735	.|.	.|.	ENSG00000058668|ENSG00000058668	ENST00000367218;ENST00000367219;ENST00000391954;ENST00000341360|ENST00000356729	D;D;D;D|.	0.92911|.	-3.13;-3.13;-3.13;-3.13|.	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	0.212421|.	0.23742|.	N|.	0.045009|.	T|.	0.70544|.	0.3236|.	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.997;0.985|.	D;D|.	0.79108|.	0.992;0.981|.	T|.	0.70139|.	-0.4954|.	10|.	0.87932|.	D|.	0|.	.|.	14.5464|14.5464	0.68032|0.68032	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1106;1106|.	P23634;B1APW5|.	AT2B4_HUMAN;.|.	A|Q	1106;1094;1070;1106|71	ENSP00000356187:V1106A;ENSP00000356188:V1094A;ENSP00000375816:V1070A;ENSP00000340930:V1106A|.	ENSP00000340930:V1106A|.	V|X	+|+	2|1	0|0	ATP2B4|ATP2B4	201968981|201968981	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.843000|7.843000	0.86859|0.86859	2.108000|2.108000	0.64289|0.64289	0.533000|0.533000	0.62120|0.62120	GTA|TAA	.	.		0.473	ATP2B4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087463.1	NM_001001396	
RCOR3	55758	hgsc.bcm.edu	37	1	211486854	211486854	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:211486854T>A	ENST00000367005.4	+	11	1373	c.1232T>A	c.(1231-1233)cTg>cAg	p.L411Q	RCOR3_ENST00000526255.1_3'UTR|RCOR3_ENST00000367006.4_Silent_p.S388S|RCOR3_ENST00000419091.2_Missense_Mutation_p.L469Q	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	411	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		ATTGCCACTCTGAACCAGCCT	0.627																																					p.L469Q		Atlas-SNP	.											.	RCOR3	51	.	0			c.T1406A						.						143.0	108.0	120.0					1																	211486854		2203	4300	6503	SO:0001583	missense	55758	exon12			CCACTCTGAACCA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.1232T>A	chr1.hg19:g.211486854T>A	ENSP00000355972:p.Leu411Gln	97.0	0.0		203.0	68.0	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.472798	0.26423	.	.	ENSG00000117625	ENST00000419091;ENST00000367005;ENST00000529763	T;T	0.31510	1.49;1.53	5.07	5.07	0.68467	.	0.380245	0.23893	N	0.043536	T	0.40119	0.1104	.	.	.	0.30833	N	0.736454	D;P	0.58620	0.983;0.79	P;B	0.58331	0.837;0.202	T	0.28073	-1.0055	9	0.13470	T	0.59	-7.4012	14.8169	0.70041	0.0:0.0:0.0:1.0	.	469;411	Q9P2K3-3;Q9P2K3	.;RCOR3_HUMAN	Q	469;411;187	ENSP00000413929:L469Q;ENSP00000355972:L411Q	ENSP00000355972:L411Q	L	+	2	0	RCOR3	209553477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.712000	0.74681	1.910000	0.55303	0.528000	0.53228	CTG	.	.		0.627	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254	
ZBTB18	10472	hgsc.bcm.edu	37	1	244218375	244218375	+	Silent	SNP	C	C	A	rs375286592		TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr1:244218375C>A	ENST00000358704.4	+	2	1448	c.1299C>A	c.(1297-1299)acC>acA	p.T433T		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	424					cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCATGTACACCCTCAAGCGCC	0.632																																					p.T433T		Atlas-SNP	.											.	.	.	.	0			c.C1299A						.	C	,	0,4406		0,0,2203	71.0	73.0	72.0		1272,1299	-1.3	1.0	1		72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ZNF238	NM_006352.3,NM_205768.2	,	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	,	424/523,433/532	244218375	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10472	exon2			GTACACCCTCAAG	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1299C>A	chr1.hg19:g.244218375C>A		205.0	0.0		528.0	246.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Silent	SNP	ENST00000358704.4	hg19	CCDS1622.1																																																																																			.	.		0.632	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768	
CLHC1	130162	hgsc.bcm.edu	37	2	55402927	55402927	+	Nonstop_Mutation	SNP	T	T	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:55402927T>C	ENST00000401408.1	-	13	2105	c.1760A>G	c.(1759-1761)tAg>tGg	p.*587W	CLHC1_ENST00000494539.1_5'UTR|CLHC1_ENST00000406076.1_Nonstop_Mutation_p.*465W|CLHC1_ENST00000407122.1_Nonstop_Mutation_p.*587W|CLHC1_ENST00000406437.2_Nonstop_Mutation_p.*138W	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	0																	GATATAGAACTACCAAAACAC	0.368																																					p.X587W		Atlas-SNP	.											.	.	.	.	0			c.A1760G						.						100.0	91.0	94.0					2																	55402927		2203	4300	6503	SO:0001578	stop_lost	130162	exon13			TAGAACTACCAAA		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.1760A>G	chr2.hg19:g.55402927T>C	ENSP00000384869:p.*587Serext*7	105.0	0.0		136.0	58.0	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	hg19	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.848614	0.71603	.	.	ENSG00000162994	ENST00000406437;ENST00000407122;ENST00000401408;ENST00000406076	.	.	.	5.8	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2414	0.43314	0.1477:0.0:0.0:0.8523	.	.	.	.	W	138;587;587;465	.	.	X	-	2	0	C2orf63	55256431	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.888000	0.63164	1.010000	0.39314	0.528000	0.53228	TAG	.	.		0.368	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
ALMS1	7840	hgsc.bcm.edu	37	2	73681090	73681090	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:73681090T>A	ENST00000264448.6	+	8	7544	c.7433T>A	c.(7432-7434)cTg>cAg	p.L2478Q	ALMS1_ENST00000377715.1_Missense_Mutation_p.L2478Q|ALMS1_ENST00000409009.1_Missense_Mutation_p.L2436Q|ALMS1-IT1_ENST00000441587.2_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2478					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GTAGATTCACTGGCTGCACAT	0.453																																					p.L2478Q		Atlas-SNP	.											.	ALMS1	384	.	0			c.T7433A						.						116.0	115.0	115.0					2																	73681090		1949	4140	6089	SO:0001583	missense	7840	exon8			ATTCACTGGCTGC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7433T>A	chr2.hg19:g.73681090T>A	ENSP00000264448:p.Leu2478Gln	125.0	0.0		195.0	10.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	T	18.50	3.638306	0.67130	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.35605	2.22;2.22;1.3	5.9	5.9	0.94986	.	0.000000	0.39146	N	0.001453	T	0.52725	0.1752	L	0.48642	1.525	0.41976	D	0.990779	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.55515	-0.8129	10	0.87932	D	0	.	12.7235	0.57156	0.0:0.0:0.0:1.0	.	2478;2436;2478	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	Q	2436;2478;2478	ENSP00000386627:L2436Q;ENSP00000264448:L2478Q;ENSP00000366944:L2478Q	ENSP00000264448:L2478Q	L	+	2	0	ALMS1	73534598	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	4.517000	0.60503	2.264000	0.75181	0.533000	0.62120	CTG	.	.		0.453	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
NFE2L2	4780	hgsc.bcm.edu	37	2	178098809	178098810	+	Missense_Mutation	DNP	TC	TC	AA			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:178098809_178098810TC>AA	ENST00000397062.3	-	2	789_790	c.235_236GA>TT	c.(235-237)GAg>TTg	p.E79L	NFE2L2_ENST00000423513.1_Missense_Mutation_p.E63L|NFE2L2_ENST00000446151.2_Missense_Mutation_p.E63L|NFE2L2_ENST00000464747.1_Missense_Mutation_p.E63L|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E63L	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	79					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E79K(10)|p.E79Q(10)|p.E79G(1)|p.E79_T80insE(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TTCACCTGTCTCTTCATCTAGT	0.441			Mis		"""NSCLC, HNSCC"""					HNSCC(56;0.16)																											p.E79V|p.E79X		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,bladder,carcinoma,-1,3|NFE2L2,bladder,carcinoma,0,21	NFE2L2	225	.	22	Substitution - Missense(21)|Insertion - In frame(1)	lung(13)|oesophagus(5)|upper_aerodigestive_tract(2)|urinary_tract(1)|cervix(1)	c.A236T|c.G235T						.																																			SO:0001583	missense	4780	exon2			CCTGTCTCTTCAT|CTGTCTCTTCATC		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"""basic leucine zipper proteins"""	7782	protein-coding gene	gene with protein product	"""NF-E2-related factor 2"""	600492	"""nuclear factor (erythroid-derived 2)-like 2"""			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.235_236delinsAA	chr2.hg19:g.178098809_178098810delinsAA	ENSP00000380252:p.Glu79Leu	47.0|48.0	0.0		64.0	26.0|27.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1																																																																																			.	.		0.441	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164	
SPEG	10290	hgsc.bcm.edu	37	2	220342149	220342149	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:220342149G>T	ENST00000312358.7	+	20	4843	c.4711G>T	c.(4711-4713)Gag>Tag	p.E1571*	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1571	Ig-like 8.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTGCAAAGCAGAGTTGGCTGT	0.612																																					p.E1571X		Atlas-SNP	.											.	SPEG	272	.	0			c.G4711T						.						32.0	38.0	36.0					2																	220342149		2082	4217	6299	SO:0001587	stop_gained	10290	exon20			AAAGCAGAGTTGG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4711G>T	chr2.hg19:g.220342149G>T	ENSP00000311684:p.Glu1571*	105.0	0.0		120.0	50.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Nonsense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	47	13.211917	0.99727	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	.	.	.	5.35	5.35	0.76521	.	0.457119	0.16376	N	0.217101	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	.	19.0677	0.93119	0.0:0.0:1.0:0.0	.	.	.	.	X	1571	.	ENSP00000265327:E1571X	E	+	1	0	SPEG	220050393	1.000000	0.71417	0.967000	0.41034	0.995000	0.86356	9.613000	0.98350	2.506000	0.84524	0.655000	0.94253	GAG	.	.		0.612	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
DOCK10	55619	hgsc.bcm.edu	37	2	225653873	225653873	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:225653873C>A	ENST00000258390.7	-	48	5393	c.5326G>T	c.(5326-5328)Gga>Tga	p.G1776*	DOCK10_ENST00000409592.3_Nonsense_Mutation_p.G1770*	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1776	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GCTGGCCATCCCATAGAGAAC	0.383																																					p.G1776X		Atlas-SNP	.											.	DOCK10	308	.	0			c.G5326T						.						138.0	117.0	123.0					2																	225653873		1877	4103	5980	SO:0001587	stop_gained	55619	exon48			GCCATCCCATAGA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5326G>T	chr2.hg19:g.225653873C>A	ENSP00000258390:p.Gly1776*	86.0	0.0		110.0	54.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Nonsense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	47	13.299214	0.99733	.	.	ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.2079	0.98282	0.0:1.0:0.0:0.0	.	.	.	.	X	1770;1776;281	.	ENSP00000258390:G1776X	G	-	1	0	DOCK10	225362117	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.476000	0.81055	2.781000	0.95711	0.655000	0.94253	GGA	.	.		0.383	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
LRIG1	26018	hgsc.bcm.edu	37	3	66465346	66465346	+	Silent	SNP	T	T	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr3:66465346T>C	ENST00000273261.3	-	5	1169	c.645A>G	c.(643-645)caA>caG	p.Q215Q	LRIG1_ENST00000383703.3_Silent_p.Q215Q	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	215					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GTACTCACAGTTGTGTCAGCC	0.488																																					p.Q215Q		Atlas-SNP	.											.	LRIG1	138	.	0			c.A645G						.						172.0	158.0	163.0					3																	66465346		2203	4300	6503	SO:0001819	synonymous_variant	26018	exon5			TCACAGTTGTGTC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.645A>G	chr3.hg19:g.66465346T>C		73.0	0.0		114.0	32.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	hg19	CCDS33783.1																																																																																			.	.		0.488	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
ZNF654	55279	hgsc.bcm.edu	37	3	88189316	88189316	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr3:88189316G>A	ENST00000309495.5	+	1	1063	c.856G>A	c.(856-858)Gcc>Acc	p.A286T	CGGBP1_ENST00000462901.1_Intron	NM_018293.2	NP_060763.2	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	286					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(2)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(3)	12		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		GTTCCAGCTTGCCCAGCACAC	0.393																																					p.A286T		Atlas-SNP	.											.	ZNF654	56	.	0			c.G856A						.						117.0	108.0	111.0					3																	88189316		1874	4112	5986	SO:0001583	missense	55279	exon1			CAGCTTGCCCAGC	AF543494	CCDS46874.1	3p11.1	2005-01-10			ENSG00000175105	ENSG00000175105			25612	protein-coding gene	gene with protein product							Standard	NM_018293		Approved	FLJ10997, FLJ21142	uc003dqv.3	Q8IZM8	OTTHUMG00000159097	ENST00000309495.5:c.856G>A	chr3.hg19:g.88189316G>A	ENSP00000312141:p.Ala286Thr	74.0	0.0		70.0	19.0	NM_018293	Q9H791|Q9NV14	Missense_Mutation	SNP	ENST00000309495.5	hg19	CCDS46874.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.871297	0.33069	.	.	ENSG00000175105	ENST00000309495	T	0.36157	1.27	5.87	4.99	0.66335	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.617472	0.17613	N	0.167998	T	0.19127	0.0459	N	0.12831	0.26	0.80722	D	1	B	0.29909	0.261	B	0.20577	0.03	T	0.07347	-1.0777	10	0.10636	T	0.68	.	14.4059	0.67081	0.0715:0.0:0.9285:0.0	.	286	Q8IZM8	ZN654_HUMAN	T	286	ENSP00000312141:A286T	ENSP00000312141:A286T	A	+	1	0	ZNF654	88272006	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.261000	0.43276	2.785000	0.95823	0.655000	0.94253	GCC	.	.		0.393	ZNF654-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353285.2	NM_018293	
DZIP3	9666	hgsc.bcm.edu	37	3	108373044	108373044	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr3:108373044C>T	ENST00000361582.3	+	19	2316	c.2086C>T	c.(2086-2088)Cac>Tac	p.H696Y	DZIP3_ENST00000463306.1_Missense_Mutation_p.H696Y	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	696					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						AGCAAATCCACACTCAGTCAG	0.378																																					p.H696Y		Atlas-SNP	.											.	DZIP3	111	.	0			c.C2086T						.						154.0	136.0	142.0					3																	108373044		2203	4300	6503	SO:0001583	missense	9666	exon19			AATCCACACTCAG	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30938	protein-coding gene	gene with protein product	"""human RNA-binding ubiquitin ligase of 138 kDa"", ""protein phosphatase 1, regulatory subunit 66"""	608672	"""DAZ interacting protein 3, zinc finger"""			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2086C>T	chr3.hg19:g.108373044C>T	ENSP00000355028:p.His696Tyr	143.0	0.0		149.0	43.0	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	hg19	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.566819	0.28003	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	T;T	0.30714	1.52;1.52	4.81	0.747	0.18371	.	1.249520	0.05584	N	0.573414	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23904	-1.0175	10	0.38643	T	0.18	0.0012	3.1826	0.06589	0.1921:0.4828:0.0:0.3251	.	314;696	D3DN61;Q86Y13	.;DZIP3_HUMAN	Y	696	ENSP00000355028:H696Y;ENSP00000419981:H696Y	ENSP00000355028:H696Y	H	+	1	0	DZIP3	109855734	0.000000	0.05858	0.000000	0.03702	0.613000	0.37349	-0.670000	0.05256	-0.052000	0.13311	0.585000	0.79938	CAC	.	.		0.378	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648	
HTT	3064	hgsc.bcm.edu	37	4	3123007	3123007	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr4:3123007C>A	ENST00000355072.5	+	9	1266	c.1121C>A	c.(1120-1122)aCc>aAc	p.T374N		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	374					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AATGTTGTGACCGGAGCCCTG	0.522																																					p.T374N		Atlas-SNP	.											.	HTT	221	.	0			c.C1121A						.						66.0	68.0	67.0					4																	3123007		1965	4170	6135	SO:0001583	missense	3064	exon9			TTGTGACCGGAGC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1121C>A	chr4.hg19:g.3123007C>A	ENSP00000347184:p.Thr374Asn	85.0	0.0		115.0	45.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.905103	0.72868	.	.	ENSG00000197386	ENST00000355072	T	0.64618	-0.11	4.52	4.52	0.55395	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69251	0.3090	L	0.33624	1.015	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.65985	-0.6035	10	0.25106	T	0.35	.	17.2061	0.86918	0.0:1.0:0.0:0.0	.	374	P42858	HD_HUMAN	N	374	ENSP00000347184:T374N	ENSP00000347184:T374N	T	+	2	0	HTT	3092805	1.000000	0.71417	0.965000	0.40720	0.976000	0.68499	7.260000	0.78391	2.233000	0.73108	0.655000	0.94253	ACC	.	.		0.522	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
ZNF827	152485	hgsc.bcm.edu	37	4	146695657	146695657	+	Splice_Site	SNP	C	C	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr4:146695657C>G	ENST00000508784.1	-	11	3088		c.e11+1		ZNF827_ENST00000379448.4_Splice_Site|ZNF827_ENST00000513320.1_Splice_Site			Q17R98	ZN827_HUMAN	zinc finger protein 827						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(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					GGAATGGTCACCTGTGTGCTT	0.562																																					.		Atlas-SNP	.											.	ZNF827	102	.	0			c.2860+1G>C						.						258.0	174.0	202.0					4																	146695657		2203	4300	6503	SO:0001630	splice_region_variant	152485	exon12			TGGTCACCTGTGT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"""Zinc fingers, C2H2-type"""	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2860+1G>C	chr4.hg19:g.146695657C>G		132.0	0.0		148.0	42.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Splice_Site	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.8	4.331918	0.81801	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000511659;ENST00000440280	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2789	0.98501	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF827	146915107	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.412000	0.80091	2.788000	0.95919	0.650000	0.86243	.	.	.		0.562	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835	Intron
CDH9	1007	hgsc.bcm.edu	37	5	26881251	26881251	+	Silent	SNP	T	T	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr5:26881251T>G	ENST00000231021.4	-	12	2536	c.2364A>C	c.(2362-2364)cgA>cgC	p.R788R		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	788					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CCTCTTAGTCTCGGTCACTAT	0.413																																					p.R788R	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A2364C						.						135.0	129.0	131.0					5																	26881251		2203	4300	6503	SO:0001819	synonymous_variant	1007	exon12			TTAGTCTCGGTCA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2364A>C	chr5.hg19:g.26881251T>G		89.0	0.0		152.0	56.0	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	hg19	CCDS3893.1																																																																																			.	.		0.413	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
GZMA	3001	hgsc.bcm.edu	37	5	54401400	54401400	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr5:54401400G>A	ENST00000274306.6	+	2	204	c.169G>A	c.(169-171)Gct>Act	p.A57T		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	57	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				CTGTGCTGGGGCTTTGATTGC	0.388																																					p.A57T		Atlas-SNP	.											.	GZMA	60	.	0			c.G169A						.						104.0	96.0	99.0					5																	54401400		2203	4300	6503	SO:0001583	missense	3001	exon2			GCTGGGGCTTTGA		CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"""CTL tryptase"", ""Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"""	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.169G>A	chr5.hg19:g.54401400G>A	ENSP00000274306:p.Ala57Thr	51.0	0.0		45.0	21.0	NM_006144	A4PHN1|Q6IB36	Missense_Mutation	SNP	ENST00000274306.6	hg19	CCDS3965.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.468773	0.26335	.	.	ENSG00000145649	ENST00000274306	D	0.89196	-2.48	5.07	5.07	0.68467	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.235594	0.41605	D	0.000858	T	0.66557	0.2801	N	0.00859	-1.14	0.40122	D	0.976618	P	0.37158	0.585	B	0.30105	0.111	T	0.73332	-0.4016	10	0.24483	T	0.36	.	12.6488	0.56749	0.0801:0.0:0.9199:0.0	.	57	P12544	GRAA_HUMAN	T	57	ENSP00000274306:A57T	ENSP00000274306:A57T	A	+	1	0	GZMA	54437157	0.628000	0.27138	0.987000	0.45799	0.442000	0.32017	1.022000	0.30052	2.615000	0.88500	0.655000	0.94253	GCT	.	.		0.388	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144	
NR3C1	2908	hgsc.bcm.edu	37	5	142779486	142779486	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr5:142779486G>C	ENST00000343796.2	-	2	1912	c.919C>G	c.(919-921)Cct>Gct	p.P307A	NR3C1_ENST00000231509.3_Missense_Mutation_p.P307A|NR3C1_ENST00000416954.2_Intron|NR3C1_ENST00000415690.2_Missense_Mutation_p.P307A|NR3C1_ENST00000394466.2_Missense_Mutation_p.P307A|NR3C1_ENST00000503201.1_Missense_Mutation_p.P307A|NR3C1_ENST00000504572.1_Missense_Mutation_p.P307A|NR3C1_ENST00000394464.2_Missense_Mutation_p.P307A|NR3C1_ENST00000424646.2_Missense_Mutation_p.P307A	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	307	Modulating.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|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 positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TTTGCTCCAGGAAAGCTTGCC	0.428																																					p.P307A		Atlas-SNP	.											.	NR3C1	124	.	0			c.C919G						.						77.0	80.0	79.0					5																	142779486		2203	4300	6503	SO:0001583	missense	2908	exon2			CTCCAGGAAAGCT	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"""Nuclear hormone receptors"""	7978	protein-coding gene	gene with protein product		138040	"""nuclear receptor subfamily 3, group C, member 1"""	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.919C>G	chr5.hg19:g.142779486G>C	ENSP00000343205:p.Pro307Ala	72.0	0.0		87.0	4.0	NM_001018074	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	hg19	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.402063	0.25291	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000361001;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000503201	T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.65	2.04	0.26737	.	0.290828	0.39544	N	0.001337	T	0.16769	0.0403	N	0.19112	0.55	0.80722	D	1	B;B;B	0.21147	0.052;0.012;0.015	B;B;B	0.23574	0.047;0.014;0.028	T	0.07829	-1.0752	10	0.14252	T	0.57	.	8.8019	0.34914	0.707:0.0:0.293:0.0	.	307;307;307	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	A	307	ENSP00000377977:P307A;ENSP00000343205:P307A;ENSP00000387672:P307A;ENSP00000405282:P307A;ENSP00000422518:P307A;ENSP00000377979:P307A;ENSP00000231509:P307A;ENSP00000427672:P307A	ENSP00000231509:P307A	P	-	1	0	NR3C1	142759679	0.998000	0.40836	1.000000	0.80357	0.878000	0.50629	0.620000	0.24403	0.421000	0.25980	-0.312000	0.09012	CCT	.	.		0.428	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1		
PHIP	55023	hgsc.bcm.edu	37	6	79752610	79752610	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr6:79752610A>T	ENST00000275034.4	-	7	717	c.550T>A	c.(550-552)Tca>Aca	p.S184T		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	184					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TACACAGATGACAAGTGTCCA	0.353																																					p.S184T		Atlas-SNP	.											.	PHIP	177	.	0			c.T550A						.						165.0	159.0	161.0					6																	79752610		2203	4299	6502	SO:0001583	missense	55023	exon7			CAGATGACAAGTG	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.550T>A	chr6.hg19:g.79752610A>T	ENSP00000275034:p.Ser184Thr	70.0	0.0		75.0	4.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.961330	0.92791	.	.	ENSG00000146247	ENST00000275034	T	0.27720	1.65	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000013	T	0.34571	0.0902	L	0.41356	1.27	0.80722	D	1	D;D	0.57257	0.979;0.979	D;D	0.74023	0.982;0.982	T	0.07271	-1.0781	9	.	.	.	-9.4383	14.3835	0.66926	1.0:0.0:0.0:0.0	.	184;184	A7J992;Q8WWQ0	.;PHIP_HUMAN	T	184	ENSP00000275034:S184T	.	S	-	1	0	PHIP	79809329	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	8.880000	0.92407	1.994000	0.58287	0.533000	0.62120	TCA	.	.		0.353	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
ARID1B	57492	hgsc.bcm.edu	37	6	157522055	157522055	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr6:157522055A>G	ENST00000350026.5	+	17	4289	c.4288A>G	c.(4288-4290)Atc>Gtc	p.I1430V	ARID1B_ENST00000275248.4_Missense_Mutation_p.I1425V|ARID1B_ENST00000367148.1_Missense_Mutation_p.I1483V|ARID1B_ENST00000346085.5_Missense_Mutation_p.I1443V	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1430					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GACACACGGAATCCCGCCTCA	0.637																																					p.I1443V		Atlas-SNP	.											.	ARID1B	320	.	0			c.A4327G						.						28.0	32.0	31.0					6																	157522055		2203	4296	6499	SO:0001583	missense	57492	exon18			CACGGAATCCCGC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.4288A>G	chr6.hg19:g.157522055A>G	ENSP00000055163:p.Ile1430Val	179.0	0.0		216.0	90.0	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	A	1.491	-0.554755	0.03996	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.01981	4.86;4.86;4.85;4.85;4.52	5.08	-4.85	0.03142	.	0.267066	0.41823	N	0.000816	T	0.00440	0.0014	N	0.22421	0.69	0.09310	N	0.999995	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.46748	-0.9169	10	0.16896	T	0.51	.	8.7325	0.34507	0.4103:0.4637:0.126:0.0	.	1430;1443;1425	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	V	1443;1430;1483;1425;952	ENSP00000344546:I1443V;ENSP00000055163:I1430V;ENSP00000356116:I1483V;ENSP00000275248:I1425V;ENSP00000412835:I952V	ENSP00000275248:I1425V	I	+	1	0	ARID1B	157563747	0.589000	0.26807	0.017000	0.16124	0.037000	0.13140	1.471000	0.35365	-0.553000	0.06158	-0.326000	0.08463	ATC	.	.		0.637	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
LPA	4018	hgsc.bcm.edu	37	6	161016508	161016508	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr6:161016508G>T	ENST00000316300.5	-	21	3391	c.3347C>A	c.(3346-3348)aCc>aAc	p.T1116N	LPA_ENST00000447678.1_Missense_Mutation_p.T1116N			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3624	Kringle 10. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GGGATCCATGGTGTAACACCA	0.517																																					p.T1116N		Atlas-SNP	.											.	LPA	237	.	0			c.C3347A						.						107.0	105.0	106.0					6																	161016508		2123	4259	6382	SO:0001583	missense	4018	exon22			TCCATGGTGTAAC	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.3347C>A	chr6.hg19:g.161016508G>T	ENSP00000321334:p.Thr1116Asn	84.0	0.0		143.0	29.0	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	g	11.47	1.648034	0.29336	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.70986	-0.53;-0.53	2.31	2.31	0.28768	Kringle (4);Kringle-like fold (1);	.	.	.	.	D	0.82416	0.5032	H	0.95816	3.725	0.23739	N	0.996974	D	0.76494	0.999	D	0.97110	1.0	T	0.70454	-0.4867	9	0.87932	D	0	.	8.0392	0.30511	0.0:0.0:1.0:0.0	.	3624	P08519	APOA_HUMAN	N	1116	ENSP00000321334:T1116N;ENSP00000395608:T1116N	ENSP00000321334:T1116N	T	-	2	0	LPA	160936498	1.000000	0.71417	0.217000	0.23759	0.314000	0.28054	5.905000	0.69893	1.265000	0.44215	0.205000	0.17691	ACC	.	.		0.517	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
THSD7A	221981	hgsc.bcm.edu	37	7	11446000	11446000	+	Silent	SNP	A	A	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr7:11446000A>G	ENST00000423059.4	-	22	4415	c.4164T>C	c.(4162-4164)tgT>tgC	p.C1388C	AC004538.3_ENST00000445839.1_RNA|AC004160.4_ENST00000425837.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1388	TSP type-1 14. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CAATGTCAGCACAGAATTCCT	0.443										HNSCC(18;0.044)																											p.C1388C		Atlas-SNP	.											.	THSD7A	219	.	0			c.T4164C						.						114.0	116.0	115.0					7																	11446000		1923	4154	6077	SO:0001819	synonymous_variant	221981	exon21			GTCAGCACAGAAT		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.4164T>C	chr7.hg19:g.11446000A>G		71.0	0.0		155.0	56.0	NM_015204		Silent	SNP	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.		0.443	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
FKBP9	11328	hgsc.bcm.edu	37	7	33014908	33014908	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr7:33014908G>A	ENST00000242209.4	+	3	651	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Missense_Mutation_p.R214Q|FKBP9_ENST00000538443.1_Missense_Mutation_p.R23Q	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	161					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			AGTTGCCCTCGGACCATCCAG	0.473																																					p.R161Q		Atlas-SNP	.											FKBP9,brain,glioma,0,9	FKBP9	335	.	0			c.G482A						.						99.0	87.0	91.0					7																	33014908		2203	4300	6503	SO:0001583	missense	11328	exon3			GCCCTCGGACCAT	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"""EF-hand domain containing"""	3725	protein-coding gene	gene with protein product			"""FK506-binding protein 9 (63 kD)"""			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.482G>A	chr7.hg19:g.33014908G>A	ENSP00000242209:p.Arg161Gln	93.0	2.0		140.0	6.0	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	hg19	CCDS5439.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.720086	0.89205	.	.	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443	D;D;D	0.86164	-2.08;-2.08;-2.08	5.36	5.36	0.76844	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	0.000000	0.85682	D	0.000000	D	0.92714	0.7684	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.92752	0.6217	10	0.56958	D	0.05	-4.2611	19.0957	0.93249	0.0:0.0:1.0:0.0	.	214;161;161	B7Z6H3;O95302;B3KQQ0	.;FKBP9_HUMAN;.	Q	161;214;23	ENSP00000242209:R161Q;ENSP00000439250:R214Q;ENSP00000437504:R23Q	ENSP00000242209:R161Q	R	+	2	0	FKBP9	32981433	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	9.809000	0.99208	2.524000	0.85096	0.650000	0.86243	CGG	.	.		0.473	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270	
GSR	2936	hgsc.bcm.edu	37	8	30538494	30538494	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr8:30538494G>T	ENST00000221130.5	-	12	1436	c.1346C>A	c.(1345-1347)cCg>cAg	p.P449Q	GSR_ENST00000546342.1_Missense_Mutation_p.P420Q|GSR_ENST00000537535.1_Missense_Mutation_p.P367Q|GSR_ENST00000414019.1_Missense_Mutation_p.P406Q|GSR_ENST00000541648.1_Missense_Mutation_p.P396Q	NM_000637.3|NM_001195102.1|NM_001195103.1	NP_000628.2|NP_001182031.1|NP_001182032.1	P00390	GSHR_HUMAN	glutathione reductase	449					cell redox homeostasis (GO:0045454)|glutathione metabolic process (GO:0006749)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|glutathione-disulfide reductase activity (GO:0004362)|NADP binding (GO:0050661)	p.P449Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	23				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Flavin adenine dinucleotide(DB03147)|Glutathione(DB00143)	GTGATACATCGGGGTAAAGCT	0.338																																					p.P449Q		Atlas-SNP	.											.	GSR	53	.	1	Substitution - Missense(1)	lung(1)	c.C1346A						.						253.0	240.0	244.0					8																	30538494		2201	4300	6501	SO:0001583	missense	2936	exon12			TACATCGGGGTAA		CCDS34877.1, CCDS56530.1, CCDS56531.1, CCDS56532.1	8p21.1	2012-10-02			ENSG00000104687	ENSG00000104687	1.8.1.7		4623	protein-coding gene	gene with protein product		138300					Standard	NM_000637		Approved		uc003xih.2	P00390	OTTHUMG00000163946	ENST00000221130.5:c.1346C>A	chr8.hg19:g.30538494G>T	ENSP00000221130:p.Pro449Gln	81.0	0.0		82.0	4.0	NM_000637	C8KIL8|C8KIL9|C8KIM0|D3DSV3|Q7Z5C9|Q9NP63	Missense_Mutation	SNP	ENST00000221130.5	hg19	CCDS34877.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611051	0.66558	.	.	ENSG00000104687	ENST00000221130;ENST00000414019;ENST00000546342;ENST00000541648;ENST00000537535	D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04	5.35	5.35	0.76521	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (2);	0.000000	0.85682	D	0.000000	D	0.96987	0.9016	M	0.92880	3.355	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97760	1.0220	10	0.72032	D	0.01	-25.7309	16.6411	0.85127	0.0:0.0:1.0:0.0	.	449	P00390	GSHR_HUMAN	Q	449;406;420;396;367	ENSP00000221130:P449Q;ENSP00000390065:P406Q;ENSP00000445516:P420Q;ENSP00000444559:P396Q;ENSP00000438845:P367Q	ENSP00000221130:P449Q	P	-	2	0	GSR	30658036	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	8.914000	0.92735	2.511000	0.84671	0.650000	0.86243	CCG	.	.		0.338	GSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376519.1		
OPLAH	26873	hgsc.bcm.edu	37	8	145106719	145106719	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr8:145106719G>C	ENST00000426825.1	-	27	3712	c.3631C>G	c.(3631-3633)Cct>Gct	p.P1211A	CTD-3065J16.6_ENST00000561181.1_RNA|CTD-3065J16.6_ENST00000528912.1_RNA|OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	1211					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CGGGCGCCAGGCTCGCCCCCT	0.741																																					p.P1211A		Atlas-SNP	.											.	OPLAH	78	.	0			c.C3631G						.						13.0	15.0	14.0					8																	145106719		1811	4057	5868	SO:0001583	missense	26873	exon27			CGCCAGGCTCGCC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.3631C>G	chr8.hg19:g.145106719G>C	ENSP00000475943:p.Pro1211Ala	29.0	0.0		47.0	15.0	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	hg19		.	.	.	.	.	.	.	.	.	.	g	8.918	0.960411	0.18507	.	.	ENSG00000178814	ENST00000426825	.	.	.	4.64	3.72	0.42706	.	0.447039	0.24242	N	0.040254	T	0.40015	0.1100	L	0.33339	1.005	0.31266	N	0.6923779999999999	B	0.14805	0.011	B	0.16289	0.015	T	0.51020	-0.8758	8	0.41790	T	0.15	.	10.7779	0.46361	0.0:0.1917:0.8083:0.0	.	1211	O14841	OPLA_HUMAN	A	1211	.	ENSP00000412071:P1211A	P	-	1	0	OPLAH	145178707	0.900000	0.30661	0.953000	0.39169	0.259000	0.26198	1.523000	0.35932	2.126000	0.65437	0.472000	0.43445	CCT	.	.		0.741	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
SVEP1	79987	hgsc.bcm.edu	37	9	113173981	113173981	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr9:113173981G>T	ENST00000401783.2	-	37	6346	c.6010C>A	c.(6010-6012)Ctg>Atg	p.L2004M	SVEP1_ENST00000374469.1_Missense_Mutation_p.L1981M|SVEP1_ENST00000297826.5_De_novo_Start_InFrame	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2004	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCGTCGGCCAGGCATTCAATG	0.493																																					p.L2004M		Atlas-SNP	.											.	SVEP1	326	.	0			c.C6010A						.						27.0	29.0	28.0					9																	113173981		1953	4144	6097	SO:0001583	missense	79987	exon37			CGGCCAGGCATTC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.6010C>A	chr9.hg19:g.113173981G>T	ENSP00000384917:p.Leu2004Met	89.0	0.0		100.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.934540	0.34189	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.66460	-0.21;-0.21	5.58	2.75	0.32379	Complement control module (2);Sushi/SCR/CCP (3);	0.140827	0.48286	D	0.000193	T	0.53610	0.1807	L	0.55213	1.73	0.80722	D	1	P	0.35192	0.489	B	0.33620	0.167	T	0.49969	-0.8882	10	0.42905	T	0.14	.	3.2306	0.06747	0.3981:0.0:0.4234:0.1785	.	2004	Q4LDE5	SVEP1_HUMAN	M	2004;1981	ENSP00000384917:L2004M;ENSP00000363593:L1981M	ENSP00000363593:L1981M	L	-	1	2	SVEP1	112213802	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.370000	0.44240	0.726000	0.32339	-0.218000	0.12543	CTG	.	.		0.493	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
WDFY4	57705	hgsc.bcm.edu	37	10	50022050	50022050	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr10:50022050G>A	ENST00000325239.5	+	30	5290	c.5263G>A	c.(5263-5265)Gaa>Aaa	p.E1755K	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1755						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						GCACCACCAGGAAGAAGTCCT	0.587											OREG0007651	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.E1755K		Atlas-SNP	.											.	WDFY4	205	.	0			c.G5263A						.						41.0	45.0	44.0					10																	50022050		692	1591	2283	SO:0001583	missense	57705	exon31			CACCAGGAAGAAG	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5263G>A	chr10.hg19:g.50022050G>A	ENSP00000320563:p.Glu1755Lys	29.0	0.0	966	63.0	13.0	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	hg19	CCDS44385.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.82|11.82	1.752185|1.752185	0.31046|0.31046	.|.	.|.	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002;ENST00000374161	T|.	0.55588|.	0.51|.	5.83|5.83	3.97|3.97	0.46021|0.46021	.|.	0.293904|.	0.31335|.	N|.	0.007827|.	T|T	0.57651|0.57651	0.2068|0.2068	L|L	0.54323|0.54323	1.7|1.7	0.42832|0.42832	D|D	0.994025|0.994025	P;B|.	0.38078|.	0.617;0.335|.	B;B|.	0.39660|.	0.306;0.039|.	T|T	0.53725|0.53725	-0.8398|-0.8398	9|5	.|.	.|.	.|.	.|.	7.4541|7.4541	0.27255|0.27255	0.0944:0.2125:0.6931:0.0|0.0944:0.2125:0.6931:0.0	.|.	283;1755|.	F2Z372;Q6ZS81|.	.;WDFY4_HUMAN|.	K|E	1755|845;301	ENSP00000320563:E1755K|.	.|.	E|G	+|+	1|2	0|0	WDFY4|WDFY4	49692056|49692056	0.998000|0.998000	0.40836|0.40836	0.508000|0.508000	0.27688|0.27688	0.839000|0.839000	0.47603|0.47603	3.941000|3.941000	0.56607|0.56607	0.794000|0.794000	0.33899|0.33899	0.591000|0.591000	0.81541|0.81541	GAA|GGA	.	.		0.587	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
ABTB2	25841	hgsc.bcm.edu	37	11	34189528	34189528	+	Silent	SNP	T	T	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr11:34189528T>G	ENST00000435224.2	-	6	1999	c.1575A>C	c.(1573-1575)ccA>ccC	p.P525P	ABTB2_ENST00000298992.2_Silent_p.P339P	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	525					cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CGTACATCAGTGGCGTCATAC	0.542																																					p.P525P		Atlas-SNP	.											.	ABTB2	101	.	0			c.A1575C						.						155.0	94.0	115.0					11																	34189528		2202	4298	6500	SO:0001819	synonymous_variant	25841	exon6			CATCAGTGGCGTC	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.1575A>C	chr11.hg19:g.34189528T>G		84.0	0.0		121.0	18.0	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Silent	SNP	ENST00000435224.2	hg19	CCDS7890.2																																																																																			.	.		0.542	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
LRP4	4038	hgsc.bcm.edu	37	11	46921839	46921839	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr11:46921839T>A	ENST00000378623.1	-	3	532	c.290A>T	c.(289-291)gAg>gTg	p.E97V		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	97	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CGAGTCATCCTCACAGTCGTT	0.532																																					p.E97V		Atlas-SNP	.											.	LRP4	160	.	0			c.A290T						.						131.0	114.0	120.0					11																	46921839		2201	4299	6500	SO:0001583	missense	4038	exon3			TCATCCTCACAGT	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.290A>T	chr11.hg19:g.46921839T>A	ENSP00000367888:p.Glu97Val	120.0	0.0		190.0	74.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	15.73	2.918894	0.52546	.	.	ENSG00000134569	ENST00000378623;ENST00000534404	D;D	0.95690	-3.78;-3.78	5.63	5.63	0.86233	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.140677	0.47852	D	0.000201	D	0.94411	0.8202	L	0.38649	1.16	0.52501	D	0.999956	P;D	0.59357	0.692;0.985	B;P	0.51453	0.22;0.67	D	0.93936	0.7219	10	0.38643	T	0.18	.	15.841	0.78845	0.0:0.0:0.0:1.0	.	142;97	C9JRN7;O75096	.;LRP4_HUMAN	V	97;48	ENSP00000367888:E97V;ENSP00000434763:E48V	ENSP00000367888:E97V	E	-	2	0	LRP4	46878415	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.209000	0.58493	2.146000	0.66826	0.459000	0.35465	GAG	.	.		0.532	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
MYRF	745	hgsc.bcm.edu	37	11	61547742	61547742	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr11:61547742G>C	ENST00000278836.5	+	18	2481	c.2385G>C	c.(2383-2385)gaG>gaC	p.E795D	MYRF_ENST00000327797.1_Missense_Mutation_p.G478R|MYRF_ENST00000265460.5_Missense_Mutation_p.E786D|MYRF_ENST00000389602.4_Missense_Mutation_p.E186D|TMEM258_ENST00000535042.1_Intron	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	795					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCACAGAGGAGGACCTGGTAG	0.612																																					p.E795D		Atlas-SNP	.											.	.	.	.	0			c.G2385C						.						87.0	68.0	75.0					11																	61547742		2202	4299	6501	SO:0001583	missense	745	exon18			AGAGGAGGACCTG		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.2385G>C	chr11.hg19:g.61547742G>C	ENSP00000278836:p.Glu795Asp	241.0	0.0		387.0	71.0	NM_001127392	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	hg19	CCDS44622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.15|11.15	1.554032|1.554032	0.27739|0.27739	.|.	.|.	ENSG00000124920|ENSG00000124920	ENST00000278836;ENST00000265460;ENST00000389602|ENST00000327797	T;T;T|T	0.32988|0.40225	1.44;1.45;1.43|1.04	4.86|4.86	1.92|1.92	0.25849|0.25849	.|.	0.109296|.	0.64402|.	D|.	0.000007|.	T|T	0.33323|0.33323	0.0859|0.0859	L|L	0.29908|0.29908	0.895|0.895	0.26322|0.26322	N|N	0.977664|0.977664	P;P;B|.	0.37688|.	0.605;0.459;0.011|.	B;B;B|.	0.39590|.	0.18;0.304;0.01|.	T|T	0.29731|0.29731	-1.0002|-1.0002	10|7	0.22109|0.87932	T|D	0.4|0	-34.3974|-34.3974	5.9653|5.9653	0.19322|0.19322	0.225:0.0:0.6412:0.1338|0.225:0.0:0.6412:0.1338	.|.	186;786;795|.	B4DHB2;Q9Y2G1-2;Q9Y2G1|.	.;.;MRF_HUMAN|.	D|R	795;786;186|478	ENSP00000278836:E795D;ENSP00000265460:E786D;ENSP00000374253:E186D|ENSP00000333261:G478R	ENSP00000265460:E786D|ENSP00000333261:G478R	E|G	+|+	3|1	2|0	C11orf9|C11orf9	61304318|61304318	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.816000|0.816000	0.46133|0.46133	1.460000|1.460000	0.35244|0.35244	0.587000|0.587000	0.29643|0.29643	-0.258000|-0.258000	0.10820|0.10820	GAG|GGA	.	.		0.612	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
KRT79	338785	hgsc.bcm.edu	37	12	53216820	53216820	+	Silent	SNP	A	A	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr12:53216820A>G	ENST00000330553.5	-	7	1381	c.1347T>C	c.(1345-1347)ctT>ctC	p.L449L		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	449	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGCTCTCCAGAAGCTTGCGGT	0.657																																					p.L449L		Atlas-SNP	.											.	KRT79	78	.	0			c.T1347C						.						58.0	55.0	56.0					12																	53216820		2203	4300	6503	SO:0001819	synonymous_variant	338785	exon7			CTCCAGAAGCTTG	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1347T>C	chr12.hg19:g.53216820A>G		60.0	0.0		65.0	18.0	NM_175834	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	hg19	CCDS8839.1																																																																																			.	.		0.657	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
CRY1	1407	hgsc.bcm.edu	37	12	107393336	107393336	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr12:107393336C>G	ENST00000008527.5	-	7	1997	c.1130G>C	c.(1129-1131)gGa>gCa	p.G377A		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	377	Required for inhibition of CLOCK- ARNTL/BMAL1-mediated transcription. {ECO:0000250}.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						TACCTTCATTCCTTCTTCCCA	0.413																																					p.G377A		Atlas-SNP	.											.	CRY1	74	.	0			c.G1130C						.						84.0	78.0	80.0					12																	107393336		2203	4300	6503	SO:0001583	missense	1407	exon7			TTCATTCCTTCTT	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"""cryptochrome 1 (photolyase-like)"""	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.1130G>C	chr12.hg19:g.107393336C>G	ENSP00000008527:p.Gly377Ala	93.0	0.0		80.0	29.0	NM_004075		Missense_Mutation	SNP	ENST00000008527.5	hg19	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708209	0.89018	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.79	5.79	0.91817	DNA photolyase, FAD-binding/Cryptochrome, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.90017	0.6883	H	0.96489	3.83	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92455	0.5973	9	0.87932	D	0	-17.7008	20.0308	0.97536	0.0:1.0:0.0:0.0	.	377	Q16526	CRY1_HUMAN	A	377	.	ENSP00000008527:G377A	G	-	2	0	CRY1	105917466	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.818000	0.86416	2.732000	0.93576	0.585000	0.79938	GGA	.	.		0.413	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075	
HECTD4	283450	hgsc.bcm.edu	37	12	112601506	112601506	+	Missense_Mutation	SNP	C	C	T	rs564542020		TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr12:112601506C>T	ENST00000430131.2	-	73	12616	c.11471G>A	c.(11470-11472)cGg>cAg	p.R3824Q	HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000550722.1_Missense_Mutation_p.R4100Q|HECTD4_ENST00000377560.5_Missense_Mutation_p.R4074Q			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3824	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CCGCAGGCTCCGGATGGCTGC	0.682													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17361	0.0		0.0	False		,,,				2504	0.0				p.R4112Q		Atlas-SNP	.											.	.	.	.	0			c.G12335A						.						5.0	9.0	7.0					12																	112601506		1490	2933	4423	SO:0001583	missense	283450	exon74			AGGCTCCGGATGG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.11471G>A	chr12.hg19:g.112601506C>T	ENSP00000404379:p.Arg3824Gln	70.0	0.0		64.0	22.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.822958	0.96989	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000547085	T;T;T	0.57436	0.4;0.4;0.4	5.73	5.73	0.89815	HECT (4);	.	.	.	.	T	0.64416	0.2596	L	0.31664	0.95	0.58432	D	0.999999	D	0.69078	0.997	D	0.72982	0.979	T	0.66432	-0.5925	9	0.72032	D	0.01	.	19.8984	0.96975	0.0:1.0:0.0:0.0	.	3824	Q9Y4D8	K0614_HUMAN	Q	4074;3824;4100;289	ENSP00000366783:R4074Q;ENSP00000404379:R3824Q;ENSP00000449784:R4100Q	ENSP00000366783:R4074Q	R	-	2	0	C12orf51	111085889	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.597000	0.67577	2.713000	0.92767	0.655000	0.94253	CGG	.	.		0.682	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
EBPL	84650	hgsc.bcm.edu	37	13	50235138	50235138	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr13:50235138T>G	ENST00000242827.6	-	4	637	c.587A>C	c.(586-588)cAg>cCg	p.Q196P	EBPL_ENST00000495963.2_5'UTR|EBPL_ENST00000378270.5_3'UTR|EBPL_ENST00000378284.2_3'UTR|EBPL_ENST00000378272.5_3'UTR	NM_032565.3	NP_115954.1	Q9BY08	EBPL_HUMAN	emopamil binding protein-like	196					sterol metabolic process (GO:0016125)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholestenol delta-isomerase activity (GO:0047750)	p.Q196P(2)		endometrium(8)|kidney(6)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		GGTTTCTTTCTGATGCATTTT	0.383																																					p.Q196P	NSCLC(39;857 1083 36109 42364 51411)	Atlas-SNP	.											EBPL,NS,carcinoma,0,2	EBPL	44	.	2	Substitution - Missense(2)	endometrium(2)	c.A587C						.						73.0	73.0	73.0					13																	50235138		2203	4300	6503	SO:0001583	missense	84650	exon4			TCTTTCTGATGCA	AF243433	CCDS9420.1, CCDS61334.1	13q12-q13	2008-02-05			ENSG00000123179	ENSG00000123179			18061	protein-coding gene	gene with protein product							Standard	NM_032565		Approved	EBRP	uc001vdg.3	Q9BY08	OTTHUMG00000016920	ENST00000242827.6:c.587A>C	chr13.hg19:g.50235138T>G	ENSP00000242827:p.Gln196Pro	96.0	1.0		82.0	4.0	NM_032565	A6NJ59|Q569H7|Q5JVN2|Q5JVN3|Q5JVN4|Q5JVN5|Q5JVN6	Missense_Mutation	SNP	ENST00000242827.6	hg19	CCDS9420.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.722268	0.48728	.	.	ENSG00000123179	ENST00000242827	D	0.97994	-4.65	5.61	-2.45	0.06481	.	1.466260	0.03646	N	0.240220	D	0.94876	0.8344	L	0.47716	1.5	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	D	0.86530	0.1821	10	0.30078	T	0.28	-0.1548	6.1064	0.20075	0.3657:0.0:0.2518:0.3825	.	196	Q9BY08	EBPL_HUMAN	P	196	ENSP00000242827:Q196P	ENSP00000242827:Q196P	Q	-	2	0	EBPL	49133139	0.002000	0.14202	0.003000	0.11579	0.996000	0.88848	-0.059000	0.11731	-0.151000	0.11176	0.528000	0.53228	CAG	.	.		0.383	EBPL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044932.2	NM_032565	
CLN5	1203	hgsc.bcm.edu	37	13	77566254	77566254	+	Silent	SNP	G	G	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr13:77566254G>C	ENST00000377453.3	+	1	1460	c.168G>C	c.(166-168)acG>acC	p.T56T	CLN5_ENST00000485938.1_3'UTR	NM_006493.2	NP_006484.1	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5	7					brain development (GO:0007420)|cell death (GO:0008219)|glycosylation (GO:0070085)|lysosomal lumen acidification (GO:0007042)|neurogenesis (GO:0022008)|neuron maturation (GO:0042551)|protein catabolic process (GO:0030163)|signal peptide processing (GO:0006465)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|vacuolar lumen (GO:0005775)	mannose binding (GO:0005537)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)		AGGTAGACACGGCACAGGGCG	0.741																																					p.T56T		Atlas-SNP	.											.	CLN5	32	.	0			c.G168C						.						11.0	14.0	13.0					13																	77566254		2161	4235	6396	SO:0001819	synonymous_variant	1203	exon1			AGACACGGCACAG		CCDS9456.1	13q21.2-q32	2014-09-17			ENSG00000102805	ENSG00000102805			2076	protein-coding gene	gene with protein product		608102				7942847, 8661106	Standard	NM_006493		Approved		uc001vkc.3	O75503	OTTHUMG00000017100	ENST00000377453.3:c.168G>C	chr13.hg19:g.77566254G>C		25.0	0.0		32.0	5.0	NM_006493	B3KQK7	Silent	SNP	ENST00000377453.3	hg19	CCDS9456.1																																																																																			.	.		0.741	CLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045318.1	NM_006493	
SLC10A2	6555	hgsc.bcm.edu	37	13	103705045	103705045	+	Silent	SNP	A	A	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr13:103705045A>T	ENST00000245312.3	-	3	1106	c.510T>A	c.(508-510)gtT>gtA	p.V170V		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	170					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	CAACGAGAGAAACCAGAGATG	0.398																																					p.V170V		Atlas-SNP	.											.	SLC10A2	67	.	0			c.T510A						.						167.0	152.0	157.0					13																	103705045		2203	4300	6503	SO:0001819	synonymous_variant	6555	exon3			GAGAGAAACCAGA	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"""Solute carriers"""	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.510T>A	chr13.hg19:g.103705045A>T		87.0	0.0		94.0	25.0	NM_000452	A1L4F4|Q13839	Silent	SNP	ENST00000245312.3	hg19	CCDS9506.1																																																																																			.	.		0.398	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1		
BAZ1A	11177	hgsc.bcm.edu	37	14	35255190	35255190	+	Silent	SNP	A	A	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr14:35255190A>G	ENST00000382422.2	-	13	1951	c.1624T>C	c.(1624-1626)Ttg>Ctg	p.L542L	BAZ1A_ENST00000358716.4_Silent_p.L510L|BAZ1A_ENST00000360310.1_Silent_p.L542L			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	542					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TCAAGATCCAAACTTTTCAAA	0.313																																					p.L542L		Atlas-SNP	.											.	BAZ1A	128	.	0			c.T1624C						.						44.0	43.0	43.0					14																	35255190		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon14			GATCCAAACTTTT	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.1624T>C	chr14.hg19:g.35255190A>G		30.0	0.0		16.0	4.0	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	hg19	CCDS9651.1																																																																																			.	.		0.313	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
TLN2	83660	hgsc.bcm.edu	37	15	63029258	63029258	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr15:63029258T>G	ENST00000561311.1	+	28	3770	c.3540T>G	c.(3538-3540)gaT>gaG	p.D1180E	TLN2_ENST00000559908.1_3'UTR|TLN2_ENST00000306829.6_Missense_Mutation_p.D1180E			Q9Y4G6	TLN2_HUMAN	talin 2	1180	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CACCTGGAGATGCAGAGCGTC	0.557																																					p.D1180E		Atlas-SNP	.											.	TLN2	253	.	0			c.T3540G						.						63.0	57.0	59.0					15																	63029258		2203	4300	6503	SO:0001583	missense	83660	exon26			TGGAGATGCAGAG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.3540T>G	chr15.hg19:g.63029258T>G	ENSP00000453508:p.Asp1180Glu	141.0	0.0		279.0	55.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.610404	0.46527	.	.	ENSG00000171914	ENST00000306829	T	0.16073	2.37	5.12	-1.57	0.08506	.	0.000000	0.85682	D	0.000000	T	0.18841	0.0452	M	0.64630	1.985	0.43133	D	0.994872	B	0.32731	0.382	B	0.35607	0.206	T	0.06215	-1.0839	10	0.45353	T	0.12	-17.8071	13.5526	0.61740	0.0:0.5273:0.0:0.4727	.	1180	Q9Y4G6	TLN2_HUMAN	E	1180	ENSP00000303476:D1180E	ENSP00000303476:D1180E	D	+	3	2	TLN2	60816550	0.361000	0.24972	0.892000	0.35008	0.972000	0.66771	-0.357000	0.07651	-0.486000	0.06744	-0.347000	0.07816	GAT	.	.		0.557	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
CELF6	60677	hgsc.bcm.edu	37	15	72582280	72582280	+	Splice_Site	SNP	C	C	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr15:72582280C>T	ENST00000569547.1	-	5	674	c.603G>A	c.(601-603)gcG>gcA	p.A201A	RP11-106M3.2_ENST00000379915.4_RNA|RP11-106M3.3_ENST00000570175.1_RNA|CELF6_ENST00000569311.1_5'UTR|CELF6_ENST00000543764.2_Splice_Site_p.A86A|CELF6_ENST00000567083.1_Splice_Site_p.A201A|CELF6_ENST00000395258.2_Splice_Site_p.A88A|CELF6_ENST00000287202.5_Splice_Site_p.A201A|CELF6_ENST00000539635.1_Splice_Site_p.A62A			Q96J87	CELF6_HUMAN	CUGBP, Elav-like family member 6	201	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(2)	13						CCGCCCTCACCGCCATGGTCC	0.687																																					p.A201A		Atlas-SNP	.											.	CELF6	30	.	0			c.G603A						.						12.0	14.0	13.0					15																	72582280		2163	4258	6421	SO:0001630	splice_region_variant	60677	exon5			CCTCACCGCCATG	AF425606	CCDS10242.1, CCDS53955.1, CCDS53956.1	15q24	2013-02-12	2010-02-19	2010-02-19	ENSG00000140488	ENSG00000140488		"""RNA binding motif (RRM) containing"""	14059	protein-coding gene	gene with protein product		612681	"""Bruno (Drosophila) -like 6, RNA binding protein"", ""bruno-like 6, RNA binding protein (Drosophila)"""	BRUNOL6		10893231	Standard	NM_052840		Approved		uc002auh.2	Q96J87	OTTHUMG00000133444	ENST00000569547.1:c.603+1G>A	chr15.hg19:g.72582280C>T		78.0	0.0		91.0	5.0	NM_001172684	B4DG28|B4DJB6|Q6PII4|Q6ZNJ7|Q8N607	Silent	SNP	ENST00000569547.1	hg19	CCDS10242.1																																																																																			.	.		0.687	CELF6-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000420180.1	NM_052840	Silent
GFOD2	81577	hgsc.bcm.edu	37	16	67709857	67709857	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr16:67709857A>G	ENST00000268797.7	-	3	704	c.359T>C	c.(358-360)gTa>gCa	p.V120A	GFOD2_ENST00000602377.1_5'UTR	NM_030819.3	NP_110446.3	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain containing 2	120					extracellular matrix organization (GO:0030198)	proteinaceous extracellular matrix (GO:0005578)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		CACGTTCCCTACCAGGCTCAT	0.567																																					p.V120A		Atlas-SNP	.											.	GFOD2	36	.	0			c.T359C						.						95.0	72.0	80.0					16																	67709857		2198	4300	6498	SO:0001583	missense	81577	exon3			TTCCCTACCAGGC	AK074382	CCDS10845.1, CCDS59268.1	16q22.1	2008-02-05			ENSG00000141098	ENSG00000141098			28159	protein-coding gene	gene with protein product						12975309	Standard	NM_030819		Approved	FLJ23802, MGC11335	uc002eub.3	Q3B7J2	OTTHUMG00000137537	ENST00000268797.7:c.359T>C	chr16.hg19:g.67709857A>G	ENSP00000268797:p.Val120Ala	128.0	0.0		146.0	45.0	NM_030819	Q69YL9|Q6UXX6|Q7L648|Q8TE86|Q9BQ07|R4GNG5	Missense_Mutation	SNP	ENST00000268797.7	hg19	CCDS10845.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.583781	0.65992	.	.	ENSG00000141098	ENST00000268797	T	0.29655	1.56	5.01	5.01	0.66863	NAD(P)-binding domain (1);	0.049892	0.85682	D	0.000000	T	0.41190	0.1148	M	0.68317	2.08	0.58432	D	0.999999	P	0.42203	0.773	P	0.45794	0.493	T	0.42565	-0.9444	10	0.72032	D	0.01	-30.6441	14.6786	0.69001	1.0:0.0:0.0:0.0	.	120	Q3B7J2	GFOD2_HUMAN	A	120	ENSP00000268797:V120A	ENSP00000268797:V120A	V	-	2	0	GFOD2	66267358	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.307000	0.96226	2.007000	0.58848	0.460000	0.39030	GTA	.	.		0.567	GFOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268868.2	NM_030819	
MED13	9969	hgsc.bcm.edu	37	17	60064481	60064481	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr17:60064481G>A	ENST00000397786.2	-	12	2348	c.2272C>T	c.(2272-2274)Cgc>Tgc	p.R758C		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	758					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTAGTAGGGCGTGGAGCATCT	0.433																																					p.R758C		Atlas-SNP	.											.	MED13	181	.	0			c.C2272T						.						61.0	57.0	58.0					17																	60064481		1862	4100	5962	SO:0001583	missense	9969	exon12			TAGGGCGTGGAGC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.2272C>T	chr17.hg19:g.60064481G>A	ENSP00000380888:p.Arg758Cys	134.0	0.0		189.0	57.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100342	0.56183	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.74947	-0.89	5.12	5.12	0.69794	.	0.059122	0.64402	D	0.000002	T	0.69646	0.3134	L	0.43152	1.355	0.80722	D	1	B	0.22983	0.078	B	0.11329	0.006	T	0.67317	-0.5701	10	0.56958	D	0.05	-20.273	18.9313	0.92566	0.0:0.0:1.0:0.0	.	758	Q9UHV7	MED13_HUMAN	C	758;757	ENSP00000380888:R758C	ENSP00000262436:R757C	R	-	1	0	MED13	57419263	1.000000	0.71417	0.992000	0.48379	0.901000	0.52897	7.277000	0.78572	2.560000	0.86352	0.655000	0.94253	CGC	.	.		0.433	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647263	34647263	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr18:34647263G>C	ENST00000280020.5	+	7	1009	c.987G>C	c.(985-987)aaG>aaC	p.K329N	KIAA1328_ENST00000543923.1_Missense_Mutation_p.K221N|KIAA1328_ENST00000435985.2_Missense_Mutation_p.K45N|KIAA1328_ENST00000586135.1_Missense_Mutation_p.K45N|KIAA1328_ENST00000586501.1_Missense_Mutation_p.K45N|KIAA1328_ENST00000591619.1_Missense_Mutation_p.K325N	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	329										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		AACATCCTAAGACACATCCAG	0.468																																					p.K329N		Atlas-SNP	.											.	KIAA1328	39	.	0			c.G987C						.						111.0	106.0	108.0					18																	34647263		2089	4215	6304	SO:0001583	missense	57536	exon7			TCCTAAGACACAT	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.987G>C	chr18.hg19:g.34647263G>C	ENSP00000280020:p.Lys329Asn	196.0	0.0		229.0	18.0	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	hg19	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	G	7.573	0.667232	0.14710	.	.	ENSG00000150477	ENST00000543923;ENST00000280020;ENST00000383055;ENST00000435985	T;T;T	0.45276	0.9;0.9;0.9	6.17	-0.189	0.13260	.	0.681821	0.14788	N	0.298395	T	0.36331	0.0963	L	0.50333	1.59	0.09310	N	1	B;B;P;B	0.46142	0.023;0.023;0.873;0.01	B;B;P;B	0.44990	0.023;0.023;0.466;0.007	T	0.18840	-1.0324	10	0.41790	T	0.15	.	6.9251	0.24410	0.4411:0.0:0.4455:0.1135	.	45;329;45;329	Q86T90-4;A8K8C3;Q86T90-3;Q86T90	.;.;.;K1328_HUMAN	N	221;329;329;45	ENSP00000441359:K221N;ENSP00000280020:K329N;ENSP00000390515:K45N	ENSP00000280020:K329N	K	+	3	2	KIAA1328	32901261	0.007000	0.16637	0.017000	0.16124	0.028000	0.11728	-0.117000	0.10708	-0.080000	0.12685	-0.150000	0.13652	AAG	.	.		0.468	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
TIMM13	26517	hgsc.bcm.edu	37	19	2427289	2427289	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr19:2427289C>T	ENST00000215570.3	-	2	514	c.154G>A	c.(154-156)Ggg>Agg	p.G52R	LMNB2_ENST00000475819.1_5'Flank|TIMM13_ENST00000591871.1_Missense_Mutation_p.G37R	NM_012458.2	NP_036590.1	Q9Y5L4	TIM13_HUMAN	translocase of inner mitochondrial membrane 13 homolog (yeast)	52					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space protein transporter complex (GO:0042719)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	zinc ion binding (GO:0008270)			endometrium(1)|prostate(1)	2		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)		CCAGGTTTCCCTATACACTTC	0.667																																					p.G52R		Atlas-SNP	.											.	TIMM13	7	.	0			c.G154A						.						96.0	110.0	105.0					19																	2427289		2203	4300	6503	SO:0001583	missense	26517	exon2			GTTTCCCTATACA	AF152352	CCDS12089.1	19p13.3	2008-07-04	2001-11-28	2002-03-17		ENSG00000099800			11816	protein-coding gene	gene with protein product		607383	"""translocase of inner mitochondrial membrane 13 (yeast) homolog B"""	TIMM13B		10552927, 17329230	Standard	NM_012458		Approved	Tim13	uc002lvx.1	Q9Y5L4		ENST00000215570.3:c.154G>A	chr19.hg19:g.2427289C>T	ENSP00000215570:p.Gly52Arg	39.0	0.0		73.0	25.0	NM_012458	P62206|Q9UHL8|Q9WTL1	Missense_Mutation	SNP	ENST00000215570.3	hg19	CCDS12089.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.493180	0.44352	.	.	ENSG00000099800	ENST00000215570	T	0.62498	0.02	3.44	3.44	0.39384	.	0.000000	0.85682	D	0.000000	T	0.48169	0.1485	.	.	.	0.58432	D	0.999999	B	0.21753	0.06	B	0.23716	0.048	T	0.41716	-0.9493	9	0.23302	T	0.38	-23.6549	12.7718	0.57426	0.0:1.0:0.0:0.0	.	52	Q9Y5L4	TIM13_HUMAN	R	52	ENSP00000215570:G52R	ENSP00000215570:G52R	G	-	1	0	TIMM13	2378289	1.000000	0.71417	0.999000	0.59377	0.870000	0.49936	4.117000	0.57877	1.922000	0.55676	0.491000	0.48974	GGG	.	.		0.667	TIMM13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451333.1		
UNC13A	23025	hgsc.bcm.edu	37	19	17720864	17720864	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr19:17720864G>A	ENST00000519716.2	-	43	4695	c.4696C>T	c.(4696-4698)Cgg>Tgg	p.R1566W	UNC13A_ENST00000252773.7_Missense_Mutation_p.R1566W|UNC13A_ENST00000428389.2_Missense_Mutation_p.R1654W|UNC13A_ENST00000550896.1_Missense_Mutation_p.R1539W|UNC13A_ENST00000552293.1_Missense_Mutation_p.R1560W|UNC13A_ENST00000551649.1_Missense_Mutation_p.R1585W	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1566	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						ATGAACGGCCGGAAGATGCCA	0.517																																					p.R1566W		Atlas-SNP	.											.	UNC13A	299	.	0			c.C4696T						.						122.0	130.0	127.0					19																	17720864		2154	4277	6431	SO:0001583	missense	23025	exon41			ACGGCCGGAAGAT	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.4696C>T	chr19.hg19:g.17720864G>A	ENSP00000429562:p.Arg1566Trp	118.0	0.0		199.0	73.0	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007738	0.75046	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	4.13	4.13	0.48395	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.84005	0.5377	M	0.89968	3.075	0.46981	D	0.999273	D	0.89917	1.0	D	0.85130	0.997	D	0.87780	0.2611	10	0.87932	D	0	-17.1577	13.9527	0.64129	0.0:0.0:1.0:0.0	.	1566	Q9UPW8	UN13A_HUMAN	W	1566;1654;1566;1585;1560;1539	ENSP00000429562:R1566W;ENSP00000400409:R1654W;ENSP00000252773:R1566W;ENSP00000447236:R1585W;ENSP00000447572:R1560W;ENSP00000446831:R1539W	ENSP00000252773:R1566W	R	-	1	2	UNC13A	17581864	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.923000	0.56469	1.869000	0.54173	0.478000	0.44815	CGG	.	.		0.517	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39914693	39914693	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr19:39914693G>A	ENST00000409794.3	+	19	3770	c.2920G>A	c.(2920-2922)Gat>Aat	p.D974N	CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.D945N|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.D915N	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	974					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AACTTTCTCTGATCAAGGCCA	0.567																																					p.D974N		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G2920A						.						93.0	97.0	96.0					19																	39914693		2203	4300	6503	SO:0001583	missense	64857	exon19			TTCTCTGATCAAG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.2920G>A	chr19.hg19:g.39914693G>A	ENSP00000386733:p.Asp974Asn	130.0	0.0		167.0	82.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	16.20	3.056851	0.55325	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508	T;T;T	0.78816	-1.03;-1.1;-1.21	3.82	2.75	0.32379	.	0.949809	0.08659	N	0.912730	T	0.77691	0.4168	L	0.39898	1.24	0.09310	N	0.999999	D;P;P	0.55385	0.971;0.952;0.952	P;P;P	0.52514	0.701;0.505;0.601	T	0.65331	-0.6194	10	0.87932	D	0	.	9.3484	0.38122	0.0:0.2186:0.7814:0.0	.	945;974;915	Q9H7P9-3;Q9H7P9;E7ESZ3	.;PKHG2_HUMAN;.	N	974;945;915	ENSP00000386733:D974N;ENSP00000392906:D945N;ENSP00000408857:D915N	ENSP00000386733:D974N	D	+	1	0	PLEKHG2	44606533	0.000000	0.05858	0.011000	0.14972	0.042000	0.13812	0.588000	0.23924	1.165000	0.42670	0.591000	0.81541	GAT	.	.		0.567	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
BPIFB2	80341	hgsc.bcm.edu	37	20	31600638	31600638	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr20:31600638G>A	ENST00000170150.3	+	4	428	c.233G>A	c.(232-234)cGc>cAc	p.R78H		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	78						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CATGTGCCCCGCCTCCACCTG	0.537																																					p.R78H		Atlas-SNP	.											.	.	.	.	0			c.G233A						.						197.0	187.0	190.0					20																	31600638		2203	4300	6503	SO:0001583	missense	80341	exon4			TGCCCCGCCTCCA	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.233G>A	chr20.hg19:g.31600638G>A	ENSP00000170150:p.Arg78His	126.0	0.0		280.0	36.0	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	hg19	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	G	3.151	-0.174123	0.06421	.	.	ENSG00000078898	ENST00000170150	T	0.05786	3.39	4.41	-5.21	0.02815	.	1.608980	0.03461	N	0.212134	T	0.02380	0.0073	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44436	-0.9328	10	0.13470	T	0.59	0.0364	7.6161	0.28158	0.2661:0.0:0.5834:0.1505	.	78	Q8N4F0	BPIB2_HUMAN	H	78	ENSP00000170150:R78H	ENSP00000170150:R78H	R	+	2	0	BPIFB2	31064299	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.003000	0.03682	-1.155000	0.02822	-0.302000	0.09304	CGC	.	.		0.537	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
LAMA5	3911	hgsc.bcm.edu	37	20	60893664	60893664	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr20:60893664T>G	ENST00000252999.3	-	53	7151	c.7085A>C	c.(7084-7086)gAg>gCg	p.E2362A		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2362	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGCCTGGTTCTCCTCCCAGAG	0.672																																					p.E2362A		Atlas-SNP	.											.	LAMA5	268	.	0			c.A7085C						.						30.0	37.0	35.0					20																	60893664		2183	4270	6453	SO:0001583	missense	3911	exon53			TGGTTCTCCTCCC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7085A>C	chr20.hg19:g.60893664T>G	ENSP00000252999:p.Glu2362Ala	129.0	0.0		251.0	27.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	-	11.66	1.706313	0.30232	.	.	ENSG00000130702	ENST00000252999	T	0.14144	2.53	3.88	2.73	0.32206	Laminin I (1);	0.993490	0.08172	U	0.986761	T	0.13114	0.0318	L	0.43923	1.385	0.31105	N	0.710572	B	0.29481	0.245	B	0.31946	0.138	T	0.28681	-1.0036	10	0.48119	T	0.1	.	4.6545	0.12611	0.0:0.1485:0.407:0.4445	.	2362	O15230	LAMA5_HUMAN	A	2362	ENSP00000252999:E2362A	ENSP00000252999:E2362A	E	-	2	0	LAMA5	60327059	0.985000	0.35326	0.993000	0.49108	0.428000	0.31595	2.380000	0.44327	0.467000	0.27218	0.358000	0.22013	GAG	.	.		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ZNRF3	84133	hgsc.bcm.edu	37	22	29440871	29440871	+	Missense_Mutation	SNP	G	G	A	rs372884606		TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr22:29440871G>A	ENST00000544604.2	+	5	912	c.737G>A	c.(736-738)cGc>cAc	p.R246H	ZNRF3_ENST00000332811.4_Missense_Mutation_p.R146H|ZNRF3_ENST00000402174.1_Missense_Mutation_p.R146H|ZNRF3_ENST00000406323.3_Missense_Mutation_p.R146H	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	246					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						AAGCAGCGACGCAGTCAGGTA	0.517																																					p.R246H		Atlas-SNP	.											.	ZNRF3	75	.	0			c.G737A						.	G	HIS/ARG,HIS/ARG	1,4143		0,1,2071	111.0	113.0	113.0		737,437	5.3	1.0	22		113	0,8382		0,0,4191	no	missense,missense	ZNRF3	NM_001206998.1,NM_032173.3	29,29	0,1,6262	AA,AG,GG		0.0,0.0241,0.0080	probably-damaging,probably-damaging	246/937,146/837	29440871	1,12525	2072	4191	6263	SO:0001583	missense	84133	exon5			AGCGACGCAGTCA	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"""RING-type (C3HC4) zinc fingers"""	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.737G>A	chr22.hg19:g.29440871G>A	ENSP00000443824:p.Arg246His	103.0	0.0		158.0	47.0	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835791	0.91117	2.41E-4	0.0	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000402174;ENST00000406323	T;T;T;T	0.12039	2.82;2.72;2.72;2.72	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.25269	0.0614	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.02743	-1.1116	10	0.33940	T	0.23	-14.7992	18.0498	0.89344	0.0:0.0:1.0:0.0	.	246	Q9ULT6	ZNRF3_HUMAN	H	246;146;146;146	ENSP00000443824:R246H;ENSP00000328614:R146H;ENSP00000384456:R146H;ENSP00000384553:R146H	ENSP00000328614:R146H	R	+	2	0	ZNRF3	27770871	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.814000	0.91968	2.515000	0.84797	0.655000	0.94253	CGC	.	.		0.517	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972	
BMX	660	hgsc.bcm.edu	37	X	15560134	15560134	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chrX:15560134T>A	ENST00000357607.2	+	15	1612	c.1424T>A	c.(1423-1425)tTc>tAc	p.F475Y	BMX_ENST00000342014.6_Missense_Mutation_p.F475Y|BMX_ENST00000348343.6_Missense_Mutation_p.F475Y			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	475	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					CTGGTTAAATTCTATGGAGTG	0.393																																					p.F475Y		Atlas-SNP	.											.	BMX	73	.	0			c.T1424A						.						123.0	117.0	119.0					X																	15560134		2203	4299	6502	SO:0001583	missense	660	exon15			TTAAATTCTATGG	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1079	protein-coding gene	gene with protein product	"""BTK-like on X chromosome"""	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.1424T>A	chrX.hg19:g.15560134T>A	ENSP00000350224:p.Phe475Tyr	98.0	0.0		124.0	93.0	NM_001721	A6NIH9|O60564|Q12871	Missense_Mutation	SNP	ENST00000357607.2	hg19	CCDS14168.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.455164	0.84209	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	D;D;D	0.89270	-2.49;-2.49;-2.49	4.84	4.84	0.62591	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.134965	0.37669	N	0.001999	D	0.89192	0.6645	L	0.39147	1.195	0.40456	D	0.98019	P	0.49783	0.928	P	0.54372	0.75	D	0.90436	0.4428	10	0.87932	D	0	.	12.3781	0.55291	0.0:0.0:0.0:1.0	.	475	P51813	BMX_HUMAN	Y	475	ENSP00000350224:F475Y;ENSP00000308774:F475Y;ENSP00000340082:F475Y	ENSP00000340082:F475Y	F	+	2	0	BMX	15470055	1.000000	0.71417	0.998000	0.56505	0.821000	0.46438	7.837000	0.86796	1.593000	0.50029	0.481000	0.45027	TTC	.	.		0.393	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721	
SEC31B	25956	hgsc.bcm.edu	37	10	102265220	102265221	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr10:102265220_102265221insA	ENST00000370345.3	-	10	1173_1174	c.1076_1077insT	c.(1075-1077)ctcfs	p.L359fs	SEC31B_ENST00000451524.1_Frame_Shift_Ins_p.L359fs	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	359					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GCAGTGGTGGGAGAGGCTGGCC	0.515																																					p.L359fs		Atlas-Indel,Pindel	.											.	SEC31B	84	.	0			c.1077_1078insT						.																																			SO:0001589	frameshift_variant	25956	exon10			.	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1077dupT	chr10.hg19:g.102265221_102265221dupA	ENSP00000359370:p.Leu359fs	55.0	0.0		95.0	23.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Frame_Shift_Ins	INS	ENST00000370345.3	hg19	CCDS7495.1																																																																																			.	.		0.515	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209217426	209217426	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr2:209217426delA	ENST00000264380.4	+	39	5922	c.5764delA	c.(5764-5766)aagfs	p.K1922fs		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1922	Catalytic.|PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						AATTGGTTATAAGAACTCTCA	0.373																																					p.Y1921X		Atlas-INDEL	.											.	PIKFYVE	223	.	0			c.5763delT						.						80.0	83.0	82.0					2																	209217426		2202	4300	6502	SO:0001589	frameshift_variant	200576	exon39			.	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5764delA	chr2.hg19:g.209217426delA	ENSP00000264380:p.Lys1922fs	45.0	0.0		43.0	16.0	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Frame_Shift_Del	DEL	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	.		0.373	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
CYSLTR1	10800	hgsc.bcm.edu	37	X	77528826	77528827	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chrX:77528826_77528827insT	ENST00000373304.3	-	3	709_710	c.417_418insA	c.(415-420)aaagccfs	p.A140fs		NM_001282187.1|NM_001282188.1|NM_006639.3	NP_001269116.1|NP_001269117.1|NP_006630.1	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	140					defense response (GO:0006952)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory gaseous exchange (GO:0007585)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene receptor activity (GO:0004974)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14					Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	ACAAACCTGGCTTTTTTCTGTG	0.366																																					p.A140fs		Atlas-Indel,Pindel	.											.	CYSLTR1	59	.	0			c.418_419insA						.																																			SO:0001589	frameshift_variant	10800	exon3			.	AF119711	CCDS14439.1	Xq13-q21	2012-08-10			ENSG00000173198	ENSG00000173198		"""GPCR / Class A : Leukotriene receptors"""	17451	protein-coding gene	gene with protein product		300201				10391245, 10462554	Standard	NM_006639		Approved	CysLT1, CysLT(1), CYSLT1R	uc004edb.3	Q9Y271	OTTHUMG00000021889	ENST00000373304.3:c.418dupA	chrX.hg19:g.77528832_77528832dupT	ENSP00000362401:p.Ala140fs	71.0	0.0		62.0	41.0	NM_006639	B2R954|D3DTE4|Q5JS94|Q8IV19	Frame_Shift_Ins	INS	ENST00000373304.3	hg19	CCDS14439.1																																																																																			.	.		0.366	CYSLTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057315.1		
UGT2B4	7363	hgsc.bcm.edu	37	4	70352328	70352330	+	Splice_Site	DEL	AAG	AAG	-			TCGA-DD-A4NO-01A-11D-A28X-10	TCGA-DD-A4NO-10A-01D-A28X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c36b12b9-c709-4e3d-acec-e6c2dfedbb5c	f388d82f-63e0-41b8-8514-839e3359602a	g.chr4:70352328_70352330delAAG	ENST00000305107.6	-	4	1133_1135	c.1087_1089delCTT	c.(1087-1089)cttdel	p.L363del	UGT2B4_ENST00000506580.1_5'UTR|UGT2B4_ENST00000381096.3_Splice_Site_p.L227del|UGT2B4_ENST00000512583.1_Splice_Site_p.L363del	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	363					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	GAGACTTACCAAGAAGATCATTC	0.34																																					p.363_364del		Atlas-Indel,Pindel	.											.	UGT2B4	105	.	0			c.1088_1090del						.																																			SO:0001630	splice_region_variant	7363	exon4			.	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.1090+1CTT>-	chr4.hg19:g.70352331_70352333delAAG		100.0	0.0		84.0	22.0	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	In_Frame_Del	DEL	ENST00000305107.6	hg19	CCDS43234.1																																																																																			.	.		0.340	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	In_Frame_Del
