#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
HP1BP3	50809	hgsc.bcm.edu	37	1	21072039	21072039	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:21072039C>G	ENST00000312239.5	-	12	1503	c.1364G>C	c.(1363-1365)aGa>aCa	p.R455T	RP5-930J4.4_ENST00000413451.1_RNA|HP1BP3_ENST00000375003.2_Missense_Mutation_p.R303T	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	455	Lys-rich.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TCCACACCTTCTCTTAGGTGG	0.448																																					p.R455T		Atlas-SNP	.											.	HP1BP3	47	.	0			c.G1364C						.						109.0	96.0	101.0					1																	21072039		2203	4300	6503	SO:0001583	missense	50809	exon12			CACCTTCTCTTAG	BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.1364G>C	chr1.hg19:g.21072039C>G	ENSP00000312625:p.Arg455Thr	78.0	0.0		56.0	34.0	NM_016287	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Missense_Mutation	SNP	ENST00000312239.5	hg19	CCDS30621.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310845	0.60414	.	.	ENSG00000127483	ENST00000312239;ENST00000375004;ENST00000375003	T;T	0.52057	0.68;0.71	5.87	4.75	0.60458	.	0.273767	0.47093	D	0.000250	T	0.30727	0.0774	L	0.27053	0.805	0.80722	D	1	B	0.27498	0.18	B	0.24974	0.057	T	0.12016	-1.0564	10	0.41790	T	0.15	.	6.5213	0.22277	0.0:0.8336:0.0:0.1664	.	455	Q5SSJ5	HP1B3_HUMAN	T	455;417;303	ENSP00000312625:R455T;ENSP00000364142:R303T	ENSP00000312625:R455T	R	-	2	0	HP1BP3	20944626	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.517000	0.45529	2.941000	0.99782	0.655000	0.94253	AGA	.	.		0.448	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287	
ZNF436	80818	hgsc.bcm.edu	37	1	23689582	23689582	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:23689582C>T	ENST00000314011.4	-	4	429	c.293G>A	c.(292-294)aGc>aAc	p.S98N	ZNF436_ENST00000374608.3_Missense_Mutation_p.S98N	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CCTATCTCCGCTTTCAAAGCC	0.443																																					p.S98N		Atlas-SNP	.											.	ZNF436	49	.	0			c.G293A						.						186.0	188.0	187.0					1																	23689582		2203	4300	6503	SO:0001583	missense	80818	exon4			TCTCCGCTTTCAA	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"""Zinc fingers, C2H2-type"", ""-"""	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.293G>A	chr1.hg19:g.23689582C>T	ENSP00000313582:p.Ser98Asn	105.0	0.0		57.0	34.0	NM_001077195	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	hg19	CCDS233.1	.	.	.	.	.	.	.	.	.	.	C	1.135	-0.651148	0.03506	.	.	ENSG00000125945	ENST00000314011;ENST00000374609;ENST00000374608	T;T;T	0.06608	3.28;3.51;3.28	5.85	0.137	0.14787	.	0.751927	0.12633	N	0.452002	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47459	-0.9116	10	0.21014	T	0.42	-7.1493	5.3217	0.15885	0.0:0.3878:0.1439:0.4683	.	98	Q9C0F3	ZN436_HUMAN	N	98	ENSP00000313582:S98N;ENSP00000363737:S98N;ENSP00000363736:S98N	ENSP00000313582:S98N	S	-	2	0	ZNF436	23562169	0.000000	0.05858	0.034000	0.17996	0.769000	0.43574	-0.935000	0.03950	-0.145000	0.11294	0.655000	0.94253	AGC	.	.		0.443	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634	
TTLL7	79739	hgsc.bcm.edu	37	1	84386928	84386928	+	Splice_Site	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:84386928A>G	ENST00000260505.8	-	11	1668		c.e11+1		TTLL7_ENST00000477524.1_Splice_Site	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		AAACTTTCATACCAACTCTTC	0.388																																					.		Atlas-SNP	.											.	TTLL7	93	.	0			c.1290+2T>C						.						93.0	94.0	94.0					1																	84386928		2203	4299	6502	SO:0001630	splice_region_variant	79739	exon12			TTTCATACCAACT	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"""Tubulin tyrosine ligase-like family"""	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.1290+1T>C	chr1.hg19:g.84386928A>G		107.0	0.0		108.0	41.0	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Splice_Site	SNP	ENST00000260505.8	hg19	CCDS690.2	.	.	.	.	.	.	.	.	.	.	A	23.5	4.423474	0.83559	.	.	ENSG00000137941	ENST00000260505;ENST00000370704;ENST00000370703	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5427	0.84406	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TTLL7	84159516	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.585000	0.90802	2.363000	0.80096	0.523000	0.50628	.	.	.		0.388	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686	Intron
TMEM56	148534	hgsc.bcm.edu	37	1	95609526	95609526	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:95609526C>G	ENST00000370203.4	+	2	360	c.69C>G	c.(67-69)ttC>ttG	p.F23L	TMEM56_ENST00000463375.1_3'UTR|RP11-57H12.6_ENST00000604534.1_Missense_Mutation_p.F23L	NM_001199679.1|NM_152487.2	NP_001186608.1|NP_689700.1	Q96MV1	TMM56_HUMAN	transmembrane protein 56	23						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(2)|skin(1)|urinary_tract(1)	12		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)		AGCTTCTTTTCTACTTTGTAA	0.353																																					p.F23L		Atlas-SNP	.											.	TMEM56	24	.	0			c.C69G						.						110.0	109.0	109.0					1																	95609526		2202	4299	6501	SO:0001583	missense	148534	exon2			TCTTTTCTACTTT		CCDS753.1	1p21.3	2008-02-05			ENSG00000152078	ENSG00000152078			26477	protein-coding gene	gene with protein product							Standard	NM_152487		Approved	FLJ31842	uc001drb.3	Q96MV1	OTTHUMG00000010847	ENST00000370203.4:c.69C>G	chr1.hg19:g.95609526C>G	ENSP00000359222:p.Phe23Leu	148.0	0.0		118.0	51.0	NM_001199679	B2RPI2|D3DT48	Missense_Mutation	SNP	ENST00000370203.4	hg19	CCDS753.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.446642	0.84101	.	.	ENSG00000152078	ENST00000370203;ENST00000456991;ENST00000455656	.	.	.	5.45	5.45	0.79879	.	0.095798	0.64402	D	0.000001	T	0.78136	0.4236	M	0.82056	2.57	0.45806	D	0.998687	D;D	0.89917	1.0;0.985	D;P	0.77004	0.989;0.863	T	0.74697	-0.3578	8	0.24483	T	0.36	-24.5126	18.0671	0.89394	0.0:1.0:0.0:0.0	.	23;23	C9JJM2;Q96MV1	.;TMM56_HUMAN	L	23	.	ENSP00000359222:F23L	F	+	3	2	TMEM56	95382114	1.000000	0.71417	0.995000	0.50966	0.962000	0.63368	2.211000	0.42825	2.545000	0.85829	0.650000	0.86243	TTC	.	.		0.353	TMEM56-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029935.1	NM_152487	
AMPD1	270	hgsc.bcm.edu	37	1	115223060	115223060	+	Missense_Mutation	SNP	C	C	T	rs149424604		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:115223060C>T	ENST00000520113.2	-	6	701	c.686G>A	c.(685-687)cGa>cAa	p.R229Q	AMPD1_ENST00000353928.6_Missense_Mutation_p.R196Q|AMPD1_ENST00000369538.3_Missense_Mutation_p.R225Q			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	229					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	GTTGTCTGTTCGGAAGGGGTC	0.423													C|||	1	0.000199681	0.0	0.0	5008	,	,		19044	0.0		0.0	False		,,,				2504	0.001				p.R229Q		Atlas-SNP	.											AMPD1_ENST00000520113,colon,carcinoma,0,4	AMPD1	223	.	0			c.G686A						.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	121.0	120.0	120.0		686,674	0.6	0.3	1	dbSNP_134	120	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	43,43	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	229/781,225/777	115223060	2,13004	2203	4300	6503	SO:0001583	missense	270	exon6			TCTGTTCGGAAGG	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.686G>A	chr1.hg19:g.115223060C>T	ENSP00000430075:p.Arg229Gln	146.0	0.0		119.0	31.0	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	hg19	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	10.79	1.450420	0.26074	2.27E-4	1.16E-4	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.86865	-2.18;-2.18;-2.18	6.07	0.651	0.17817	.	0.560054	0.20388	N	0.093306	T	0.62196	0.2408	L	0.33485	1.01	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.52866	-0.8518	10	0.20519	T	0.43	-0.3344	11.336	0.49505	0.0:0.5997:0.0:0.4003	.	225;196	Q5TF02;P23109	.;AMPD1_HUMAN	Q	229;225;196	ENSP00000430075:R229Q;ENSP00000358551:R225Q;ENSP00000316520:R196Q	ENSP00000316520:R196Q	R	-	2	0	AMPD1	115024583	0.003000	0.15002	0.273000	0.24645	0.985000	0.73830	0.135000	0.15952	-0.111000	0.12001	-0.224000	0.12420	CGA	.	C|1.000;T|0.000		0.423	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
NOTCH2	4853	hgsc.bcm.edu	37	1	120484359	120484359	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:120484359C>A	ENST00000256646.2	-	18	2990	c.2771G>T	c.(2770-2772)gGt>gTt	p.G924V		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	924	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATACAGGAACCTCCATTCTG	0.433			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.G924V		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.G2771T						.						59.0	56.0	57.0					1																	120484359		2203	4300	6503	SO:0001583	missense	4853	exon18	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CAGGAACCTCCAT	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.2771G>T	chr1.hg19:g.120484359C>A	ENSP00000256646:p.Gly924Val	268.0	0.0		280.0	109.0	NM_001200001	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.933683	0.73442	.	.	ENSG00000134250	ENST00000256646	D	0.97455	-4.39	6.08	4.16	0.48862	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.211734	0.23672	U	0.045707	D	0.98422	0.9475	H	0.95645	3.7	0.80722	D	1	P;D	0.52996	0.526;0.957	P;P	0.57324	0.61;0.818	D	0.99560	1.0968	10	0.87932	D	0	.	14.4364	0.67284	0.0:0.4895:0.5105:0.0	.	924;924	Q6IQ50;Q04721	.;NOTC2_HUMAN	V	924	ENSP00000256646:G924V	ENSP00000256646:G924V	G	-	2	0	NOTCH2	120285882	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	2.613000	0.46351	1.571000	0.49722	0.591000	0.81541	GGT	.	.		0.433	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
PFDN2	5202	hgsc.bcm.edu	37	1	161070507	161070507	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:161070507G>T	ENST00000368010.3	-	4	515	c.431C>A	c.(430-432)gCt>gAt	p.A144D	PFDN2_ENST00000468311.1_5'UTR	NM_012394.3	NP_036526.2	Q9UHV9	PFD2_HUMAN	prefoldin subunit 2	144					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	unfolded protein binding (GO:0051082)			lung(1)|skin(1)	2	all_cancers(52;1.84e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			GCTGGCCTTAGCCCCAGCCCC	0.458																																					p.A144D		Atlas-SNP	.											.	PFDN2	10	.	0			c.C431A						.						110.0	105.0	107.0					1																	161070507		2203	4300	6503	SO:0001583	missense	5202	exon4			GCCTTAGCCCCAG	AF165883	CCDS1217.1	1q23.3	2008-02-05	2006-02-24		ENSG00000143256	ENSG00000143256			8867	protein-coding gene	gene with protein product		613466	"""prefoldin 2"""			10051400	Standard	NM_012394		Approved		uc001fxu.3	Q9UHV9	OTTHUMG00000031481	ENST00000368010.3:c.431C>A	chr1.hg19:g.161070507G>T	ENSP00000356989:p.Ala144Asp	140.0	0.0		128.0	6.0	NM_012394	Q9P0P7|Q9UN05	Missense_Mutation	SNP	ENST00000368010.3	hg19	CCDS1217.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.985728	0.35036	.	.	ENSG00000143256	ENST00000368010	.	.	.	5.24	5.24	0.73138	.	0.112377	0.64402	D	0.000013	T	0.29882	0.0747	N	0.22421	0.69	0.46336	D	0.99899	B	0.31893	0.345	B	0.34180	0.177	T	0.13282	-1.0515	9	0.15066	T	0.55	-5.9868	16.3815	0.83462	0.0:0.0:1.0:0.0	.	144	Q9UHV9	PFD2_HUMAN	D	144	.	ENSP00000356989:A144D	A	-	2	0	PFDN2	159337131	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.817000	0.86213	2.724000	0.93272	0.561000	0.74099	GCT	.	.		0.458	PFDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077100.1	NM_012394	
C1orf226	400793	hgsc.bcm.edu	37	1	162353116	162353116	+	Silent	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:162353116A>G	ENST00000458626.2	+	2	634	c.462A>G	c.(460-462)ccA>ccG	p.P154P	C1orf226_ENST00000426197.2_Silent_p.P197P	NM_001085375.1	NP_001078844.1	A1L170	CA226_HUMAN	chromosome 1 open reading frame 226	154										central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12						GGACAGAGCCATCACCTGGGC	0.602																																					p.P197P		Atlas-SNP	.											.	C1orf226	49	.	0			c.A591G						.						35.0	39.0	38.0					1																	162353116		1997	4169	6166	SO:0001819	synonymous_variant	400793	exon3			AGAGCCATCACCT	AI480219, AK023199, AK125122, AL512785, BC127743	CCDS44268.1, CCDS53422.1	1q23.3	2013-10-11			ENSG00000239887	ENSG00000239887			34351	protein-coding gene	gene with protein product						14702039	Standard	NM_001085375		Approved	FLJ13137	uc010pkt.1	A1L170	OTTHUMG00000031376	ENST00000458626.2:c.462A>G	chr1.hg19:g.162353116A>G		170.0	0.0		191.0	73.0	NM_001135240	B4DF31	Silent	SNP	ENST00000458626.2	hg19	CCDS53422.1																																																																																			.	.		0.602	C1orf226-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076793.2	NM_001085375	
DENND1B	163486	hgsc.bcm.edu	37	1	197704827	197704827	+	Intron	SNP	A	A	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:197704827A>T	ENST00000367396.3	-	3	252				DENND1B_ENST00000400967.2_5'Flank|DENND1B_ENST00000477581.1_5'UTR|DENND1B_ENST00000235453.4_5'UTR	NM_144977.4	NP_659414.2	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B						positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|kidney(2)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	22						GGGAGGCGCTACGCCAGGACC	0.567																																					p.V61E		Atlas-SNP	.											.	DENND1B	108	.	0			c.T182A						.						36.0	29.0	31.0					1																	197704827		692	1591	2283	SO:0001627	intron_variant	163486	exon3			GGCGCTACGCCAG	BC016588	CCDS41452.2, CCDS72996.1, CCDS72997.1	1q31.3	2012-10-03	2005-08-17	2005-08-17	ENSG00000213047	ENSG00000213047		"""DENN/MADD domain containing"""	28404	protein-coding gene	gene with protein product		613292	"""family with sequence similarity 31, member B"", ""chromosome 1 open reading frame 218"""	FAM31B, C1orf218		12477932	Standard	NM_144977		Approved	MGC27044, FLJ20054	uc021pgu.1	Q6P3S1	OTTHUMG00000035653	ENST00000367396.3:c.83-20623T>A	chr1.hg19:g.197704827A>T		61.0	0.0		60.0	19.0	NM_001195216	B5MD89|D3PFD5|Q5T3B8|Q5T3B9|Q5T3C1|Q5TAI8|Q6B0I8|Q8NDT1|Q8TBE6|Q9H774|Q9NXU2	Missense_Mutation	SNP	ENST00000367396.3	hg19	CCDS41452.2																																																																																			.	.		0.567	DENND1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086539.1	NM_144977	
NVL	4931	hgsc.bcm.edu	37	1	224415337	224415337	+	Silent	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:224415337G>A	ENST00000281701.6	-	23	2821	c.2562C>T	c.(2560-2562)ctC>ctT	p.L854L	NVL_ENST00000340871.4_Silent_p.L665L|NVL_ENST00000482491.1_Silent_p.L578L|NVL_ENST00000391875.2_Silent_p.L748L|NVL_ENST00000469075.1_Silent_p.L763L|RP11-365O16.6_ENST00000420350.1_RNA	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	854						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		ATCACCGGCTGAGGGACTCCT	0.547																																					p.L854L		Atlas-SNP	.											.	NVL	74	.	0			c.C2562T						.						60.0	56.0	57.0					1																	224415337		2203	4300	6503	SO:0001819	synonymous_variant	4931	exon23			CCGGCTGAGGGAC	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"""ATPases / AAA-type"""	8070	protein-coding gene	gene with protein product	"""Nuclear valosin-containing protein-like"", ""nuclear VCP-like protein"""	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.2562C>T	chr1.hg19:g.224415337G>A		420.0	0.0		362.0	103.0	NM_002533	B4DMC4|B4DP98|Q96EM7	Silent	SNP	ENST00000281701.6	hg19	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	G	7.535	0.659437	0.14645	.	.	ENSG00000143748	ENST00000469968	.	.	.	4.9	1.7	0.24286	.	.	.	.	.	.	.	.	.	.	.	0.48571	D	0.99967	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.3407	6.6129	0.22761	0.0974:0.3502:0.5523:0.0	.	.	.	.	X	737	.	.	Q	-	1	0	NVL	222481960	0.360000	0.24964	0.262000	0.24481	0.302000	0.27658	0.335000	0.19806	0.560000	0.29169	0.655000	0.94253	CAG	.	.		0.547	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533	
OBSCN	84033	hgsc.bcm.edu	37	1	228487195	228487195	+	Intron	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:228487195G>A	ENST00000422127.1	+	43	11703				RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000570156.2_Silent_p.E4482E|OBSCN_ENST00000359599.6_3'UTR|OBSCN_ENST00000366707.4_Silent_p.E1172E	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTGGGCAGGAGAGGACCTCAG	0.537																																					p.E4482E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G13446A						.						193.0	163.0	172.0					1																	228487195		876	1991	2867	SO:0001627	intron_variant	84033	exon50			GCAGGAGAGGACC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11659+4451G>A	chr1.hg19:g.228487195G>A		29.0	0.0		38.0	7.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.537	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
EXOC8	149371	hgsc.bcm.edu	37	1	231472537	231472537	+	Nonsense_Mutation	SNP	C	C	A	rs144793875	byFrequency	TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:231472537C>A	ENST00000360394.2	-	1	1041	c.955G>T	c.(955-957)Gaa>Taa	p.E319*	SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank|EXOC8_ENST00000366645.1_Nonsense_Mutation_p.E315*|SPRTN_ENST00000391858.4_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	319	Poly-Glu.				cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				ACAGCTGGTTCTTCTTCTTCG	0.552																																					p.E319X		Atlas-SNP	.											.	EXOC8	42	.	0			c.G955T						.						139.0	122.0	128.0					1																	231472537		2203	4300	6503	SO:0001587	stop_gained	149371	exon1			CTGGTTCTTCTTC	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.955G>T	chr1.hg19:g.231472537C>A	ENSP00000353564:p.Glu319*	98.0	0.0		95.0	36.0	NM_175876	B3KU33|Q5TE82	Nonsense_Mutation	SNP	ENST00000360394.2	hg19	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	C	36	5.960066	0.97145	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	.	.	.	5.55	4.62	0.57501	.	0.268239	0.28940	N	0.013649	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-13.2016	15.9135	0.79491	0.0:0.8641:0.1359:0.0	.	.	.	.	X	319;315	.	ENSP00000353564:E319X	E	-	1	0	EXOC8	229539160	1.000000	0.71417	0.131000	0.22000	0.852000	0.48524	7.017000	0.76399	1.287000	0.44583	0.561000	0.74099	GAA	.	C|0.997;G|0.003		0.552	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876	
MOGS	7841	hgsc.bcm.edu	37	2	74692368	74692368	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:74692368G>A	ENST00000233616.4	-	1	169	c.7C>T	c.(7-9)Cgg>Tgg	p.R3W	MOGS_ENST00000535045.1_Missense_Mutation_p.R3W|MOGS_ENST00000452063.2_Intron|MOGS_ENST00000409065.1_Missense_Mutation_p.R3W|MOGS_ENST00000462443.1_Intron	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	3					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						CGCTCGCCCCGAGCCATCCTG	0.781																																					p.R3W		Atlas-SNP	.											.	MOGS	58	.	0			c.C7T						.						5.0	6.0	5.0					2																	74692368		1176	2657	3833	SO:0001583	missense	7841	exon1			CGCCCCGAGCCAT	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.7C>T	chr2.hg19:g.74692368G>A	ENSP00000233616:p.Arg3Trp	249.0	1.0		187.0	86.0	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	hg19	CCDS42700.1	.	.	.	.	.	.	.	.	.	.	G	35	5.459894	0.96240	.	.	ENSG00000115275	ENST00000233616;ENST00000409065;ENST00000535045	T	0.42900	0.96	4.72	4.72	0.59763	.	0.154600	0.39274	N	0.001408	T	0.43277	0.1240	N	0.08118	0	0.39413	D	0.966781	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.948	T	0.54879	-0.8227	10	0.87932	D	0	-20.6456	13.0502	0.58950	0.0:0.0:1.0:0.0	.	3;3	B4E3B8;Q13724	.;MOGS_HUMAN	W	3	ENSP00000233616:R3W	ENSP00000233616:R3W	R	-	1	2	MOGS	74545876	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.432000	0.59922	2.448000	0.82819	0.643000	0.83706	CGG	.	.		0.781	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
M1AP	130951	hgsc.bcm.edu	37	2	74842177	74842177	+	Silent	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:74842177G>A	ENST00000290536.5	-	3	456	c.340C>T	c.(340-342)Ctg>Ttg	p.L114L	M1AP_ENST00000409585.1_Silent_p.L114L|M1AP_ENST00000358434.2_5'UTR|M1AP_ENST00000536235.1_Silent_p.L114L	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	114					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											TCTACTGCCAGCCGCAGAGAA	0.512																																					p.L114L		Atlas-SNP	.											.	.	.	.	0			c.C340T						.						186.0	161.0	170.0					2																	74842177		2203	4300	6503	SO:0001819	synonymous_variant	130951	exon3			CTGCCAGCCGCAG		CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"""meiosis 1 arresting protein"", ""spermatogenesis associated 37"""		"""chromosome 2 open reading frame 65"""	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.340C>T	chr2.hg19:g.74842177G>A		127.0	0.0		112.0	42.0	NM_138804	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Silent	SNP	ENST00000290536.5	hg19	CCDS33229.1																																																																																			.	.		0.512	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804	
SCN2A	6326	hgsc.bcm.edu	37	2	166172100	166172100	+	Silent	SNP	G	G	T	rs267598958		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:166172100G>T	ENST00000375437.2	+	11	1793	c.1503G>T	c.(1501-1503)ctG>ctT	p.L501L	SCN2A_ENST00000283256.6_Silent_p.L501L|SCN2A_ENST00000375427.2_Silent_p.L501L|SCN2A_ENST00000357398.3_Silent_p.L501L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	501					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAAAAGAGCTGAaaaacagaa	0.393																																					p.L501L		Atlas-SNP	.											.	SCN2A	589	.	0			c.G1503T						.						44.0	47.0	46.0					2																	166172100		2203	4300	6503	SO:0001819	synonymous_variant	6326	exon10			AGAGCTGAAAAAC	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1503G>T	chr2.hg19:g.166172100G>T		178.0	0.0		155.0	53.0	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	hg19	CCDS33314.1																																																																																			.	.		0.393	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
TTN	7273	hgsc.bcm.edu	37	2	179474547	179474547	+	Silent	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:179474547C>A	ENST00000591111.1	-	222	46904	c.46680G>T	c.(46678-46680)ctG>ctT	p.L15560L	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Silent_p.L14633L|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.L8328L|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Silent_p.L17201L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Silent_p.L8261L|TTN_ENST00000460472.2_Silent_p.L8136L			Q8WZ42	TITIN_HUMAN	titin	15560	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATTGGTACCAGGTGTTCAT	0.478																																					p.L17201L		Atlas-SNP	.											.	TTN	18412	.	0			c.G51603T						.						447.0	426.0	433.0					2																	179474547		1926	4144	6070	SO:0001819	synonymous_variant	7273	exon272			TGGTACCAGGTGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.46680G>T	chr2.hg19:g.179474547C>A		186.0	0.0		159.0	35.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ABI2	10152	hgsc.bcm.edu	37	2	204267450	204267450	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:204267450G>C	ENST00000422511.2	+	9	1117	c.1086G>C	c.(1084-1086)caG>caC	p.Q362H	ABI2_ENST00000261017.5_Missense_Mutation_p.Q328H|ABI2_ENST00000430418.1_Missense_Mutation_p.Q340H|ABI2_ENST00000261016.6_Missense_Mutation_p.Q283H|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000424558.1_Missense_Mutation_p.Q389H|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000295851.5_Missense_Mutation_p.Q395H|ABI2_ENST00000261018.7_Missense_Mutation_p.Q181H			Q9NYB9	ABI2_HUMAN	abl-interactor 2	395	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						TTTATAGCCAGAATCCAGGTT	0.373																																					p.Q328H		Atlas-SNP	.											ABI2,colon,carcinoma,0,1	ABI2	44	.	0			c.G984C						.						102.0	100.0	101.0					2																	204267450		2203	4300	6503	SO:0001583	missense	10152	exon7			TAGCCAGAATCCA	AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1086G>C	chr2.hg19:g.204267450G>C	ENSP00000396249:p.Gln362His	191.0	0.0		165.0	58.0	NM_005759	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Missense_Mutation	SNP	ENST00000422511.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.104458|4.104458	0.77096|0.77096	.|.	.|.	ENSG00000138443|ENSG00000138443	ENST00000295851;ENST00000261017;ENST00000430418;ENST00000424558;ENST00000261016;ENST00000417864;ENST00000422511;ENST00000261018|ENST00000451591;ENST00000454023	T;T;T;T;T;T;T;T|.	0.48836|.	1.02;1.08;1.16;1.02;0.93;1.25;1.07;0.8|.	5.6|5.6	4.72|4.72	0.59763|0.59763	.|.	0.050825|.	0.85682|.	D|.	0.000000|.	T|T	0.64962|0.64962	0.2646|0.2646	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	B;D;D;D;D;D;D;D;P|.	0.69078|.	0.435;0.997;0.99;0.995;0.988;0.976;0.995;0.98;0.816|.	B;D;D;P;D;D;D;D;P|.	0.77004|.	0.109;0.921;0.979;0.862;0.977;0.923;0.989;0.948;0.866|.	T|T	0.62872|0.62872	-0.6762|-0.6762	10|5	0.87932|.	D|.	0|.	-9.7717|-9.7717	12.2155|12.2155	0.54404|0.54404	0.078:0.0:0.922:0.0|0.078:0.0:0.922:0.0	.|.	181;230;120;272;389;340;283;395;328|.	B7Z5L1;B7Z612;B4DMM5;B7Z836;Q9NYB9-4;E9PEZ7;Q9NYB9-3;Q9NYB9;Q9NYB9-2|.	.;.;.;.;.;.;.;ABI2_HUMAN;.|.	H|T	395;328;340;389;283;395;362;181|199;175	ENSP00000295851:Q395H;ENSP00000261017:Q328H;ENSP00000408898:Q340H;ENSP00000391433:Q389H;ENSP00000261016:Q283H;ENSP00000414703:Q395H;ENSP00000396249:Q362H;ENSP00000261018:Q181H|.	ENSP00000261016:Q283H|.	Q|R	+|+	3|2	2|0	ABI2|ABI2	203975695|203975695	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.249000|5.249000	0.65427|0.65427	2.636000|2.636000	0.89361|0.89361	0.655000|0.655000	0.94253|0.94253	CAG|AGA	.	.		0.373	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759	
PSMD1	5707	hgsc.bcm.edu	37	2	232028365	232028365	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:232028365A>G	ENST00000308696.6	+	21	2567	c.2405A>G	c.(2404-2406)tAt>tGt	p.Y802C	PSMD1_ENST00000373635.4_Intron|PSMD1_ENST00000409643.1_Intron	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	802					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	AAAGTTCAGTATAAATCGAAC	0.383																																					p.Y802C		Atlas-SNP	.											.	PSMD1	77	.	0			c.A2405G						.						110.0	108.0	108.0					2																	232028365		2203	4300	6503	SO:0001583	missense	5707	exon21			TTCAGTATAAATC	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"""Proteasome (prosome, macropain) subunits"""	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.2405A>G	chr2.hg19:g.232028365A>G	ENSP00000309474:p.Tyr802Cys	122.0	0.0		81.0	33.0	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Missense_Mutation	SNP	ENST00000308696.6	hg19	CCDS2482.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.130568	0.77549	.	.	ENSG00000173692	ENST00000308696	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.63757	0.2538	L	0.59436	1.845	0.80722	D	1	D	0.59357	0.985	P	0.51193	0.662	T	0.69379	-0.5161	9	0.87932	D	0	-13.8533	14.5377	0.67973	1.0:0.0:0.0:0.0	.	802	Q99460	PSMD1_HUMAN	C	802	.	ENSP00000309474:Y802C	Y	+	2	0	PSMD1	231736609	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.139000	0.94554	2.002000	0.58637	0.454000	0.30748	TAT	.	.		0.383	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2		
ALPI	248	hgsc.bcm.edu	37	2	233323747	233323747	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr2:233323747G>A	ENST00000295463.3	+	11	1555	c.1478G>A	c.(1477-1479)tGc>tAc	p.C493Y		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	493					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TACACGGCCTGCGACCTGGCG	0.726																																					p.C493Y		Atlas-SNP	.											.	ALPI	64	.	0			c.G1478A						.						18.0	18.0	18.0					2																	233323747		2136	4212	6348	SO:0001583	missense	248	exon11			CGGCCTGCGACCT	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.1478G>A	chr2.hg19:g.233323747G>A	ENSP00000295463:p.Cys493Tyr	121.0	0.0		76.0	37.0	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	hg19	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248887	0.80024	.	.	ENSG00000163295	ENST00000295463	D	0.95690	-3.78	4.84	4.84	0.62591	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.217378	0.49305	D	0.000157	D	0.95802	0.8634	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.96792	0.9583	10	0.62326	D	0.03	.	17.9391	0.89021	0.0:0.0:1.0:0.0	.	493	P09923	PPBI_HUMAN	Y	493	ENSP00000295463:C493Y	ENSP00000295463:C493Y	C	+	2	0	ALPI	233031991	1.000000	0.71417	0.117000	0.21633	0.051000	0.14879	4.944000	0.63561	2.213000	0.71641	0.591000	0.81541	TGC	.	.		0.726	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
IL17RC	84818	hgsc.bcm.edu	37	3	9975230	9975230	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:9975230C>T	ENST00000295981.3	+	19	2547	c.2329C>T	c.(2329-2331)Cgc>Tgc	p.R777C	IL17RC_ENST00000403601.3_Missense_Mutation_p.R706C|IL17RC_ENST00000416074.2_Missense_Mutation_p.R532C|RP11-1020A11.1_ENST00000602411.1_RNA|CRELD1_ENST00000397170.3_5'Flank|CRELD1_ENST00000383811.3_5'Flank|CRELD1_ENST00000326434.5_5'Flank|IL17RC_ENST00000413608.1_Missense_Mutation_p.R693C|IL17RC_ENST00000498214.1_3'UTR|CRELD1_ENST00000452070.1_5'Flank|IL17RC_ENST00000383812.4_Missense_Mutation_p.R691C|IL17RC_ENST00000455057.1_Missense_Mutation_p.R674C	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	777					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CGCGCCGGGACGCGGGGTGGG	0.672																																					p.R777C		Atlas-SNP	.											.	IL17RC	55	.	0			c.C2329T						.						6.0	8.0	8.0					3																	9975230		1761	3844	5605	SO:0001583	missense	84818	exon19			CCGGGACGCGGGG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.2329C>T	chr3.hg19:g.9975230C>T	ENSP00000295981:p.Arg777Cys	104.0	0.0		80.0	22.0	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	hg19	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.928411	0.34002	.	.	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T	0.47528	1.83;1.81;1.83;0.84;1.83	4.22	-1.66	0.08265	.	3.416830	0.01360	N	0.012212	T	0.32912	0.0845	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B;B;B	0.09022	0.001;0.001;0.001;0.001;0.001;0.001;0.002;0.001	B;B;B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.0;0.001;0.0;0.001	T	0.34079	-0.9843	10	0.72032	D	0.01	1.8744	5.5264	0.16960	0.0:0.2842:0.4943:0.2215	.	532;674;676;693;532;691;777;706	F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;B4E008;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;I17RC_HUMAN;.	C	691;777;706;532;674;693	ENSP00000373323:R691C;ENSP00000295981:R777C;ENSP00000384969:R706C;ENSP00000407894:R674C;ENSP00000396064:R693C	ENSP00000295981:R777C	R	+	1	0	IL17RC	9950230	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.088000	0.14979	-0.113000	0.11958	-0.266000	0.10368	CGC	.	.		0.672	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
SATB1	6304	hgsc.bcm.edu	37	3	18390666	18390666	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:18390666T>C	ENST00000338745.6	-	11	4022	c.2288A>G	c.(2287-2289)gAc>gGc	p.D763G	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.D763G|SATB1_ENST00000417717.2_Missense_Mutation_p.D795G	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	763					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						TTTATCTCAGTCTTTCAAATC	0.353																																					p.D795G		Atlas-SNP	.											.	SATB1	96	.	0			c.A2384G						.						104.0	101.0	102.0					3																	18390666		2203	4300	6503	SO:0001583	missense	6304	exon12			TCTCAGTCTTTCA		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"""Homeoboxes / CUT class"""	10541	protein-coding gene	gene with protein product		602075	"""special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"""			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.2288A>G	chr3.hg19:g.18390666T>C	ENSP00000341024:p.Asp763Gly	138.0	0.0		125.0	42.0	NM_001195470	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	4.989	0.183690	0.09495	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	T;T;T	0.55052	0.62;0.62;0.54	5.7	5.7	0.88788	.	0.107977	0.64402	D	0.000009	T	0.41259	0.1151	N	0.19112	0.55	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.001	T	0.26677	-1.0096	10	0.66056	D	0.02	-10.4461	15.9579	0.79902	0.0:0.0:0.0:1.0	.	795;763	Q01826-2;Q01826	.;SATB1_HUMAN	G	763;763;795	ENSP00000341024:D763G;ENSP00000399708:D763G;ENSP00000399518:D795G	ENSP00000341024:D763G	D	-	2	0	SATB1	18365670	1.000000	0.71417	1.000000	0.80357	0.146000	0.21551	6.979000	0.76154	2.178000	0.69098	0.533000	0.62120	GAC	.	.		0.353	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010	
RNF123	63891	hgsc.bcm.edu	37	3	49753432	49753432	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:49753432C>T	ENST00000327697.6	+	33	3472	c.3328C>T	c.(3328-3330)Cgt>Tgt	p.R1110C	RNF123_ENST00000433785.1_Missense_Mutation_p.R222C	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	1110					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GCTGCTGCGGCGTCTTGCACA	0.602																																					p.R1110C		Atlas-SNP	.											.	RNF123	100	.	0			c.C3328T						.						100.0	94.0	96.0					3																	49753432		2203	4300	6503	SO:0001583	missense	63891	exon33			CTGCGGCGTCTTG	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.3328C>T	chr3.hg19:g.49753432C>T	ENSP00000328287:p.Arg1110Cys	48.0	0.0		51.0	23.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496586	0.85069	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000433785	D	0.84730	-1.89	5.97	5.07	0.68467	.	0.051043	0.85682	D	0.000000	D	0.90899	0.7140	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.91249	0.5028	10	0.87932	D	0	-13.933	14.3919	0.66986	0.2506:0.7494:0.0:0.0	.	1110	Q5XPI4	RN123_HUMAN	C	1110;1110;222	ENSP00000328287:R1110C	ENSP00000328287:R1110C	R	+	1	0	RNF123	49728436	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.474000	0.60203	2.828000	0.97474	0.655000	0.94253	CGT	.	.		0.602	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
MST1R	4486	hgsc.bcm.edu	37	3	49932696	49932696	+	Silent	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:49932696G>A	ENST00000296474.3	-	14	3202	c.3175C>T	c.(3175-3177)Cta>Tta	p.L1059L	MST1R_ENST00000344206.4_Silent_p.L1010L	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	1059					cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		AGGTCCCTTAGCTGGATGGAC	0.542																																					p.L1059L		Atlas-SNP	.											.	MST1R	205	.	0			c.C3175T						.						166.0	163.0	164.0					3																	49932696		2203	4300	6503	SO:0001819	synonymous_variant	4486	exon14			CCCTTAGCTGGAT	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"""CD molecules"""	7381	protein-coding gene	gene with protein product		600168	"""PTK8 protein tyrosine kinase 8"""	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.3175C>T	chr3.hg19:g.49932696G>A		114.0	0.0		146.0	43.0	NM_002447	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	hg19	CCDS2807.1																																																																																			.	.		0.542	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
CPOX	1371	hgsc.bcm.edu	37	3	98299597	98299597	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:98299597G>A	ENST00000264193.2	-	7	1513	c.1295C>T	c.(1294-1296)tCa>tTa	p.S432L		NM_000097.5	NP_000088.3	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	432					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to arsenic-containing substance (GO:0046685)|response to insecticide (GO:0017085)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to methylmercury (GO:0051597)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	coproporphyrinogen oxidase activity (GO:0004109)|protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CTCTGAGGGTGAATGCATGTA	0.403																																					p.S432L	Esophageal Squamous(75;7 1223 22300 43648 48951)	Atlas-SNP	.											.	CPOX	34	.	0			c.C1295T						.						82.0	72.0	76.0					3																	98299597		2203	4300	6503	SO:0001583	missense	1371	exon7			GAGGGTGAATGCA	BC017210	CCDS2932.1	3q12	2012-10-02		2004-01-30		ENSG00000080819	1.3.3.3		2321	protein-coding gene	gene with protein product	"""coproporphyria"""	612732	"""coproporphyrinogen oxidase (coproporphyria, harderoporphyria)"""	CPO		7757079, 8407975	Standard	NM_000097		Approved	CPX, HCP	uc003dsx.3	P36551		ENST00000264193.2:c.1295C>T	chr3.hg19:g.98299597G>A	ENSP00000264193:p.Ser432Leu	111.0	0.0		105.0	30.0	NM_000097	A8K275|B4DSD5|Q14060|Q53F08|Q8IZ45|Q96AF3	Missense_Mutation	SNP	ENST00000264193.2	hg19	CCDS2932.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.558600	0.45590	.	.	ENSG00000080819	ENST00000264193	D	0.93247	-3.19	5.62	4.75	0.60458	.	0.285416	0.39407	N	0.001363	D	0.89332	0.6685	L	0.45581	1.43	0.28967	N	0.889478	B	0.10296	0.003	B	0.12837	0.008	T	0.82546	-0.0403	10	0.44086	T	0.13	-6.4579	8.5325	0.33344	0.1742:0.0:0.8258:0.0	.	432	P36551	HEM6_HUMAN	L	432	ENSP00000264193:S432L	ENSP00000264193:S432L	S	-	2	0	CPOX	99782287	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.130000	0.50508	1.361000	0.45981	0.655000	0.94253	TCA	.	.		0.403	CPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358900.1	NM_000097	
POLQ	10721	hgsc.bcm.edu	37	3	121208342	121208342	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:121208342C>T	ENST00000264233.5	-	16	3564	c.3436G>A	c.(3436-3438)Gtg>Atg	p.V1146M		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1146					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TGACAAGTCACATTTTTACTC	0.353								DNA polymerases (catalytic subunits)																													p.V1146M	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G3436A						.						129.0	128.0	129.0					3																	121208342		2203	4300	6503	SO:0001583	missense	10721	exon16			AAGTCACATTTTT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3436G>A	chr3.hg19:g.121208342C>T	ENSP00000264233:p.Val1146Met	140.0	0.0		119.0	45.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	2.541	-0.306331	0.05458	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.51574	0.7	5.24	-2.31	0.06765	.	1.657830	0.03438	N	0.208881	T	0.29620	0.0739	N	0.14661	0.345	0.09310	N	1	B;B	0.22480	0.07;0.003	B;B	0.15870	0.014;0.009	T	0.20371	-1.0277	10	0.39692	T	0.17	.	7.3718	0.26806	0.0:0.5966:0.11:0.2934	.	1146;318	O75417;O75417-2	DPOLQ_HUMAN;.	M	769;1146;1282	ENSP00000264233:V1146M	ENSP00000264233:V1146M	V	-	1	0	POLQ	122691032	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.450000	0.06803	-0.331000	0.08501	-0.471000	0.05019	GTG	.	.		0.353	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
OSBPL11	114885	hgsc.bcm.edu	37	3	125271474	125271474	+	Missense_Mutation	SNP	T	T	C	rs375600104		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:125271474T>C	ENST00000296220.5	-	9	1494	c.1205A>G	c.(1204-1206)tAt>tGt	p.Y402C		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	402					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						AAAGTCTGCATACATTTCCAG	0.403																																					p.Y402C		Atlas-SNP	.											.	OSBPL11	64	.	0			c.A1205G						.	T	CYS/TYR	0,4406		0,0,2203	103.0	100.0	101.0		1205	3.8	1.0	3		101	1,8599	1.2+/-3.3	0,1,4299	no	missense	OSBPL11	NM_022776.4	194	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	402/748	125271474	1,13005	2203	4300	6503	SO:0001583	missense	114885	exon9			TCTGCATACATTT	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.1205A>G	chr3.hg19:g.125271474T>C	ENSP00000296220:p.Tyr402Cys	127.0	0.0		133.0	40.0	NM_022776	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	hg19	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	T	17.83	3.485106	0.63962	0.0	1.16E-4	ENSG00000144909	ENST00000296220	T	0.29142	1.58	5.07	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.58977	0.2160	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66756	-0.5843	10	0.87932	D	0	-18.2334	11.3851	0.49780	0.1349:0.0:0.0:0.8651	.	402	Q9BXB4	OSB11_HUMAN	C	402	ENSP00000296220:Y402C	ENSP00000296220:Y402C	Y	-	2	0	OSBPL11	126754164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.721000	0.84768	2.134000	0.65973	0.482000	0.46254	TAT	.	.		0.403	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776	
EFCC1	79825	hgsc.bcm.edu	37	3	128753168	128753168	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:128753168A>G	ENST00000480450.1	+	5	1445	c.1445A>G	c.(1444-1446)gAg>gGg	p.E482G	EFCC1_ENST00000436022.2_Missense_Mutation_p.E45G			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	482							calcium ion binding (GO:0005509)										ACCTCTGAGGAGGAGGTCAGC	0.597																																					p.E482G		Atlas-SNP	.											.	.	.	.	0			c.A1445G						.						39.0	39.0	39.0					3																	128753168		2203	4300	6503	SO:0001583	missense	79825	exon5			CTGAGGAGGAGGT	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"""EF-hand domain containing"""	25692	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 73"", ""coiled-coil domain containing 48"""	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1445A>G	chr3.hg19:g.128753168A>G	ENSP00000420075:p.Glu482Gly	81.0	0.0		53.0	24.0	NM_024768	A8MYE2	Missense_Mutation	SNP	ENST00000480450.1	hg19	CCDS3054.2	.	.	.	.	.	.	.	.	.	.	A	15.79	2.938030	0.52972	.	.	ENSG00000114654	ENST00000480450;ENST00000436022	T;T	0.49720	0.78;0.77	4.29	3.1	0.35709	.	0.586195	0.15359	N	0.266511	T	0.37839	0.1018	L	0.47716	1.5	0.24165	N	0.995645	B	0.11235	0.004	B	0.09377	0.004	T	0.29088	-1.0023	10	0.56958	D	0.05	.	6.7895	0.23692	0.8829:0.0:0.1171:0.0	.	482	Q9HA90	CCD48_HUMAN	G	482;45	ENSP00000420075:E482G;ENSP00000414597:E45G	ENSP00000414597:E45G	E	+	2	0	CCDC48	130235858	1.000000	0.71417	0.858000	0.33744	0.515000	0.34225	5.818000	0.69236	1.687000	0.51057	0.260000	0.18958	GAG	.	.		0.597	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768	
EFCAB12	90288	hgsc.bcm.edu	37	3	129127685	129127685	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:129127685A>G	ENST00000505956.1	-	6	1214	c.1052T>C	c.(1051-1053)aTc>aCc	p.I351T	EFCAB12_ENST00000326085.3_Missense_Mutation_p.I351T	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	351							calcium ion binding (GO:0005509)										CGTGTACTGGATGGAGGGGAT	0.587																																					p.I351T		Atlas-SNP	.											.	.	.	.	0			c.T1052C						.						50.0	52.0	51.0					3																	129127685		2108	4221	6329	SO:0001583	missense	90288	exon6			TACTGGATGGAGG	AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.1052T>C	chr3.hg19:g.129127685A>G	ENSP00000420854:p.Ile351Thr	119.0	0.0		118.0	56.0	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	hg19	CCDS54638.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.784466	0.31593	.	.	ENSG00000172771	ENST00000505956;ENST00000326085	T;T	0.02656	4.21;4.21	4.82	3.66	0.41972	.	0.584995	0.14920	N	0.290738	T	0.07773	0.0195	L	0.32530	0.975	0.22066	N	0.999389	D	0.76494	0.999	D	0.80764	0.994	T	0.26326	-1.0106	10	0.72032	D	0.01	-31.2919	8.3798	0.32463	0.9081:0.0:0.0919:0.0	.	351	Q6NXP0	CC025_HUMAN	T	351	ENSP00000420854:I351T;ENSP00000324241:I351T	ENSP00000324241:I351T	I	-	2	0	C3orf25	130610375	0.999000	0.42202	0.993000	0.49108	0.096000	0.18686	2.061000	0.41403	0.691000	0.31592	-0.264000	0.10439	ATC	.	.		0.587	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
MBNL1	4154	hgsc.bcm.edu	37	3	152173338	152173338	+	Intron	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr3:152173338A>G	ENST00000463374.1	+	7	1526				MBNL1_ENST00000282488.7_Intron|RP11-362A9.3_ENST00000463255.1_RNA|MBNL1_ENST00000324210.5_Missense_Mutation_p.I323M|MBNL1_ENST00000492948.1_Missense_Mutation_p.I323M|MBNL1_ENST00000355460.2_Intron|MBNL1_ENST00000357472.3_Missense_Mutation_p.I323M|MBNL1_ENST00000485910.1_Intron|MBNL1_ENST00000324196.5_Intron|MBNL1_ENST00000498502.1_Intron|MBNL1_ENST00000545754.1_Missense_Mutation_p.I255M|MBNL1_ENST00000282486.6_Intron|MBNL1_ENST00000485509.1_Intron|MBNL1_ENST00000493459.1_Missense_Mutation_p.I284M	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1						alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CAGGCTCAATATTGTGCATGA	0.413																																					p.I323M		Atlas-SNP	.											.	MBNL1	100	.	0			c.A969G						.						238.0	212.0	221.0					3																	152173338		2203	4300	6503	SO:0001627	intron_variant	4154	exon7			CTCAATATTGTGC	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"""Zinc fingers, CCCH-type domain containing"""	6923	protein-coding gene	gene with protein product		606516	"""muscleblind (Drosophila)-like"", ""muscleblind-like (Drosophila)"""	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.1016-718A>G	chr3.hg19:g.152173338A>G		104.0	0.0		97.0	30.0	NM_021038	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.924937	0.34002	.	.	ENSG00000152601	ENST00000493459;ENST00000324210;ENST00000545754;ENST00000357472;ENST00000465907;ENST00000492948;ENST00000478535	.	.	.	5.7	4.49	0.54785	.	.	.	.	.	T	0.19287	0.0463	N	0.00991	-1.07	0.31524	N	0.662024	B;B;B;P	0.45715	0.066;0.009;0.356;0.865	B;B;B;P	0.46253	0.066;0.011;0.197;0.509	T	0.21177	-1.0253	8	0.48119	T	0.1	.	14.1329	0.65266	0.8669:0.133:0.0:0.0	.	255;323;284;323	Q96RE3;Q86UV8;Q86VM6;Q96P92	.;.;.;.	M	284;323;255;323;255;323;191	.	ENSP00000319429:I323M	I	+	3	3	MBNL1	153656028	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.611000	0.67674	2.168000	0.68352	0.533000	0.62120	ATA	.	.		0.413	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038	
LDB2	9079	hgsc.bcm.edu	37	4	16900005	16900005	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:16900005A>G	ENST00000304523.5	-	1	427	c.104T>C	c.(103-105)aTg>aCg	p.M35T	LDB2_ENST00000502640.1_Missense_Mutation_p.M35T|LDB2_ENST00000515064.1_Missense_Mutation_p.M35T|LDB2_ENST00000441778.2_Missense_Mutation_p.M35T	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2	35					epithelial structure maintenance (GO:0010669)|hair follicle development (GO:0001942)|positive regulation of cellular component biogenesis (GO:0044089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell maintenance (GO:0035019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	LIM domain binding (GO:0030274)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						TCTCTTGTTCATCTCATAGAT	0.448																																					p.M35T		Atlas-SNP	.											.	LDB2	129	.	0			c.T104C						.						202.0	179.0	187.0					4																	16900005		2203	4300	6503	SO:0001583	missense	9079	exon1			TTGTTCATCTCAT	AF068651	CCDS3420.1, CCDS47031.1	4p16	2008-08-01			ENSG00000169744	ENSG00000169744			6533	protein-coding gene	gene with protein product		603450				9853615, 9880598, 10861853	Standard	NM_001290		Approved	CLIM1, LDB1	uc003goz.3	O43679	OTTHUMG00000048212	ENST00000304523.5:c.104T>C	chr4.hg19:g.16900005A>G	ENSP00000306772:p.Met35Thr	145.0	0.0		104.0	31.0	NM_001290	O60619|O75480	Missense_Mutation	SNP	ENST00000304523.5	hg19	CCDS3420.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.270647	0.59540	.	.	ENSG00000169744	ENST00000515064;ENST00000441778;ENST00000304523;ENST00000502640;ENST00000506732	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.57902	0.2085	L	0.47190	1.495	0.80722	D	1	B;P;P;P;B	0.40197	0.029;0.706;0.506;0.657;0.247	B;P;B;B;B	0.44921	0.085;0.464;0.333;0.409;0.247	T	0.63242	-0.6681	9	0.87932	D	0	-13.2894	13.9753	0.64268	1.0:0.0:0.0:0.0	.	1;35;35;35;35	B7Z6D0;E9PFI4;G5E9Y7;O43679-2;O43679	.;.;.;.;LDB2_HUMAN	T	35;35;35;35;11	.	ENSP00000306772:M35T	M	-	2	0	LDB2	16509103	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.790000	0.91844	1.883000	0.54544	0.377000	0.23210	ATG	.	.		0.448	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250321.2		
PDS5A	23244	hgsc.bcm.edu	37	4	39904058	39904058	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:39904058C>A	ENST00000303538.8	-	13	1947	c.1408G>T	c.(1408-1410)Gct>Tct	p.A470S	PDS5A_ENST00000503396.1_Missense_Mutation_p.A470S	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						AGATACTGAGCAAAGATTTTC	0.308																																					p.A470S		Atlas-SNP	.											.	PDS5A	114	.	0			c.G1408T						.						97.0	93.0	94.0					4																	39904058		1821	4079	5900	SO:0001583	missense	23244	exon13			ACTGAGCAAAGAT	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1408G>T	chr4.hg19:g.39904058C>A	ENSP00000303427:p.Ala470Ser	271.0	0.0		197.0	72.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.54|14.54	2.566126|2.566126	0.45694|0.45694	.|.	.|.	ENSG00000121892|ENSG00000121892	ENST00000303538;ENST00000503396|ENST00000513798	.|.	.|.	.|.	5.47|5.47	5.47|5.47	0.80525|0.80525	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67069|0.67069	0.2854|0.2854	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	D|D	1|1	B;P|.	0.50272|.	0.05;0.933|.	B;P|.	0.55222|.	0.037;0.771|.	T|T	0.62324|0.62324	-0.6878|-0.6878	8|5	.|.	.|.	.|.	-12.0649|-12.0649	19.313|19.313	0.94199|0.94199	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	470;470|.	Q29RF7-3;Q29RF7|.	.;PDS5A_HUMAN|.	S|F	470|107	.|.	.|.	A|L	-|-	1|3	0|2	PDS5A|PDS5A	39580453|39580453	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.818000|7.818000	0.86416|0.86416	2.570000|2.570000	0.86706|0.86706	0.655000|0.655000	0.94253|0.94253	GCT|TTG	.	.		0.308	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
ANKRD17	26057	hgsc.bcm.edu	37	4	73943157	73943157	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:73943157T>G	ENST00000358602.4	-	32	7618	c.7502A>C	c.(7501-7503)gAg>gCg	p.E2501A	ANKRD17_ENST00000330838.6_Missense_Mutation_p.E2250A|ANKRD17_ENST00000509867.2_Missense_Mutation_p.E2388A	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2501					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACTATCTCGCTCCATTGCTTG	0.458																																					p.E2501A		Atlas-SNP	.											.	ANKRD17	214	.	0			c.A7502C						.						195.0	175.0	182.0					4																	73943157		2203	4300	6503	SO:0001583	missense	26057	exon32			TCTCGCTCCATTG	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.7502A>C	chr4.hg19:g.73943157T>G	ENSP00000351416:p.Glu2501Ala	132.0	0.0		73.0	6.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	hg19	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	18.72	3.684889	0.68157	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867	T;T;T	0.75154	-0.91;-0.87;-0.87	5.65	5.65	0.86999	.	0.174226	0.39083	N	0.001469	T	0.69351	0.3101	L	0.49778	1.585	0.43014	D	0.994559	P;P;P;B	0.37330	0.59;0.59;0.455;0.319	B;B;B;B	0.33121	0.158;0.158;0.076;0.076	T	0.74160	-0.3755	10	0.87932	D	0	.	15.8801	0.79197	0.0:0.0:0.0:1.0	.	2500;2250;2501;2388	O75179-2;G5E964;O75179;E7EUV3	.;.;ANR17_HUMAN;.	A	2501;1908;2250;2388	ENSP00000351416:E2501A;ENSP00000332265:E2250A;ENSP00000427151:E2388A	ENSP00000332265:E2250A	E	-	2	0	ANKRD17	74162021	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.127000	0.77210	2.166000	0.68216	0.460000	0.39030	GAG	.	.		0.458	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
TRPC3	7222	hgsc.bcm.edu	37	4	122853582	122853582	+	Silent	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:122853582C>T	ENST00000379645.3	-	2	904	c.831G>A	c.(829-831)agG>agA	p.R277R	TRPC3_ENST00000264811.5_Silent_p.R204R|TRPC3_ENST00000513531.1_Silent_p.R204R	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	192					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.R204R(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AGGAGTCGTGCCTCTGCTTCT	0.592																																					p.R277R		Atlas-SNP	.											TRPC3_ENST00000379645,NS,carcinoma,-1,1	TRPC3	201	.	1	Substitution - coding silent(1)	endometrium(1)	c.G831A						.						51.0	46.0	47.0					4																	122853582		2203	4300	6503	SO:0001819	synonymous_variant	7222	exon2			GTCGTGCCTCTGC	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.831G>A	chr4.hg19:g.122853582C>T		177.0	0.0		105.0	9.0	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	hg19	CCDS47130.1																																																																																			.	.		0.592	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
FAT4	79633	hgsc.bcm.edu	37	4	126336041	126336041	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:126336041A>T	ENST00000394329.3	+	5	5936	c.5923A>T	c.(5923-5925)Atc>Ttc	p.I1975F	FAT4_ENST00000335110.5_Missense_Mutation_p.I273F	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1975	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AATTTCAGGCATCAACTCTCA	0.358																																					p.I1975F		Atlas-SNP	.											.	FAT4	1752	.	0			c.A5923T						.						64.0	68.0	67.0					4																	126336041		2203	4300	6503	SO:0001583	missense	79633	exon5			TCAGGCATCAACT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5923A>T	chr4.hg19:g.126336041A>T	ENSP00000377862:p.Ile1975Phe	164.0	0.0		92.0	6.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	9.485	1.099278	0.20552	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.51325	0.71;0.71	5.23	-1.08	0.09936	Cadherin (4);Cadherin-like (1);	0.871371	0.09306	U	0.820226	T	0.24353	0.0590	N	0.13352	0.335	0.20703	N	0.999868	B;B	0.09022	0.0;0.002	B;B	0.09377	0.003;0.004	T	0.21075	-1.0256	10	0.56958	D	0.05	.	0.8668	0.01205	0.208:0.2089:0.3295:0.2536	.	273;1975	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	F	1975;273	ENSP00000377862:I1975F;ENSP00000335169:I273F	ENSP00000335169:I273F	I	+	1	0	FAT4	126555491	0.000000	0.05858	0.916000	0.36221	0.926000	0.56050	-0.377000	0.07456	-0.170000	0.10816	0.528000	0.53228	ATC	.	.		0.358	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
JADE1	79960	hgsc.bcm.edu	37	4	129778563	129778563	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:129778563C>A	ENST00000226319.6	+	8	1215	c.935C>A	c.(934-936)gCg>gAg	p.A312E	PHF17_ENST00000452328.2_Missense_Mutation_p.A300E|PHF17_ENST00000511647.1_Missense_Mutation_p.A312E|PHF17_ENST00000512960.1_Missense_Mutation_p.A312E|PHF17_ENST00000413543.2_Missense_Mutation_p.A312E	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AGCCGGTGGGCGCTAGTGTGC	0.532																																					p.A312E		Atlas-SNP	.											.	PHF17	63	.	0			c.C935A						.						157.0	161.0	160.0					4																	129778563		2203	4300	6503	SO:0001583	missense	79960	exon8			GGTGGGCGCTAGT																												ENST00000226319.6:c.935C>A	chr4.hg19:g.129778563C>A	ENSP00000226319:p.Ala312Glu	151.0	0.0		96.0	50.0	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	hg19	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366421	0.61513	.	.	ENSG00000077684	ENST00000226319;ENST00000511647;ENST00000452328;ENST00000512960;ENST00000535321;ENST00000413543	T;T;T;T;T	0.13089	2.62;2.62;2.62;2.62;2.62	4.54	4.54	0.55810	.	0.111121	0.64402	D	0.000008	T	0.29749	0.0743	L	0.43554	1.36	0.80722	D	1	P;D;P	0.69078	0.908;0.997;0.455	P;D;B	0.74348	0.855;0.983;0.387	T	0.01099	-1.1452	9	.	.	.	.	17.8247	0.88661	0.0:1.0:0.0:0.0	.	300;312;312	Q6IE81-2;Q6IE81;Q6IE81-3	.;JADE1_HUMAN;.	E	312;312;300;312;312;312	ENSP00000226319:A312E;ENSP00000423737:A312E;ENSP00000388015:A300E;ENSP00000425730:A312E;ENSP00000404211:A312E	.	A	+	2	0	PHF17	129998013	1.000000	0.71417	0.969000	0.41365	0.114000	0.19823	6.966000	0.76073	2.496000	0.84212	0.655000	0.94253	GCG	.	.		0.532	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
ABCE1	6059	hgsc.bcm.edu	37	4	146041189	146041189	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:146041189A>C	ENST00000296577.4	+	11	1543	c.1028A>C	c.(1027-1029)aAa>aCa	p.K343T	OTUD4_ENST00000455611.2_Intron|ABCE1_ENST00000502803.1_3'UTR	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	343	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					GAAGAAGTTAAAAAGATGTGT	0.338																																					p.K343T		Atlas-SNP	.											.	ABCE1	47	.	0			c.A1028C						.						59.0	63.0	62.0					4																	146041189		2202	4300	6502	SO:0001583	missense	6059	exon11			AAGTTAAAAAGAT	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"""ATP binding cassette transporters / subfamily E"""	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.1028A>C	chr4.hg19:g.146041189A>C	ENSP00000296577:p.Lys343Thr	253.0	1.0		156.0	77.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Missense_Mutation	SNP	ENST00000296577.4	hg19	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.025636	0.54683	.	.	ENSG00000164163	ENST00000296577	D	0.94232	-3.38	5.31	5.31	0.75309	ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.88243	0.6384	N	0.20685	0.6	0.80722	D	1	B	0.16802	0.019	B	0.20955	0.032	D	0.84372	0.0544	10	0.41790	T	0.15	-18.4169	15.548	0.76123	1.0:0.0:0.0:0.0	.	343	P61221	ABCE1_HUMAN	T	343	ENSP00000296577:K343T	ENSP00000296577:K343T	K	+	2	0	ABCE1	146260639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.232000	0.95325	2.120000	0.65058	0.454000	0.30748	AAA	.	.		0.338	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940	
PLCXD3	345557	hgsc.bcm.edu	37	5	41382514	41382514	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:41382514A>T	ENST00000377801.3	-	2	300	c.226T>A	c.(226-228)Tgg>Agg	p.W76R	PLCXD3_ENST00000328457.3_Missense_Mutation_p.W76R			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	76	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GTGGCTAACCATTTCCGCATG	0.463																																					p.W76R		Atlas-SNP	.											.	PLCXD3	86	.	0			c.T226A						.						59.0	65.0	63.0					5																	41382514		2203	4300	6503	SO:0001583	missense	345557	exon2			CTAACCATTTCCG		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.226T>A	chr5.hg19:g.41382514A>T	ENSP00000367032:p.Trp76Arg	114.0	0.0		89.0	33.0	NM_001005473	A6NL04	Missense_Mutation	SNP	ENST00000377801.3	hg19	CCDS34150.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178619	0.78564	.	.	ENSG00000182836	ENST00000377801;ENST00000328457	.	.	.	6.07	6.07	0.98685	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (1);	0.000000	0.85682	D	0.000000	D	0.86577	0.5966	M	0.93150	3.385	0.80722	D	1	D	0.67145	0.996	D	0.79108	0.992	D	0.89906	0.4048	9	0.87932	D	0	-3.2113	16.6406	0.85098	1.0:0.0:0.0:0.0	.	76	Q63HM9	PLCX3_HUMAN	R	76	.	ENSP00000333751:W76R	W	-	1	0	PLCXD3	41418271	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.923000	0.92808	2.326000	0.78906	0.533000	0.62120	TGG	.	.		0.463	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875	
ZNF474	133923	hgsc.bcm.edu	37	5	121488330	121488330	+	Silent	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:121488330C>T	ENST00000296600.4	+	2	1028	c.645C>T	c.(643-645)acC>acT	p.T215T	ZNF474_ENST00000514925.1_Intron|CTC-441N14.2_ENST00000504829.1_RNA|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	215							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		GTAGTGGAACCCCAGCCCGAC	0.488																																					p.T215T		Atlas-SNP	.											.	ZNF474	43	.	0			c.C645T						.						98.0	97.0	97.0					5																	121488330		2203	4300	6503	SO:0001819	synonymous_variant	133923	exon2			TGGAACCCCAGCC	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.645C>T	chr5.hg19:g.121488330C>T		133.0	0.0		118.0	46.0	NM_207317	A8K4M0|Q96M07	Silent	SNP	ENST00000296600.4	hg19	CCDS4130.1																																																																																			.	.		0.488	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140768944	140768944	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:140768944A>G	ENST00000519479.1	+	1	1493	c.1493A>G	c.(1492-1494)gAg>gGg	p.E498G	PCDHGA7_ENST00000518325.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	498	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCAGCGGGAGCTGTCATCC	0.617																																					p.E498G		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.A1493G						.						59.0	66.0	64.0					5																	140768944		2015	4167	6182	SO:0001583	missense	8641	exon1			AGCGGGAGCTGTC	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1493A>G	chr5.hg19:g.140768944A>G	ENSP00000428288:p.Glu498Gly	135.0	0.0		139.0	45.0	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	hg19	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	10.27	1.305186	0.23736	.	.	ENSG00000253953	ENST00000519479	T	0.61158	0.13	5.18	2.04	0.26737	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.44435	0.1293	N	0.20986	0.625	0.19575	N	0.999965	B;B	0.20368	0.035;0.044	B;B	0.29524	0.062;0.103	T	0.45745	-0.9240	9	0.87932	D	0	.	8.4986	0.33144	0.2723:0.6484:0.0:0.0794	.	498;498	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	G	498	ENSP00000428288:E498G	ENSP00000428288:E498G	E	+	2	0	PCDHGB4	140749128	0.435000	0.25577	0.499000	0.27577	0.009000	0.06853	0.922000	0.28734	0.588000	0.29660	-1.142000	0.01873	GAG	.	.		0.617	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
DPCR1	135656	hgsc.bcm.edu	37	6	30918187	30918187	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:30918187C>T	ENST00000462446.1	+	2	1974	c.1946C>T	c.(1945-1947)gCc>gTc	p.A649V	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	196						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						GAAATGACAGCCAACGAGAAG	0.488																																					p.A649V		Atlas-SNP	.											.	DPCR1	99	.	0			c.C1946T						.						181.0	203.0	196.0					6																	30918187		692	1591	2283	SO:0001583	missense	135656	exon2			TGACAGCCAACGA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1946C>T	chr6.hg19:g.30918187C>T	ENSP00000417182:p.Ala649Val	158.0	0.0		114.0	47.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	7.090	0.571884	0.13623	.	.	ENSG00000168631	ENST00000462446	T	0.53423	0.62	1.43	-2.86	0.05717	.	.	.	.	.	T	0.15046	0.0363	L	0.27053	0.805	0.09310	N	0.999998	D	0.58620	0.983	P	0.51170	0.661	T	0.03662	-1.1015	9	0.23891	T	0.37	.	0.5364	0.00637	0.2429:0.3319:0.2406:0.1846	.	649	E9PEI6	.	V	649	ENSP00000417182:A649V	ENSP00000417182:A649V	A	+	2	0	DPCR1	31026166	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-1.035000	0.03564	-0.789000	0.04498	0.109000	0.15622	GCC	.	.		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
C2	717	hgsc.bcm.edu	37	6	31895872	31895872	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:31895872C>A	ENST00000299367.5	+	2	463	c.187C>A	c.(187-189)Ctg>Atg	p.L63M	CFB_ENST00000556679.1_Missense_Mutation_p.L63M|CFB_ENST00000456570.1_Missense_Mutation_p.L63M|C2_ENST00000418949.2_Missense_Mutation_p.L63M|C2_ENST00000442278.2_Intron|C2_ENST00000452323.2_Intron|C2_ENST00000469372.1_Intron|CFB_ENST00000477310.1_Missense_Mutation_p.L63M	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	63	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		AGCATCACGGCTGTGCAAGAG	0.642																																					p.L63M		Atlas-SNP	.											.	C2	50	.	0			c.C187A						.						26.0	28.0	27.0					6																	31895872		2203	4300	6503	SO:0001583	missense	717	exon2			TCACGGCTGTGCA		CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"""Complement system"""	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.187C>A	chr6.hg19:g.31895872C>A	ENSP00000299367:p.Leu63Met	74.0	0.0		58.0	22.0	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.602958	0.46423	.	.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000413154;ENST00000299367;ENST00000447952;ENST00000418949;ENST00000556679;ENST00000456570;ENST00000477310	T;T;T;T;T;T;T	0.50548	0.92;0.74;0.92;0.74;0.92;0.92;0.74	5.22	-2.13	0.07144	Complement control module (2);Sushi/SCR/CCP (2);	0.959111	0.08454	N	0.943421	T	0.10852	0.0265	.	.	.	0.09310	N	1	B;B;B	0.22276	0.067;0.005;0.017	B;B;B	0.21546	0.035;0.014;0.008	T	0.27297	-1.0078	9	0.41790	T	0.15	-3.6602	0.6883	0.00887	0.3716:0.1977:0.2444:0.1863	.	63;63;63	B4E1Z4;P06681;Q8N6L6	.;CO2_HUMAN;.	M	63	ENSP00000403325:L63M;ENSP00000299367:L63M;ENSP00000391354:L63M;ENSP00000406190:L63M;ENSP00000451848:L63M;ENSP00000410815:L63M;ENSP00000418996:L63M	ENSP00000299367:L63M	L	+	1	2	CFB;C2;XXbac-BPG116M5.17	32003851	0.000000	0.05858	0.057000	0.19452	0.551000	0.35334	-0.820000	0.04457	-0.277000	0.09193	0.655000	0.94253	CTG	.	.		0.642	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9		
ATF6B	1388	hgsc.bcm.edu	37	6	32085446	32085446	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:32085446C>T	ENST00000375203.3	-	13	1482	c.1450G>A	c.(1450-1452)Gcc>Acc	p.A484T	ATF6B_ENST00000375201.4_Missense_Mutation_p.A481T	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	484					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						AGCTCCTTGGCGCCCCCAGGG	0.562																																					p.A484T		Atlas-SNP	.											.	ATF6B	40	.	0			c.G1450A						.						53.0	58.0	56.0					6																	32085446		2203	4300	6503	SO:0001583	missense	1388	exon13			CCTTGGCGCCCCC		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.1450G>A	chr6.hg19:g.32085446C>T	ENSP00000364349:p.Ala484Thr	89.0	0.0		92.0	4.0	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Missense_Mutation	SNP	ENST00000375203.3	hg19	CCDS4737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.365|6.365	0.435387|0.435387	0.12045|0.12045	.|.	.|.	ENSG00000213676|ENSG00000213676	ENST00000375192;ENST00000375203;ENST00000375201|ENST00000453203	T;T|.	0.55588|.	0.51;1.25|.	5.58|5.58	1.6|1.6	0.23607|0.23607	.|.	1.089090|.	0.07216|.	N|.	0.860079|.	T|T	0.14743|0.14743	0.0356|0.0356	L|L	0.31294|0.31294	0.92|0.92	0.21355|0.21355	N|N	0.999715|0.999715	B;B;B|.	0.16396|.	0.017;0.006;0.01|.	B;B;B|.	0.11329|.	0.006;0.002;0.002|.	T|T	0.28964|0.28964	-1.0027|-1.0027	9|5	.|.	.|.	.|.	-5.3948|-5.3948	9.2689|9.2689	0.37659|0.37659	0.0:0.6772:0.0:0.3228|0.0:0.6772:0.0:0.3228	.|.	481;484;484|.	Q99941-2;Q99941;Q6AZW6|.	.;ATF6B_HUMAN;.|.	T|H	87;484;481|20	ENSP00000364349:A484T;ENSP00000364347:A481T|.	.|.	A|R	-|-	1|2	0|0	ATF6B|ATF6B	32193424|32193424	0.000000|0.000000	0.05858|0.05858	0.121000|0.121000	0.21740|0.21740	0.928000|0.928000	0.56348|0.56348	-0.526000|-0.526000	0.06207|0.06207	-0.004000|-0.004000	0.14419|0.14419	-0.126000|-0.126000	0.14955|0.14955	GCC|CGC	.	.		0.562	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2		
C6orf222	389384	hgsc.bcm.edu	37	6	36298079	36298079	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:36298079G>A	ENST00000437635.2	-	2	566	c.389C>T	c.(388-390)tCc>tTc	p.S130F		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	130										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						CGGATGCTGGGAGATACCCTC	0.607																																					p.S130F		Atlas-SNP	.											.	C6orf222	72	.	0			c.C389T						.						73.0	66.0	68.0					6																	36298079		2203	4300	6503	SO:0001583	missense	389384	exon2			TGCTGGGAGATAC		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.389C>T	chr6.hg19:g.36298079G>A	ENSP00000418983:p.Ser130Phe	66.0	0.0		70.0	27.0	NM_001010903	B2RTY8	Missense_Mutation	SNP	ENST00000437635.2	hg19	CCDS34439.1	.	.	.	.	.	.	.	.	.	.	G	4.432	0.079968	0.08533	.	.	ENSG00000189325	ENST00000437635	T	0.49139	0.79	3.55	1.72	0.24424	.	0.512563	0.16611	N	0.206908	T	0.18215	0.0437	L	0.46157	1.445	0.09310	N	1	P	0.45011	0.848	B	0.37989	0.262	T	0.06180	-1.0841	10	0.87932	D	0	-28.1982	5.2395	0.15464	0.2704:0.0:0.7296:0.0	.	130	P0C671	CF222_HUMAN	F	130	ENSP00000418983:S130F	ENSP00000418983:S130F	S	-	2	0	C6orf222	36406057	0.000000	0.05858	0.003000	0.11579	0.074000	0.17049	0.087000	0.14958	0.834000	0.34852	0.289000	0.19496	TCC	.	.		0.607	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903	
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42796515	42796515	+	Silent	SNP	C	C	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:42796515C>G	ENST00000314073.5	+	6	620	c.444C>G	c.(442-444)tcC>tcG	p.S148S	GLTSCR1L_ENST00000394168.1_Silent_p.S148S			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	148																	CATCAGCATCCTTTACTCAGG	0.463																																					p.S148S		Atlas-SNP	.											.	.	.	.	0			c.C444G						.						147.0	134.0	138.0					6																	42796515		2203	4300	6503	SO:0001819	synonymous_variant	23506	exon5			AGCATCCTTTACT	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"""KIAA0240"""	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.444C>G	chr6.hg19:g.42796515C>G		121.0	0.0		105.0	41.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	hg19	CCDS34451.1																																																																																			.	.		0.463	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	
TBX18	9096	hgsc.bcm.edu	37	6	85446578	85446578	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:85446578G>T	ENST00000369663.5	-	8	1986	c.1649C>A	c.(1648-1650)tCc>tAc	p.S550Y	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	550					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		ACTTCCTTGGGAAGAAACAAT	0.507																																					p.S550Y		Atlas-SNP	.											.	TBX18	131	.	0			c.C1649A						.						67.0	77.0	74.0					6																	85446578		2203	4300	6503	SO:0001583	missense	9096	exon8			CCTTGGGAAGAAA	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1649C>A	chr6.hg19:g.85446578G>T	ENSP00000358677:p.Ser550Tyr	208.0	0.0		160.0	62.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	hg19	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.554023	0.65425	.	.	ENSG00000112837	ENST00000369663	D	0.87650	-2.28	5.26	5.26	0.73747	.	0.150436	0.64402	D	0.000006	D	0.82728	0.5100	L	0.27053	0.805	0.54753	D	0.999982	D	0.61080	0.989	P	0.50708	0.648	D	0.85861	0.1410	10	0.72032	D	0.01	.	18.8443	0.92198	0.0:0.0:1.0:0.0	.	550	O95935	TBX18_HUMAN	Y	550	ENSP00000358677:S550Y	ENSP00000358677:S550Y	S	-	2	0	TBX18	85503297	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	6.968000	0.76086	2.453000	0.82957	0.585000	0.79938	TCC	.	.		0.507	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
ASF1A	25842	hgsc.bcm.edu	37	6	119228720	119228720	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:119228720T>C	ENST00000229595.5	+	4	750	c.556T>C	c.(556-558)Tgg>Cgg	p.W186R	MCM9_ENST00000316316.6_Intron	NM_014034.2	NP_054753.1	Q9Y294	ASF1A_HUMAN	anti-silencing function 1A histone chaperone	186	Required for interaction with HIRA.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|muscle cell differentiation (GO:0042692)|negative regulation of chromatin silencing (GO:0031936)|nucleosome assembly (GO:0006334)|osteoblast differentiation (GO:0001649)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)			endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0633)|OV - Ovarian serous cystadenocarcinoma(136;0.188)		ATCAAAGGGATGGTCCACATC	0.388																																					p.W186R		Atlas-SNP	.											.	ASF1A	16	.	0			c.T556C						.						113.0	105.0	107.0					6																	119228720		1910	4120	6030	SO:0001583	missense	25842	exon4			AAGGGATGGTCCA	AF279306	CCDS47469.1	6q22.31	2013-05-01	2013-05-01		ENSG00000111875	ENSG00000111875			20995	protein-coding gene	gene with protein product		609189	"""ASF1 anti-silencing function 1 homolog A (S. cerevisiae)"""			10810093, 11042152	Standard	NM_014034		Approved	DKFZP547E2110, CIA	uc011ebn.2	Q9Y294	OTTHUMG00000015470	ENST00000229595.5:c.556T>C	chr6.hg19:g.119228720T>C	ENSP00000229595:p.Trp186Arg	272.0	0.0		120.0	66.0	NM_014034	Q6IA08|Q9P014	Missense_Mutation	SNP	ENST00000229595.5	hg19	CCDS47469.1	.	.	.	.	.	.	.	.	.	.	T	12.91	2.080082	0.36662	.	.	ENSG00000111875	ENST00000229595	.	.	.	6.01	6.01	0.97437	.	0.000000	0.64402	D	0.000002	T	0.18841	0.0452	N	0.08118	0	0.58432	D	0.999999	B	0.31910	0.346	B	0.28709	0.093	T	0.11397	-1.0589	9	0.25106	T	0.35	-3.3821	16.5285	0.84344	0.0:0.0:0.0:1.0	.	186	Q9Y294	ASF1A_HUMAN	R	186	.	ENSP00000229595:W186R	W	+	1	0	ASF1A	119270419	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.435000	0.59941	2.307000	0.77673	0.528000	0.53228	TGG	.	.		0.388	ASF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361910.1	NM_014034	
SERAC1	84947	hgsc.bcm.edu	37	6	158535862	158535862	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr6:158535862T>C	ENST00000367104.3	-	15	1774	c.1643A>G	c.(1642-1644)tAt>tGt	p.Y548C	SERAC1_ENST00000367102.2_3'UTR|SERAC1_ENST00000367101.1_3'UTR	NM_032861.3	NP_116250.3	Q96JX3	SRAC1_HUMAN	serine active site containing 1	548					extracellular matrix organization (GO:0030198)|GPI anchor metabolic process (GO:0006505)|intracellular protein transport (GO:0006886)|phospholipid biosynthetic process (GO:0008654)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	15		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		GAAGAGAAGATAGCGAATATT	0.368																																					p.Y548C		Atlas-SNP	.											.	SERAC1	31	.	0			c.A1643G						.						163.0	166.0	165.0					6																	158535862		2203	4300	6503	SO:0001583	missense	84947	exon15			AGAAGATAGCGAA	BC001705	CCDS5255.1	6q25.3	2003-05-12			ENSG00000122335	ENSG00000122335			21061	protein-coding gene	gene with protein product		614725					Standard	NM_032861		Approved	FLJ14917	uc003qrc.2	Q96JX3	OTTHUMG00000015905	ENST00000367104.3:c.1643A>G	chr6.hg19:g.158535862T>C	ENSP00000356071:p.Tyr548Cys	165.0	0.0		88.0	39.0	NM_032861	Q49AT1|Q5VTX3|Q6PKF3	Missense_Mutation	SNP	ENST00000367104.3	hg19	CCDS5255.1	.	.	.	.	.	.	.	.	.	.	.	19.12	3.765764	0.69878	.	.	ENSG00000122335	ENST00000367104;ENST00000435180	D;D	0.95205	-3.64;-3.62	6.08	6.08	0.98989	.	0.114120	0.64402	D	0.000007	D	0.95909	0.8668	M	0.77616	2.38	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.95682	0.8733	10	0.48119	T	0.1	-23.1776	10.3822	0.44119	0.2517:0.0:0.0:0.7483	.	548	Q96JX3	SRAC1_HUMAN	C	548;123	ENSP00000356071:Y548C;ENSP00000391168:Y123C	ENSP00000356071:Y548C	Y	-	2	0	SERAC1	158455850	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.709000	0.54853	2.333000	0.79357	0.533000	0.62120	TAT	.	.		0.368	SERAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042862.1	NM_032861	
USP42	84132	hgsc.bcm.edu	37	7	6189723	6189723	+	Silent	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:6189723G>A	ENST00000306177.5	+	13	2054	c.1896G>A	c.(1894-1896)gtG>gtA	p.V632V		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	632					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		GTACGATTGTGAGCTCCCACT	0.582																																					p.V632V		Atlas-SNP	.											.	USP42	138	.	0			c.G1896A						.						32.0	39.0	36.0					7																	6189723		2032	4174	6206	SO:0001819	synonymous_variant	84132	exon13			GATTGTGAGCTCC	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.1896G>A	chr7.hg19:g.6189723G>A		107.0	0.0		85.0	19.0	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.		0.582	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
DLX5	1749	hgsc.bcm.edu	37	7	96650094	96650094	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:96650094C>T	ENST00000222598.4	-	3	1297	c.824G>A	c.(823-825)gGc>gAc	p.G275D	DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	275					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	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)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CTGTAAGGAGCCCGGCGGCGG	0.572																																					p.G275D		Atlas-SNP	.											.	DLX5	52	.	0			c.G824A						.						47.0	54.0	51.0					7																	96650094		2203	4300	6503	SO:0001583	missense	1749	exon3			AAGGAGCCCGGCG		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"""Homeoboxes / ANTP class : NKL subclass"""	2918	protein-coding gene	gene with protein product		600028	"""distal-less homeo box 5"""			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.824G>A	chr7.hg19:g.96650094C>T	ENSP00000222598:p.Gly275Asp	114.0	0.0		96.0	32.0	NM_005221	B7Z4P3|Q9UPL1	Missense_Mutation	SNP	ENST00000222598.4	hg19	CCDS5647.1	.	.	.	.	.	.	.	.	.	.	C	8.944	0.966557	0.18659	.	.	ENSG00000105880	ENST00000222598	D	0.89123	-2.47	5.34	4.45	0.53987	.	0.177624	0.51477	D	0.000085	D	0.82926	0.5143	L	0.43152	1.355	0.38939	D	0.958102	B	0.21071	0.051	B	0.16722	0.016	T	0.79169	-0.1914	10	0.39692	T	0.17	-13.3977	9.004	0.36100	0.0:0.6517:0.2722:0.0761	.	275	P56178	DLX5_HUMAN	D	275	ENSP00000222598:G275D	ENSP00000222598:G275D	G	-	2	0	DLX5	96488030	1.000000	0.71417	0.996000	0.52242	0.453000	0.32348	1.942000	0.40243	2.659000	0.90383	0.655000	0.94253	GGC	.	.		0.572	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2		
AGFG2	3268	hgsc.bcm.edu	37	7	100160302	100160302	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:100160302G>A	ENST00000300176.4	+	8	1206	c.1084G>A	c.(1084-1086)Gga>Aga	p.G362R	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	362					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCTGGCCTTTGGAGGTGAGTC	0.657																																					p.G362R		Atlas-SNP	.											.	AGFG2	44	.	0			c.G1084A						.						20.0	22.0	21.0					7																	100160302		2202	4300	6502	SO:0001583	missense	3268	exon8			GCCTTTGGAGGTG	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1084G>A	chr7.hg19:g.100160302G>A	ENSP00000300176:p.Gly362Arg	48.0	0.0		25.0	12.0	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577412	0.86645	.	.	ENSG00000106351	ENST00000300176	T	0.28666	1.6	5.0	5.0	0.66597	.	0.299228	0.30830	N	0.008794	T	0.51941	0.1704	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.52147	-0.8614	10	0.66056	D	0.02	-4.2535	13.7212	0.62728	0.0:0.0:1.0:0.0	.	362	O95081	AGFG2_HUMAN	R	362	ENSP00000300176:G362R	ENSP00000300176:G362R	G	+	1	0	AGFG2	99998238	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.235000	0.58666	2.610000	0.88304	0.549000	0.68633	GGA	.	.		0.657	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
TRIM56	81844	hgsc.bcm.edu	37	7	100732328	100732328	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:100732328G>A	ENST00000306085.6	+	3	2032	c.1735G>A	c.(1735-1737)Gtg>Atg	p.V579M		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	579					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					CAACGGCGAAGTGCAGTGGCG	0.716																																					p.V579M	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.G1735A						.						53.0	59.0	57.0					7																	100732328		2102	4203	6305	SO:0001583	missense	81844	exon3			GGCGAAGTGCAGT	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19028	protein-coding gene	gene with protein product			"""tripartite motif-containing 56"""				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.1735G>A	chr7.hg19:g.100732328G>A	ENSP00000305161:p.Val579Met	31.0	0.0		31.0	10.0	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Missense_Mutation	SNP	ENST00000306085.6	hg19	CCDS43625.1	.	.	.	.	.	.	.	.	.	.	G	9.141	1.013807	0.19277	.	.	ENSG00000169871	ENST00000306085	T	0.32988	1.43	3.87	2.98	0.34508	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	T	0.19927	0.0479	N	0.14661	0.345	0.24224	N	0.995424	P	0.44627	0.839	B	0.43575	0.424	T	0.05886	-1.0858	9	0.56958	D	0.05	.	7.2567	0.26181	0.1196:0.0:0.8804:0.0	.	579	Q9BRZ2	TRI56_HUMAN	M	579	ENSP00000305161:V579M	ENSP00000305161:V579M	V	+	1	0	TRIM56	100519048	0.999000	0.42202	0.948000	0.38648	0.317000	0.28152	1.146000	0.31589	1.219000	0.43474	0.586000	0.80456	GTG	.	.		0.716	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
DLD	1738	hgsc.bcm.edu	37	7	107558474	107558474	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:107558474G>A	ENST00000205402.5	+	12	1623	c.1342G>A	c.(1342-1344)Gac>Aac	p.D448N	DLD_ENST00000440410.1_Missense_Mutation_p.D425N|DLD_ENST00000537148.1_Missense_Mutation_p.D349N|DLD_ENST00000437604.2_Missense_Mutation_p.D400N	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	448					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	GAAATCGACAGACAGAGTACT	0.398																																					p.D448N		Atlas-SNP	.											.	DLD	72	.	0			c.G1342A						.						134.0	126.0	129.0					7																	107558474		2203	4300	6503	SO:0001583	missense	1738	exon12			TCGACAGACAGAG	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"""E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"""	238331	"""dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"""	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.1342G>A	chr7.hg19:g.107558474G>A	ENSP00000205402:p.Asp448Asn	201.0	0.0		176.0	34.0	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Missense_Mutation	SNP	ENST00000205402.5	hg19	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	G	32	5.177864	0.94846	.	.	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000537148;ENST00000440410;ENST00000437604;ENST00000539590	D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08	6.07	5.19	0.71726	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (2);	0.000000	0.85682	D	0.000000	D	0.95408	0.8509	M	0.62088	1.915	0.80722	D	1	D;P;D	0.89917	1.0;0.853;1.0	D;P;D	0.97110	1.0;0.874;1.0	D	0.95850	0.8874	10	0.87932	D	0	-7.9006	17.4012	0.87460	0.0:0.1247:0.8753:0.0	.	425;400;448	E9PEX6;B4DT69;P09622	.;.;DLDH_HUMAN	N	448;448;349;425;400;398	ENSP00000205402:D448N;ENSP00000390667:D448N;ENSP00000442399:D349N;ENSP00000417016:D425N;ENSP00000387542:D400N	ENSP00000205402:D448N	D	+	1	0	DLD	107345710	1.000000	0.71417	0.940000	0.37924	0.982000	0.71751	9.869000	0.99810	1.556000	0.49512	0.655000	0.94253	GAC	.	.		0.398	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108	
NRCAM	4897	hgsc.bcm.edu	37	7	107818532	107818532	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:107818532C>A	ENST00000425651.2	-	23	2876	c.2877G>T	c.(2875-2877)aaG>aaT	p.K959N	NRCAM_ENST00000379028.3_Missense_Mutation_p.K959N|NRCAM_ENST00000379024.4_Missense_Mutation_p.K940N|NRCAM_ENST00000351718.4_Missense_Mutation_p.K943N|NRCAM_ENST00000413765.2_Missense_Mutation_p.K940N|NRCAM_ENST00000379022.4_Missense_Mutation_p.K959N	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	959	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GATTCACAATCTTCAAAGACG	0.428																																					p.K959N		Atlas-SNP	.											.	NRCAM	267	.	0			c.G2877T						.						83.0	73.0	77.0					7																	107818532		2203	4300	6503	SO:0001583	missense	4897	exon23			CACAATCTTCAAA		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2877G>T	chr7.hg19:g.107818532C>A	ENSP00000401244:p.Lys959Asn	176.0	0.0		154.0	53.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.033160	0.35893	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022	T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31	6.05	5.16	0.70880	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.195360	0.53938	D	0.000043	T	0.48095	0.1481	L	0.41492	1.28	0.42549	D	0.993103	B;B;B;B;B	0.22909	0.077;0.003;0.009;0.007;0.014	B;B;B;B;B	0.28991	0.097;0.017;0.034;0.011;0.067	T	0.43097	-0.9412	10	0.31617	T	0.26	.	9.3878	0.38354	0.1435:0.7841:0.0:0.0724	.	959;940;940;943;959	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	N	959;959;940;959;943;940;959;959	ENSP00000368314:K959N;ENSP00000407858:K940N;ENSP00000325269:K943N;ENSP00000368310:K940N;ENSP00000401244:K959N;ENSP00000368308:K959N	ENSP00000325269:K943N	K	-	3	2	NRCAM	107605768	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	0.743000	0.26231	1.533000	0.49186	0.650000	0.86243	AAG	.	.		0.428	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
RALYL	138046	hgsc.bcm.edu	37	8	85774619	85774619	+	Silent	SNP	A	A	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr8:85774619A>C	ENST00000521268.1	+	6	1607	c.502A>C	c.(502-504)Agg>Cgg	p.R168R	RALYL_ENST00000522455.1_Silent_p.R168R|RALYL_ENST00000517638.1_Silent_p.R181R|RALYL_ENST00000518566.1_Silent_p.R157R|RALYL_ENST00000521376.1_Silent_p.R79R|RALYL_ENST00000521695.1_Silent_p.R168R|RALYL_ENST00000523850.1_Silent_p.R95R	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	168							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						AACGACTCGCAGGGGGAAAGG	0.473																																					p.R181R		Atlas-SNP	.											.	RALYL	123	.	0			c.A541C						.						59.0	63.0	62.0					8																	85774619		1920	4138	6058	SO:0001819	synonymous_variant	138046	exon6			ACTCGCAGGGGGA		CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"""RNA binding motif (RRM) containing"""	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.502A>C	chr8.hg19:g.85774619A>C		71.0	0.0		119.0	16.0	NM_001100391	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Silent	SNP	ENST00000521268.1	hg19	CCDS55253.1																																																																																			.	.		0.473	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1		
CDH17	1015	hgsc.bcm.edu	37	8	95182668	95182668	+	Silent	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr8:95182668C>T	ENST00000027335.3	-	9	1147	c.1023G>A	c.(1021-1023)ccG>ccA	p.P341P	CDH17_ENST00000441892.2_Intron|CDH17_ENST00000450165.2_Silent_p.P341P	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	341	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TTACTGGTGACGGACATGTAG	0.418																																					p.P341P		Atlas-SNP	.											.	CDH17	119	.	0			c.G1023A						.						158.0	146.0	150.0					8																	95182668		2203	4300	6503	SO:0001819	synonymous_variant	1015	exon9			TGGTGACGGACAT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1023G>A	chr8.hg19:g.95182668C>T		217.0	0.0		248.0	17.0	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	hg19	CCDS6260.1																																																																																			.	.		0.418	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
CCIN	881	hgsc.bcm.edu	37	9	36169649	36169649	+	Silent	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:36169649C>A	ENST00000335119.2	+	1	261	c.150C>A	c.(148-150)tcC>tcA	p.S50S		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	50	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			CTGCTGTCTCCCCACTGGTGA	0.537																																					p.S50S		Atlas-SNP	.											.	CCIN	56	.	0			c.C150A						.						132.0	122.0	125.0					9																	36169649		2203	4300	6503	SO:0001819	synonymous_variant	881	exon1			TGTCTCCCCACTG	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"""BTB/POZ domain containing"""	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.150C>A	chr9.hg19:g.36169649C>A		179.0	0.0		152.0	62.0	NM_005893	Q9BXG7	Silent	SNP	ENST00000335119.2	hg19	CCDS6599.1																																																																																			.	.		0.537	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893	
FOXB2	442425	hgsc.bcm.edu	37	9	79635418	79635418	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:79635418T>A	ENST00000376708.1	+	1	848	c.848T>A	c.(847-849)gTg>gAg	p.V283E		NM_001013735.1	NP_001013757.1	Q5VYV0	FOXB2_HUMAN	forkhead box B2	283					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(8)|ovary(1)	10						TACAAGGGCGTGCTGCAGGCT	0.697																																					p.V283E		Atlas-SNP	.											.	FOXB2	71	.	0			c.T848A						.						42.0	42.0	42.0					9																	79635418		2203	4300	6503	SO:0001583	missense	442425	exon1			AGGGCGTGCTGCA		CCDS35045.1	9q21.2	2008-02-05			ENSG00000204612	ENSG00000204612		"""Forkhead boxes"""	23315	protein-coding gene	gene with protein product							Standard	NM_001013735		Approved	bA159H20.4	uc004ako.1	Q5VYV0	OTTHUMG00000020051	ENST00000376708.1:c.848T>A	chr9.hg19:g.79635418T>A	ENSP00000365898:p.Val283Glu	97.0	0.0		74.0	24.0	NM_001013735		Missense_Mutation	SNP	ENST00000376708.1	hg19	CCDS35045.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064103	0.55432	.	.	ENSG00000204612	ENST00000376708	D	0.96232	-3.95	3.41	3.41	0.39046	.	0.000000	0.37178	U	0.002206	D	0.95169	0.8434	L	0.42245	1.32	0.43885	D	0.996504	D	0.65815	0.995	D	0.70487	0.969	D	0.91991	0.5603	10	0.07482	T	0.82	.	5.851	0.18694	0.2354:0.0:0.0:0.7645	.	283	Q5VYV0	FOXB2_HUMAN	E	283	ENSP00000365898:V283E	ENSP00000365898:V283E	V	+	2	0	FOXB2	78825238	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.523000	0.45580	1.400000	0.46741	0.379000	0.24179	GTG	.	.		0.697	FOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052745.1	NM_001013735	
VPS13A	23230	hgsc.bcm.edu	37	9	79922965	79922965	+	Silent	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:79922965A>G	ENST00000360280.3	+	35	4325	c.4065A>G	c.(4063-4065)caA>caG	p.Q1355Q	VPS13A_ENST00000423463.2_3'UTR|VPS13A_ENST00000376636.3_Silent_p.Q1316Q|VPS13A_ENST00000376634.4_Silent_p.Q1355Q|VPS13A_ENST00000357409.5_Silent_p.Q1355Q	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1355					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CAAAAGACCAATACAGTGCCA	0.343																																					p.Q1355Q		Atlas-SNP	.											.	VPS13A	735	.	0			c.A4065G						.						172.0	169.0	170.0					9																	79922965		2203	4300	6503	SO:0001819	synonymous_variant	23230	exon35			AGACCAATACAGT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.4065A>G	chr9.hg19:g.79922965A>G		375.0	0.0		280.0	71.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	hg19	CCDS6655.1																																																																																			.	.		0.343	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
THNSL1	79896	hgsc.bcm.edu	37	10	25312662	25312662	+	Silent	SNP	A	A	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr10:25312662A>T	ENST00000524413.1	+	3	857	c.510A>T	c.(508-510)acA>acT	p.T170T	THNSL1_ENST00000376356.4_Silent_p.T170T			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	170						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	TAATGAAGACAGATAGGATTG	0.343																																					p.T170T		Atlas-SNP	.											.	THNSL1	70	.	0			c.A510T						.						56.0	57.0	56.0					10																	25312662		2203	4300	6503	SO:0001819	synonymous_variant	79896	exon3			GAAGACAGATAGG	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.510A>T	chr10.hg19:g.25312662A>T		71.0	0.0		54.0	20.0	NM_024838	B3KWL1|D3DRV3|Q5VV21	Silent	SNP	ENST00000524413.1	hg19	CCDS7147.1																																																																																			.	.		0.343	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
OPN4	94233	hgsc.bcm.edu	37	10	88428477	88428477	+	IGR	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr10:88428477C>A	ENST00000241891.5	+	0	2308				LDB3_ENST00000263066.6_Missense_Mutation_p.P10H|LDB3_ENST00000372066.3_Missense_Mutation_p.P10H|LDB3_ENST00000458213.2_Missense_Mutation_p.P10H|LDB3_ENST00000310944.6_Missense_Mutation_p.P10H|LDB3_ENST00000361373.4_Missense_Mutation_p.P10H|LDB3_ENST00000372056.4_Missense_Mutation_p.P10H|LDB3_ENST00000542786.1_Missense_Mutation_p.P10H|LDB3_ENST00000352360.5_Missense_Mutation_p.P10H|LDB3_ENST00000429277.2_Missense_Mutation_p.P10H	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4						phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CTGACTGGGCCCGGGCCCTGG	0.642																																					p.P10H		Atlas-SNP	.											.	LDB3	164	.	0			c.C29A						.						52.0	57.0	55.0					10																	88428477		2203	4300	6503	SO:0001628	intergenic_variant	11155	exon1			CTGGGCCCGGGCC	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654		chr10.hg19:g.88428477C>A		120.0	0.0		89.0	18.0	NM_007078	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888670	0.91814	.	.	ENSG00000122367	ENST00000539402;ENST00000429277;ENST00000458213;ENST00000352360;ENST00000372066;ENST00000263066;ENST00000372056;ENST00000310944;ENST00000361373;ENST00000542786	T;T;T;T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71	5.5	5.5	0.81552	PDZ/DHR/GLGF (3);	0.000000	0.32204	N	0.006423	T	0.65228	0.2671	H	0.94620	3.56	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.999;1.0;0.966	T	0.75844	-0.3174	10	0.87932	D	0	.	19.4084	0.94658	0.0:1.0:0.0:0.0	.	10;10;10;10;10;10;10	B4E3K3;F5H0C2;O75112-4;O75112;O75112-2;O75112-5;O75112-6	.;.;.;LDB3_HUMAN;.;.;.	H	10	ENSP00000401437:P10H;ENSP00000409148:P10H;ENSP00000263067:P10H;ENSP00000361136:P10H;ENSP00000263066:P10H;ENSP00000361126:P10H;ENSP00000311913:P10H;ENSP00000355296:P10H;ENSP00000438866:P10H	ENSP00000263066:P10H	P	+	2	0	LDB3	88418457	1.000000	0.71417	0.987000	0.45799	0.918000	0.54935	7.717000	0.84732	2.593000	0.87608	0.655000	0.94253	CCC	.	.		0.642	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
IFITM3	10410	hgsc.bcm.edu	37	11	320798	320798	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:320798G>A	ENST00000399808.4	-	1	252	c.16C>T	c.(16-18)Caa>Taa	p.Q6*	RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000526811.1_Intron|IFITM3_ENST00000602735.1_Intron|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000602429.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	6					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AAGAAGGTTTGGACAGTGTGA	0.587																																					p.Q6X		Atlas-SNP	.											.	IFITM3	132	.	0			c.C16T						.						127.0	141.0	137.0					11																	320798		1936	4144	6080	SO:0001587	stop_gained	10410	exon1			AGGTTTGGACAGT	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.16C>T	chr11.hg19:g.320798G>A	ENSP00000382707:p.Gln6*	42.0	0.0		30.0	7.0	NM_021034	Q53Y76|Q96HK8|Q96J15	Nonsense_Mutation	SNP	ENST00000399808.4	hg19	CCDS41585.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.709345	0.89018	.	.	ENSG00000142089	ENST00000399808	.	.	.	4.0	-0.68	0.11346	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	2.8102	0.05440	0.1039:0.3287:0.3958:0.1716	.	.	.	.	X	6	.	ENSP00000382707:Q6X	Q	-	1	0	IFITM3	310798	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.448000	0.21726	-0.188000	0.10499	0.405000	0.27470	CAA	.	.		0.587	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
MUC5B	727897	hgsc.bcm.edu	37	11	1275529	1275529	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:1275529C>A	ENST00000529681.1	+	34	15483	c.15425C>A	c.(15424-15426)tCc>tAc	p.S5142Y	MUC5B_ENST00000447027.1_Missense_Mutation_p.S5145Y	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5142	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CACTACAAGTCCATGGATATC	0.632																																					p.S5142Y		Atlas-SNP	.											.	MUC5B	473	.	0			c.C15425A						.						34.0	41.0	39.0					11																	1275529		2163	4263	6426	SO:0001583	missense	727897	exon34			ACAAGTCCATGGA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.15425C>A	chr11.hg19:g.1275529C>A	ENSP00000436812:p.Ser5142Tyr	47.0	0.0		49.0	16.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106012	0.37145	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.18810	2.19;2.38	4.31	3.32	0.38043	.	.	.	.	.	T	0.40423	0.1116	L	0.58101	1.795	0.09310	N	1	D;D	0.71674	0.998;0.998	D;D	0.67900	0.954;0.954	T	0.10109	-1.0644	9	0.87932	D	0	.	12.7585	0.57350	0.1639:0.836:0.0:0.0	.	5479;5145	A7Y9J9;E9PBJ0	.;.	Y	5142;5145;5086;41;4854	ENSP00000436812:S5142Y;ENSP00000415793:S5145Y	ENSP00000343037:S5086Y	S	+	2	0	MUC5B	1232105	0.008000	0.16893	0.057000	0.19452	0.716000	0.41182	1.502000	0.35704	2.119000	0.64992	0.400000	0.26472	TCC	.	.		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ELP4	26610	hgsc.bcm.edu	37	11	31653846	31653846	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:31653846A>C	ENST00000350638.5	+	7	856	c.821A>C	c.(820-822)aAt>aCt	p.N274T	ELP4_ENST00000395934.2_Missense_Mutation_p.N274T|ELP4_ENST00000379163.5_Missense_Mutation_p.N275T	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	274					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					TGTGCAGAAAATGGTGGCAAC	0.418																																					p.N274T		Atlas-SNP	.											.	ELP4	78	.	0			c.A821C						.						119.0	115.0	116.0					11																	31653846		1910	4131	6041	SO:0001583	missense	26610	exon7			CAGAAAATGGTGG	AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"""Elongator acetyltransferase complex subunits"""	1171	protein-coding gene	gene with protein product		606985	"""chromosome 11 open reading frame 19"", ""elongation protein 4 homolog (S. cerevisiae)"""	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.821A>C	chr11.hg19:g.31653846A>C	ENSP00000298937:p.Asn274Thr	118.0	0.0		110.0	30.0	NM_019040	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Missense_Mutation	SNP	ENST00000350638.5	hg19	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	A	5.186	0.219839	0.09863	.	.	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	T;T;T	0.41065	1.01;1.01;1.01	5.85	2.35	0.29111	.	0.464639	0.26708	N	0.022907	T	0.20780	0.0500	N	0.16368	0.405	0.23943	N	0.996399	B;B;B	0.30914	0.3;0.062;0.028	B;B;B	0.25987	0.065;0.05;0.027	T	0.13335	-1.0513	10	0.21540	T	0.41	-5.0039	6.5047	0.22188	0.5829:0.1821:0.2349:0.0	.	275;274;274	B4E3W0;G5E9D4;Q96EB1	.;.;ELP4_HUMAN	T	274;275;274	ENSP00000298937:N274T;ENSP00000368461:N275T;ENSP00000379267:N274T	ENSP00000298937:N274T	N	+	2	0	ELP4	31610422	0.502000	0.26107	0.455000	0.27031	0.345000	0.29048	0.704000	0.25661	0.487000	0.27698	0.528000	0.53228	AAT	.	.		0.418	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040	
ATM	472	hgsc.bcm.edu	37	11	108117798	108117798	+	Missense_Mutation	SNP	C	C	T	rs138398778		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:108117798C>T	ENST00000452508.2	+	9	1198	c.1009C>T	c.(1009-1011)Cgt>Tgt	p.R337C	ATM_ENST00000278616.4_Missense_Mutation_p.R337C			Q13315	ATM_HUMAN	ATM serine/threonine kinase	337			R -> C (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.|R -> H (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R337C(3)|p.R337S(2)|p.F336_A340del(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTCAGGATTTCGTAATATTGC	0.323			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.R337C		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,NS,adenocarcinoma,-1,16	ATM	1657	.	6	Substitution - Missense(5)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(3)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)	c.C1009T						.	C	CYS/ARG	0,4402		0,0,2201	60.0	61.0	61.0		1009	5.7	1.0	11	dbSNP_134	61	1,8595	1.2+/-3.3	0,1,4297	yes	missense	ATM	NM_000051.3	180	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	337/3057	108117798	1,12997	2201	4298	6499	SO:0001583	missense	472	exon8	Familial Cancer Database	AT, Louis-Bar syndrome	GGATTTCGTAATA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.1009C>T	chr11.hg19:g.108117798C>T	ENSP00000388058:p.Arg337Cys	239.0	0.0		208.0	66.0	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568847	0.86439	0.0	1.16E-4	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.02369	4.32;4.62;4.62	5.72	5.72	0.89469	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.00022	-1.2342	10	0.87932	D	0	.	19.8868	0.96915	0.0:1.0:0.0:0.0	.	337	Q13315	ATM_HUMAN	C	337	ENSP00000435747:R337C;ENSP00000278616:R337C;ENSP00000388058:R337C	ENSP00000278616:R337C	R	+	1	0	ATM	107623008	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.213000	0.58520	2.709000	0.92574	0.655000	0.94253	CGT	.	C|1.000;T|0.000		0.323	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
ROBO3	64221	hgsc.bcm.edu	37	11	124743649	124743649	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:124743649C>T	ENST00000397801.1	+	11	1867	c.1675C>T	c.(1675-1677)Ccc>Tcc	p.P559S	ROBO3_ENST00000538940.1_Missense_Mutation_p.P537S	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	559	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		TCCGGGGGCTCCCTCTCAGCC	0.527																																					p.P559S		Atlas-SNP	.											.	ROBO3	199	.	0			c.C1675T						.						35.0	38.0	37.0					11																	124743649		1864	4085	5949	SO:0001583	missense	64221	exon11			GGGGCTCCCTCTC	AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13433	protein-coding gene	gene with protein product		608630	"""roundabout (axon guidance receptor, Drosophila) homolog 3"", ""horizontal gaze palsy with progressive scoliosis"""	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.1675C>T	chr11.hg19:g.124743649C>T	ENSP00000380903:p.Pro559Ser	69.0	0.0		66.0	23.0	NM_022370		Missense_Mutation	SNP	ENST00000397801.1	hg19	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.853629	0.71719	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	D;D	0.95069	-3.6;-3.6	5.71	5.71	0.89125	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41001	D	0.000976	D	0.98005	0.9343	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98715	1.0706	10	0.87932	D	0	.	18.6381	0.91385	0.0:1.0:0.0:0.0	.	559	Q96MS0	ROBO3_HUMAN	S	559;537	ENSP00000380903:P559S;ENSP00000441797:P537S	ENSP00000380903:P559S	P	+	1	0	ROBO3	124248859	1.000000	0.71417	1.000000	0.80357	0.368000	0.29767	7.721000	0.84768	2.702000	0.92279	0.563000	0.77884	CCC	.	.		0.527	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663	
BARX2	8538	hgsc.bcm.edu	37	11	129306802	129306802	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr11:129306802C>A	ENST00000281437.4	+	2	440	c.344C>A	c.(343-345)gCc>gAc	p.A115D	BARX2_ENST00000526127.1_5'UTR	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	115					cartilage condensation (GO:0001502)|catagen (GO:0042637)|myotube differentiation (GO:0014902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		GGGGGCGAGGCCCTAGCCAGC	0.687																																					p.A115D		Atlas-SNP	.											.	BARX2	40	.	0			c.C344A						.						35.0	41.0	39.0					11																	129306802		2201	4296	6497	SO:0001583	missense	8538	exon2			GCGAGGCCCTAGC	AF031924	CCDS8481.1	11q24.3	2011-06-20	2007-07-09		ENSG00000043039	ENSG00000043039		"""Homeoboxes / ANTP class : NKL subclass"""	956	protein-coding gene	gene with protein product		604823	"""BarH-like homeobox 2"""			10644443	Standard	NM_003658		Approved		uc001qfc.4	Q9UMQ3	OTTHUMG00000165776	ENST00000281437.4:c.344C>A	chr11.hg19:g.129306802C>A	ENSP00000281437:p.Ala115Asp	163.0	0.0		173.0	17.0	NM_003658	O43518|Q6NT51	Missense_Mutation	SNP	ENST00000281437.4	hg19	CCDS8481.1	.	.	.	.	.	.	.	.	.	.	C	7.481	0.648643	0.14516	.	.	ENSG00000043039	ENST00000281437	D	0.90504	-2.68	5.76	3.86	0.44501	Homeodomain-related (1);	0.371999	0.26130	N	0.026177	T	0.79125	0.4393	N	0.24115	0.695	0.80722	D	1	B	0.28713	0.22	B	0.24006	0.05	T	0.67764	-0.5586	10	0.12766	T	0.61	.	5.3255	0.15905	0.1594:0.6283:0.1364:0.076	.	115	Q9UMQ3	BARX2_HUMAN	D	115	ENSP00000281437:A115D	ENSP00000281437:A115D	A	+	2	0	BARX2	128812012	0.994000	0.37717	0.338000	0.25549	0.101000	0.19017	3.148000	0.50647	0.746000	0.32786	0.655000	0.94253	GCC	.	.		0.687	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386153.1	NM_003658	
IQSEC3	440073	hgsc.bcm.edu	37	12	248119	248119	+	Silent	SNP	C	C	A	rs548532490		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:248119C>A	ENST00000538872.1	+	4	1708	c.1590C>A	c.(1588-1590)ggC>ggA	p.G530G	IQSEC3_ENST00000382841.2_Silent_p.G227G|IQSEC3_ENST00000326261.4_Silent_p.G530G|RP11-598F7.4_ENST00000505893.2_RNA|RP11-598F7.4_ENST00000508953.2_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	530					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		CCGAGCAGGGCGAGACCTCTG	0.751																																					p.G530G		Atlas-SNP	.											.	IQSEC3	154	.	0			c.C1590A						.						14.0	13.0	14.0					12																	248119		2161	4216	6377	SO:0001819	synonymous_variant	440073	exon4			GCAGGGCGAGACC	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.1590C>A	chr12.hg19:g.248119C>A		69.0	0.0		68.0	27.0	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	hg19	CCDS53728.1																																																																																			.	.		0.751	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
SLC6A12	6539	hgsc.bcm.edu	37	12	301770	301770	+	Silent	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:301770G>A	ENST00000428720.1	-	15	2318	c.1575C>T	c.(1573-1575)taC>taT	p.Y525Y	SLC6A12_ENST00000397296.2_Silent_p.Y525Y|RP11-283I3.1_ENST00000544067.1_RNA|SLC6A12_ENST00000536824.1_Silent_p.Y525Y|SLC6A12_ENST00000424061.2_Silent_p.Y525Y|SLC6A12_ENST00000359674.4_Silent_p.Y525Y	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	525					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AGACGTTGTTGTACTTGAGGG	0.572																																					p.Y525Y		Atlas-SNP	.											.	SLC6A12	60	.	0			c.C1575T						.						111.0	115.0	113.0					12																	301770		2203	4300	6503	SO:0001819	synonymous_variant	6539	exon15			GTTGTTGTACTTG	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.1575C>T	chr12.hg19:g.301770G>A		173.0	0.0		194.0	55.0	NM_001122848	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	hg19	CCDS8501.1																																																																																			.	.		0.572	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
TROAP	10024	hgsc.bcm.edu	37	12	49725143	49725143	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:49725143G>C	ENST00000257909.3	+	14	2321	c.2245G>C	c.(2245-2247)Gtc>Ctc	p.V749L	TROAP_ENST00000547923.1_Missense_Mutation_p.V428L|TROAP_ENST00000551245.1_Missense_Mutation_p.V839L	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	749					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						CCCCACCCGGGTCTGCACCAA	0.602											OREG0021792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V749L		Atlas-SNP	.											.	TROAP	80	.	0			c.G2245C						.						52.0	50.0	50.0					12																	49725143		2203	4300	6503	SO:0001583	missense	10024	exon14			ACCCGGGTCTGCA	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.2245G>C	chr12.hg19:g.49725143G>C	ENSP00000257909:p.Val749Leu	74.0	0.0	964	95.0	30.0	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	hg19	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903822	0.52333	.	.	ENSG00000135451	ENST00000551245;ENST00000257909;ENST00000547923	.	.	.	5.93	1.62	0.23740	.	0.707580	0.12780	N	0.439766	T	0.22589	0.0545	L	0.35854	1.095	0.25243	N	0.989735	B;B;B	0.33940	0.433;0.433;0.157	B;B;B	0.27887	0.084;0.084;0.05	T	0.19712	-1.0297	9	0.72032	D	0.01	-6.1667	4.072	0.09887	0.2873:0.1736:0.5391:0.0	.	839;428;749	F8W130;F8W1U0;Q12815	.;.;TROAP_HUMAN	L	839;749;428	.	ENSP00000257909:V749L	V	+	1	0	TROAP	48011410	0.983000	0.35010	0.964000	0.40570	0.961000	0.63080	0.270000	0.18607	0.848000	0.35191	0.561000	0.74099	GTC	.	.		0.602	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
PFDN5	5204	hgsc.bcm.edu	37	12	53691669	53691669	+	Silent	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:53691669C>T	ENST00000551018.1	+	4	520	c.243C>T	c.(241-243)caC>caT	p.H81H	PFDN5_ENST00000334478.4_Silent_p.H81H|C12orf10_ENST00000267103.5_5'Flank|PFDN5_ENST00000351500.3_Silent_p.H36H|PFDN5_ENST00000550846.1_Intron|C12orf10_ENST00000549488.1_5'Flank|RP11-680A11.5_ENST00000550263.1_RNA|C12orf10_ENST00000548632.1_5'Flank	NM_002624.3	NP_002615.2	Q99471	PFD5_HUMAN	prefoldin subunit 5	81					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	transcription corepressor activity (GO:0003714)			kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)	8						ATGTGGAACACGTGCTCATCG	0.512																																					p.H81H		Atlas-SNP	.											.	PFDN5	16	.	0			c.C243T						.						182.0	166.0	172.0					12																	53691669		2203	4300	6503	SO:0001819	synonymous_variant	5204	exon4			GGAACACGTGCTC	D89667	CCDS8853.1, CCDS8854.1	12q13.13	2008-05-14	2006-02-24						8869	protein-coding gene	gene with protein product		604899	"""prefoldin 5"""			9630229, 9792694	Standard	NM_002624		Approved	PFD5, MM-1	uc001scl.3	Q99471	OTTHUMG00000169675	ENST00000551018.1:c.243C>T	chr12.hg19:g.53691669C>T		119.0	0.0		105.0	11.0	NM_002624	A8K9A8|Q54AA8|Q9C083|Q9C084	Silent	SNP	ENST00000551018.1	hg19	CCDS8853.1																																																																																			.	.		0.512	PFDN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405368.2		
SP1	6667	hgsc.bcm.edu	37	12	53776141	53776141	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:53776141C>T	ENST00000327443.4	+	3	508	c.410C>T	c.(409-411)tCc>tTc	p.S137F	SP1_ENST00000426431.2_Missense_Mutation_p.S130F	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	137	Ser/Thr-rich.				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|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)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		AGTGAGTCTTCCAAGAATCGC	0.537																																					p.S137F		Atlas-SNP	.											.	SP1	57	.	0			c.C410T						.						65.0	66.0	66.0					12																	53776141		2203	4300	6503	SO:0001583	missense	6667	exon3			AGTCTTCCAAGAA	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11205	protein-coding gene	gene with protein product	"""specificity protein 1"""	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.410C>T	chr12.hg19:g.53776141C>T	ENSP00000329357:p.Ser137Phe	132.0	0.0		103.0	35.0	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Missense_Mutation	SNP	ENST00000327443.4	hg19	CCDS8857.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977718	0.53720	.	.	ENSG00000185591	ENST00000327443;ENST00000426431	T;T	0.09911	2.96;2.93	4.13	4.13	0.48395	.	0.000000	0.53938	D	0.000048	T	0.12689	0.0308	L	0.46157	1.445	0.46298	D	0.998978	D	0.54772	0.968	B	0.42062	0.374	T	0.04495	-1.0947	10	0.87932	D	0	.	15.6957	0.77494	0.0:1.0:0.0:0.0	.	137	P08047	SP1_HUMAN	F	137;130	ENSP00000329357:S137F;ENSP00000404263:S130F	ENSP00000329357:S137F	S	+	2	0	SP1	52062408	0.002000	0.14202	1.000000	0.80357	0.945000	0.59286	1.251000	0.32862	2.306000	0.77630	0.467000	0.42956	TCC	.	.		0.537	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1		
ATP2A2	488	hgsc.bcm.edu	37	12	110778773	110778773	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr12:110778773C>T	ENST00000539276.2	+	14	2180	c.2071C>T	c.(2071-2073)Cag>Tag	p.Q691*	ATP2A2_ENST00000395494.2_Nonsense_Mutation_p.Q664*|ATP2A2_ENST00000308664.6_Nonsense_Mutation_p.Q691*			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	691					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						AGAATTTCTTCAGTCTTTTGA	0.473																																					p.Q691X		Atlas-SNP	.											.	ATP2A2	78	.	0			c.C2071T						.						42.0	44.0	43.0					12																	110778773		2203	4300	6503	SO:0001587	stop_gained	488	exon14			TTTCTTCAGTCTT		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"""ATPases / P-type"""	812	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 2"", ""calcium pump 2"""	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.2071C>T	chr12.hg19:g.110778773C>T	ENSP00000440045:p.Gln691*	146.0	0.0		136.0	36.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Nonsense_Mutation	SNP	ENST00000539276.2	hg19	CCDS9144.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.430852|6.430852	0.97559|0.97559	.|.	.|.	ENSG00000174437|ENSG00000174437	ENST00000308664;ENST00000395494;ENST00000539276|ENST00000548169	.|.	.|.	.|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.80037	.|0.4550	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.77705	.|-0.2488	.|3	0.21540|.	T|.	0.41|.	.|.	20.0784|20.0784	0.97758|0.97758	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	691;664;691|581	.|.	ENSP00000311186:Q691X|.	Q|S	+|+	1|2	0|0	ATP2A2|ATP2A2	109263156|109263156	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.999000|0.999000	0.98932|0.98932	7.818000|7.818000	0.86416|0.86416	2.736000|2.736000	0.93811|0.93811	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.	.		0.473	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681	
AQP9	366	hgsc.bcm.edu	37	15	58430833	58430833	+	Silent	SNP	G	G	A	rs370186994		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:58430833G>A	ENST00000219919.4	+	1	439	c.69G>A	c.(67-69)gcG>gcA	p.A23A	ALDH1A2_ENST00000558231.1_Intron|AQP9_ENST00000559443.1_3'UTR|AQP9_ENST00000536493.1_Silent_p.A23A|AQP9_ENST00000558772.1_Intron	NM_020980.3	NP_066190.2	O43315	AQP9_HUMAN	aquaporin 9	23					amine transport (GO:0015837)|canalicular bile acid transport (GO:0015722)|carboxylic acid transport (GO:0046942)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|glycerol transport (GO:0015793)|immune response (GO:0006955)|metabolic process (GO:0008152)|polyol transport (GO:0015791)|purine nucleobase transport (GO:0006863)|pyrimidine nucleobase transport (GO:0015855)|pyrimidine-containing compound transmembrane transport (GO:0072531)|response to mercury ion (GO:0046689)|response to organic substance (GO:0010033)|response to osmotic stress (GO:0006970)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water homeostasis (GO:0030104)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carboxylic acid transmembrane transporter activity (GO:0046943)|glycerol channel activity (GO:0015254)|polyol transmembrane transporter activity (GO:0015166)|porin activity (GO:0015288)|purine nucleobase transmembrane transporter activity (GO:0005345)|pyrimidine nucleobase transmembrane transporter activity (GO:0005350)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)	21				GBM - Glioblastoma multiforme(80;0.16)		GCAGCTTAGCGAAAGAAACCC	0.483																																					p.A23A		Atlas-SNP	.											.	AQP9	39	.	0			c.G69A						.	G		0,4384		0,0,2192	148.0	148.0	148.0		69	-6.1	0.1	15		148	1,8583		0,1,4291	no	coding-synonymous	AQP9	NM_020980.3		0,1,6483	AA,AG,GG		0.0116,0.0,0.0077		23/296	58430833	1,12967	2192	4292	6484	SO:0001819	synonymous_variant	366	exon1			CTTAGCGAAAGAA	AF016495	CCDS10165.1	15q	2005-09-20			ENSG00000103569	ENSG00000103569		"""Ion channels / Aquaporins"""	643	protein-coding gene	gene with protein product		602914					Standard	NM_020980		Approved	SSC1, HsT17287	uc002aez.2	O43315	OTTHUMG00000132631	ENST00000219919.4:c.69G>A	chr15.hg19:g.58430833G>A		153.0	0.0		150.0	49.0	NM_020980	Q9NP32	Silent	SNP	ENST00000219919.4	hg19	CCDS10165.1																																																																																			.	.		0.483	AQP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255878.2	NM_020980	
IGDCC4	57722	hgsc.bcm.edu	37	15	65702586	65702586	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:65702586G>A	ENST00000352385.2	-	3	702	c.493C>T	c.(493-495)Cac>Tac	p.H165Y		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	165	Ig-like C2-type 2.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CCTTCAATGTGGCACTCAAAG	0.612																																					p.H165Y		Atlas-SNP	.											.	IGDCC4	95	.	0			c.C493T						.						91.0	78.0	83.0					15																	65702586		2201	4299	6500	SO:0001583	missense	57722	exon3			CAATGTGGCACTC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.493C>T	chr15.hg19:g.65702586G>A	ENSP00000319623:p.His165Tyr	54.0	0.0		30.0	6.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947320	0.34377	.	.	ENSG00000103742	ENST00000352385	T	0.67171	-0.25	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.253764	0.41001	D	0.000975	T	0.59676	0.2211	L	0.42744	1.35	0.37722	D	0.92495	B	0.10296	0.003	B	0.15052	0.012	T	0.57590	-0.7785	10	0.19590	T	0.45	-18.2775	17.1439	0.86761	0.0:0.0:1.0:0.0	.	165	Q8TDY8	IGDC4_HUMAN	Y	165	ENSP00000319623:H165Y	ENSP00000319623:H165Y	H	-	1	0	IGDCC4	63489639	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.072000	0.76777	2.576000	0.86940	0.655000	0.94253	CAC	.	.		0.612	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
DNAJA4	55466	hgsc.bcm.edu	37	15	78568034	78568034	+	Silent	SNP	T	T	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:78568034T>C	ENST00000394852.3	+	5	1031	c.841T>C	c.(841-843)Ttg>Ctg	p.L281L	DNAJA4_ENST00000446172.2_Silent_p.L254L|DNAJA4_ENST00000343789.3_Silent_p.L281L|DNAJA4_ENST00000394855.3_Silent_p.L310L	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	281					negative regulation of inclusion body assembly (GO:0090084)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	8						GATAAAAACATTGGACAATCG	0.363																																					p.L310L		Atlas-SNP	.											.	DNAJA4	63	.	0			c.T928C						.						118.0	112.0	114.0					15																	78568034		2196	4293	6489	SO:0001819	synonymous_variant	55466	exon6			AAAACATTGGACA	AF116663	CCDS10299.2, CCDS45316.1, CCDS45317.1	15q24.1	2011-09-02			ENSG00000140403	ENSG00000140403		"""Heat shock proteins / DNAJ (HSP40)"""	14885	protein-coding gene	gene with protein product						11147971	Standard	NM_018602		Approved	PRO1472	uc002bdi.3	Q8WW22	OTTHUMG00000143733	ENST00000394852.3:c.841T>C	chr15.hg19:g.78568034T>C		69.0	0.0		65.0	19.0	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Silent	SNP	ENST00000394852.3	hg19	CCDS45316.1																																																																																			.	.		0.363	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602	
RGMA	56963	hgsc.bcm.edu	37	15	93588470	93588470	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr15:93588470C>A	ENST00000329082.7	-	4	1382	c.1111G>T	c.(1111-1113)Gag>Tag	p.E371*	RGMA_ENST00000557301.1_Nonsense_Mutation_p.E379*|RGMA_ENST00000425933.2_Nonsense_Mutation_p.E355*|RGMA_ENST00000542321.2_Nonsense_Mutation_p.E355*|RGMA_ENST00000556658.1_Nonsense_Mutation_p.E262*|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000538818.1_Nonsense_Mutation_p.E262*|RGMA_ENST00000543599.1_Nonsense_Mutation_p.E355*	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	371					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|neural tube closure (GO:0001843)|regulation of BMP signaling pathway (GO:0030510)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			TACAGGTCCTCCACCGGCAGC	0.647																																					p.E379X		Atlas-SNP	.											.	RGMA	49	.	0			c.G1135T						.						34.0	37.0	36.0					15																	93588470		2116	4233	6349	SO:0001587	stop_gained	56963	exon4			GGTCCTCCACCGG	AL390083	CCDS45357.1, CCDS53973.1, CCDS53974.1	15q26.1	2013-11-06	2013-11-06			ENSG00000182175			30308	protein-coding gene	gene with protein product		607362	"""RGM domain family, member A"""			15975920	Standard	NM_020211		Approved	RGM, RGMa	uc010urc.2	Q96B86		ENST00000329082.7:c.1111G>T	chr15.hg19:g.93588470C>A	ENSP00000330005:p.Glu371*	129.0	0.0		113.0	34.0	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Nonsense_Mutation	SNP	ENST00000329082.7	hg19	CCDS45357.1	.	.	.	.	.	.	.	.	.	.	C	42	9.237840	0.99110	.	.	ENSG00000182175	ENST00000543599;ENST00000425933;ENST00000329082;ENST00000542321;ENST00000538818;ENST00000557301	.	.	.	4.87	4.87	0.63330	.	0.050013	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-13.1226	17.6076	0.88042	0.0:1.0:0.0:0.0	.	.	.	.	X	355;355;371;355;262;379	.	ENSP00000330005:E371X	E	-	1	0	RGMA	91389474	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.879000	0.63100	2.240000	0.73641	0.491000	0.48974	GAG	.	.		0.647	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211	
GNPTG	84572	hgsc.bcm.edu	37	16	1411878	1411878	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr16:1411878A>C	ENST00000204679.4	+	5	282	c.239A>C	c.(238-240)aAg>aCg	p.K80T	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	80	PRKCSH.				carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				CCCAGGTACAAGTATGAGTTC	0.657																																					p.K80T		Atlas-SNP	.											.	GNPTG	18	.	0			c.A239C						.						58.0	54.0	55.0					16																	1411878		2199	4300	6499	SO:0001583	missense	84572	exon5			GGTACAAGTATGA	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"""GlcNAc-phosphotransferase gamma-subunit"""	607838	"""N-acetylglucosamine-1-phosphotransferase, gamma subunit"", ""chromosome 16 open reading frame 27"""	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835	ENST00000204679.4:c.239A>C	chr16.hg19:g.1411878A>C	ENSP00000204679:p.Lys80Thr	63.0	0.0		42.0	12.0	NM_032520	B2R556|Q6XYD7|Q96L13	Missense_Mutation	SNP	ENST00000204679.4	hg19	CCDS10436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.92|15.92	2.975758|2.975758	0.53720|0.53720	.|.	.|.	ENSG00000090581|ENSG00000090581	ENST00000204679|ENST00000529110	D|.	0.81659|.	-1.52|.	5.28|5.28	5.28|5.28	0.74379|0.74379	Mannose-6-phosphate receptor, binding (1);Glucosidase II beta subunit-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.57932|0.57932	0.2087|0.2087	L|L	0.41492|0.41492	1.28|1.28	0.52099|0.52099	D|D	0.999946|0.999946	P|.	0.51057|.	0.941|.	P|.	0.58520|.	0.84|.	T|T	0.55471|0.55471	-0.8136|-0.8136	10|5	0.41790|.	T|.	0.15|.	-50.8171|-50.8171	13.1571|13.1571	0.59524|0.59524	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	80|.	Q9UJJ9|.	GNPTG_HUMAN|.	T|H	80|102	ENSP00000204679:K80T|.	ENSP00000204679:K80T|.	K|Q	+|+	2|3	0|2	GNPTG|GNPTG	1351879|1351879	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.868000|0.868000	0.49771|0.49771	8.397000|8.397000	0.90193|0.90193	2.003000|2.003000	0.58678|0.58678	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.		0.657	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520	
GUCY2D	3000	hgsc.bcm.edu	37	17	7916472	7916472	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:7916472G>A	ENST00000254854.4	+	11	2315	c.2165G>A	c.(2164-2166)cGg>cAg	p.R722Q		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	722	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> W (in dbSNP:rs34331388).		intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				CTGGAGCGCCGGGGAACGCTG	0.657																																					p.R722Q		Atlas-SNP	.											.	GUCY2D	82	.	0			c.G2165A						.						37.0	35.0	36.0					17																	7916472		2203	4300	6503	SO:0001583	missense	3000	exon11			AGCGCCGGGGAAC	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.2165G>A	chr17.hg19:g.7916472G>A	ENSP00000254854:p.Arg722Gln	77.0	0.0		48.0	29.0	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	hg19	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479356	0.44044	.	.	ENSG00000132518	ENST00000254854	T	0.62232	0.04	4.97	1.75	0.24633	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.315714	0.23211	N	0.050671	T	0.42899	0.1223	L	0.33624	1.015	0.25727	N	0.98531	B	0.24483	0.104	B	0.19391	0.025	T	0.17992	-1.0351	10	0.13470	T	0.59	.	7.4891	0.27452	0.3553:0.0:0.6447:0.0	.	722	Q02846	GUC2D_HUMAN	Q	722	ENSP00000254854:R722Q	ENSP00000254854:R722Q	R	+	2	0	GUCY2D	7857197	0.000000	0.05858	0.993000	0.49108	0.971000	0.66376	0.071000	0.14594	0.698000	0.31739	0.561000	0.74099	CGG	.	.		0.657	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
CDC27	996	hgsc.bcm.edu	37	17	45219595	45219595	+	Splice_Site	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:45219595C>A	ENST00000066544.3	-	11	1471	c.1378G>T	c.(1378-1380)Gaa>Taa	p.E460*	CDC27_ENST00000531206.1_Splice_Site_p.E466*|CDC27_ENST00000446365.2_Splice_Site_p.E399*|CDC27_ENST00000527547.1_Splice_Site_p.G460C	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	460				Missing (in Ref. 1; AAA60471). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAAACAGACCTGCTGCTGCT	0.294																																					p.E466X		Atlas-SNP	.											.	CDC27	337	.	0			c.G1396T						.						25.0	25.0	25.0					17																	45219595		2199	4292	6491	SO:0001630	splice_region_variant	996	exon11			ACAGACCTGCTGC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1378+1G>T	chr17.hg19:g.45219595C>A		276.0	0.0		272.0	78.0	NM_001114091	G3V1C4|Q16349|Q96F35	Nonsense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.663474|6.663474	0.97743|0.97743	.|.	.|.	ENSG00000004897|ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365|ENST00000527547	.|T	.|0.75154	.|-0.91	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	0.053451|.	0.64402|.	D|.	0.000001|.	.|D	.|0.86322	.|0.5905	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	.|D	.|0.86259	.|0.1654	.|6	.|.	.|.	.|.	-0.6453|-0.6453	17.0728|17.0728	0.86579|0.86579	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|460	.|G5EA36	.|.	X|C	460;466;399|460	.|ENSP00000437339:G460C	.|.	E|G	-|-	1|1	0|0	CDC27|CDC27	42574594|42574594	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	7.429000|7.429000	0.80309|0.80309	2.632000|2.632000	0.89209|0.89209	0.557000|0.557000	0.71058|0.71058	GAA|GGT	.	.		0.294	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Nonsense_Mutation
KCNH6	81033	hgsc.bcm.edu	37	17	61620964	61620964	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:61620964C>T	ENST00000583023.1	+	10	2187	c.2176C>T	c.(2176-2178)Cga>Tga	p.R726*	KCNH6_ENST00000581784.1_Nonsense_Mutation_p.R673*|KCNH6_ENST00000314672.5_Nonsense_Mutation_p.R726*|KCNH6_ENST00000456941.2_Nonsense_Mutation_p.R673*	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	726					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CTCATCCCCCCGACAGGCTCC	0.597																																					p.R726X		Atlas-SNP	.											.	KCNH6	122	.	0			c.C2176T						.						59.0	64.0	63.0					17																	61620964		2203	4300	6503	SO:0001587	stop_gained	81033	exon10			TCCCCCCGACAGG	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2176C>T	chr17.hg19:g.61620964C>T	ENSP00000463533:p.Arg726*	176.0	0.0		169.0	60.0	NM_030779	Q9BRD7	Nonsense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	C	31	5.081806	0.94050	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	.	.	.	4.92	3.88	0.44766	.	2.951240	0.03137	U	0.166020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0816	0.48064	0.1842:0.8158:0.0:0.0	.	.	.	.	X	726;673	.	ENSP00000318212:R726X	R	+	1	2	KCNH6	58974696	0.008000	0.16893	0.953000	0.39169	0.371000	0.29859	0.148000	0.16224	2.442000	0.82660	0.655000	0.94253	CGA	.	.		0.597	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
GRIN2C	2905	hgsc.bcm.edu	37	17	72846852	72846852	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr17:72846852A>G	ENST00000293190.5	-	5	1314	c.1168T>C	c.(1168-1170)Tac>Cac	p.Y390H	GRIN2C_ENST00000347612.4_Missense_Mutation_p.Y390H|GRIN2C_ENST00000578159.1_5'Flank	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	390					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GAGGCACTGTAGCGAGGCCAC	0.657																																					p.Y390H		Atlas-SNP	.											.	GRIN2C	144	.	0			c.T1168C						.						69.0	49.0	56.0					17																	72846852		2203	4300	6503	SO:0001583	missense	2905	exon5			CACTGTAGCGAGG		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.1168T>C	chr17.hg19:g.72846852A>G	ENSP00000293190:p.Tyr390His	187.0	0.0		177.0	48.0	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	hg19	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	A	14.51	2.555626	0.45487	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.07567	3.18	4.28	4.28	0.50868	.	0.069729	0.64402	D	0.000015	T	0.29749	0.0743	M	0.84433	2.695	0.47511	D	0.999449	D;D	0.76494	0.999;0.994	D;D	0.68483	0.958;0.947	T	0.07616	-1.0763	10	0.39692	T	0.17	.	13.5423	0.61681	1.0:0.0:0.0:0.0	.	424;390	Q8IW23;Q14957	.;NMDE3_HUMAN	H	390;424	ENSP00000293190:Y390H	ENSP00000293190:Y390H	Y	-	1	0	GRIN2C	70358447	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	9.079000	0.94032	1.922000	0.55676	0.454000	0.30748	TAC	.	.		0.657	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
HAUS1	115106	hgsc.bcm.edu	37	18	43708091	43708091	+	Nonstop_Mutation	SNP	A	A	G			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr18:43708091A>G	ENST00000282058.6	+	9	917	c.837A>G	c.(835-837)tgA>tgG	p.*279W	HAUS1_ENST00000588704.1_3'UTR|HAUS1_ENST00000585518.1_3'UTR	NM_138443.3	NP_612452.1	Q96CS2	HAUS1_HUMAN	HAUS augmin-like complex, subunit 1	0					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						TGGAACTGTGACAAAAGCCAA	0.348																																					p.X279W	NSCLC(79;183 1423 5813 15597 38427)	Atlas-SNP	.											.	HAUS1	22	.	0			c.A837G						.						100.0	85.0	90.0					18																	43708091		2203	4297	6500	SO:0001578	stop_lost	115106	exon9			ACTGTGACAAAAG	AY360137	CCDS11928.1	18q21.1	2013-10-11	2009-04-20	2009-04-20	ENSG00000152240	ENSG00000152240		"""HAUS augmin-like complex subunits"""	25174	protein-coding gene	gene with protein product		608775	"""coiled-coil domain containing 5 (spindle associated)"""	CCDC5		19427217	Standard	NR_026978		Approved	HEI-C, HsT1461, FLJ40084	uc002lbu.3	Q96CS2	OTTHUMG00000132638	ENST00000282058.6:c.837A>G	chr18.hg19:g.43708091A>G	ENSP00000282058:p.*279Trpext*10	452.0	0.0		397.0	88.0	NM_138443	B2RDM7|Q8N837	Missense_Mutation	SNP	ENST00000282058.6	hg19	CCDS11928.1	.	.	.	.	.	.	.	.	.	.	A	8.756	0.922472	0.17982	.	.	ENSG00000152240	ENST00000282058	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4884	0.50367	1.0:0.0:0.0:0.0	.	.	.	.	W	279	.	.	X	+	3	0	HAUS1	41962089	1.000000	0.71417	0.996000	0.52242	0.145000	0.21501	4.442000	0.59988	2.026000	0.59711	0.477000	0.44152	TGA	.	.		0.348	HAUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255885.1	NM_138443	
LOXHD1	125336	hgsc.bcm.edu	37	18	44137363	44137363	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr18:44137363C>A	ENST00000398722.4	-	14	2471	c.2472G>T	c.(2470-2472)tgG>tgT	p.W824C	LOXHD1_ENST00000536736.1_Missense_Mutation_p.W1102C|LOXHD1_ENST00000441893.2_Missense_Mutation_p.W35C|LOXHD1_ENST00000441551.2_Missense_Mutation_p.W896C|LOXHD1_ENST00000582408.1_5'UTR|LOXHD1_ENST00000300591.6_5'UTR|LOXHD1_ENST00000579038.1_5'Flank			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	824	PLAT 6. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						TGTCCAGGAACCAGCCTGCTC	0.567																																					p.W1102C		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G3306T						.						228.0	198.0	207.0					18																	44137363		692	1591	2283	SO:0001583	missense	125336	exon21			CAGGAACCAGCCT	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.2472G>T	chr18.hg19:g.44137363C>A	ENSP00000381707:p.Trp824Cys	149.0	0.0		165.0	28.0	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.57|13.57	2.278123|2.278123	0.40294|0.40294	.|.	.|.	ENSG00000167210|ENSG00000167210	ENST00000441551|ENST00000398722;ENST00000536736;ENST00000441893;ENST00000335730	.|T;T;T	.|0.80214	.|-1.35;-1.35;-1.35	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	.|0.124248	.|0.64402	.|D	.|0.000017	D|D	0.93910|0.93910	0.8051|0.8051	H|H	0.98295|0.98295	4.195|4.195	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.97110	.|1.0;0.998;0.998	D|D	0.96199|0.96199	0.9144|0.9144	5|10	.|0.87932	.|D	.|0	.|.	16.5132|16.5132	0.84292|0.84292	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1102;35;824	.|F5GZB4;F8WA52;Q8IVV2-2	.|.;.;.	F|C	1083|824;1102;35;824	.|ENSP00000381707:W824C;ENSP00000444586:W1102C;ENSP00000409062:W35C	.|ENSP00000338222:W824C	V|W	-|-	1|3	0|0	LOXHD1|LOXHD1	42391361|42391361	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	7.727000|7.727000	0.84838|0.84838	2.436000|2.436000	0.82500|0.82500	0.484000|0.484000	0.47621|0.47621	GTT|TGG	.	.		0.567	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
MBP	4155	hgsc.bcm.edu	37	18	74728894	74728894	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr18:74728894T>C	ENST00000397869.3	-	1	117	c.71A>G	c.(70-72)cAt>cGt	p.H24R	MBP_ENST00000397866.4_Missense_Mutation_p.H24R|MBP_ENST00000354542.4_Missense_Mutation_p.H24R|MBP_ENST00000578193.1_Missense_Mutation_p.H24R|MBP_ENST00000527041.1_Missense_Mutation_p.H24R|MBP_ENST00000355994.2_Missense_Mutation_p.H157R|MBP_ENST00000359645.3_Missense_Mutation_p.H24R|MBP_ENST00000397865.5_Missense_Mutation_p.H24R|MBP_ENST00000397863.1_Missense_Mutation_p.H157R|MBP_ENST00000580402.1_Missense_Mutation_p.H157R|MBP_ENST00000487778.1_5'Flank|MBP_ENST00000526111.1_Intron|MBP_ENST00000397875.3_Missense_Mutation_p.H24R|MBP_ENST00000579129.1_Missense_Mutation_p.H157R|MBP_ENST00000397860.3_Missense_Mutation_p.H157R|MBP_ENST00000528160.1_Missense_Mutation_p.H24R|MBP_ENST00000382582.3_Missense_Mutation_p.H24R			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	ATGCCTGGCATGGTCCATGGT	0.622																																					p.H157R	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.A470G						.						112.0	91.0	98.0					18																	74728894		2203	4300	6503	SO:0001583	missense	4155	exon4			CTGGCATGGTCCA		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.71A>G	chr18.hg19:g.74728894T>C	ENSP00000380967:p.His24Arg	138.0	0.0		96.0	24.0	NM_001025100	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000397869.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.56	3.420651	0.62622	.	.	ENSG00000197971	ENST00000382582;ENST00000355994;ENST00000397875;ENST00000397866;ENST00000397865;ENST00000527041;ENST00000359645;ENST00000528160;ENST00000397869;ENST00000354542;ENST00000397868;ENST00000498683;ENST00000397863;ENST00000397860	.	.	.	5.06	5.06	0.68205	.	0.063133	0.64402	D	0.000004	T	0.75087	0.3802	L	0.55990	1.75	0.39451	D	0.967407	D;D;D;P;D;D	0.67145	0.996;0.993;0.996;0.907;0.995;0.995	D;P;D;P;D;D	0.87578	0.998;0.824;0.99;0.45;0.996;0.996	T	0.79186	-0.1907	9	0.87932	D	0	-6.6509	14.8857	0.70567	0.0:0.0:0.0:1.0	.	24;157;157;24;24;24	B7Z3Y6;P02686;P02686-2;P02686-6;P02686-4;P02686-3	.;MBP_HUMAN;.;.;.;.	R	24;157;24;24;24;24;24;24;24;24;24;24;157;157	.	ENSP00000346545:H24R	H	-	2	0	MBP	72857882	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	5.071000	0.64382	1.912000	0.55364	0.456000	0.33151	CAT	.	.		0.622	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081	
ZNF441	126068	hgsc.bcm.edu	37	19	11891553	11891553	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:11891553A>T	ENST00000357901.4	+	4	1016	c.914A>T	c.(913-915)gAt>gTt	p.D305V	ZNF441_ENST00000454339.2_Missense_Mutation_p.D238V	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CACACTGGAGATGGGCCTCAT	0.403																																					p.D305V		Atlas-SNP	.											.	ZNF441	123	.	0			c.A914T						.						100.0	102.0	101.0					19																	11891553		2203	4300	6503	SO:0001583	missense	126068	exon4			CTGGAGATGGGCC	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"""Zinc fingers, C2H2-type"", ""-"""	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.914A>T	chr19.hg19:g.11891553A>T	ENSP00000350576:p.Asp305Val	140.0	0.0		81.0	29.0	NM_152355		Missense_Mutation	SNP	ENST00000357901.4	hg19	CCDS12266.2	.	.	.	.	.	.	.	.	.	.	-	18.46	3.629913	0.67015	.	.	ENSG00000197044	ENST00000409902;ENST00000357901;ENST00000454339	T;T	0.17691	2.26;2.26	0.998	0.998	0.19857	Zinc finger, C2H2 (1);	.	.	.	.	T	0.15652	0.0377	N	0.20610	0.595	0.45205	D	0.998217	P	0.47350	0.894	P	0.51701	0.677	T	0.06881	-1.0802	9	0.62326	D	0.03	.	7.5239	0.27643	1.0:0.0:0.0:0.0	.	305	Q8N8Z8	ZN441_HUMAN	V	261;305;238	ENSP00000350576:D305V;ENSP00000403738:D238V	ENSP00000350576:D305V	D	+	2	0	ZNF441	11752553	0.905000	0.30787	0.005000	0.12908	0.799000	0.45148	2.685000	0.46959	0.703000	0.31848	0.248000	0.18094	GAT	.	.		0.403	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355	
GIPC1	10755	hgsc.bcm.edu	37	19	14591237	14591237	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:14591237C>A	ENST00000393033.4	-	6	804	c.535G>T	c.(535-537)Gag>Tag	p.E179*	GIPC1_ENST00000586027.1_Nonsense_Mutation_p.E179*|GIPC1_ENST00000393028.1_Nonsense_Mutation_p.E82*|GIPC1_ENST00000345425.2_Nonsense_Mutation_p.E179*|GIPC1_ENST00000591349.1_Nonsense_Mutation_p.E82*|GIPC1_ENST00000393029.3_Nonsense_Mutation_p.E82*	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	179	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.E179K(1)		endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						TTAATGGCCTCGATCATGTCG	0.667											OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E179X	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											GIPC1,NS,carcinoma,0,1	GIPC1	21	.	1	Substitution - Missense(1)	lung(1)	c.G535T						.						74.0	75.0	74.0					19																	14591237		2203	4300	6503	SO:0001587	stop_gained	10755	exon5			TGGCCTCGATCAT	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.535G>T	chr19.hg19:g.14591237C>A	ENSP00000376753:p.Glu179*	146.0	1.0	696	122.0	40.0	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Nonsense_Mutation	SNP	ENST00000393033.4	hg19	CCDS12310.1	.	.	.	.	.	.	.	.	.	.	C	39	7.440191	0.98286	.	.	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-7.024	15.6737	0.77297	0.0:1.0:0.0:0.0	.	.	.	.	X	179;179;82;82;179	.	ENSP00000340698:E179X	E	-	1	0	GIPC1	14452237	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.189000	0.77747	2.311000	0.77944	0.561000	0.74099	GAG	.	.		0.667	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		
ZNF507	22847	hgsc.bcm.edu	37	19	32845669	32845669	+	Silent	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:32845669C>T	ENST00000311921.4	+	2	2125	c.1933C>T	c.(1933-1935)Ctg>Ttg	p.L645L	ZNF507_ENST00000544431.1_Silent_p.L645L|ZNF507_ENST00000355898.5_Silent_p.L645L	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	645					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					CCGTTGCCGCCTGTGTCACTA	0.527																																					p.L645L		Atlas-SNP	.											.	ZNF507	92	.	0			c.C1933T						.						153.0	119.0	131.0					19																	32845669		2203	4300	6503	SO:0001819	synonymous_variant	22847	exon3			TGCCGCCTGTGTC	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"""Zinc fingers, C2H2-type"""	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.1933C>T	chr19.hg19:g.32845669C>T		168.0	0.0		135.0	35.0	NM_001136156	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Silent	SNP	ENST00000311921.4	hg19	CCDS32985.1																																																																																			.	.		0.527	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910	
FCGBP	8857	hgsc.bcm.edu	37	19	40368348	40368348	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:40368348C>T	ENST00000221347.6	-	28	13007	c.13000G>A	c.(13000-13002)Gcc>Acc	p.A4334T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4334						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ACCCCAGCGGCCTGGCAGGCG	0.647																																					p.A4334T		Atlas-SNP	.											.	FCGBP	416	.	0			c.G13000A						.						175.0	185.0	181.0					19																	40368348		2203	4300	6503	SO:0001583	missense	8857	exon28			CAGCGGCCTGGCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13000G>A	chr19.hg19:g.40368348C>T	ENSP00000221347:p.Ala4334Thr	343.0	0.0		323.0	51.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	9.235	1.036807	0.19669	.	.	ENSG00000090920	ENST00000221347	T	0.78003	-1.14	4.08	4.08	0.47627	Uncharacterised domain, cysteine-rich (2);	0.349619	0.25768	U	0.028439	D	0.82273	0.5001	M	0.73217	2.22	0.26109	N	0.980703	D	0.63046	0.992	P	0.62491	0.903	T	0.71646	-0.4530	10	0.17369	T	0.5	.	9.3858	0.38342	0.0:0.898:0.0:0.102	.	4334	Q9Y6R7	FCGBP_HUMAN	T	4334	ENSP00000221347:A4334T	ENSP00000221347:A4334T	A	-	1	0	FCGBP	45060188	0.000000	0.05858	0.994000	0.49952	0.123000	0.20343	-0.051000	0.11885	2.279000	0.76181	0.305000	0.20034	GCC	.	.		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF135	7694	hgsc.bcm.edu	37	19	58579348	58579348	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:58579348G>A	ENST00000313434.5	+	5	1597	c.1496G>A	c.(1495-1497)tGc>tAc	p.C499Y	RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000439855.2_Missense_Mutation_p.C499Y|ZNF135_ENST00000511556.1_Missense_Mutation_p.C511Y|ZNF135_ENST00000401053.4_Missense_Mutation_p.C523Y|ZNF135_ENST00000359978.6_Intron|ZNF135_ENST00000506786.1_Missense_Mutation_p.C457Y	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	499					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		TGCAATGACTGCGGCAAGGCA	0.562																																					p.C523Y		Atlas-SNP	.											ZNF135_ENST00000401053,NS,carcinoma,0,2	ZNF135	159	.	0			c.G1568A						.						90.0	81.0	84.0					19																	58579348		2203	4300	6503	SO:0001583	missense	7694	exon4			ATGACTGCGGCAA	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"""Zinc fingers, C2H2-type"", ""-"""	12919	protein-coding gene	gene with protein product		604077	"""zinc finger protein 61"", ""zinc finger protein 135 (clone pHZ-17)"""	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1496G>A	chr19.hg19:g.58579348G>A	ENSP00000321406:p.Cys499Tyr	107.0	0.0		92.0	29.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.49|10.49	1.365473|1.365473	0.24684|0.24684	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000391699|ENST00000401053;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	.|D;D;D;D;D	.|0.85861	.|-2.04;-2.04;-2.04;-2.04;-2.04	3.26|3.26	2.16|2.16	0.27623|0.27623	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	D|D	0.93844|0.93844	0.8031|0.8031	H|H	0.96365|0.96365	3.81|3.81	0.34095|0.34095	D|D	0.661122|0.661122	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.998	D|D	0.94796|0.94796	0.7966|0.7966	5|9	.|0.87932	.|D	.|0	.|.	9.9698|9.9698	0.41747|0.41747	0.1088:0.0:0.8912:0.0|0.1088:0.0:0.8912:0.0	.|.	.|511;499	.|E9PEV2;P52742	.|.;ZN135_HUMAN	T|Y	517|523;499;499;511;457	.|ENSP00000441410:C523Y;ENSP00000444828:C499Y;ENSP00000321406:C499Y;ENSP00000422074:C511Y;ENSP00000427691:C457Y	.|ENSP00000321406:C499Y	A|C	+|+	1|2	0|0	ZNF135|ZNF135	63271160|63271160	1.000000|1.000000	0.71417|0.71417	0.499000|0.499000	0.27577|0.27577	0.010000|0.010000	0.07245|0.07245	4.121000|4.121000	0.57904|0.57904	0.671000|0.671000	0.31185|0.31185	0.557000|0.557000	0.71058|0.71058	GCG|TGC	.	.		0.562	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
ZCCHC3	85364	hgsc.bcm.edu	37	20	278367	278367	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr20:278367T>C	ENST00000382352.3	+	1	631	c.140T>C	c.(139-141)cTa>cCa	p.L47P		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	47							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GTGAAGAATCTAGCCGAGAAG	0.791																																					p.L47P		Atlas-SNP	.											.	ZCCHC3	20	.	0			c.T140C						.						1.0	2.0	1.0					20																	278367		805	2014	2819	SO:0001583	missense	85364	exon1			AGAATCTAGCCGA	AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"""Zinc fingers, CCHC domain containing"""	16230	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 99"""	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.140T>C	chr20.hg19:g.278367T>C	ENSP00000371789:p.Leu47Pro	80.0	0.0		75.0	16.0	NM_033089	Q3B7J3|Q6NT79	Missense_Mutation	SNP	ENST00000382352.3	hg19	CCDS42844.1	.	.	.	.	.	.	.	.	.	.	T	13.71	2.318499	0.40996	.	.	ENSG00000177764	ENST00000382352	.	.	.	4.08	2.95	0.34219	.	0.209202	0.22922	N	0.054011	T	0.36880	0.0983	N	0.14661	0.345	0.52501	D	0.999956	D	0.61080	0.989	P	0.50825	0.651	T	0.24333	-1.0163	9	0.87932	D	0	-16.2416	8.1946	0.31389	0.1792:0.0:0.0:0.8207	.	47	Q9NUD5	ZCHC3_HUMAN	P	47	.	ENSP00000371789:L47P	L	+	2	0	ZCCHC3	226367	0.986000	0.35501	0.998000	0.56505	0.757000	0.42996	0.903000	0.28475	0.691000	0.31592	0.379000	0.24179	CTA	.	.		0.791	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1		
CDH4	1002	hgsc.bcm.edu	37	20	60448832	60448832	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr20:60448832C>A	ENST00000360469.5	+	7	1014	c.926C>A	c.(925-927)aCg>aAg	p.T309K	CDH4_ENST00000543233.1_Missense_Mutation_p.T235K	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	309	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GACAGCACCACGGCCAACGGG	0.602																																					p.T309K		Atlas-SNP	.											.	CDH4	172	.	0			c.C926A						.						150.0	116.0	127.0					20																	60448832		2203	4300	6503	SO:0001583	missense	1002	exon7			GCACCACGGCCAA	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.926C>A	chr20.hg19:g.60448832C>A	ENSP00000353656:p.Thr309Lys	91.0	0.0		85.0	35.0	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	hg19	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546761	0.86022	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.53206	0.63;0.63	4.76	4.76	0.60689	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.74176	0.3682	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79926	-0.1597	9	.	.	.	.	17.8138	0.88624	0.0:1.0:0.0:0.0	.	309	P55283	CADH4_HUMAN	K	309;217;235	ENSP00000353656:T309K;ENSP00000443301:T235K	.	T	+	2	0	CDH4	59882227	1.000000	0.71417	0.995000	0.50966	0.938000	0.57974	4.621000	0.61233	2.196000	0.70406	0.460000	0.39030	ACG	.	.		0.602	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
COL18A1	80781	hgsc.bcm.edu	37	21	46912479	46912479	+	Splice_Site	SNP	G	G	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr21:46912479G>A	ENST00000359759.4	+	22	3453		c.e22+1		COL18A1_ENST00000400337.2_Splice_Site|COL18A1_ENST00000355480.5_Splice_Site			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGGACCTGAGGTATGTGCCTG	0.607																																					.		Atlas-SNP	.											.	COL18A1	129	.	0			c.2187+1G>A						.						126.0	138.0	134.0					21																	46912479		1935	4129	6064	SO:0001630	splice_region_variant	80781	exon23			CCTGAGGTATGTG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3432+1G>A	chr21.hg19:g.46912479G>A		136.0	0.0		75.0	11.0	NM_130445	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Splice_Site	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	G	12.70	2.017299	0.35606	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	.	.	.	3.15	3.15	0.36227	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0448	0.42180	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL18A1	45736907	1.000000	0.71417	0.472000	0.27241	0.011000	0.07611	3.908000	0.56355	1.795000	0.52594	0.556000	0.70494	.	.	.		0.607	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		Intron
PNPLA5	150379	hgsc.bcm.edu	37	22	44282291	44282291	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr22:44282291C>T	ENST00000597664.1	-	6	970	c.841G>A	c.(841-843)Ggc>Agc	p.G281S	PNPLA5_ENST00000381198.2_Missense_Mutation_p.G167S|PNPLA5_ENST00000593866.1_Missense_Mutation_p.G167S|PNPLA5_ENST00000216177.4_Missense_Mutation_p.G281S			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	281					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TGGTCACAGCCAGCATCCCAG	0.587																																					p.G281S		Atlas-SNP	.											.	PNPLA5	46	.	0			c.G841A						.						95.0	83.0	87.0					22																	44282291		2203	4300	6503	SO:0001583	missense	150379	exon6			CACAGCCAGCATC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.841G>A	chr22.hg19:g.44282291C>T	ENSP00000471069:p.Gly281Ser	70.0	0.0		70.0	12.0	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.64	1.699025	0.30142	.	.	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.44083	1.45;0.93;1.71	3.86	2.79	0.32731	.	1.332370	0.05078	N	0.482968	T	0.31949	0.0813	L	0.41356	1.27	0.09310	N	1	P;P;B	0.40970	0.473;0.734;0.036	B;B;B	0.35470	0.091;0.203;0.023	T	0.14896	-1.0456	10	0.14656	T	0.56	-9.7781	8.5041	0.33177	0.2318:0.7682:0.0:0.0	.	189;167;281	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	S	281;167;189	ENSP00000216177:G281S;ENSP00000370595:G167S;ENSP00000405732:G189S	ENSP00000216177:G281S	G	-	1	0	PNPLA5	42613624	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	0.774000	0.26675	0.906000	0.36621	0.491000	0.48974	GGC	.	.		0.587	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
SPANXC	64663	hgsc.bcm.edu	37	X	140336533	140336533	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chrX:140336533C>A	ENST00000358993.2	-	1	96	c.58G>T	c.(58-60)Gag>Tag	p.E20*		NM_022661.2	NP_073152.1	Q9NY87	SPNXC_HUMAN	SPANX family, member C	20						cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(2)|lung(3)|pancreas(1)	6	Acute lymphoblastic leukemia(192;7.65e-05)					TCATTCACCTCGTTGGATTCA	0.493																																					p.E20X		Atlas-SNP	.											.	SPANXC	8	.	0			c.G58T						.						81.0	115.0	103.0					X																	140336533		2173	4253	6426	SO:0001587	stop_gained	64663	exon1			TCACCTCGTTGGA	AJ238277	CCDS14673.1	Xq27.2	2009-03-25			ENSG00000198573	ENSG00000198573			14331	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 3"""	300330				10626816	Standard	NM_022661		Approved	CTp11, CT11.3	uc004fbk.3	Q9NY87	OTTHUMG00000022556	ENST00000358993.2:c.58G>T	chrX.hg19:g.140336533C>A	ENSP00000351884:p.Glu20*	310.0	1.0		287.0	209.0	NM_022661	Q32WL9|Q5JX88	Nonsense_Mutation	SNP	ENST00000358993.2	hg19	CCDS14673.1	.	.	.	.	.	.	.	.	.	.	c	10.43	1.348209	0.24426	.	.	ENSG00000198573	ENST00000358993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	.	.	.	.	.	.	.	X	20	.	ENSP00000351884:E20X	E	-	1	0	SPANXC	140164199	0.082000	0.21442	0.000000	0.03702	0.000000	0.00434	-1.577000	0.02127	-0.759000	0.04684	-0.773000	0.03387	GAG	.	.		0.493	SPANXC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058590.1	NM_022661	
LYST	1130	hgsc.bcm.edu	37	1	235916449	235916451	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:235916449_235916451delAGA	ENST00000389794.3	-	26	7527_7529	c.7353_7355delTCT	c.(7351-7356)cttctc>ctc	p.2451_2452LL>L	LYST_ENST00000389793.2_In_Frame_Del_p.2451_2452LL>L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2451	Poly-Leu.				blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TAAAATTTGGAGAAGAAGTAAAA	0.365																																					p.2452_2452del		Atlas-INDEL	.											.,1	LYST	370	.	0			c.7354_7356del						.			14,4252		7,0,2126						-2.1	1.0			69	29,8213		14,1,4106	no	coding	LYST	NM_000081.2		21,1,6232	A1A1,A1R,RR		0.3519,0.3282,0.3438				43,12465				SO:0001651	inframe_deletion	1130	exon26			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.7353_7355delTCT	chr1.hg19:g.235916452_235916454delAGA	ENSP00000374444:p.Leu2452del	381.0	0.0		375.0	118.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	In_Frame_Del	DEL	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.365	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
HARS2	23438	hgsc.bcm.edu	37	5	140075365	140075365	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr5:140075365delG	ENST00000230771.3	+	6	791	c.568delG	c.(568-570)gcafs	p.A190fs	HARS2_ENST00000508522.1_Frame_Shift_Del_p.A165fs|HARS2_ENST00000435019.2_Frame_Shift_Del_p.A150fs|HARS2_ENST00000437649.2_Frame_Shift_Del_p.A116fs|HARS2_ENST00000448069.2_Frame_Shift_Del_p.A51fs|HARS2_ENST00000432671.2_Frame_Shift_Del_p.A76fs	NM_012208.2	NP_036340.1	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2, mitochondrial	190					gene expression (GO:0010467)|histidyl-tRNA aminoacylation (GO:0006427)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|histidine-tRNA ligase activity (GO:0004821)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|large_intestine(5)|lung(10)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATCCCCGATGCAGAGTGTTT	0.443																																					p.D189fs		Atlas-INDEL	.											.	HARS2	41	.	0			c.567delT						.						185.0	177.0	180.0					5																	140075365		2203	4300	6503	SO:0001589	frameshift_variant	23438	exon6			.	U18937	CCDS4238.1, CCDS64267.1	5q31.3	2012-07-20	2012-07-20	2007-02-23	ENSG00000112855	ENSG00000112855	6.1.1.21	"""Aminoacyl tRNA synthetases / Class II"""	4817	protein-coding gene	gene with protein product	"""histidine tRNA ligase 2, mitochondrial (putative)"""	600783	"""histidyl-tRNA synthetase-like"""	HARSL		7755634, 21464306	Standard	NM_012208		Approved	HO3, HARSR	uc003lgx.3	P49590	OTTHUMG00000129500	ENST00000230771.3:c.568delG	chr5.hg19:g.140075365delG	ENSP00000230771:p.Ala190fs	155.0	0.0		130.0	42.0	NM_012208	B4DDY8	Frame_Shift_Del	DEL	ENST00000230771.3	hg19	CCDS4238.1																																																																																			.	.		0.443	HARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251670.2	NM_012208	
NHS	4810	hgsc.bcm.edu	37	X	17745169	17745169	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chrX:17745169delA	ENST00000380060.3	+	6	3218	c.2880delA	c.(2878-2880)ccafs	p.P960fs	NHS_ENST00000398097.3_Frame_Shift_Del_p.P804fs	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	981					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TCAAATCTCCAGAGAGCTCTG	0.423																																					p.P960fs		Atlas-INDEL	.											.	NHS	302	.	0			c.2879delC						.						80.0	78.0	78.0					X																	17745169		2203	4300	6503	SO:0001589	frameshift_variant	4810	exon6			.		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.2880delA	chrX.hg19:g.17745169delA	ENSP00000369400:p.Pro960fs	144.0	0.0		124.0	93.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Frame_Shift_Del	DEL	ENST00000380060.3	hg19	CCDS14181.1																																																																																			.	.		0.423	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51633222	51633222	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr19:51633222delG	ENST00000250360.3	+	7	1345	c.1278delG	c.(1276-1278)gtgfs	p.V426fs	SIGLEC9_ENST00000440804.3_Intron	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	426					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GCTCCTCAGTGGGGGAAGGAG	0.612																																					p.V426fs		Atlas-INDEL	.											.	SIGLEC9	85	.	0			c.1277delT						.						67.0	68.0	68.0					19																	51633222		2203	4300	6503	SO:0001589	frameshift_variant	27180	exon7			.	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.1278delG	chr19.hg19:g.51633222delG	ENSP00000250360:p.Val426fs	73.0	0.0		67.0	21.0	NM_014441	Q6GTU4|Q9BYI9	Frame_Shift_Del	DEL	ENST00000250360.3	hg19	CCDS12825.1																																																																																			.	.		0.612	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
MED28	80306	hgsc.bcm.edu	37	4	17616334	17616342	+	In_Frame_Del	DEL	CCCGCCGGG	CCCGCCGGG	-	rs375191348		TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	CCCGCCGGG	CCCGCCGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr4:17616334_17616342delCCCGCCGGG	ENST00000237380.7	+	1	81_89	c.57_65delCCCGCCGGG	c.(55-66)gccccgccgggc>gcc	p.PPG20del	AC006160.5_ENST00000511010.1_RNA	NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	20					negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						CCCCTCAGGCCCCGCCGGGCCTTCCGGGC	0.612																																					p.19_22del		Atlas-INDEL	.											.	MED28	16	.	0			c.56_64del						.																																			SO:0001651	inframe_deletion	80306	exon1			.	AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579			24628	protein-coding gene	gene with protein product		610311	"""mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)"""			11779215, 15467741	Standard	NM_025205		Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.57_65delCCCGCCGGG	chr4.hg19:g.17616334_17616342delCCCGCCGGG	ENSP00000237380:p.Pro20_Gly22del	139.0	0.0		108.0	42.0	NM_025205	Q9BZJ5	In_Frame_Del	DEL	ENST00000237380.7	hg19	CCDS33963.1																																																																																			.	.		0.612	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360055.3	NM_025205	
SRRT	51593	hgsc.bcm.edu	37	7	100483551	100483552	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr7:100483551_100483552insA	ENST00000347433.4	+	12	1605_1606	c.1447_1448insA	c.(1447-1449)cagfs	p.Q483fs	SRRT_ENST00000388793.4_Frame_Shift_Ins_p.Q482fs|SRRT_ENST00000457580.2_Frame_Shift_Ins_p.Q483fs|SRRT_ENST00000432932.1_Frame_Shift_Ins_p.Q482fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	483					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TTGGAACCTGCAGAACATCCGT	0.495																																					p.Q483fs		Atlas-INDEL	.											.	SRRT	108	.	0			c.1447_1448insA						.																																			SO:0001589	frameshift_variant	51593	exon12			.		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.1448dupA	chr7.hg19:g.100483552_100483552dupA	ENSP00000314491:p.Gln483fs	141.0	0.0		100.0	36.0	NM_001128853	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Ins	INS	ENST00000347433.4	hg19	CCDS34709.1																																																																																			.	.		0.495	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
WDR38	401551	hgsc.bcm.edu	37	9	127619833	127619834	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr9:127619833_127619834insA	ENST00000373574.1	+	9	925_926	c.869_870insA	c.(868-873)ttagtgfs	p.V291fs		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	291					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GGGAAAATCTTAGTGTCTGGAG	0.554																																					p.L291fs		Atlas-INDEL	.											.	WDR38	21	.	0			c.872_873insA						.																																			SO:0001589	frameshift_variant	401551	exon9			.		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"""WD repeat domain containing"""	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.870dupA	chr9.hg19:g.127619834_127619834dupA	ENSP00000362677:p.Val291fs	95.0	0.0		89.0	15.0	NM_001276374	A0PK24	Frame_Shift_Ins	INS	ENST00000373574.1	hg19	CCDS43876.1																																																																																			.	.		0.554	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476	
ARID1A	8289	hgsc.bcm.edu	37	1	27023388	27023388	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-AADR-01A-11D-A40R-10	TCGA-DD-AADR-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	78443fc5-5436-4636-afe8-df7854f7d17e	eb002cc9-e23b-4133-aac1-7b82257351cd	g.chr1:27023388delC	ENST00000324856.7	+	1	865	c.494delC	c.(493-495)gcgfs	p.A167fs	RP5-968P14.2_ENST00000569378.1_RNA|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.A167fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	167					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCCGCCGCCGCGGCCGCCGTC	0.766			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.A165fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.493delG						.						2.0	3.0	3.0					1																	27023388		1260	2903	4163	SO:0001589	frameshift_variant	8289	exon1			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.494delC	chr1.hg19:g.27023388delC	ENSP00000320485:p.Ala167fs	69.0	0.0		36.0	18.0	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.766	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
