#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
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919960	12919960	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:12919960C>T	ENST00000240189.2	+	3	787	c.700C>T	c.(700-702)Ctt>Ttt	p.L234F		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	234					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GATGAAGACTCTTTGCAAACT	0.423																																					p.L234F		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.C700T						.						110.0	114.0	113.0					1																	12919960		2203	4299	6502	SO:0001583	missense	65122	exon3			AAGACTCTTTGCA		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.700C>T	chr1.hg19:g.12919960C>T	ENSP00000240189:p.Leu234Phe	171.0	0.0		145.0	32.0	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	hg19	CCDS149.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.356756	0.24598	.	.	ENSG00000120952	ENST00000240189	T	0.02863	4.13	0.842	-0.495	0.12030	.	0.181875	0.36409	N	0.002604	T	0.13114	0.0318	M	0.90483	3.12	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.04242	-1.0966	10	0.87932	D	0	.	4.5732	0.12219	0.0:0.5898:0.4102:0.0	.	234	O60811	PRAM2_HUMAN	F	234	ENSP00000240189:L234F	ENSP00000240189:L234F	L	+	1	0	PRAMEF2	12842547	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-1.613000	0.02059	-0.146000	0.11274	0.194000	0.17425	CTT	.	.		0.423	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
FHAD1	114827	hgsc.bcm.edu	37	1	15684641	15684641	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:15684641A>T	ENST00000375998.4	+	19	2532	c.2532A>T	c.(2530-2532)ttA>ttT	p.L844F	FHAD1_ENST00000314740.8_Missense_Mutation_p.L97F|FHAD1_ENST00000417793.1_Missense_Mutation_p.L808F|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000358897.4_Missense_Mutation_p.L844F|FHAD1_ENST00000375999.3_Missense_Mutation_p.L844F			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	844										skin(1)|stomach(1)	2						AGGACGTTTTAAATAATAAAT	0.358																																					p.L844F		Atlas-SNP	.											.	FHAD1	78	.	0			c.A2532T						.						48.0	44.0	45.0					1																	15684641		692	1591	2283	SO:0001583	missense	114827	exon20			CGTTTTAAATAAT	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.2532A>T	chr1.hg19:g.15684641A>T	ENSP00000365166:p.Leu844Phe	134.0	0.0		64.0	13.0	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.53|13.53	2.265329|2.265329	0.40095|0.40095	.|.	.|.	ENSG00000142621|ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668|ENST00000444385	T;T;T;T;T;T;T|.	0.49139|.	0.79;0.79;0.79;0.79;0.79;0.79;0.79|.	5.14|5.14	4.01|4.01	0.46588|0.46588	.|.	.|.	.|.	.|.	.|.	T|.	0.53769|.	0.1817|.	M|M	0.72118|0.72118	2.19|2.19	0.28856|0.28856	N|N	0.89579|0.89579	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.91635|.	0.999;0.997|.	T|.	0.51276|.	-0.8726|.	9|.	0.23302|.	T|.	0.38|.	.|.	7.9946|7.9946	0.30261|0.30261	0.9055:0.0:0.0945:0.0|0.9055:0.0:0.0945:0.0	.|.	97;844|.	B7WPP2;B1AJZ9|.	.;FHAD1_HUMAN|.	F|L	844;808;844;844;115;97;79|163	ENSP00000351770:L844F;ENSP00000407615:L808F;ENSP00000365167:L844F;ENSP00000365166:L844F;ENSP00000434909:L115F;ENSP00000322979:L97F;ENSP00000318812:L79F|.	ENSP00000318812:L79F|.	L|X	+|+	3|2	2|2	FHAD1|FHAD1	15557228|15557228	0.994000|0.994000	0.37717|0.37717	0.921000|0.921000	0.36526|0.36526	0.047000|0.047000	0.14425|0.14425	1.269000|1.269000	0.33074|0.33074	0.905000|0.905000	0.36596|0.36596	0.482000|0.482000	0.46254|0.46254	TTA|TAA	.	.		0.358	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
CDA	978	hgsc.bcm.edu	37	1	20940334	20940334	+	Splice_Site	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:20940334G>A	ENST00000375071.3	+	3	448		c.e3-1		CDA_ENST00000461985.1_Intron	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase						cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	TGCTTCCCCAGTGACATGCAA	0.473																																					.	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.267-1G>A						.						132.0	110.0	118.0					1																	20940334		2203	4300	6503	SO:0001630	splice_region_variant	978	exon3			TCCCCAGTGACAT	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.267-1G>A	chr1.hg19:g.20940334G>A		137.0	0.0		104.0	20.0	NM_001785		Splice_Site	SNP	ENST00000375071.3	hg19	CCDS210.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645639	0.67358	.	.	ENSG00000158825	ENST00000375071	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6118	0.68522	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDA	20812921	1.000000	0.71417	0.997000	0.53966	0.746000	0.42486	8.114000	0.89570	2.523000	0.85059	0.491000	0.48974	.	.	.		0.473	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785	Intron
HTR1D	3352	hgsc.bcm.edu	37	1	23519871	23519871	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:23519871A>T	ENST00000374619.1	-	1	1351	c.842T>A	c.(841-843)cTt>cAt	p.L281H	HTR1D_ENST00000314113.3_Missense_Mutation_p.L281H	NM_000864.4	NP_000855.1	P28221	5HT1D_HUMAN	5-hydroxytryptamine (serotonin) receptor 1D, G protein-coupled	281					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intestine smooth muscle contraction (GO:0014827)|regulation of behavior (GO:0050795)|regulation of locomotion (GO:0040012)|response to toxic substance (GO:0009636)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000779)|all_lung(284;0.00135)|Breast(348;0.0385)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.69e-27)|Colorectal(126;4.86e-08)|COAD - Colon adenocarcinoma(152;2.86e-06)|GBM - Glioblastoma multiforme(114;0.00012)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(1967;0.00122)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.083)|LUSC - Lung squamous cell carcinoma(448;0.185)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Naratriptan(DB00952)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	ACTGTCAGCAAGCTTGATTTT	0.557																																					p.L281H		Atlas-SNP	.											.	HTR1D	36	.	0			c.T842A						.						87.0	89.0	89.0					1																	23519871		2203	4300	6503	SO:0001583	missense	3352	exon1			TCAGCAAGCTTGA	M89955	CCDS231.1	1p36.3-p34.3	2012-08-08	2012-02-03		ENSG00000179546	ENSG00000179546		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5289	protein-coding gene	gene with protein product		182133	"""5-hydroxytryptamine (serotonin) receptor 1D"""	HTRL		2541503, 1662665	Standard	NM_000864		Approved	RDC4, HT1DA, 5-HT1D	uc001bgn.3	P28221	OTTHUMG00000003235	ENST00000374619.1:c.842T>A	chr1.hg19:g.23519871A>T	ENSP00000363748:p.Leu281His	96.0	0.0		61.0	14.0	NM_000864		Missense_Mutation	SNP	ENST00000374619.1	hg19	CCDS231.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.680737	0.47886	.	.	ENSG00000179546	ENST00000314113;ENST00000374619	T;T	0.70869	-0.52;-0.52	5.34	5.34	0.76211	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.78181	0.4243	L	0.42686	1.345	0.50813	D	0.999899	D	0.76494	0.999	D	0.76071	0.987	T	0.76945	-0.2771	10	0.36615	T	0.2	.	14.5065	0.67755	1.0:0.0:0.0:0.0	.	281	P28221	5HT1D_HUMAN	H	281	ENSP00000313661:L281H;ENSP00000363748:L281H	ENSP00000313661:L281H	L	-	2	0	HTR1D	23392458	1.000000	0.71417	0.997000	0.53966	0.859000	0.49053	7.576000	0.82467	2.037000	0.60232	0.528000	0.53228	CTT	.	.		0.557	HTR1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008924.1	NM_000864	
RSRP1	57035	hgsc.bcm.edu	37	1	25570119	25570119	+	Silent	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:25570119C>A	ENST00000243189.7	-	4	954	c.678G>T	c.(676-678)tcG>tcT	p.S226S	C1orf63_ENST00000417642.2_Silent_p.S227S	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		226										breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTACCTTTTCCGACAGCTAGA	0.333																																					p.S226S		Atlas-SNP	.											.	C1orf63	17	.	0			c.G678T						.						202.0	179.0	187.0					1																	25570119		2203	4300	6503	SO:0001819	synonymous_variant	57035	exon4			CTTTTCCGACAGC																												ENST00000243189.7:c.678G>T	chr1.hg19:g.25570119C>A		175.0	0.0		108.0	5.0	NM_020317	A8K917|Q49AA4|Q5TH71|Q9GZP6	Silent	SNP	ENST00000243189.7	hg19	CCDS260.1																																																																																			.	.		0.333	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2		
HMGB4	127540	hgsc.bcm.edu	37	1	34330001	34330001	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:34330001G>A	ENST00000522796.1	+	4	2114	c.209G>A	c.(208-210)cGa>cAa	p.R70Q	CSMD2_ENST00000373381.4_Intron|HMGB4_ENST00000425537.1_3'UTR|HMGB4_ENST00000519684.1_Missense_Mutation_p.R70Q			Q8WW32	HMGB4_HUMAN	high mobility group box 4	70						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GACAAAGCCCGATACCAGGAA	0.468																																					p.R70Q		Atlas-SNP	.											HMGB4,NS,malignant_melanoma,0,1	HMGB4	27	.	0			c.G209A						.						123.0	141.0	135.0					1																	34330001		2203	4300	6503	SO:0001583	missense	127540	exon2			AAGCCCGATACCA		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"""High-mobility group / Canonical"""	24954	protein-coding gene	gene with protein product			"""high-mobility group box 4"""				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.209G>A	chr1.hg19:g.34330001G>A	ENSP00000430919:p.Arg70Gln	119.0	0.0		89.0	18.0	NM_145205	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	hg19	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.244721	0.79912	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	T;T	0.15017	2.46;2.46	5.58	2.7	0.31948	.	0.000000	0.64402	D	0.000001	T	0.19604	0.0471	M	0.72894	2.215	0.43824	D	0.996393	P	0.52170	0.951	B	0.44133	0.442	T	0.01771	-1.1277	10	0.56958	D	0.05	.	5.8675	0.18783	0.1663:0.1562:0.6774:0.0	.	70	B2R4X7	.	Q	70	ENSP00000429214:R70Q;ENSP00000430919:R70Q	ENSP00000429214:R70Q	R	+	2	0	HMGB4	34102588	1.000000	0.71417	0.469000	0.27204	0.989000	0.77384	5.402000	0.66332	0.459000	0.27016	0.609000	0.83330	CGA	.	.		0.468	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205	
C1orf94	84970	hgsc.bcm.edu	37	1	34667800	34667800	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:34667800C>T	ENST00000488417.1	+	4	1506	c.1386C>T	c.(1384-1386)ctC>ctT	p.L462L	C1orf94_ENST00000373374.3_Silent_p.L272L	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	462										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CACTCTGGCTCAACCTGAACT	0.532																																					p.L462L		Atlas-SNP	.											.	C1orf94	156	.	0			c.C1386T						.						189.0	159.0	169.0					1																	34667800		2203	4300	6503	SO:0001819	synonymous_variant	84970	exon4			CTGGCTCAACCTG	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1386C>T	chr1.hg19:g.34667800C>T		293.0	0.0		215.0	47.0	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	hg19	CCDS44108.1																																																																																			.	.		0.532	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
GNL2	29889	hgsc.bcm.edu	37	1	38033329	38033329	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:38033329C>T	ENST00000373062.3	-	15	2086	c.1988G>A	c.(1987-1989)aGg>aAg	p.R663K	GNL2_ENST00000462812.1_5'UTR	NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	663					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				TTCCTCTTCCCTTTGTGCCTT	0.398																																					p.R663K		Atlas-SNP	.											.	GNL2	58	.	0			c.G1988A						.						208.0	196.0	200.0					1																	38033329		2203	4300	6503	SO:0001583	missense	29889	exon15			TCTTCCCTTTGTG	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.1988G>A	chr1.hg19:g.38033329C>T	ENSP00000362153:p.Arg663Lys	142.0	0.0		115.0	24.0	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	hg19	CCDS421.1	.	.	.	.	.	.	.	.	.	.	C	5.665	0.307227	0.10733	.	.	ENSG00000134697	ENST00000373062	T	0.20738	2.05	4.88	2.48	0.30137	.	0.315524	0.36893	N	0.002345	T	0.07279	0.0184	N	0.11427	0.14	0.21256	N	0.999745	B	0.02656	0.0	B	0.04013	0.001	T	0.32587	-0.9901	10	0.08179	T	0.78	-8.7647	2.502	0.04636	0.3076:0.4952:0.0:0.1971	.	663	Q13823	NOG2_HUMAN	K	663	ENSP00000362153:R663K	ENSP00000362153:R663K	R	-	2	0	GNL2	37805916	1.000000	0.71417	0.997000	0.53966	0.521000	0.34408	2.081000	0.41596	1.119000	0.41883	0.591000	0.81541	AGG	.	.		0.398	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285	
C1orf228	339541	hgsc.bcm.edu	37	1	45163762	45163762	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:45163762G>A	ENST00000458657.2	+	5	610	c.303G>A	c.(301-303)gaG>gaA	p.E101E	C1orf228_ENST00000444751.1_Intron|C1orf228_ENST00000535358.1_Silent_p.E101E			Q6PIY5	CA228_HUMAN	chromosome 1 open reading frame 228	101										central_nervous_system(1)	1						AATTTCTTGAGGTTGGAGGTG	0.418																																					p.E101E		Atlas-SNP	.											.	C1orf228	15	.	0			c.G303A						.						139.0	117.0	123.0					1																	45163762		692	1591	2283	SO:0001819	synonymous_variant	339541	exon4			TCTTGAGGTTGGA	AL122004, AY254217, BC026115	CCDS53311.1	1p34.1	2011-02-22	2009-03-17	2009-03-17	ENSG00000198520	ENSG00000198520			34345	protein-coding gene	gene with protein product			"""non-protein coding RNA 82"""	NCRNA00082		12477932	Standard	NM_001145636		Approved	MGC33556, p40	uc001cmf.2	Q6PIY5	OTTHUMG00000007834	ENST00000458657.2:c.303G>A	chr1.hg19:g.45163762G>A		138.0	0.0		99.0	18.0	NM_001145636	A1KXE5	Silent	SNP	ENST00000458657.2	hg19	CCDS53311.1																																																																																			.	.		0.418	C1orf228-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023125.2	NM_001145636	
LEPR	3953	hgsc.bcm.edu	37	1	66102182	66102182	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:66102182A>G	ENST00000349533.6	+	20	3167	c.2982A>G	c.(2980-2982)aaA>aaG	p.K994K	LEPR_ENST00000406510.3_Silent_p.K61K	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GCAACTCTAAACCAAGTGAAA	0.428																																					p.K994K		Atlas-SNP	.											.	LEPR	284	.	0			c.A2982G						.						66.0	64.0	65.0					1																	66102182		2203	4300	6503	SO:0001819	synonymous_variant	3953	exon20			CTCTAAACCAAGT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.2982A>G	chr1.hg19:g.66102182A>G		56.0	0.0		36.0	7.0	NM_002303	Q6FHL5	Silent	SNP	ENST00000349533.6	hg19	CCDS631.1																																																																																			.	.		0.428	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
MIER1	57708	hgsc.bcm.edu	37	1	67436586	67436586	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:67436586G>A	ENST00000355356.3	+	8	858	c.709G>A	c.(709-711)Gat>Aat	p.D237N	MIER1_ENST00000371016.1_Missense_Mutation_p.D254N|MIER1_ENST00000357692.2_Missense_Mutation_p.D254N|MIER1_ENST00000371018.3_Missense_Mutation_p.D254N|MIER1_ENST00000401041.1_Missense_Mutation_p.D290N|MIER1_ENST00000371014.1_Missense_Mutation_p.D290N|MIER1_ENST00000401042.3_Missense_Mutation_p.D237N|MIER1_ENST00000355977.6_Missense_Mutation_p.D174N	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	237	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.			D -> G (in Ref. 4; CAH10526). {ECO:0000305}.	positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						AAGAACAGGTGATGAGAAGGG	0.363																																					p.D290N		Atlas-SNP	.											.	MIER1	86	.	0			c.G868A						.						107.0	102.0	104.0					1																	67436586		1849	4107	5956	SO:0001583	missense	57708	exon9			ACAGGTGATGAGA		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"""mesoderm induction early response 1 homolog (Xenopus laevis)"""			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.709G>A	chr1.hg19:g.67436586G>A	ENSP00000347514:p.Asp237Asn	136.0	0.0		77.0	5.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Missense_Mutation	SNP	ENST00000355356.3	hg19	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.657597	0.47467	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000355977;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000401042;ENST00000355356	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.52	5.52	0.82312	ELM2 domain (1);	0.089115	0.85682	D	0.000000	T	0.20129	0.0484	N	0.17379	0.485	0.58432	D	0.999997	B;P;P;P;P;P;P;B;B	0.46395	0.019;0.877;0.873;0.59;0.455;0.799;0.873;0.021;0.007	B;B;B;B;B;B;B;B;B	0.43360	0.016;0.417;0.385;0.223;0.111;0.214;0.298;0.016;0.024	T	0.02371	-1.1169	10	0.16896	T	0.51	-25.6678	19.4162	0.94700	0.0:0.0:1.0:0.0	.	254;254;237;237;174;261;254;290;290	Q5TAD2;Q32NC4;Q8N108-3;Q8N108-6;Q08AE0;Q8N108;Q8N108-10;Q5TAD5;Q5TAD4	.;.;.;.;.;MIER1_HUMAN;.;.;.	N	258;254;174;254;290;254;290;237;237	ENSP00000360057:D254N;ENSP00000348253:D174N;ENSP00000350321:D254N;ENSP00000383820:D290N;ENSP00000360055:D254N;ENSP00000360053:D290N;ENSP00000383821:D237N;ENSP00000347514:D237N	ENSP00000347514:D237N	D	+	1	0	MIER1	67209174	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.629000	0.83207	2.764000	0.94973	0.650000	0.86243	GAT	.	.		0.363	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	
ZNHIT6	54680	hgsc.bcm.edu	37	1	86123530	86123530	+	Splice_Site	SNP	C	C	A	rs139368369		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:86123530C>A	ENST00000370574.3	-	9	1505	c.1372G>T	c.(1372-1374)Gtg>Ttg	p.V458L	ZNHIT6_ENST00000431532.2_Splice_Site_p.V419L			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	458					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						TTACACTTACCTTGGTGAAGA	0.328																																					p.V458L		Atlas-SNP	.											.	ZNHIT6	42	.	0			c.G1372T						.	C	LEU/VAL,LEU/VAL	0,4404		0,0,2202	121.0	123.0	122.0		1255,1372	4.8	1.0	1	dbSNP_134	122	1,8581	1.2+/-3.3	0,1,4290	no	missense-near-splice,missense-near-splice	ZNHIT6	NM_001170670.1,NM_017953.3	32,32	0,1,6492	AA,AC,CC		0.0117,0.0,0.0077	benign,benign	419/432,458/471	86123530	1,12985	2202	4291	6493	SO:0001630	splice_region_variant	54680	exon9			ACTTACCTTGGTG	AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"""Zinc fingers, HIT-type"""	26089	protein-coding gene	gene with protein product	"""box C/D snoRNA essential 1 homolog (S. cerevisiae)"""		"""chromosome 1 open reading frame 181"", ""zinc finger, HIT type 6"""	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.1372+1G>T	chr1.hg19:g.86123530C>A		55.0	0.0		54.0	13.0	NM_017953	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Missense_Mutation	SNP	ENST00000370574.3	hg19	CCDS707.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052131	0.36181	0.0	1.17E-4	ENSG00000117174	ENST00000431532;ENST00000370574	T;T	0.45276	0.94;0.9	5.67	4.76	0.60689	.	0.811253	0.11117	N	0.597822	T	0.19685	0.0473	L	0.53249	1.67	0.29441	N	0.859165	B;B	0.26672	0.035;0.156	B;B	0.22386	0.018;0.039	T	0.11155	-1.0599	9	.	.	.	-0.8053	9.9337	0.41539	0.0:0.8427:0.0:0.1573	.	419;458	B4DP13;Q9NWK9	.;BCD1_HUMAN	L	419;458	ENSP00000414344:V419L;ENSP00000359606:V458L	.	V	-	1	0	ZNHIT6	85896118	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.259000	0.43259	1.540000	0.49301	0.655000	0.94253	GTG	.	C|1.000;A|0.000		0.328	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953	Missense_Mutation
RPAP2	79871	hgsc.bcm.edu	37	1	92789745	92789745	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:92789745G>A	ENST00000610020.1	+	8	1377	c.1268G>A	c.(1267-1269)tGg>tAg	p.W423*		NM_024813.2	NP_079089.2	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	423					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|snRNA transcription (GO:0009301)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleolus (GO:0005730)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	22		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		TTCCCTGCCTGGAGGGAATCT	0.418																																					p.W423X		Atlas-SNP	.											.	RPAP2	48	.	0			c.G1268A						.						73.0	76.0	75.0					1																	92789745		2203	4300	6503	SO:0001587	stop_gained	79871	exon8			CTGCCTGGAGGGA	AK023212	CCDS740.1	1p22.1	2014-01-28	2007-07-26	2007-07-26	ENSG00000122484	ENSG00000122484			25791	protein-coding gene	gene with protein product		611476	"""chromosome 1 open reading frame 82"""	C1orf82		17643375	Standard	NM_024813		Approved	FLJ13150	uc001dot.2	Q8IXW5	OTTHUMG00000010288	ENST00000610020.1:c.1268G>A	chr1.hg19:g.92789745G>A	ENSP00000476948:p.Trp423*	110.0	0.0		80.0	21.0	NM_024813	C9JKB5|Q49AS7|Q9H8Y2	Nonsense_Mutation	SNP	ENST00000610020.1	hg19	CCDS740.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236952	0.58886	.	.	ENSG00000122484	ENST00000370343;ENST00000394482	.	.	.	5.63	-3.36	0.04913	.	1.138040	0.06667	N	0.765441	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	1.4894	2.7472	0.05271	0.278:0.064:0.338:0.32	.	.	.	.	X	423	.	ENSP00000359368:W423X	W	+	2	0	RPAP2	92562333	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	-0.492000	0.06467	-0.118000	0.11851	0.655000	0.94253	TGG	.	.		0.418	RPAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028368.2	NM_024813	
SPAG17	200162	hgsc.bcm.edu	37	1	118558673	118558673	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:118558673T>G	ENST00000336338.5	-	29	4267	c.4202A>C	c.(4201-4203)aAt>aCt	p.N1401T		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1401						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GCCGATCCGATTTCCTTCAGG	0.463																																					p.N1401T		Atlas-SNP	.											.	SPAG17	263	.	0			c.A4202C						.						171.0	177.0	175.0					1																	118558673		2203	4300	6503	SO:0001583	missense	200162	exon29			ATCCGATTTCCTT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4202A>C	chr1.hg19:g.118558673T>G	ENSP00000337804:p.Asn1401Thr	320.0	0.0		218.0	49.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	3.268	-0.149720	0.06585	.	.	ENSG00000155761	ENST00000336338	T	0.17213	2.29	4.72	0.71	0.18157	.	1.384010	0.04043	N	0.303385	T	0.04227	0.0117	L	0.44542	1.39	0.21064	N	0.999798	B	0.12013	0.005	B	0.09377	0.004	T	0.36089	-0.9762	10	0.29301	T	0.29	.	1.3661	0.02201	0.1536:0.1161:0.3462:0.3841	.	1401	Q6Q759	SPG17_HUMAN	T	1401	ENSP00000337804:N1401T	ENSP00000337804:N1401T	N	-	2	0	SPAG17	118360196	0.505000	0.26131	0.948000	0.38648	0.262000	0.26303	0.556000	0.23438	0.694000	0.31654	0.377000	0.23210	AAT	.	.		0.463	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144931551	144931551	+	Intron	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:144931551T>C	ENST00000369354.3	-	6	826				PDE4DIP_ENST00000529945.1_Missense_Mutation_p.K53R|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.K53R|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000479408.2_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000530740.1_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAAAGCACACTTGCTGCAAGC	0.517			T	PDGFRB	MPD																																p.K53R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A158G						.						98.0	100.0	100.0					1																	144931551		2203	4300	6503	SO:0001627	intron_variant	9659	exon1			GCACACTTGCTGC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.637-7730A>G	chr1.hg19:g.144931551T>C		240.0	0.0		267.0	13.0	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477935	0.84747	.	.	ENSG00000178104	ENST00000369353;ENST00000313431;ENST00000529945	T;T	0.31247	1.5;1.54	5.3	5.3	0.74995	.	.	.	.	.	T	0.44519	0.1297	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.49331	-0.8951	9	0.87932	D	0	.	13.1866	0.59684	0.0:0.0:0.0:1.0	.	53	Q5VU43-2	.	R	53	ENSP00000316434:K53R;ENSP00000433392:K53R	ENSP00000316434:K53R	K	-	2	0	PDE4DIP	143642908	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	8.040000	0.89188	1.996000	0.58369	0.379000	0.24179	AAG	.	.		0.517	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PRKAB2	5565	hgsc.bcm.edu	37	1	146634090	146634090	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:146634090T>C	ENST00000254101.3	-	6	739	c.601A>G	c.(601-603)Aga>Gga	p.R201G	PRKAB2_ENST00000496858.1_5'Flank|PRKAB2_ENST00000425272.2_Missense_Mutation_p.R119G	NM_005399.3	NP_005390.1	O43741	AAKB2_HUMAN	protein kinase, AMP-activated, beta 2 non-catalytic subunit	201					carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)|regulation of fatty acid biosynthetic process (GO:0042304)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)	p.R201*(1)		NS(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.0487)				Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)	GATTTGAATCTTTCCTCAGAT	0.408																																					p.R201G		Atlas-SNP	.											PRKAB2,mouth,carcinoma,0,1	PRKAB2	26	.	1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	c.A601G						.						108.0	105.0	106.0					1																	146634090		2203	4300	6503	SO:0001583	missense	5565	exon6			TGAATCTTTCCTC	BC053610	CCDS925.1	1q21.2	2008-02-05			ENSG00000131791	ENSG00000131791			9379	protein-coding gene	gene with protein product	"""AMPK beta 2"""	602741				8557660	Standard	NM_005399		Approved		uc001epe.3	O43741	OTTHUMG00000014032	ENST00000254101.3:c.601A>G	chr1.hg19:g.146634090T>C	ENSP00000254101:p.Arg201Gly	104.0	0.0		143.0	14.0	NM_005399	A8K9V5|B4DH06|Q5VXY0	Missense_Mutation	SNP	ENST00000254101.3	hg19	CCDS925.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.959026	0.53400	.	.	ENSG00000131791	ENST00000254101;ENST00000425272	.	.	.	5.74	3.59	0.41128	5-AMP-activated protein kinase, beta subunit, interaction domain (1);	0.048455	0.85682	D	0.000000	T	0.28732	0.0712	L	0.43923	1.385	0.52099	D	0.999943	B;B	0.17465	0.005;0.022	B;B	0.18263	0.008;0.021	T	0.15521	-1.0434	9	0.56958	D	0.05	.	6.3918	0.21591	0.1209:0.0:0.4538:0.4254	.	119;201	B4DH06;O43741	.;AAKB2_HUMAN	G	201;119	.	ENSP00000254101:R201G	R	-	1	2	PRKAB2	145100714	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.991000	0.56973	0.472000	0.27344	0.533000	0.62120	AGA	.	.		0.408	PRKAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039471.1	NM_005399	
VPS45	11311	hgsc.bcm.edu	37	1	150054035	150054035	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:150054035A>G	ENST00000369130.3	+	9	1438	c.892A>G	c.(892-894)Aaa>Gaa	p.K298E	VPS45_ENST00000369128.5_Missense_Mutation_p.K193E|VPS45_ENST00000535106.1_Missense_Mutation_p.K229E	NM_001279354.1|NM_007259.3	NP_001266283.1|NP_009190.2	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45 homolog (S. cerevisiae)	298				K -> R (in Ref. 1; AAC50931). {ECO:0000305}.	blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|vesicle docking involved in exocytosis (GO:0006904)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCAGAAGAAGAAACCAAAAGA	0.338																																					p.K298E		Atlas-SNP	.											.	VPS45	47	.	0			c.A892G						.						71.0	69.0	70.0					1																	150054035		2202	4300	6502	SO:0001583	missense	11311	exon9			AAGAAGAAACCAA	U35246	CCDS944.1, CCDS60244.1, CCDS72904.1	1q21.2	2008-02-05	2006-12-19	2006-12-19	ENSG00000136631	ENSG00000136631			14579	protein-coding gene	gene with protein product		610035	"""vacuolar protein sorting 45A (yeast homolog)"", ""vacuolar protein sorting 45A (yeast)"""	VPS45B, VPS45A		8996080	Standard	NM_007259		Approved	h-vps45, H1	uc001etp.3	Q9NRW7	OTTHUMG00000012511	ENST00000369130.3:c.892A>G	chr1.hg19:g.150054035A>G	ENSP00000358126:p.Lys298Glu	129.0	0.0		205.0	14.0	NM_007259	D3DUZ9|F5H8K1|Q15715|Q53FR8|Q5T4P6|Q9Y4Z6	Missense_Mutation	SNP	ENST00000369130.3	hg19	CCDS944.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.085144	0.55861	.	.	ENSG00000136631	ENST00000369130;ENST00000369128;ENST00000543996;ENST00000535106;ENST00000419023	T;T;T;T	0.76060	1.55;-0.99;1.55;1.55	5.54	5.54	0.83059	.	0.176312	0.64402	D	0.000008	T	0.69477	0.3115	M	0.68952	2.095	0.58432	D	0.999996	P;B;B;B	0.37423	0.594;0.03;0.065;0.03	B;B;B;B	0.43623	0.425;0.102;0.145;0.102	T	0.71384	-0.4609	10	0.38643	T	0.18	.	15.0164	0.71588	1.0:0.0:0.0:0.0	.	193;298;118;298	F5H8K1;Q53FR8;A0AR27;Q9NRW7	.;.;.;VPS45_HUMAN	E	298;193;173;229;229	ENSP00000358126:K298E;ENSP00000358124:K193E;ENSP00000440690:K229E;ENSP00000400143:K229E	ENSP00000358124:K193E	K	+	1	0	VPS45	148320659	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.467000	0.90390	2.326000	0.78906	0.533000	0.62120	AAA	.	.		0.338	VPS45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034964.1	NM_007259	
SETDB1	9869	hgsc.bcm.edu	37	1	150915464	150915464	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:150915464T>C	ENST00000271640.5	+	7	1000	c.810T>C	c.(808-810)gaT>gaC	p.D270D	SETDB1_ENST00000368969.4_Silent_p.D270D|SETDB1_ENST00000368962.2_Silent_p.D270D|SETDB1_ENST00000459773.1_Intron|SETDB1_ENST00000368963.1_Intron	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	270	Tudor 1.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			AATACAAAGATGGGAATCAGG	0.502																																					p.D270D		Atlas-SNP	.											.	SETDB1	204	.	0			c.T810C						.						151.0	141.0	144.0					1																	150915464		2203	4300	6503	SO:0001819	synonymous_variant	9869	exon7			CAAAGATGGGAAT	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Tudor domain containing"""	10761	protein-coding gene	gene with protein product	"""tudor domain containing 21"""	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.810T>C	chr1.hg19:g.150915464T>C		210.0	0.0		384.0	37.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Silent	SNP	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.		0.502	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2		
FLG	2312	hgsc.bcm.edu	37	1	152286777	152286777	+	Silent	SNP	G	G	A	rs375267392		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:152286777G>A	ENST00000368799.1	-	3	620	c.585C>T	c.(583-585)gaC>gaT	p.D195D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	195					establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTTCCTATTGTCTCCTAATC	0.318									Ichthyosis																												p.D195D		Atlas-SNP	.											.	FLG	900	.	0			c.C585T						.						87.0	94.0	91.0					1																	152286777		2203	4298	6501	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTATTGTCTCCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.585C>T	chr1.hg19:g.152286777G>A		143.0	0.0		282.0	31.0	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	hg19	CCDS30860.1																																																																																			.	.		0.318	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG2	388698	hgsc.bcm.edu	37	1	152327323	152327323	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:152327323C>G	ENST00000388718.5	-	3	3011	c.2939G>C	c.(2938-2940)gGc>gCc	p.G980A	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	980	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTTTCCTGAGCCTGACTCATG	0.498																																					p.G980A		Atlas-SNP	.											.	FLG2	431	.	0			c.G2939C						.						258.0	260.0	259.0					1																	152327323		2203	4300	6503	SO:0001583	missense	388698	exon3			CCTGAGCCTGACT	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2939G>C	chr1.hg19:g.152327323C>G	ENSP00000373370:p.Gly980Ala	300.0	0.0		520.0	40.0	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	8.274	0.813954	0.16537	.	.	ENSG00000143520	ENST00000388718	T	0.39787	1.06	3.96	2.02	0.26589	.	.	.	.	.	T	0.12603	0.0306	M	0.65498	2.005	0.09310	N	1	P	0.34977	0.478	B	0.30105	0.111	T	0.33085	-0.9882	9	0.05833	T	0.94	1.3468	6.3918	0.21591	0.0:0.7628:0.0:0.2372	.	980	Q5D862	FILA2_HUMAN	A	980	ENSP00000373370:G980A	ENSP00000373370:G980A	G	-	2	0	FLG2	150593947	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	0.317000	0.19487	0.878000	0.35920	0.561000	0.74099	GGC	.	.		0.498	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
LCE1B	353132	hgsc.bcm.edu	37	1	152785131	152785131	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:152785131C>T	ENST00000360090.3	+	1	685	c.209C>T	c.(208-210)tCt>tTt	p.S70F		NM_178349.1	NP_848126.1	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	70	Gly-rich.				keratinization (GO:0031424)					breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|skin(2)	18	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCTGCAGTTCTGGGGGAGGT	0.677																																					p.S70F		Atlas-SNP	.											.	LCE1B	45	.	0			c.C209T						.						44.0	52.0	49.0					1																	152785131		2203	4300	6503	SO:0001583	missense	353132	exon1			GCAGTTCTGGGGG	BI670515	CCDS1027.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000196734	ENSG00000196734		"""Late cornified envelopes"""	16611	protein-coding gene	gene with protein product		612604	"""small proline rich-like (epidermal differentiation complex) 2A"""	SPRL2A		11698679	Standard	NM_178349		Approved	LEP2	uc001faq.3	Q5T7P3	OTTHUMG00000014402	ENST00000360090.3:c.209C>T	chr1.hg19:g.152785131C>T	ENSP00000353203:p.Ser70Phe	72.0	0.0		98.0	4.0	NM_178349	A4IF40	Missense_Mutation	SNP	ENST00000360090.3	hg19	CCDS1027.1	.	.	.	.	.	.	.	.	.	.	C	7.359	0.624493	0.14193	.	.	ENSG00000196734	ENST00000360090;ENST00000439693	T	0.06294	3.32	4.35	4.35	0.52113	.	0.000000	0.36519	N	0.002551	T	0.17704	0.0425	M	0.87180	2.865	0.27475	N	0.952748	D	0.76494	0.999	D	0.83275	0.996	T	0.01925	-1.1246	10	0.87932	D	0	.	12.2361	0.54516	0.0:1.0:0.0:0.0	.	70	Q5T7P3	LCE1B_HUMAN	F	70;62	ENSP00000353203:S70F	ENSP00000353203:S70F	S	+	2	0	LCE1B	151051755	1.000000	0.71417	1.000000	0.80357	0.271000	0.26615	1.683000	0.37638	2.256000	0.74724	0.650000	0.86243	TCT	.	.		0.677	LCE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040060.1	NM_178349	
NPR1	4881	hgsc.bcm.edu	37	1	153653162	153653162	+	Missense_Mutation	SNP	C	C	T	rs561449958		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:153653162C>T	ENST00000368680.3	+	2	1379	c.907C>T	c.(907-909)Cgc>Tgc	p.R303C		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	303					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	TGTCAGTGCCCGCCAGGCCTT	0.577																																					p.R303C	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											NPR1,caecum,carcinoma,0,1	NPR1	104	.	0			c.C907T						.						34.0	34.0	34.0					1																	153653162		2203	4300	6503	SO:0001583	missense	4881	exon2			AGTGCCCGCCAGG	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.907C>T	chr1.hg19:g.153653162C>T	ENSP00000357669:p.Arg303Cys	44.0	0.0		91.0	19.0	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	hg19	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	C	8.961	0.970610	0.18659	.	.	ENSG00000169418	ENST00000368680	T	0.76186	-1.0	4.47	2.5	0.30297	Extracellular ligand-binding receptor (1);	0.416519	0.22134	N	0.064153	T	0.76364	0.3977	M	0.80982	2.52	0.45097	D	0.998116	D	0.76494	0.999	P	0.59171	0.853	T	0.77792	-0.2455	10	0.62326	D	0.03	.	6.5876	0.22630	0.3253:0.5062:0.1686:0.0	.	303	P16066	ANPRA_HUMAN	C	303	ENSP00000357669:R303C	ENSP00000357669:R303C	R	+	1	0	NPR1	151919786	0.000000	0.05858	0.996000	0.52242	0.037000	0.13140	-0.541000	0.06099	2.317000	0.78254	0.557000	0.71058	CGC	.	.		0.577	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
CHRNB2	1141	hgsc.bcm.edu	37	1	154543704	154543704	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:154543704C>T	ENST00000368476.3	+	5	669	c.405C>T	c.(403-405)gcC>gcT	p.A135A		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	135					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	ATTCCAATGCCGTGGTCTCCT	0.532																																					p.A135A		Atlas-SNP	.											.	CHRNB2	74	.	0			c.C405T						.						132.0	121.0	125.0					1																	154543704		2203	4300	6503	SO:0001819	synonymous_variant	1141	exon5			CAATGCCGTGGTC	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1962	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 2 (neuronal)"""	118507	"""cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"""			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.405C>T	chr1.hg19:g.154543704C>T		152.0	0.0		240.0	26.0	NM_000748	Q9UEH9	Silent	SNP	ENST00000368476.3	hg19	CCDS1070.1																																																																																			.	.		0.532	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748	
TRIM46	80128	hgsc.bcm.edu	37	1	155145067	155145067	+	5'Flank	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:155145067C>A	ENST00000334634.4	+	0	0				TRIM46_ENST00000368382.1_5'Flank|TRIM46_ENST00000368383.3_5'Flank|TRIM46_ENST00000368385.4_5'Flank|RP11-201K10.3_ENST00000473363.2_Missense_Mutation_p.D170Y|TRIM46_ENST00000545012.1_5'Flank|KRTCAP2_ENST00000490672.1_5'UTR|TRIM46_ENST00000392451.2_5'Flank|TRIM46_ENST00000543729.1_5'Flank|KRTCAP2_ENST00000295682.4_Missense_Mutation_p.G92V	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46							intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGCTTGGAATCCTTTGCCAAA	0.443																																					p.G92V		Atlas-SNP	.											.	KRTCAP2	15	.	0			c.G275T						.						112.0	113.0	113.0					1																	155145067		2203	4300	6503	SO:0001631	upstream_gene_variant	200185	exon3			TGGAATCCTTTGC		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680		chr1.hg19:g.155145067C>A	Exception_encountered	157.0	0.0		282.0	16.0	NM_173852	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039061	0.93630	.	.	ENSG00000163463	ENST00000295682	T	0.53206	0.63	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.63988	0.2558	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68002	-0.5524	10	0.87932	D	0	-2.9392	13.7846	0.63102	0.0:1.0:0.0:0.0	.	92	Q8N6L1	KTAP2_HUMAN	V	92	ENSP00000295682:G92V	ENSP00000295682:G92V	G	-	2	0	KRTCAP2	153411691	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.172000	0.77604	2.708000	0.92522	0.467000	0.42956	GGA	.	.		0.443	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	
NES	10763	hgsc.bcm.edu	37	1	156639411	156639411	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:156639411C>T	ENST00000368223.3	-	4	4701	c.4569G>A	c.(4567-4569)atG>atA	p.M1523I		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1523	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTGCATCCTCCATCCCACTGG	0.577																																					p.M1523I		Atlas-SNP	.											.	NES	196	.	0			c.G4569A						.						74.0	66.0	69.0					1																	156639411		2203	4300	6503	SO:0001583	missense	10763	exon4			ATCCTCCATCCCA	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4569G>A	chr1.hg19:g.156639411C>T	ENSP00000357206:p.Met1523Ile	133.0	0.0		297.0	60.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	5.254	0.232304	0.09969	.	.	ENSG00000132688	ENST00000368223	D	0.84298	-1.83	4.56	-2.47	0.06442	.	.	.	.	.	T	0.53769	0.1817	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49380	-0.8946	9	0.72032	D	0.01	.	5.5637	0.17158	0.1198:0.5102:0.0:0.37	.	1523	P48681	NEST_HUMAN	I	1523	ENSP00000357206:M1523I	ENSP00000357206:M1523I	M	-	3	0	NES	154906035	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.449000	0.06812	-0.543000	0.06240	0.313000	0.20887	ATG	.	.		0.577	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
NES	10763	hgsc.bcm.edu	37	1	156641300	156641300	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:156641300A>T	ENST00000368223.3	-	4	2812	c.2680T>A	c.(2680-2682)Tct>Act	p.S894T		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	894	Tail.			QGAMNPLEKEIQEPLESVEVNQETFRLLEEENQESLRSLGA WNLENLRSPEE -> KSGGNESSRKGNSRTTGVCGSEPRDI QTPGRGESGIIEISGSMEPGEFEISRG (in Ref. 1; CAA46780). {ECO:0000305}.	brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GCTCCCAGAGATCTCAATGAT	0.458																																					p.S894T		Atlas-SNP	.											.	NES	196	.	0			c.T2680A						.						65.0	69.0	68.0					1																	156641300		2203	4300	6503	SO:0001583	missense	10763	exon4			CCAGAGATCTCAA	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.2680T>A	chr1.hg19:g.156641300A>T	ENSP00000357206:p.Ser894Thr	129.0	0.0		204.0	17.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	hg19	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.903430	0.52333	.	.	ENSG00000132688	ENST00000368223	D	0.90732	-2.72	5.16	-1.46	0.08800	.	.	.	.	.	D	0.82944	0.5147	M	0.65498	2.005	0.09310	N	1	P	0.47409	0.895	P	0.46975	0.533	T	0.75709	-0.3223	9	0.72032	D	0.01	.	5.6531	0.17627	0.2996:0.4436:0.2568:0.0	.	894	P48681	NEST_HUMAN	T	894	ENSP00000357206:S894T	ENSP00000357206:S894T	S	-	1	0	NES	154907924	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	-0.444000	0.06854	-0.270000	0.09285	-0.371000	0.07208	TCT	.	.		0.458	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
OR10T2	128360	hgsc.bcm.edu	37	1	158368322	158368322	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:158368322T>G	ENST00000334438.1	-	1	934	c.935A>C	c.(934-936)aAg>aCg	p.K312T		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	312			K -> N (in dbSNP:rs6692949).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					TTAGCTCATCTTGGTTGCCAC	0.358																																					p.K312T		Atlas-SNP	.											.	OR10T2	76	.	0			c.A935C						.						24.0	23.0	23.0					1																	158368322		2203	4300	6503	SO:0001583	missense	128360	exon1			CTCATCTTGGTTG	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.935A>C	chr1.hg19:g.158368322T>G	ENSP00000334115:p.Lys312Thr	57.0	0.0		94.0	12.0	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	hg19	CCDS30895.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.402698	0.62288	.	.	ENSG00000186306	ENST00000334438	T	0.00305	8.18	4.45	4.45	0.53987	.	0.000000	0.43919	D	0.000520	T	0.00109	0.0003	N	0.08118	0	0.21675	N	0.999599	D	0.76494	0.999	D	0.63488	0.915	T	0.55003	-0.8208	10	0.59425	D	0.04	.	11.3382	0.49516	0.0:0.0:0.0:1.0	.	312	Q8NGX3	O10T2_HUMAN	T	312	ENSP00000334115:K312T	ENSP00000334115:K312T	K	-	2	0	OR10T2	156634946	0.811000	0.29063	0.095000	0.20976	0.394000	0.30568	1.174000	0.31932	1.858000	0.53909	0.533000	0.62120	AAG	.	.		0.358	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
IGSF9	57549	hgsc.bcm.edu	37	1	159901621	159901621	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:159901621G>A	ENST00000368094.1	-	11	1540	c.1343C>T	c.(1342-1344)cCt>cTt	p.P448L	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.P432L	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	448	Ig-like 5.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			AGAGACAACAGGAGGAGGGTC	0.612																																					p.P448L		Atlas-SNP	.											.	IGSF9	123	.	0			c.C1343T						.						49.0	55.0	53.0					1																	159901621		2203	4300	6503	SO:0001583	missense	57549	exon11			ACAACAGGAGGAG	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1343C>T	chr1.hg19:g.159901621G>A	ENSP00000357073:p.Pro448Leu	50.0	0.0		113.0	9.0	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.674034	0.47781	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.71461	-0.57;-0.57	4.41	4.41	0.53225	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.190730	0.25780	N	0.028343	D	0.85526	0.5717	M	0.93328	3.405	0.58432	D	0.999999	D;D	0.89917	0.992;1.0	D;D	0.83275	0.937;0.996	D	0.89524	0.3780	9	.	.	.	-2.2744	14.5219	0.67856	0.0:0.0:1.0:0.0	.	448;448	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	432;448;448	ENSP00000355049:P432L;ENSP00000357073:P448L	.	P	-	2	0	IGSF9	158168245	1.000000	0.71417	0.366000	0.25914	0.078000	0.17371	8.951000	0.93025	2.003000	0.58678	0.561000	0.74099	CCT	.	.		0.612	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
ATP1A4	480	hgsc.bcm.edu	37	1	160141549	160141549	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:160141549T>C	ENST00000368081.4	+	12	2325		c.e12+2		ATP1A4_ENST00000418334.1_Splice_Site	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide						ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGAATTAAGGTAAATACTTGC	0.488																																					.		Atlas-SNP	.											.	ATP1A4	167	.	0			c.1854+2T>C						.						76.0	79.0	78.0					1																	160141549		2203	4300	6503	SO:0001630	splice_region_variant	480	exon12			TTAAGGTAAATAC	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1854+2T>C	chr1.hg19:g.160141549T>C		42.0	0.0		96.0	12.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Splice_Site	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.087669	0.36855	.	.	ENSG00000132681	ENST00000368081	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5356	0.50634	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP1A4	158408173	1.000000	0.71417	0.998000	0.56505	0.311000	0.27955	7.656000	0.83736	1.898000	0.54952	0.533000	0.62120	.	.	.		0.488	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	Intron
DNM3	26052	hgsc.bcm.edu	37	1	172357765	172357765	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:172357765C>G	ENST00000355305.5	+	20	2513	c.2356C>G	c.(2356-2358)Ctc>Gtc	p.L786V	DNM3_ENST00000367731.1_Missense_Mutation_p.L776V|DNM3_ENST00000358155.4_Missense_Mutation_p.L780V			Q9UQ16	DYN3_HUMAN	dynamin 3	786					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						AAGTGCTCCCCTCGCAAGGCC	0.592																																					p.L780V		Atlas-SNP	.											.	DNM3	85	.	0			c.C2338G						.						52.0	62.0	59.0					1																	172357765		1961	4154	6115	SO:0001583	missense	26052	exon20			GCTCCCCTCGCAA	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"""Pleckstrin homology (PH) domain containing"""	29125	protein-coding gene	gene with protein product	"""Dyna III"""	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2356C>G	chr1.hg19:g.172357765C>G	ENSP00000347457:p.Leu786Val	67.0	0.0		126.0	11.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	C	9.514	1.106573	0.20714	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000355305;ENST00000367731;ENST00000485254	D;D;D;T	0.92397	-3.03;-3.03;-3.03;-0.6	5.32	5.32	0.75619	.	0.489617	0.19509	N	0.112551	T	0.77246	0.4102	N	0.08118	0	0.80722	D	1	B;B;B	0.24258	0.018;0.061;0.1	B;B;B	0.25614	0.004;0.062;0.026	T	0.77180	-0.2682	10	0.59425	D	0.04	.	12.6485	0.56748	0.1653:0.8347:0.0:0.0	.	786;776;780	Q9UQ16;Q9UQ16-2;Q9UQ16-3	DYN3_HUMAN;.;.	V	790;780;786;776;149	ENSP00000350876:L780V;ENSP00000347457:L786V;ENSP00000356705:L776V;ENSP00000429165:L149V	ENSP00000347457:L786V	L	+	1	0	DNM3	170624388	0.537000	0.26386	0.897000	0.35233	0.044000	0.14063	2.298000	0.43602	2.493000	0.84123	0.591000	0.81541	CTC	.	.		0.592	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569	
TDRD5	163589	hgsc.bcm.edu	37	1	179659883	179659883	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:179659883T>C	ENST00000367614.1	+	17	3110	c.2751T>C	c.(2749-2751)gcT>gcC	p.A917A	TDRD5_ENST00000444136.1_Silent_p.A971A|TDRD5_ENST00000294848.8_Silent_p.A917A	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	917					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						GCAGCCGTGCTATTACATTGT	0.398																																					p.A971A		Atlas-SNP	.											.	TDRD5	149	.	0			c.T2913C						.						85.0	83.0	84.0					1																	179659883		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon18			CCGTGCTATTACA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2751T>C	chr1.hg19:g.179659883T>C		70.0	0.0		148.0	12.0	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.398	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
CACNA1E	777	hgsc.bcm.edu	37	1	181706682	181706682	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:181706682C>T	ENST00000367573.2	+	23	3444	c.3444C>T	c.(3442-3444)taC>taT	p.Y1148Y	CACNA1E_ENST00000367567.4_Silent_p.Y755Y|CACNA1E_ENST00000357570.5_Silent_p.Y1099Y|CACNA1E_ENST00000367570.1_Silent_p.Y1148Y|CACNA1E_ENST00000526775.1_Silent_p.Y1129Y|CACNA1E_ENST00000360108.3_Silent_p.Y1129Y|CACNA1E_ENST00000358338.5_Silent_p.Y1080Y	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1148					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CCTGCCACTACATCGTGAACC	0.627																																					p.Y1148Y		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C3444T						.						59.0	67.0	64.0					1																	181706682		2114	4225	6339	SO:0001819	synonymous_variant	777	exon23			CCACTACATCGTG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3444C>T	chr1.hg19:g.181706682C>T		173.0	0.0		259.0	28.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.627	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
RGSL1	353299	hgsc.bcm.edu	37	1	182442708	182442708	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:182442708A>G	ENST00000294854.8	+	6	483		c.e6-1		RGSL1_ENST00000542961.1_Splice_Site	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1						termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)				central_nervous_system(2)|skin(4)	6						TATTATTTCCAGAGTCCCTCC	0.428																																					.	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Atlas-SNP	.											.	RGSL1	111	.	0			c.464-2A>G						.						28.0	22.0	24.0					1																	182442708		692	1591	2283	SO:0001630	splice_region_variant	353299	exon6			ATTTCCAGAGTCC	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.464-1A>G	chr1.hg19:g.182442708A>G		61.0	0.0		132.0	19.0	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Splice_Site	SNP	ENST00000294854.8	hg19	CCDS58049.1																																																																																			.	.		0.428	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	Intron
RGS8	85397	hgsc.bcm.edu	37	1	182617399	182617399	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:182617399A>G	ENST00000483095.2	-	6	490	c.233T>C	c.(232-234)tTc>tCc	p.F78S	RGS8_ENST00000258302.4_Missense_Mutation_p.F96S|RGS8_ENST00000367557.4_Missense_Mutation_p.F78S|RGS8_ENST00000367556.1_Missense_Mutation_p.F78S			P57771	RGS8_HUMAN	regulator of G-protein signaling 8	78	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	5						CTCCTCACTGAACTCCGTCTT	0.488																																					p.F96S	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											.	RGS8	51	.	0			c.T287C						.						194.0	194.0	194.0					1																	182617399		2203	4300	6503	SO:0001583	missense	85397	exon5			TCACTGAACTCCG	AF297015	CCDS1349.1, CCDS41443.1	1q25	2008-07-18	2007-08-14		ENSG00000135824	ENSG00000135824		"""Regulators of G-protein signaling"""	16810	protein-coding gene	gene with protein product		607189	"""regulator of G-protein signalling 8"""			11318611	Standard	NM_001102450		Approved	MGC119067, MGC119068, MGC119069	uc001gpm.1	P57771	OTTHUMG00000035219	ENST00000483095.2:c.233T>C	chr1.hg19:g.182617399A>G	ENSP00000426289:p.Phe78Ser	121.0	0.0		223.0	20.0	NM_033345	B4DGL9|Q3SYD2	Missense_Mutation	SNP	ENST00000483095.2	hg19	CCDS41443.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.903908	0.92035	.	.	ENSG00000135824	ENST00000483095;ENST00000258302;ENST00000367557;ENST00000367556	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.55	5.55	0.83447	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.93939	3.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.76418	-0.2966	10	0.87932	D	0	.	15.3412	0.74300	1.0:0.0:0.0:0.0	.	78;96	P57771;P57771-2	RGS8_HUMAN;.	S	78;96;78;78	ENSP00000426289:F78S;ENSP00000258302:F96S;ENSP00000356528:F78S;ENSP00000356527:F78S	ENSP00000258302:F96S	F	-	2	0	RGS8	180884022	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.020000	0.93667	2.101000	0.63845	0.460000	0.39030	TTC	.	.		0.488	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345	
HMCN1	83872	hgsc.bcm.edu	37	1	186099815	186099815	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:186099815A>T	ENST00000271588.4	+	85	13445	c.13216A>T	c.(13216-13218)Atc>Ttc	p.I4406F	HMCN1_ENST00000367492.2_Missense_Mutation_p.I4406F	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4406	Ig-like C2-type 43.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTCCCTGGCCATCTATGGCAC	0.498																																					p.I4406F		Atlas-SNP	.											.	HMCN1	797	.	0			c.A13216T						.						76.0	78.0	77.0					1																	186099815		2203	4300	6503	SO:0001583	missense	83872	exon85			CTGGCCATCTATG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13216A>T	chr1.hg19:g.186099815A>T	ENSP00000271588:p.Ile4406Phe	51.0	0.0		93.0	11.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.907095	0.92107	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.79247	-1.25;-1.25	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.87912	0.6297	M	0.78049	2.395	0.80722	D	1	D	0.61697	0.99	D	0.75484	0.986	D	0.88832	0.3306	10	0.56958	D	0.05	.	15.8623	0.79035	1.0:0.0:0.0:0.0	.	4406	Q96RW7	HMCN1_HUMAN	F	4406	ENSP00000271588:I4406F;ENSP00000356462:I4406F	ENSP00000271588:I4406F	I	+	1	0	HMCN1	184366438	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.257000	0.95545	2.205000	0.71048	0.482000	0.46254	ATC	.	.		0.498	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
PDC	5132	hgsc.bcm.edu	37	1	186413279	186413279	+	Silent	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:186413279G>T	ENST00000391997.2	-	4	660	c.573C>A	c.(571-573)atC>atA	p.I191I	PDC_ENST00000340129.5_Silent_p.I191I|PDC_ENST00000456239.2_Silent_p.I139I|PDC_ENST00000497198.1_Silent_p.I139I	NM_002597.4	NP_002588.3	P20941	PHOS_HUMAN	phosducin	191	Thioredoxin fold. {ECO:0000250}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of catalytic activity (GO:0043086)|phototransduction (GO:0007602)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	phospholipase inhibitor activity (GO:0004859)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7		Breast(1374;1.53e-05)		KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.0129)		CACCTTTATAGATGAGCAGTG	0.383																																					p.I191I		Atlas-SNP	.											.	PDC	15	.	0			c.C573A						.						82.0	81.0	82.0					1																	186413279		2203	4300	6503	SO:0001819	synonymous_variant	5132	exon4			TTTATAGATGAGC	AF076464	CCDS1370.1, CCDS41447.1	1q25.2	2013-01-08			ENSG00000116703	ENSG00000116703			8759	protein-coding gene	gene with protein product		171490				8288249	Standard	NM_022576		Approved	MEKA	uc001gsa.4	P20941	OTTHUMG00000035575	ENST00000391997.2:c.573C>A	chr1.hg19:g.186413279G>T		92.0	0.0		164.0	13.0	NM_002597	Q14816|Q9UP22|Q9UP23	Silent	SNP	ENST00000391997.2	hg19	CCDS1370.1																																																																																			.	.		0.383	PDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086347.2	NM_022577	
CRB1	23418	hgsc.bcm.edu	37	1	197403858	197403858	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:197403858T>A	ENST00000367400.3	+	9	3000	c.2865T>A	c.(2863-2865)aaT>aaA	p.N955K	CRB1_ENST00000535699.1_Missense_Mutation_p.N931K|CRB1_ENST00000544212.1_Missense_Mutation_p.N436K|CRB1_ENST00000367399.2_Missense_Mutation_p.N843K|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367397.1_Missense_Mutation_p.N336K	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	955	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CTGTTTTTAATGGACAAAGCG	0.299																																					p.N955K		Atlas-SNP	.											.	CRB1	284	.	0			c.T2865A						.						66.0	71.0	70.0					1																	197403858		2202	4298	6500	SO:0001583	missense	23418	exon9			TTTTAATGGACAA		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2865T>A	chr1.hg19:g.197403858T>A	ENSP00000356370:p.Asn955Lys	122.0	0.0		181.0	15.0	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	T	4.273	0.049869	0.08243	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.34	1.69	0.24217	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.57330	0.2046	M	0.64997	1.995	0.27434	N	0.953926	B;B;P;B	0.35272	0.019;0.287;0.493;0.361	B;B;B;B	0.31101	0.022;0.053;0.124;0.024	T	0.41215	-0.9521	9	0.23891	T	0.37	.	8.9412	0.35731	0.0:0.3398:0.0:0.6602	.	931;843;604;955	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	K	931;955;843;436;336;604	ENSP00000438786:N931K;ENSP00000356370:N955K;ENSP00000356369:N843K;ENSP00000444556:N436K;ENSP00000356367:N336K	ENSP00000356367:N336K	N	+	3	2	CRB1	195670481	0.015000	0.18098	0.870000	0.34147	0.007000	0.05969	-0.067000	0.11579	0.034000	0.15491	-0.408000	0.06270	AAT	.	.		0.299	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	
NAV1	89796	hgsc.bcm.edu	37	1	201757647	201757647	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:201757647C>T	ENST00000367296.4	+	10	3467	c.3047C>T	c.(3046-3048)cCc>cTc	p.P1016L	NAV1_ENST00000367302.1_Intron|NAV1_ENST00000295624.6_Missense_Mutation_p.P1016L|NAV1_ENST00000367297.4_Missense_Mutation_p.P1016L|NAV1_ENST00000367295.1_Missense_Mutation_p.P625L|NAV1_ENST00000367300.3_Intron|NAV1_ENST00000469130.1_3'UTR|IPO9-AS1_ENST00000413035.1_RNA	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1016					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						AACAGCATCCCCACCCACGAG	0.637																																					p.P1016L		Atlas-SNP	.											.	NAV1	143	.	0			c.C3047T						.						115.0	112.0	113.0					1																	201757647		2203	4300	6503	SO:0001583	missense	89796	exon10			GCATCCCCACCCA	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3047C>T	chr1.hg19:g.201757647C>T	ENSP00000356265:p.Pro1016Leu	146.0	0.0		250.0	14.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	C	27.7	4.858535	0.91433	.	.	ENSG00000134369	ENST00000367296;ENST00000295624;ENST00000367297;ENST00000391966;ENST00000367295	T;T;T;T	0.10763	2.84;2.85;2.91;2.86	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.35158	0.0922	M	0.72118	2.19	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.994;0.996;0.999	T	0.05468	-1.0883	10	0.87932	D	0	-32.9317	18.7921	0.91978	0.0:1.0:0.0:0.0	.	1016;625;1016;524;1016	Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.;.;NAV1_HUMAN;.;.	L	1016;1016;1016;524;625	ENSP00000356265:P1016L;ENSP00000295624:P1016L;ENSP00000356266:P1016L;ENSP00000356264:P625L	ENSP00000295624:P1016L	P	+	2	0	NAV1	200024270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.744000	0.85034	2.526000	0.85167	0.561000	0.74099	CCC	.	.		0.637	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
C1orf116	79098	hgsc.bcm.edu	37	1	207198319	207198319	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:207198319C>T	ENST00000359470.5	-	3	445	c.196G>A	c.(196-198)Gac>Aac	p.D66N	C1orf116_ENST00000461135.2_5'UTR	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	66						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					AGTCCGCTGTCAGCCTCCGTG	0.582																																					p.D66N		Atlas-SNP	.											.	C1orf116	64	.	0			c.G196A						.						82.0	77.0	79.0					1																	207198319		2203	4300	6503	SO:0001583	missense	79098	exon3			CGCTGTCAGCCTC		CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"""specifically androgen-regulated gene"""	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.196G>A	chr1.hg19:g.207198319C>T	ENSP00000352447:p.Asp66Asn	87.0	0.0		177.0	8.0	NM_023938	C9JV41|Q658X3	Missense_Mutation	SNP	ENST00000359470.5	hg19	CCDS1475.1	.	.	.	.	.	.	.	.	.	.	C	33	5.267037	0.95399	.	.	ENSG00000182795	ENST00000359470	T	0.15952	2.38	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.42177	0.1191	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36089	-0.9762	10	0.87932	D	0	-24.9277	17.3149	0.87220	0.0:1.0:0.0:0.0	.	66	Q9BW04	SARG_HUMAN	N	66	ENSP00000352447:D66N	ENSP00000352447:D66N	D	-	1	0	C1orf116	205264942	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	6.452000	0.73485	2.317000	0.78254	0.655000	0.94253	GAC	.	.		0.582	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115	
KCNH1	3756	hgsc.bcm.edu	37	1	211093070	211093070	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:211093070C>A	ENST00000271751.4	-	7	1401	c.1374G>T	c.(1372-1374)atG>atT	p.M458I	KCNH1_ENST00000367007.4_Missense_Mutation_p.M431I			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	458					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TGAGGCTGGTCATTGTGAAAT	0.493																																					p.M458I		Atlas-SNP	.											.	KCNH1	199	.	0			c.G1374T						.						162.0	155.0	157.0					1																	211093070		2203	4300	6503	SO:0001583	missense	3756	exon7			GCTGGTCATTGTG	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1374G>T	chr1.hg19:g.211093070C>A	ENSP00000271751:p.Met458Ile	247.0	0.0		460.0	23.0	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.735451	0.89482	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.98249	-4.82;-4.82	5.7	5.7	0.88788	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97773	0.9269	L	0.33093	0.98	0.80722	D	1	P;P	0.47034	0.744;0.889	P;P	0.56042	0.626;0.79	D	0.98917	1.0782	10	0.72032	D	0.01	.	18.8226	0.92103	0.0:1.0:0.0:0.0	.	431;458	Q14CL3;O95259	.;KCNH1_HUMAN	I	458;431	ENSP00000271751:M458I;ENSP00000355974:M431I	ENSP00000271751:M458I	M	-	3	0	KCNH1	209159693	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.538000	0.82048	2.692000	0.91855	0.655000	0.94253	ATG	.	.		0.493	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
USH2A	7399	hgsc.bcm.edu	37	1	216172333	216172333	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:216172333G>T	ENST00000307340.3	-	34	6939	c.6553C>A	c.(6553-6555)Cat>Aat	p.H2185N	USH2A_ENST00000366943.2_Missense_Mutation_p.H2185N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2185	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTAAAATCATGTGTATGGTTT	0.323										HNSCC(13;0.011)																											p.H2185N		Atlas-SNP	.											.	USH2A	1168	.	0			c.C6553A						.						146.0	140.0	142.0					1																	216172333		2203	4300	6503	SO:0001583	missense	7399	exon34			AATCATGTGTATG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.6553C>A	chr1.hg19:g.216172333G>T	ENSP00000305941:p.His2185Asn	115.0	0.0		227.0	22.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	0.400	-0.918967	0.02396	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.52526	0.66;0.66	5.56	1.56	0.23342	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.379718	0.19202	U	0.120144	T	0.40979	0.1139	M	0.62723	1.935	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.32851	-0.9891	10	0.18276	T	0.48	.	10.4517	0.44526	0.1224:0.3076:0.57:0.0	.	2185	O75445	USH2A_HUMAN	N	2185	ENSP00000305941:H2185N;ENSP00000355910:H2185N	ENSP00000305941:H2185N	H	-	1	0	USH2A	214238956	0.004000	0.15560	0.000000	0.03702	0.178000	0.23041	1.456000	0.35201	-0.172000	0.10779	-1.273000	0.01405	CAT	.	.		0.323	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
ESRRG	2104	hgsc.bcm.edu	37	1	216850694	216850694	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:216850694C>T	ENST00000408911.3	-	2	349	c.196G>A	c.(196-198)Ggg>Agg	p.G66R	ESRRG_ENST00000366937.1_Missense_Mutation_p.G71R|ESRRG_ENST00000493603.1_Missense_Mutation_p.G43R|ESRRG_ENST00000366940.2_Missense_Mutation_p.G43R|ESRRG_ENST00000493748.1_Missense_Mutation_p.G43R|ESRRG_ENST00000366938.2_Missense_Mutation_p.G43R|ESRRG_ENST00000360012.3_Missense_Mutation_p.G43R|ESRRG_ENST00000463665.1_Missense_Mutation_p.G43R|ESRRG_ENST00000361395.2_Missense_Mutation_p.G43R|ESRRG_ENST00000359162.2_Missense_Mutation_p.G43R|ESRRG_ENST00000487276.1_Missense_Mutation_p.G43R|ESRRG_ENST00000361525.3_Missense_Mutation_p.G43R|ESRRG_ENST00000391890.3_Missense_Mutation_p.G43R	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	66					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|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)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CTGTAGCTCCCACTGGCGTCT	0.577																																					p.G71R		Atlas-SNP	.											.	ESRRG	111	.	0			c.G211A						.						118.0	105.0	109.0					1																	216850694		2203	4300	6503	SO:0001583	missense	2104	exon3			AGCTCCCACTGGC	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"""Nuclear hormone receptors"""	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.196G>A	chr1.hg19:g.216850694C>T	ENSP00000386171:p.Gly66Arg	387.0	0.0		658.0	57.0	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	hg19	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	C	35	5.473063	0.96274	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275;ENST00000469486;ENST00000459955;ENST00000481543	D;D;D;D;D;D;D;D;D;D;D;D;D;D;T;T;T	0.94828	-3.16;-3.16;-3.16;-3.17;-3.16;-3.16;-3.16;-3.16;-3.16;-3.18;-3.53;-3.16;-3.16;-2.98;0.34;0.13;0.07	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	D	0.96568	0.8880	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	0.983;1.0;1.0	P;D;D	0.91635	0.852;0.999;0.996	D	0.94728	0.7907	10	0.32370	T	0.25	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	43;71;66	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	R	43;43;71;66;43;43;43;43;43;43;43;43;43;43;43;43;43;43	ENSP00000355225:G43R;ENSP00000355907:G43R;ENSP00000355904:G71R;ENSP00000386171:G66R;ENSP00000352077:G43R;ENSP00000354584:G43R;ENSP00000355905:G43R;ENSP00000353108:G43R;ENSP00000419594:G43R;ENSP00000375761:G43R;ENSP00000418629:G43R;ENSP00000419155:G43R;ENSP00000417374:G43R;ENSP00000419514:G43R;ENSP00000417900:G43R;ENSP00000420370:G43R;ENSP00000418895:G43R	ENSP00000346386:G43R	G	-	1	0	ESRRG	214917317	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.677000	0.84024	2.937000	0.99478	0.650000	0.86243	GGG	.	.		0.577	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595	
RAB3GAP2	25782	hgsc.bcm.edu	37	1	220387288	220387288	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:220387288T>C	ENST00000358951.2	-	3	330	c.214A>G	c.(214-216)Act>Gct	p.T72A		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	72					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		AGCCAGGAAGTTTTTTGTGTT	0.383																																					p.T72A		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.A214G						.						116.0	110.0	112.0					1																	220387288		2203	4300	6503	SO:0001583	missense	25782	exon3			AGGAAGTTTTTTG	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.214A>G	chr1.hg19:g.220387288T>C	ENSP00000351832:p.Thr72Ala	147.0	0.0		282.0	32.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	T	2.570	-0.299857	0.05532	.	.	ENSG00000118873	ENST00000358951	T	0.29142	1.58	5.7	-9.62	0.00547	.	1.052410	0.07323	N	0.877924	T	0.08179	0.0204	N	0.03608	-0.345	0.09310	N	1	B;B	0.14012	0.009;0.001	B;B	0.11329	0.006;0.001	T	0.19844	-1.0293	10	0.27785	T	0.31	.	0.304	0.00277	0.3453:0.1734:0.1643:0.3169	.	72;72	Q9H2M9-2;Q9H2M9	.;RBGPR_HUMAN	A	72	ENSP00000351832:T72A	ENSP00000351832:T72A	T	-	1	0	RAB3GAP2	218453911	0.131000	0.22433	0.002000	0.10522	0.784000	0.44337	0.207000	0.17395	-1.298000	0.02348	-0.353000	0.07706	ACT	.	.		0.383	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414	
MIA3	375056	hgsc.bcm.edu	37	1	222822189	222822189	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:222822189C>T	ENST00000344922.5	+	8	3653	c.3628C>T	c.(3628-3630)Caa>Taa	p.Q1210*	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Nonsense_Mutation_p.Q88*|MIA3_ENST00000344441.6_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1210					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		TAGAGTATATCAAGGTAAATC	0.264																																					p.Q1210X		Atlas-SNP	.											.	MIA3	167	.	0			c.C3628T						.						159.0	153.0	155.0					1																	222822189		1788	4064	5852	SO:0001587	stop_gained	375056	exon8			GTATATCAAGGTA		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3628C>T	chr1.hg19:g.222822189C>T	ENSP00000340900:p.Gln1210*	52.0	0.0		68.0	11.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Nonsense_Mutation	SNP	ENST00000344922.5	hg19	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.886492|7.886492	0.98542|0.98542	.|.	.|.	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000340535|ENST00000354906	.|.	.|.	.|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|.	.|.	.|.	.|.	.|T	.|0.75004	.|0.3791	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72481	.|-0.4280	.|4	0.06365|.	T|.	0.9|.	.|.	18.5719|18.5719	0.91138|0.91138	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	1210;88|792	.|.	ENSP00000345866:Q88X|.	Q|S	+|+	1|2	0|0	MIA3|MIA3	220888812|220888812	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.906000|0.906000	0.53458|0.53458	4.440000|4.440000	0.59975|0.59975	2.738000|2.738000	0.93877|0.93877	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.		0.264	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
CCDC185	164127	hgsc.bcm.edu	37	1	223567373	223567373	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:223567373T>A	ENST00000366875.3	+	1	659	c.556T>A	c.(556-558)Tcc>Acc	p.S186T		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		186										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		CTGGTCCCCTTCCTCAGTTCC	0.602																																					p.S186T		Atlas-SNP	.											.	C1orf65	71	.	0			c.T556A						.						54.0	55.0	55.0					1																	223567373		2203	4300	6503	SO:0001583	missense	164127	exon1			TCCCCTTCCTCAG																												ENST00000366875.3:c.556T>A	chr1.hg19:g.223567373T>A	ENSP00000355840:p.Ser186Thr	244.0	0.0		475.0	50.0	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	hg19	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.201684	0.58234	.	.	ENSG00000178395	ENST00000366875	T	0.25250	1.81	4.18	3.03	0.35002	.	.	.	.	.	T	0.40145	0.1105	L	0.56769	1.78	0.19300	N	0.999974	D	0.67145	0.996	D	0.64237	0.923	T	0.11616	-1.0580	9	0.41790	T	0.15	.	7.7188	0.28721	0.0:0.0:0.213:0.787	.	186	Q8N715	CA065_HUMAN	T	186	ENSP00000355840:S186T	ENSP00000355840:S186T	S	+	1	0	C1orf65	221633996	0.077000	0.21312	0.137000	0.22149	0.043000	0.13939	0.076000	0.14712	0.605000	0.29947	0.528000	0.53228	TCC	.	.		0.602	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
GNPAT	8443	hgsc.bcm.edu	37	1	231411879	231411879	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:231411879A>G	ENST00000366647.4	+	15	2106		c.e15-1		GNPAT_ENST00000366646.3_Splice_Site|GNPAT_ENST00000469332.1_Splice_Site	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				ATTTTCTCCTAGAAATAATAA	0.284																																					.		Atlas-SNP	.											.	GNPAT	73	.	0			c.1938-2A>G						.						19.0	21.0	21.0					1																	231411879		2170	4283	6453	SO:0001630	splice_region_variant	8443	exon15			TCTCCTAGAAATA	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1938-1A>G	chr1.hg19:g.231411879A>G		201.0	0.0		345.0	33.0	NM_014236	B4DNM9|Q5TBH7|Q9BWC2	Splice_Site	SNP	ENST00000366647.4	hg19	CCDS1592.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.982392	0.53827	.	.	ENSG00000116906	ENST00000366647;ENST00000366646	.	.	.	4.76	4.76	0.60689	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6648	0.56835	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GNPAT	229478502	1.000000	0.71417	0.919000	0.36401	0.838000	0.47535	4.953000	0.63624	2.006000	0.58801	0.460000	0.39030	.	.	.		0.284	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1		Intron
RYR2	6262	hgsc.bcm.edu	37	1	237713919	237713919	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:237713919G>A	ENST00000366574.2	+	27	3459	c.3142G>A	c.(3142-3144)Gac>Aac	p.D1048N	RYR2_ENST00000360064.6_Missense_Mutation_p.D1046N|RYR2_ENST00000542537.1_Missense_Mutation_p.D1032N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1048	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATCCAACAAGGACAGCCTCCG	0.507																																					p.D1048N		Atlas-SNP	.											.	RYR2	1273	.	0			c.G3142A						.						111.0	107.0	108.0					1																	237713919		1927	4140	6067	SO:0001583	missense	6262	exon27			AACAAGGACAGCC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3142G>A	chr1.hg19:g.237713919G>A	ENSP00000355533:p.Asp1048Asn	180.0	0.0		358.0	50.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	35	5.415136	0.96092	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91464	-2.85;-2.85;-2.85	5.14	5.14	0.70334	B30.2/SPRY domain (1);Ryanodine receptor Ryr (1);	0.000000	0.56097	U	0.000028	D	0.91153	0.7214	L	0.43554	1.36	0.80722	D	1	P	0.52692	0.955	P	0.51615	0.675	D	0.91388	0.5133	10	0.49607	T	0.09	.	18.6043	0.91261	0.0:0.0:1.0:0.0	.	1048	Q92736	RYR2_HUMAN	N	1048;1046;1032	ENSP00000355533:D1048N;ENSP00000353174:D1046N;ENSP00000443798:D1032N	ENSP00000353174:D1046N	D	+	1	0	RYR2	235780542	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.731000	0.98807	2.393000	0.81446	0.563000	0.77884	GAC	.	.		0.507	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
RYR2	6262	hgsc.bcm.edu	37	1	237982484	237982484	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:237982484T>C	ENST00000366574.2	+	101	14899	c.14582T>C	c.(14581-14583)aTa>aCa	p.I4861T	RYR2_ENST00000360064.6_Missense_Mutation_p.I4867T|RYR2_ENST00000542537.1_Missense_Mutation_p.I4845T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4861					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTCTTGGCCATAATACAAGGT	0.393																																					p.I4861T		Atlas-SNP	.											.	RYR2	1273	.	0			c.T14582C						.						197.0	198.0	198.0					1																	237982484		1942	4132	6074	SO:0001583	missense	6262	exon101			TGGCCATAATACA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14582T>C	chr1.hg19:g.237982484T>C	ENSP00000355533:p.Ile4861Thr	122.0	0.0		206.0	12.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.407320	0.83230	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000536033	D;D;D	0.98437	-4.93;-4.93;-4.93	5.58	5.58	0.84498	Ion transport (1);	0.000000	0.64402	U	0.000011	D	0.98868	0.9617	M	0.81179	2.53	0.80722	D	1	P;D	0.62365	0.659;0.991	P;D	0.78314	0.477;0.991	D	0.99850	1.1070	10	0.87932	D	0	.	15.7638	0.78110	0.0:0.0:0.0:1.0	.	294;4861	F5H3C7;Q92736	.;RYR2_HUMAN	T	4861;4867;4845;294	ENSP00000355533:I4861T;ENSP00000353174:I4867T;ENSP00000443798:I4845T	ENSP00000353174:I4867T	I	+	2	0	RYR2	236049107	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.997000	0.88414	2.126000	0.65437	0.533000	0.62120	ATA	.	.		0.393	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
RGS7	6000	hgsc.bcm.edu	37	1	240966242	240966242	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:240966242A>T	ENST00000407727.1	-	15	1320	c.1321T>A	c.(1321-1323)Tcc>Acc	p.S441T	RGS7_ENST00000366565.1_Missense_Mutation_p.S441T|RGS7_ENST00000331110.7_Missense_Mutation_p.S415T|RGS7_ENST00000446183.2_Missense_Mutation_p.S357T|RGS7_ENST00000366564.1_Missense_Mutation_p.S441T|RGS7_ENST00000366562.4_Missense_Mutation_p.S441T|RGS7_ENST00000401882.1_Missense_Mutation_p.S388T|RGS7_ENST00000348120.2_Missense_Mutation_p.S388T|RGS7_ENST00000366563.1_Missense_Mutation_p.S441T			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	441	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			TAGGCACTGGATCTTATAAAA	0.348																																					p.S441T		Atlas-SNP	.											.	RGS7	308	.	0			c.T1321A						.						143.0	152.0	149.0					1																	240966242		2203	4300	6503	SO:0001583	missense	6000	exon16			CACTGGATCTTAT	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"""Regulators of G-protein signaling"""	10003	protein-coding gene	gene with protein product		602517	"""regulator of G-protein signalling 7"""			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.1321T>A	chr1.hg19:g.240966242A>T	ENSP00000384428:p.Ser441Thr	76.0	0.0		136.0	10.0	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	A	29.9	5.042600	0.93685	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	6.04	6.04	0.98038	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.103098	0.64402	D	0.000001	T	0.72645	0.3486	M	0.86268	2.805	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;1.0;0.998;1.0;0.999	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.995;1.0;0.997;1.0;0.998	T	0.77370	-0.2613	10	0.87932	D	0	.	15.7697	0.78157	1.0:0.0:0.0:0.0	.	357;415;388;441;441;441;441	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	T	415;441;441;441;272;388;357;441;441;388	ENSP00000331485:S415T;ENSP00000355523:S441T;ENSP00000355522:S441T;ENSP00000355521:S441T;ENSP00000404399:S272T;ENSP00000341242:S388T;ENSP00000390138:S357T;ENSP00000355520:S441T;ENSP00000384428:S441T;ENSP00000385508:S388T	ENSP00000331485:S415T	S	-	1	0	RGS7	239032865	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.317000	0.78254	0.460000	0.39030	TCC	.	.		0.348	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924	
OR2L2	26246	hgsc.bcm.edu	37	1	248202311	248202311	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248202311T>C	ENST00000366479.2	+	1	838	c.742T>C	c.(742-744)Tcc>Ccc	p.S248P	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CACTGTAGTGTCCTTCTACTA	0.502																																					p.S248P		Atlas-SNP	.											.	OR2L2	115	.	0			c.T742C						.						206.0	182.0	190.0					1																	248202311		2203	4300	6503	SO:0001583	missense	26246	exon1			GTAGTGTCCTTCT	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"""GPCR / Class A : Olfactory receptors"""	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.742T>C	chr1.hg19:g.248202311T>C	ENSP00000355435:p.Ser248Pro	230.0	0.0		471.0	44.0	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	hg19	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	11.36	1.616213	0.28801	.	.	ENSG00000203663	ENST00000366479	T	0.38560	1.13	1.9	-2.83	0.05769	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32287	U	0.006305	T	0.51346	0.1669	M	0.92507	3.315	0.09310	N	1	P	0.37573	0.6	P	0.46850	0.529	T	0.51172	-0.8739	10	0.56958	D	0.05	.	3.1725	0.06558	0.3251:0.0:0.1955:0.4794	.	248	Q8NH16	OR2L2_HUMAN	P	248	ENSP00000355435:S248P	ENSP00000355435:S248P	S	+	1	0	OR2L2	246268934	0.000000	0.05858	0.801000	0.32222	0.060000	0.15804	-2.297000	0.01141	-0.063000	0.13065	-1.636000	0.00776	TCC	.	.		0.502	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686	
OR2T1	26696	hgsc.bcm.edu	37	1	248569623	248569623	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248569623T>A	ENST00000366474.1	+	1	328	c.328T>A	c.(328-330)Tac>Aac	p.Y110N		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TACACCCATGTACTTCCTCCT	0.423																																					p.Y110N		Atlas-SNP	.											.	OR2T1	89	.	0			c.T328A						.						176.0	159.0	165.0					1																	248569623		2203	4300	6503	SO:0001583	missense	26696	exon1			CCCATGTACTTCC	U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"""GPCR / Class A : Olfactory receptors"""	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.328T>A	chr1.hg19:g.248569623T>A	ENSP00000355430:p.Tyr110Asn	180.0	0.0		337.0	34.0	NM_030904	Q6IEZ9	Missense_Mutation	SNP	ENST00000366474.1	hg19	CCDS31115.1	.	.	.	.	.	.	.	.	.	.	t	19.03	3.746982	0.69418	.	.	ENSG00000175143	ENST00000366474	T	0.15603	2.41	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33534	U	0.004806	T	0.46658	0.1404	M	0.87827	2.91	0.46901	D	0.99924	D	0.89917	1.0	D	0.83275	0.996	T	0.55283	-0.8165	10	0.87932	D	0	.	13.3845	0.60789	0.0:0.0:0.0:1.0	.	110	O43869	OR2T1_HUMAN	N	110	ENSP00000355430:Y110N	ENSP00000355430:Y110N	Y	+	1	0	OR2T1	246636246	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	4.233000	0.58651	1.993000	0.58246	0.528000	0.53228	TAC	.	.		0.423	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2		
OR2G6	391211	hgsc.bcm.edu	37	1	248685435	248685435	+	Missense_Mutation	SNP	C	C	A	rs568353162	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248685435C>A	ENST00000343414.4	+	1	520	c.488C>A	c.(487-489)aCt>aAt	p.T163N		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	163						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGCTCCCTCACTGTGCAGCTG	0.557																																					p.T163N		Atlas-SNP	.											.	OR2G6	124	.	0			c.C488A						.						87.0	72.0	77.0					1																	248685435		2203	4300	6503	SO:0001583	missense	391211	exon1			CCCTCACTGTGCA		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"""GPCR / Class A : Olfactory receptors"""	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.488C>A	chr1.hg19:g.248685435C>A	ENSP00000341291:p.Thr163Asn	234.0	0.0		448.0	36.0	NM_001013355	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	hg19	CCDS31119.1	.	.	.	.	.	.	.	.	.	.	N	10.77	1.443424	0.25987	.	.	ENSG00000188558	ENST00000343414	T	0.00253	8.43	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45606	U	0.000345	T	0.00815	0.0027	H	0.97611	4.04	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.19128	-1.0315	10	0.87932	D	0	.	8.3892	0.32518	0.0:0.8869:0.0:0.1131	.	163	Q5TZ20	OR2G6_HUMAN	N	163	ENSP00000341291:T163N	ENSP00000341291:T163N	T	+	2	0	OR2G6	246752058	0.000000	0.05858	0.048000	0.18961	0.274000	0.26718	-0.000000	0.12993	1.869000	0.54173	0.400000	0.26472	ACT	.	.		0.557	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842	
OR2T34	127068	hgsc.bcm.edu	37	1	248737675	248737675	+	Nonsense_Mutation	SNP	A	A	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr1:248737675A>C	ENST00000328782.2	-	1	405	c.384T>G	c.(382-384)taT>taG	p.Y128*		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AAACAGCAGCATATCGGTCAT	0.552																																					p.Y128X		Atlas-SNP	.											.	OR2T34	72	.	0			c.T384G						.						22.0	24.0	23.0					1																	248737675		2152	4264	6416	SO:0001587	stop_gained	127068	exon1			AGCAGCATATCGG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.384T>G	chr1.hg19:g.248737675A>C	ENSP00000330904:p.Tyr128*	651.0	0.0		1219.0	94.0	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Nonsense_Mutation	SNP	ENST00000328782.2	hg19	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	14.08	2.427545	0.43122	.	.	ENSG00000183310	ENST00000328782	.	.	.	2.19	-0.611	0.11601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.12	0.20148	0.7399:0.0:0.2601:0.0	.	.	.	.	X	128	.	ENSP00000330904:Y128X	Y	-	3	2	OR2T34	246804298	0.001000	0.12720	0.008000	0.14137	0.119000	0.20118	-0.342000	0.07801	-0.461000	0.06993	0.319000	0.21371	TAT	.	.		0.552	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
NBAS	51594	hgsc.bcm.edu	37	2	15307372	15307372	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:15307372T>A	ENST00000281513.5	-	52	6941	c.6916A>T	c.(6916-6918)Act>Tct	p.T2306S	NBAS_ENST00000441750.1_Missense_Mutation_p.T2186S	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2306					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TAGAAGGGAGTGGAGACACAC	0.552																																					p.T2306S		Atlas-SNP	.											.	NBAS	246	.	0			c.A6916T						.						81.0	73.0	76.0					2																	15307372		2203	4300	6503	SO:0001583	missense	51594	exon52			AGGGAGTGGAGAC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6916A>T	chr2.hg19:g.15307372T>A	ENSP00000281513:p.Thr2306Ser	180.0	0.0		213.0	23.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.010555	0.54361	.	.	ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000433283	T;T	0.30182	1.54;1.54	5.46	5.46	0.80206	.	0.048354	0.85682	D	0.000000	T	0.48892	0.1525	M	0.71581	2.175	0.53688	D	0.999974	D;P	0.57571	0.98;0.489	P;B	0.55455	0.776;0.128	T	0.53725	-0.8398	10	0.87932	D	0	.	14.7106	0.69229	0.0:0.0:0.0:1.0	.	2186;2306	A2RRP1-2;A2RRP1	.;NBAS_HUMAN	S	2186;2306;119	ENSP00000413201:T2186S;ENSP00000281513:T2306S	ENSP00000281513:T2306S	T	-	1	0	NBAS	15224823	1.000000	0.71417	0.740000	0.30986	0.216000	0.24613	5.802000	0.69122	2.062000	0.61559	0.533000	0.62120	ACT	.	.		0.552	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
KCNS3	3790	hgsc.bcm.edu	37	2	18112349	18112349	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:18112349A>G	ENST00000403915.1	+	3	525	c.74A>G	c.(73-75)aAg>aGg	p.K25R	KCNS3_ENST00000304101.4_Missense_Mutation_p.K25R|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	25					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGGGGCTTTAAGCAGTCTGTT	0.527																																					p.K25R		Atlas-SNP	.											.	KCNS3	85	.	0			c.A74G						.						106.0	101.0	103.0					2																	18112349		2203	4300	6503	SO:0001583	missense	3790	exon3			GCTTTAAGCAGTC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.74A>G	chr2.hg19:g.18112349A>G	ENSP00000385968:p.Lys25Arg	273.0	0.0		365.0	128.0	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	hg19	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	A	1.639	-0.516881	0.04200	.	.	ENSG00000170745	ENST00000403915;ENST00000304101;ENST00000419802	T;T;T	0.74632	1.14;1.14;-0.86	5.79	4.44	0.53790	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.159168	0.52532	D	0.000061	T	0.43700	0.1259	N	0.02111	-0.68	0.43394	D	0.995514	B	0.12630	0.006	B	0.15052	0.012	T	0.49808	-0.8900	10	0.02654	T	1	.	12.4181	0.55504	0.9242:0.0:0.0758:0.0	.	25	Q9BQ31	KCNS3_HUMAN	R	25	ENSP00000385968:K25R;ENSP00000305824:K25R;ENSP00000400098:K25R	ENSP00000305824:K25R	K	+	2	0	KCNS3	17975830	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.115000	0.71566	2.226000	0.72624	0.456000	0.33151	AAG	.	.		0.527	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
KLHL29	114818	hgsc.bcm.edu	37	2	23918908	23918908	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:23918908C>T	ENST00000486442.1	+	10	2546	c.1829C>T	c.(1828-1830)cCg>cTg	p.P610L		NM_052920.1	NP_443152.1	Q96CT2	KLH29_HUMAN	kelch-like family member 29	610										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|lung(1)|ovary(3)	10						TGCTGGAACCCGCAGAACAAC	0.602																																					p.P610L		Atlas-SNP	.											.	KLHL29	47	.	0			c.C1829T						.						85.0	84.0	84.0					2																	23918908		692	1591	2283	SO:0001583	missense	114818	exon10			GGAACCCGCAGAA		CCDS54335.1	2p23.3	2013-09-27	2013-02-22	2007-01-09	ENSG00000119771	ENSG00000119771		"""Kelch-like"", ""BTB/POZ domain containing"""	29404	protein-coding gene	gene with protein product			"""kelch repeat and BTB (POZ) domain containing 9"", ""kelch-like 29 (Drosophila)"""	KBTBD9		11572484	Standard	NM_052920		Approved	KIAA1921	uc010ykg.2	Q96CT2	OTTHUMG00000151899	ENST00000486442.1:c.1829C>T	chr2.hg19:g.23918908C>T	ENSP00000420659:p.Pro610Leu	135.0	0.0		118.0	34.0	NM_052920	Q8N388|Q96BF0|Q96PW7	Missense_Mutation	SNP	ENST00000486442.1	hg19	CCDS54335.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.5|21.5	4.152174|4.152174	0.78001|0.78001	.|.	.|.	ENSG00000119771|ENSG00000119771	ENST00000486442|ENST00000288548	T|.	0.69435|.	-0.4|.	4.43|4.43	3.55|3.55	0.40652|0.40652	Galactose oxidase, beta-propeller (1);|.	0.053759|.	0.85682|.	N|.	0.000000|.	T|T	0.68229|0.68229	0.2978|0.2978	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.957;1.0|.	B;D|.	0.68483|.	0.305;0.958|.	T|T	0.66444|0.66444	-0.5922|-0.5922	10|5	0.25106|.	T|.	0.35|.	.|.	12.3592|12.3592	0.55192|0.55192	0.0:0.9174:0.0:0.0826|0.0:0.9174:0.0:0.0826	.|.	390;390|.	Q96CT2;Q96CT2-2|.	KLH29_HUMAN;.|.	L|C	610|450	ENSP00000420659:P610L|.	ENSP00000420659:P610L|.	P|R	+|+	2|1	0|0	KLHL29|KLHL29	23772413|23772413	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.995000|0.995000	0.86356|0.86356	7.814000|7.814000	0.86154|0.86154	0.984000|0.984000	0.38629|0.38629	0.561000|0.561000	0.74099|0.74099	CCG|CGC	.	.		0.602	KLHL29-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324315.3	NM_052920	
GALNT14	79623	hgsc.bcm.edu	37	2	31178813	31178813	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:31178813G>A	ENST00000349752.5	-	5	1136	c.497C>T	c.(496-498)cCc>cTc	p.P166L	GALNT14_ENST00000486564.1_5'Flank|GALNT14_ENST00000406653.1_Missense_Mutation_p.P146L|GALNT14_ENST00000324589.5_Missense_Mutation_p.P171L|GALNT14_ENST00000356174.3_Missense_Mutation_p.P133L|GALNT14_ENST00000420311.2_Missense_Mutation_p.P131L	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	166	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					TTTCACCTTGGGCAACTTGAT	0.517																																					p.P171L		Atlas-SNP	.											.	GALNT14	103	.	0			c.C512T						.						215.0	200.0	205.0					2																	31178813		2203	4300	6503	SO:0001583	missense	79623	exon6			ACCTTGGGCAACT	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.497C>T	chr2.hg19:g.31178813G>A	ENSP00000288988:p.Pro166Leu	160.0	0.0		215.0	59.0	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	hg19	CCDS1773.2	.	.	.	.	.	.	.	.	.	.	G	32	5.190093	0.94923	.	.	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311;ENST00000430167	T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	5.28	5.28	0.74379	Glycosyl transferase, family 2 (1);	0.788526	0.11995	N	0.509410	D	0.82765	0.5108	M	0.85462	2.755	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.994;0.995;0.999;0.999;0.998;0.999	T	0.81178	-0.1051	10	0.44086	T	0.13	.	18.9153	0.92503	0.0:0.0:1.0:0.0	.	131;131;133;171;166;146	F5H263;B7Z5C5;Q96FL9-2;Q96FL9-3;Q96FL9;B3KV89	.;.;.;.;GLT14_HUMAN;.	L	166;171;146;133;131;133	ENSP00000288988:P166L;ENSP00000314500:P171L;ENSP00000385435:P146L;ENSP00000348497:P133L;ENSP00000415514:P131L;ENSP00000406399:P133L	ENSP00000314500:P171L	P	-	2	0	GALNT14	31032317	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.739000	0.91574	2.484000	0.83849	0.561000	0.74099	CCC	.	.		0.517	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
LHCGR	3973	hgsc.bcm.edu	37	2	48915238	48915238	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:48915238C>T	ENST00000294954.7	-	11	1719	c.1698G>A	c.(1696-1698)aaG>aaA	p.K566K	LHCGR_ENST00000405626.1_Silent_p.K539K|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Silent_p.K504K|LHCGR_ENST00000403273.1_3'UTR|LHCGR_ENST00000401907.1_3'UTR	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	566					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TCTTAGCAATCTTTGTATCTT	0.378																																					p.K566K		Atlas-SNP	.											LHCGR,NS,carcinoma,0,1	LHCGR	154	.	0			c.G1698A						.						112.0	111.0	111.0					2																	48915238		2203	4300	6503	SO:0001819	synonymous_variant	3973	exon11			AGCAATCTTTGTA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1698G>A	chr2.hg19:g.48915238C>T		151.0	0.0		169.0	19.0	NM_000233	Q14751|Q15996|Q9UEW9	Silent	SNP	ENST00000294954.7	hg19	CCDS1842.1																																																																																			.	.		0.378	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
EFEMP1	2202	hgsc.bcm.edu	37	2	56108782	56108782	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:56108782G>A	ENST00000394555.2	-	5	1040	c.605C>T	c.(604-606)cCt>cTt	p.P202L	EFEMP1_ENST00000394554.1_Missense_Mutation_p.P202L|EFEMP1_ENST00000424836.2_Missense_Mutation_p.P144L|EFEMP1_ENST00000355426.3_Missense_Mutation_p.P202L	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	202	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ATATCCAGGAGGGCACTGACA	0.512																																					p.P202L	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											EFEMP1,caecum,carcinoma,0,1	EFEMP1	81	.	0			c.C605T						.						242.0	178.0	199.0					2																	56108782		2203	4300	6503	SO:0001583	missense	2202	exon5			CCAGGAGGGCACT	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.605C>T	chr2.hg19:g.56108782G>A	ENSP00000378058:p.Pro202Leu	181.0	0.0		220.0	47.0	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Missense_Mutation	SNP	ENST00000394555.2	hg19	CCDS1857.1	.	.	.	.	.	.	.	.	.	.	G	6.568	0.473090	0.12461	.	.	ENSG00000115380	ENST00000394555;ENST00000394554;ENST00000405693;ENST00000424836;ENST00000355426	D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01	5.71	-2.15	0.07102	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.308277	0.28011	N	0.016958	D	0.84165	0.5412	L	0.55743	1.74	0.22213	N	0.999282	B;B	0.16166	0.016;0.0	B;B	0.10450	0.005;0.004	T	0.67780	-0.5582	10	0.24483	T	0.36	.	2.196	0.03911	0.2975:0.0908:0.4272:0.1846	.	144;202	B4DW75;Q12805	.;FBLN3_HUMAN	L	202;202;58;144;202	ENSP00000378058:P202L;ENSP00000378057:P202L;ENSP00000399145:P144L;ENSP00000347596:P202L	ENSP00000347596:P202L	P	-	2	0	EFEMP1	55962286	0.002000	0.14202	0.053000	0.19242	0.052000	0.14988	-0.135000	0.10420	-0.136000	0.11475	-0.143000	0.13931	CCT	.	.		0.512	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2		
CCDC142	84865	hgsc.bcm.edu	37	2	74707914	74707914	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:74707914C>T	ENST00000393965.3	-	5	1881	c.1485G>A	c.(1483-1485)aaG>aaA	p.K495K	CCDC142_ENST00000471713.1_5'UTR|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000233623.5_5'Flank|CCDC142_ENST00000290418.4_Silent_p.K488K|TTC31_ENST00000442235.2_5'Flank	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	495										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						GTGCAGTCAGCTTCTGGATCT	0.537																																					p.K488K		Atlas-SNP	.											.	CCDC142	40	.	0			c.G1464A						.						70.0	68.0	69.0					2																	74707914		2203	4300	6503	SO:0001819	synonymous_variant	84865	exon5			AGTCAGCTTCTGG	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.1485G>A	chr2.hg19:g.74707914C>T		205.0	0.0		251.0	24.0	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Silent	SNP	ENST00000393965.3	hg19																																																																																				.	.		0.537	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779	
TACR1	6869	hgsc.bcm.edu	37	2	75278382	75278382	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:75278382C>T	ENST00000305249.5	-	4	1693	c.928G>A	c.(928-930)Gac>Aac	p.D310N	TACR1_ENST00000409848.3_Missense_Mutation_p.D310N	NM_001058.3	NP_001049.1	P25103	NK1R_HUMAN	tachykinin receptor 1	310					acute inflammatory response (GO:0002526)|aggressive behavior (GO:0002118)|angiotensin-mediated drinking behavior (GO:0003051)|associative learning (GO:0008306)|behavioral response to pain (GO:0048266)|detection of abiotic stimulus (GO:0009582)|eating behavior (GO:0042755)|inflammatory response (GO:0006954)|long-term memory (GO:0007616)|operant conditioning (GO:0035106)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of action potential (GO:0045760)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|positive regulation of vasoconstriction (GO:0045907)|regulation of smooth muscle cell migration (GO:0014910)|regulation of smooth muscle cell proliferation (GO:0048660)|response to auditory stimulus (GO:0010996)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to ozone (GO:0010193)|response to progesterone (GO:0032570)|smooth muscle contraction involved in micturition (GO:0060083)|sperm ejaculation (GO:0042713)|tachykinin receptor signaling pathway (GO:0007217)	cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance P receptor activity (GO:0016496)|tachykinin receptor activity (GO:0004995)	p.D310N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(8)|ovary(1)|skin(1)	24					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	CCTCACCTGTCATTGAGGCAG	0.532																																					p.D310N	Pancreas(64;62 1268 3653 14826 43765)	Atlas-SNP	.											TACR1,NS,carcinoma,0,1	TACR1	62	.	1	Substitution - Missense(1)	lung(1)	c.G928A						.						187.0	171.0	176.0					2																	75278382		2203	4300	6503	SO:0001583	missense	6869	exon4			ACCTGTCATTGAG	M76675	CCDS1958.1, CCDS46345.1	2p13.1-p12	2012-08-08			ENSG00000115353	ENSG00000115353		"""GPCR / Class A : Tachykinin receptors"""	11526	protein-coding gene	gene with protein product		162323		TAC1R		1657150	Standard	NM_001058		Approved	SPR, NK1R, NKIR	uc002sng.2	P25103	OTTHUMG00000129973	ENST00000305249.5:c.928G>A	chr2.hg19:g.75278382C>T	ENSP00000303522:p.Asp310Asn	361.0	1.0		383.0	106.0	NM_001058	A8K150	Missense_Mutation	SNP	ENST00000305249.5	hg19	CCDS1958.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.994681	0.74703	.	.	ENSG00000115353	ENST00000305249;ENST00000409848	T;T	0.36878	1.23;1.23	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.41696	0.1170	M	0.65498	2.005	0.80722	D	1	P	0.50066	0.931	B	0.43680	0.427	T	0.19614	-1.0300	10	0.27785	T	0.31	.	17.0229	0.86438	0.0:1.0:0.0:0.0	.	310	P25103	NK1R_HUMAN	N	310	ENSP00000303522:D310N;ENSP00000386448:D310N	ENSP00000303522:D310N	D	-	1	0	TACR1	75131890	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.852000	0.55934	2.880000	0.98712	0.650000	0.86243	GAC	.	.		0.532	TACR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252239.3	NM_001058	
AFF3	3899	hgsc.bcm.edu	37	2	100194857	100194857	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:100194857C>T	ENST00000409236.2	-	16	2962	c.2850G>A	c.(2848-2850)acG>acA	p.T950T	AFF3_ENST00000409579.1_Silent_p.T975T|AFF3_ENST00000356421.2_Silent_p.T975T|AFF3_ENST00000317233.4_Silent_p.T950T			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	950					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						ACCACGGCTTCGTCTGCGGCC	0.488																																					p.T975T		Atlas-SNP	.											.	AFF3	164	.	0			c.G2925A						.						131.0	137.0	135.0					2																	100194857		2203	4300	6503	SO:0001819	synonymous_variant	3899	exon17			CGGCTTCGTCTGC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2850G>A	chr2.hg19:g.100194857C>T		135.0	0.0		204.0	66.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	hg19	CCDS42723.1																																																																																			.	.		0.488	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
IL1RL1	9173	hgsc.bcm.edu	37	2	102968228	102968228	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:102968228A>G	ENST00000233954.1	+	11	1789	c.1518A>G	c.(1516-1518)gtA>gtG	p.V506V		NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	506	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						TTATGAAAGTACAGGGGACCA	0.517																																					p.V506V		Atlas-SNP	.											.	IL1RL1	114	.	0			c.A1518G						.						48.0	48.0	48.0					2																	102968228		2203	4300	6503	SO:0001819	synonymous_variant	9173	exon11			GAAAGTACAGGGG	D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5998	protein-coding gene	gene with protein product	"""homolog of mouse growth stimulation-expressed"""	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.1518A>G	chr2.hg19:g.102968228A>G		176.0	0.0		213.0	37.0	NM_016232	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Silent	SNP	ENST00000233954.1	hg19	CCDS2057.1																																																																																			.	.		0.517	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232	
SLC9A4	389015	hgsc.bcm.edu	37	2	103090418	103090418	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:103090418T>C	ENST00000295269.4	+	1	657	c.200T>C	c.(199-201)gTg>gCg	p.V67A		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	67					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						TATGACTATGTGCAAATTCCT	0.418																																					p.V67A		Atlas-SNP	.											.	SLC9A4	115	.	0			c.T200C						.						128.0	122.0	124.0					2																	103090418		2203	4300	6503	SO:0001583	missense	389015	exon1			ACTATGTGCAAAT		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.200T>C	chr2.hg19:g.103090418T>C	ENSP00000295269:p.Val67Ala	141.0	0.0		164.0	48.0	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	hg19	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.941453	0.92526	.	.	ENSG00000180251	ENST00000295269	T	0.70749	-0.51	6.04	6.04	0.98038	.	0.122712	0.56097	D	0.000028	D	0.82797	0.5115	M	0.66939	2.045	0.58432	D	0.999996	D	0.71674	0.998	D	0.70935	0.971	D	0.84458	0.0592	10	0.87932	D	0	.	16.5885	0.84745	0.0:0.0:0.0:1.0	.	67	Q6AI14	SL9A4_HUMAN	A	67	ENSP00000295269:V67A	ENSP00000295269:V67A	V	+	2	0	SLC9A4	102456850	1.000000	0.71417	0.991000	0.47740	0.992000	0.81027	7.295000	0.78780	2.317000	0.78254	0.460000	0.39030	GTG	.	.		0.418	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
SLC9A4	389015	hgsc.bcm.edu	37	2	103124608	103124608	+	Silent	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:103124608C>A	ENST00000295269.4	+	5	1726	c.1269C>A	c.(1267-1269)atC>atA	p.I423I		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	423					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						ACCAGTGCATCATTTTCTACA	0.433																																					p.I423I		Atlas-SNP	.											.	SLC9A4	115	.	0			c.C1269A						.						171.0	165.0	167.0					2																	103124608		2203	4300	6503	SO:0001819	synonymous_variant	389015	exon5			GTGCATCATTTTC		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1269C>A	chr2.hg19:g.103124608C>A		358.0	0.0		414.0	60.0	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	hg19	CCDS33264.1																																																																																			.	.		0.433	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
SLC9A2	6549	hgsc.bcm.edu	37	2	103300730	103300730	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:103300730T>C	ENST00000233969.2	+	5	1502	c.1360T>C	c.(1360-1362)Ttt>Ctt	p.F454L		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	454					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						TGCTGCTGTGTTTCCTCGGAA	0.438																																					p.F454L		Atlas-SNP	.											.	SLC9A2	112	.	0			c.T1360C						.						259.0	242.0	248.0					2																	103300730		2203	4300	6503	SO:0001583	missense	6549	exon5			GCTGTGTTTCCTC		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"""Solute carriers"""	11072	protein-coding gene	gene with protein product		600530	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 2"""	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1360T>C	chr2.hg19:g.103300730T>C	ENSP00000233969:p.Phe454Leu	347.0	0.0		427.0	102.0	NM_003048	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	hg19	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	T	20.0	3.931198	0.73327	.	.	ENSG00000115616	ENST00000233969	T	0.13196	2.61	5.62	5.62	0.85841	Cation/H+ exchanger (1);	0.059515	0.64402	D	0.000003	T	0.23054	0.0557	L	0.31420	0.93	0.50632	D	0.99988	D	0.69078	0.997	D	0.64877	0.93	T	0.04090	-1.0978	10	0.19590	T	0.45	.	15.8096	0.78547	0.0:0.0:0.0:1.0	.	454	Q9UBY0	SL9A2_HUMAN	L	454	ENSP00000233969:F454L	ENSP00000233969:F454L	F	+	1	0	SLC9A2	102667162	1.000000	0.71417	1.000000	0.80357	0.287000	0.27160	3.184000	0.50926	2.127000	0.65507	0.533000	0.62120	TTT	.	.		0.438	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2		
RGPD4	285190	hgsc.bcm.edu	37	2	108489237	108489237	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:108489237T>A	ENST00000408999.3	+	20	4854	c.4777T>A	c.(4777-4779)Tct>Act	p.S1593T	RGPD4_ENST00000354986.4_Missense_Mutation_p.S1593T	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1593					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						CCAGAGTGGATCTGAAAGCAA	0.383																																					p.S1593T		Atlas-SNP	.											RGPD4,NS,carcinoma,0,1	RGPD4	112	.	0			c.T4777A						.						40.0	34.0	35.0					2																	108489237		691	1591	2282	SO:0001583	missense	285190	exon20			AGTGGATCTGAAA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.4777T>A	chr2.hg19:g.108489237T>A	ENSP00000386810:p.Ser1593Thr	152.0	0.0		173.0	26.0	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	10.18	1.279615	0.23307	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.38887	1.11;1.11	2.33	-2.43	0.06522	.	.	.	.	.	T	0.22551	0.0544	L	0.35414	1.06	0.21416	N	0.999698	B	0.10296	0.003	B	0.06405	0.002	T	0.25537	-1.0129	9	0.15499	T	0.54	-8.3036	2.1596	0.03821	0.2529:0.3485:0.0:0.3986	.	1593	Q7Z3J3	RGPD4_HUMAN	T	1593;1593;960	ENSP00000347081:S1593T;ENSP00000386810:S1593T	ENSP00000347081:S1593T	S	+	1	0	RGPD4	107855669	0.009000	0.17119	0.973000	0.42090	0.432000	0.31715	-0.194000	0.09559	-0.198000	0.10333	0.136000	0.15936	TCT	.	.		0.383	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
KCNH7	90134	hgsc.bcm.edu	37	2	163361023	163361023	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:163361023G>T	ENST00000332142.5	-	6	1157	c.1058C>A	c.(1057-1059)tCt>tAt	p.S353Y	KCNH7_ENST00000477019.1_5'UTR|KCNH7_ENST00000328032.4_Missense_Mutation_p.S346Y	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	353					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TTTATCTGAAGAAGGAGGTGA	0.373																																					p.S353Y	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											.	KCNH7	378	.	0			c.C1058A						.						192.0	189.0	190.0					2																	163361023		2203	4300	6503	SO:0001583	missense	90134	exon6			TCTGAAGAAGGAG	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.1058C>A	chr2.hg19:g.163361023G>T	ENSP00000331727:p.Ser353Tyr	178.0	0.0		228.0	47.0	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	hg19	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.900958	0.92035	.	.	ENSG00000184611	ENST00000332142;ENST00000328032	D;D	0.88664	-2.41;-2.41	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.91212	0.7231	L	0.43152	1.355	0.80722	D	1	P;D	0.61697	0.942;0.99	P;P	0.59703	0.637;0.862	D	0.88900	0.3352	10	0.29301	T	0.29	.	19.775	0.96388	0.0:0.0:1.0:0.0	.	346;353	Q9NS40-2;Q9NS40	.;KCNH7_HUMAN	Y	353;346	ENSP00000331727:S353Y;ENSP00000333781:S346Y	ENSP00000333781:S346Y	S	-	2	0	KCNH7	163069269	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.531000	0.73820	2.741000	0.93983	0.585000	0.79938	TCT	.	.		0.373	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272	
COBLL1	22837	hgsc.bcm.edu	37	2	165548775	165548775	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:165548775G>A	ENST00000392717.2	-	14	3488	c.3484C>T	c.(3484-3486)Ctg>Ttg	p.L1162L	COBLL1_ENST00000194871.6_Silent_p.L1191L|COBLL1_ENST00000375458.2_Silent_p.L1086L|COBLL1_ENST00000409184.3_Silent_p.L1124L|COBLL1_ENST00000342193.4_Silent_p.L1124L			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	1162	WH2. {ECO:0000255|PROSITE- ProRule:PRU00406}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						ATTGCAGTCAGCAAACTCTGT	0.443																																					p.L1124L		Atlas-SNP	.											.	COBLL1	122	.	0			c.C3370T						.						105.0	98.0	101.0					2																	165548775		2203	4300	6503	SO:0001819	synonymous_variant	22837	exon13			CAGTCAGCAAACT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.3484C>T	chr2.hg19:g.165548775G>A		150.0	0.0		169.0	56.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	hg19																																																																																				.	.		0.443	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
TTN	7273	hgsc.bcm.edu	37	2	179569674	179569674	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:179569674C>A	ENST00000591111.1	-	102	28897	c.28673G>T	c.(28672-28674)aGg>aTg	p.R9558M	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R8631M|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R9875M			Q8WZ42	TITIN_HUMAN	titin	13643					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)			CCTCTCTGACCTCTCTATTTC	0.338																																					p.R9875M		Atlas-SNP	.											.	TTN	18412	.	0			c.G29624T						.						130.0	128.0	128.0					2																	179569674		1821	4090	5911	SO:0001583	missense	7273	exon104			TCTGACCTCTCTA	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.28673G>T	chr2.hg19:g.179569674C>A	ENSP00000465570:p.Arg9558Met	183.0	0.0		258.0	34.0	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	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	8.638	0.895281	0.17613	.	.	ENSG00000155657	ENST00000342992	T	0.62941	-0.01	5.99	4.85	0.62838	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.46852	0.1414	N	0.14661	0.345	0.80722	D	1	B	0.32425	0.371	B	0.36885	0.235	T	0.49969	-0.8882	9	0.87932	D	0	.	9.4026	0.38442	0.0:0.1451:0.0:0.8549	.	9558	Q8WZ42	TITIN_HUMAN	M	8631	ENSP00000343764:R8631M	ENSP00000343764:R8631M	R	-	2	0	TTN	179277919	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	0.957000	0.29215	1.102000	0.41551	-0.302000	0.09304	AGG	.	.		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
COL5A2	1290	hgsc.bcm.edu	37	2	189901361	189901361	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:189901361T>A	ENST00000374866.3	-	52	4368	c.4094A>T	c.(4093-4095)gAt>gTt	p.D1365V		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1365	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TCTGTTCATATCAAGACCATA	0.338																																					p.D1365V		Atlas-SNP	.											.	COL5A2	230	.	0			c.A4094T						.						83.0	75.0	78.0					2																	189901361		2203	4300	6503	SO:0001583	missense	1290	exon52			TTCATATCAAGAC	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.4094A>T	chr2.hg19:g.189901361T>A	ENSP00000364000:p.Asp1365Val	73.0	0.0		100.0	20.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.142661	0.57044	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	T	0.73047	-0.71	5.98	5.98	0.97165	Fibrillar collagen, C-terminal (3);	0.000000	0.53938	D	0.000053	T	0.78394	0.4276	L	0.54908	1.71	0.80722	D	1	D;D	0.61080	0.968;0.989	P;P	0.61003	0.757;0.882	T	0.74665	-0.3589	10	0.23302	T	0.38	.	16.4696	0.84102	0.0:0.0:0.0:1.0	.	1005;1365	Q5PR22;P05997	.;CO5A2_HUMAN	V	1365;1005	ENSP00000364000:D1365V	ENSP00000364000:D1365V	D	-	2	0	COL5A2	189609606	1.000000	0.71417	0.974000	0.42286	0.987000	0.75469	4.976000	0.63785	2.289000	0.77006	0.482000	0.46254	GAT	.	.		0.338	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
STAT4	6775	hgsc.bcm.edu	37	2	191898231	191898231	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:191898231C>T	ENST00000392320.2	-	20	2151	c.1837G>A	c.(1837-1839)Gac>Aac	p.D613N	AC067945.4_ENST00000456176.1_RNA|STAT4_ENST00000358470.4_Missense_Mutation_p.D613N|STAT4_ENST00000470708.1_5'Flank	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	613	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			TCAGAATGGTCCACCCAGGTG	0.373																																					p.D613N		Atlas-SNP	.											.	STAT4	85	.	0			c.G1837A						.						54.0	57.0	56.0					2																	191898231		2203	4300	6503	SO:0001583	missense	6775	exon20			AATGGTCCACCCA		CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"""SH2 domain containing"""	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.1837G>A	chr2.hg19:g.191898231C>T	ENSP00000376134:p.Asp613Asn	92.0	0.0		128.0	36.0	NM_001243835	Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	hg19	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.092704	0.76756	.	.	ENSG00000138378	ENST00000358470;ENST00000392320	D;D	0.89050	-2.46;-2.46	5.95	5.95	0.96441	SH2 motif (4);	0.047577	0.85682	D	0.000000	T	0.81597	0.4856	N	0.12182	0.205	0.80722	D	1	P;P;P	0.43938	0.801;0.684;0.822	B;B;B	0.40825	0.272;0.272;0.341	D	0.84977	0.0886	10	0.87932	D	0	-27.3247	15.9301	0.79651	0.1357:0.8643:0.0:0.0	.	522;613;613	Q53S87;B4DV04;Q14765	.;.;STAT4_HUMAN	N	613	ENSP00000351255:D613N;ENSP00000376134:D613N	ENSP00000351255:D613N	D	-	1	0	STAT4	191606476	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.945000	0.70226	2.821000	0.97095	0.650000	0.86243	GAC	.	.		0.373	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151	
CCDC150	284992	hgsc.bcm.edu	37	2	197521532	197521532	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:197521532A>T	ENST00000389175.4	+	3	487	c.352A>T	c.(352-354)Atc>Ttc	p.I118F	CCDC150_ENST00000472405.2_Missense_Mutation_p.I15F|CCDC150_ENST00000423093.2_Intron|CCDC150_ENST00000272831.7_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	118										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						GAAGATGAACATCTTTCGGCT	0.378																																					p.I118F		Atlas-SNP	.											.	CCDC150	96	.	0			c.A352T						.						107.0	104.0	105.0					2																	197521532		1866	4100	5966	SO:0001583	missense	284992	exon3			ATGAACATCTTTC		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.352A>T	chr2.hg19:g.197521532A>T	ENSP00000373827:p.Ile118Phe	62.0	0.0		98.0	26.0	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	hg19	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.696480	0.30142	.	.	ENSG00000144395	ENST00000389175;ENST00000536389;ENST00000472405	T;T	0.30448	1.53;1.53	4.93	4.93	0.64822	.	0.184719	0.38436	N	0.001687	T	0.48554	0.1506	M	0.65975	2.015	0.80722	D	1	P;D	0.76494	0.566;0.999	B;D	0.80764	0.15;0.994	T	0.44050	-0.9353	10	0.37606	T	0.19	-6.877	8.3768	0.32447	0.9113:0.0:0.0887:0.0	.	118;118	Q8NCX0;F5H6M2	CC150_HUMAN;.	F	118;118;15	ENSP00000373827:I118F;ENSP00000441149:I15F	ENSP00000373827:I118F	I	+	1	0	CCDC150	197229777	1.000000	0.71417	0.998000	0.56505	0.674000	0.39518	1.738000	0.38207	2.082000	0.62665	0.533000	0.62120	ATC	.	.		0.378	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539	
BMPR2	659	hgsc.bcm.edu	37	2	203332240	203332240	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:203332240A>G	ENST00000374580.4	+	3	786		c.e3-1		BMPR2_ENST00000479069.1_Splice_Site|BMPR2_ENST00000374574.2_Splice_Site	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)						activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						ATTGATTTATAGGATGTTGGT	0.348																																					.		Atlas-SNP	.											.	BMPR2	142	.	0			c.248-2A>G						.						97.0	88.0	91.0					2																	203332240		2203	4300	6503	SO:0001630	splice_region_variant	659	exon3			ATTTATAGGATGT	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.248-1A>G	chr2.hg19:g.203332240A>G		85.0	0.0		115.0	47.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Splice_Site	SNP	ENST00000374580.4	hg19	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	A	15.82	2.947200	0.53186	.	.	ENSG00000204217	ENST00000374580;ENST00000374574	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3775	0.74621	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BMPR2	203040485	1.000000	0.71417	0.968000	0.41197	0.575000	0.36095	7.715000	0.84713	2.037000	0.60232	0.533000	0.62120	.	.	.		0.348	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	Intron
UNC80	285175	hgsc.bcm.edu	37	2	210786230	210786230	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:210786230T>G	ENST00000439458.1	+	33	5232	c.5152T>G	c.(5152-5154)Ttt>Gtt	p.F1718V	UNC80_ENST00000272845.6_Missense_Mutation_p.F1713V	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	1718					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						ACAGAAATCCTTTTCAGCCCG	0.448																																					p.F1718V		Atlas-SNP	.											.	UNC80	280	.	0			c.T5152G						.						77.0	66.0	69.0					2																	210786230		692	1591	2283	SO:0001583	missense	285175	exon33			AAATCCTTTTCAG	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.5152T>G	chr2.hg19:g.210786230T>G	ENSP00000391088:p.Phe1718Val	110.0	0.0		146.0	17.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Missense_Mutation	SNP	ENST00000439458.1	hg19	CCDS46504.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.758182	0.89843	.	.	ENSG00000144406	ENST00000439458;ENST00000272845	T;T	0.31510	1.49;1.49	5.67	5.67	0.87782	.	0.120542	0.56097	D	0.000032	T	0.42314	0.1197	N	0.24115	0.695	0.80722	D	1	D	0.57899	0.981	D	0.69142	0.962	T	0.39800	-0.9596	10	0.66056	D	0.02	-17.8137	16.2002	0.82067	0.0:0.0:0.0:1.0	.	1718	Q8N2C7	UNC80_HUMAN	V	1718;1713	ENSP00000391088:F1718V;ENSP00000272845:F1713V	ENSP00000272845:F1713V	F	+	1	0	UNC80	210494475	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.299000	0.78831	2.285000	0.76669	0.528000	0.53228	TTT	.	.		0.448	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
IKZF2	22807	hgsc.bcm.edu	37	2	213872617	213872617	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:213872617C>G	ENST00000434687.1	-	9	1357	c.1048G>C	c.(1048-1050)Gtt>Ctt	p.V350L	AC079610.1_ENST00000415387.1_RNA|IKZF2_ENST00000342002.2_Missense_Mutation_p.V356L|IKZF2_ENST00000457361.1_Missense_Mutation_p.V350L|IKZF2_ENST00000413091.3_3'UTR|IKZF2_ENST00000374319.4_Missense_Mutation_p.V324L|IKZF2_ENST00000374327.4_Missense_Mutation_p.V205L|IKZF2_ENST00000421754.2_Missense_Mutation_p.V276L|IKZF2_ENST00000451136.2_Missense_Mutation_p.V278L			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	350					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		GAGCTTATAACTGGGGCCACT	0.493																																					p.V350L		Atlas-SNP	.											.	IKZF2	71	.	0			c.G1048C						.						93.0	85.0	88.0					2																	213872617		2203	4300	6503	SO:0001583	missense	22807	exon8			TTATAACTGGGGC	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13177	protein-coding gene	gene with protein product		606234	"""zinc finger protein, subfamily 1A, 2 (Helios)"""	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.1048G>C	chr2.hg19:g.213872617C>G	ENSP00000412869:p.Val350Leu	155.0	0.0		193.0	41.0	NM_016260	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Missense_Mutation	SNP	ENST00000434687.1	hg19	CCDS2395.1	.	.	.	.	.	.	.	.	.	.	C	13.38	2.221082	0.39201	.	.	ENSG00000030419	ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000374327;ENST00000542010	T;T;T;T;T;T;T	0.15603	3.17;3.14;3.17;3.21;3.08;3.22;2.41	6.08	6.08	0.98989	.	0.078533	0.53938	D	0.000052	T	0.34542	0.0901	M	0.77820	2.39	0.80722	D	1	B;P;P;P;P;P	0.48162	0.27;0.717;0.899;0.906;0.803;0.73	B;B;B;P;B;B	0.48571	0.095;0.243;0.419;0.582;0.17;0.205	T	0.03673	-1.1014	10	0.59425	D	0.04	-7.3459	18.844	0.92196	0.0:1.0:0.0:0.0	.	278;276;205;324;350;128	C9JCG7;C9JTM9;F5H8M1;Q9UKS7-2;Q9UKS7;Q96LD7	.;.;.;.;IKZF2_HUMAN;.	L	350;356;350;324;278;276;205;54	ENSP00000410447:V350L;ENSP00000342876:V356L;ENSP00000412869:V350L;ENSP00000363439:V324L;ENSP00000395203:V278L;ENSP00000399574:V276L;ENSP00000363447:V205L	ENSP00000342876:V356L	V	-	1	0	IKZF2	213580862	0.911000	0.30947	1.000000	0.80357	0.990000	0.78478	1.802000	0.38853	2.894000	0.99253	0.655000	0.94253	GTT	.	.		0.493	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260	
RUFY4	285180	hgsc.bcm.edu	37	2	218947924	218947924	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:218947924G>A	ENST00000344321.7	+	11	1965	c.1447G>A	c.(1447-1449)Gga>Aga	p.G483R	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000374155.3_Missense_Mutation_p.G503R	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	483							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGAGGAGCTTGGAGGGCAGCG	0.602																																					p.G483R		Atlas-SNP	.											.	RUFY4	59	.	0			c.G1447A						.						94.0	99.0	97.0					2																	218947924		2108	4224	6332	SO:0001583	missense	285180	exon11			GAGCTTGGAGGGC	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"""Zinc fingers, FYVE domain containing"""	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1447G>A	chr2.hg19:g.218947924G>A	ENSP00000345900:p.Gly483Arg	202.0	0.0		264.0	69.0	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	hg19		.	.	.	.	.	.	.	.	.	.	G	11.12	1.543943	0.27563	.	.	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.75367	-0.93;0.9	4.27	-0.116	0.13555	Zinc finger, FYVE/PHD-type (1);	0.995534	0.08141	N	0.991689	T	0.52240	0.1722	N	0.19112	0.55	0.09310	N	1	B	0.24618	0.107	B	0.19148	0.024	T	0.30297	-0.9983	10	0.18710	T	0.47	0.0021	3.2789	0.06908	0.3808:0.2105:0.4087:0.0	.	483	Q6ZNE9	RUFY4_HUMAN	R	483;503	ENSP00000345900:G483R;ENSP00000363270:G503R	ENSP00000345900:G483R	G	+	1	0	RUFY4	218656169	0.000000	0.05858	0.119000	0.21687	0.986000	0.74619	0.563000	0.23547	0.074000	0.16767	0.555000	0.69702	GGA	.	.		0.602	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
TUBA4A	7277	hgsc.bcm.edu	37	2	220116022	220116022	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:220116022C>G	ENST00000248437.4	-	4	572	c.399G>C	c.(397-399)caG>caC	p.Q133H	TUBA4B_ENST00000490341.1_RNA|TUBA4A_ENST00000498660.1_5'UTR|TUBA4A_ENST00000392088.2_Missense_Mutation_p.Q118H	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	133					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	CCAGGAAGCCCTGAAGTCCTG	0.547																																					p.Q133H		Atlas-SNP	.											.	TUBA4A	96	.	0			c.G399C						.						45.0	49.0	47.0					2																	220116022		2189	4299	6488	SO:0001583	missense	7277	exon4			GAAGCCCTGAAGT	AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"""Tubulins"""	12407	protein-coding gene	gene with protein product		191110	"""tubulin, alpha 1 (testis specific)"", ""tubulin, alpha 1"""	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.399G>C	chr2.hg19:g.220116022C>G	ENSP00000248437:p.Gln133His	84.0	0.0		111.0	10.0	NM_006000	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	hg19	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.672479	0.29693	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000427737;ENST00000456818;ENST00000447205	T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68	5.06	3.11	0.35812	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.87374	0.6161	H	0.96430	3.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89404	0.3698	10	0.87932	D	0	.	10.3719	0.44060	0.0:0.772:0.0:0.228	.	133	P68366	TBA4A_HUMAN	H	133;118;118;156;118	ENSP00000248437:Q133H;ENSP00000375938:Q118H;ENSP00000408194:Q118H;ENSP00000416992:Q156H;ENSP00000396061:Q118H	ENSP00000248437:Q133H	Q	-	3	2	TUBA4A	219824266	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.744000	0.26245	1.375000	0.46248	0.655000	0.94253	CAG	.	.		0.547	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000	
GIGYF2	26058	hgsc.bcm.edu	37	2	233710580	233710580	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:233710580G>A	ENST00000409547.1	+	28	3755	c.3444G>A	c.(3442-3444)acG>acA	p.T1148T	GIGYF2_ENST00000409196.3_Silent_p.T1142T|GIGYF2_ENST00000373563.4_Silent_p.T1148T|GIGYF2_ENST00000373566.3_Silent_p.T1170T|GIGYF2_ENST00000409480.1_Silent_p.T1170T|GIGYF2_ENST00000409451.3_Silent_p.T1169T	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1148					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CCCTTAATACGGCAAATaact	0.463																																					p.T1169T		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G3507A						.						83.0	79.0	80.0					2																	233710580		2203	4300	6503	SO:0001819	synonymous_variant	26058	exon28			TAATACGGCAAAT	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3444G>A	chr2.hg19:g.233710580G>A		94.0	0.0		171.0	26.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.		0.463	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
COL6A3	1293	hgsc.bcm.edu	37	2	238274558	238274558	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:238274558C>G	ENST00000295550.4	-	12	6073	c.5621G>C	c.(5620-5622)aGg>aCg	p.R1874T	COL6A3_ENST00000346358.4_Missense_Mutation_p.R1674T|COL6A3_ENST00000409809.1_Missense_Mutation_p.R1668T|COL6A3_ENST00000353578.4_Missense_Mutation_p.R1668T|COL6A3_ENST00000472056.1_Missense_Mutation_p.R1267T|COL6A3_ENST00000347401.3_Missense_Mutation_p.R1673T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1874	Nonhelical region.|VWFA 10. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GCAGCTGACCCTGTGCATCTG	0.597																																					p.R1874T		Atlas-SNP	.											.	COL6A3	608	.	0			c.G5621C						.						74.0	75.0	75.0					2																	238274558		2203	4300	6503	SO:0001583	missense	1293	exon12			CTGACCCTGTGCA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5621G>C	chr2.hg19:g.238274558C>G	ENSP00000295550:p.Arg1874Thr	46.0	0.0		61.0	17.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	3.575	-0.086856	0.07097	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25	5.34	2.48	0.30137	von Willebrand factor, type A (2);	0.384789	0.22024	N	0.065682	T	0.26085	0.0636	L	0.40543	1.245	0.09310	N	1	P;P;B	0.49090	0.863;0.919;0.094	B;P;B	0.46026	0.428;0.501;0.016	T	0.07102	-1.0790	10	0.16896	T	0.51	.	3.3595	0.07181	0.0:0.4537:0.2013:0.345	.	1267;1668;1874	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	T	1874;1673;1668;1267;1668;1674	ENSP00000295550:R1874T;ENSP00000315609:R1673T;ENSP00000315873:R1668T;ENSP00000418285:R1267T;ENSP00000386844:R1668T;ENSP00000295546:R1674T	ENSP00000295550:R1874T	R	-	2	0	COL6A3	237939297	0.000000	0.05858	0.002000	0.10522	0.037000	0.13140	0.820000	0.27323	0.720000	0.32209	0.655000	0.94253	AGG	.	.		0.597	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
SCLY	51540	hgsc.bcm.edu	37	2	238990418	238990418	+	Missense_Mutation	SNP	C	C	A	rs140009501		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr2:238990418C>A	ENST00000555827.1	+	5	617	c.553C>A	c.(553-555)Cgc>Agc	p.R185S	SCLY_ENST00000429612.2_Intron|SCLY_ENST00000422984.2_Missense_Mutation_p.R91S|SCLY_ENST00000254663.6_Missense_Mutation_p.R193S|SCLY_ENST00000373332.3_Missense_Mutation_p.R103S|SCLY_ENST00000409736.2_Missense_Mutation_p.R185S			Q96I15	SCLY_HUMAN	selenocysteine lyase	185					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		CGCGGCAGTCCGCCCGACCAC	0.577																																					p.R193S	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											.	SCLY	51	.	0			c.C577A						.						109.0	91.0	97.0					2																	238990418		2203	4300	6503	SO:0001583	missense	51540	exon5			GCAGTCCGCCCGA	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.553C>A	chr2.hg19:g.238990418C>A	ENSP00000450613:p.Arg185Ser	101.0	0.0		139.0	30.0	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.7|20.7	4.036739|4.036739	0.75617|0.75617	.|.	.|.	ENSG00000132330|ENSG00000132330	ENST00000437134|ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965	.|T;T;T;D;T;T;T	.|0.86097	.|2.01;2.01;1.59;-2.07;1.59;2.01;1.59	5.84|5.84	5.84|5.84	0.93424|0.93424	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91492|0.91492	0.7314|0.7314	M|M	0.77486|0.77486	2.375|2.375	0.80722|0.80722	D|D	1|1	.|D;D;P	.|0.60575	.|0.974;0.988;0.92	.|P;P;P	.|0.59012	.|0.731;0.85;0.527	D|D	0.91579|0.91579	0.5277|0.5277	5|10	.|0.59425	.|D	.|0.04	-17.0765|-17.0765	18.9105|18.9105	0.92483|0.92483	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|91;185;185	.|E7ESG3;Q96I15;Q96I15-2	.|.;SCLY_HUMAN;.	Q|S	28|193;185;103;99;185;91;15	.|ENSP00000254663:R193S;ENSP00000450613:R185S;ENSP00000362429:R103S;ENSP00000414165:R99S;ENSP00000387162:R185S;ENSP00000416865:R91S;ENSP00000414053:R15S	.|ENSP00000254663:R185S	P|R	+|+	2|1	0|0	SCLY|SCLY	238655157|238655157	1.000000|1.000000	0.71417|0.71417	0.957000|0.957000	0.39632|0.39632	0.064000|0.064000	0.16182|0.16182	3.095000|3.095000	0.50235|0.50235	2.764000|2.764000	0.94973|0.94973	0.655000|0.655000	0.94253|0.94253	CCG|CGC	.	C|1.000;T|0.000		0.577	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
GRM7	2917	hgsc.bcm.edu	37	3	7620822	7620822	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:7620822C>T	ENST00000357716.4	+	8	2503	c.2229C>T	c.(2227-2229)gcC>gcT	p.A743A	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000486284.1_Silent_p.A743A|GRM7_ENST00000389336.4_Silent_p.A743A|GRM7_ENST00000403881.1_Silent_p.A743A|GRM7_ENST00000402647.2_Silent_p.A743A	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	743					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						CTGAGCAAGCCAGAGGGGTTC	0.428																																					p.A743A		Atlas-SNP	.											.	GRM7	223	.	0			c.C2229T						.						126.0	112.0	117.0					3																	7620822		2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			GCAAGCCAGAGGG	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2229C>T	chr3.hg19:g.7620822C>T		225.0	0.0		192.0	44.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	hg19	CCDS43042.1																																																																																			.	.		0.428	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
BRPF1	7862	hgsc.bcm.edu	37	3	9776289	9776289	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:9776289G>A	ENST00000457855.1	+	1	476	c.465G>A	c.(463-465)gaG>gaA	p.E155E	BRPF1_ENST00000424362.1_Silent_p.E155E|BRPF1_ENST00000383829.2_Silent_p.E155E|BRPF1_ENST00000302054.3_Silent_p.E155E|BRPF1_ENST00000433861.2_Silent_p.E155E			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	155	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					AGAACAAGGAGAAGCGCAAGG	0.562																																					p.E155E		Atlas-SNP	.											.	BRPF1	104	.	0			c.G465A						.						80.0	79.0	79.0					3																	9776289		2203	4300	6503	SO:0001819	synonymous_variant	7862	exon2			CAAGGAGAAGCGC	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.465G>A	chr3.hg19:g.9776289G>A		245.0	0.0		215.0	37.0	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Silent	SNP	ENST00000457855.1	hg19	CCDS2575.1																																																																																			.	.		0.562	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694	
LRRC3B	116135	hgsc.bcm.edu	37	3	26751290	26751290	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:26751290T>G	ENST00000396641.2	+	2	719	c.127T>G	c.(127-129)Tct>Gct	p.S43A	LRRC3B_ENST00000417744.1_Missense_Mutation_p.S43A|LRRC3B_ENST00000456208.2_Missense_Mutation_p.S43A|AC114877.3_ENST00000446601.1_lincRNA	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	43	LRRNT.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						TTGTTCTTCCTCTGGGGGTTT	0.438																																					p.S43A		Atlas-SNP	.											.	LRRC3B	51	.	0			c.T127G						.						148.0	141.0	143.0					3																	26751290		2203	4300	6503	SO:0001583	missense	116135	exon2			TCTTCCTCTGGGG	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.127T>G	chr3.hg19:g.26751290T>G	ENSP00000379880:p.Ser43Ala	177.0	0.0		150.0	36.0	NM_052953	Q5M8T0	Missense_Mutation	SNP	ENST00000396641.2	hg19	CCDS2644.1	.	.	.	.	.	.	.	.	.	.	T	11.53	1.667181	0.29604	.	.	ENSG00000179796	ENST00000396641;ENST00000414619;ENST00000432040;ENST00000417744;ENST00000456208	T;T;T;T	0.62105	0.2;0.05;0.2;0.2	6.17	6.17	0.99709	Leucine-rich repeat-containing N-terminal (2);	0.159349	0.64402	D	0.000019	T	0.45418	0.1341	N	0.16307	0.4	0.42957	D	0.994393	B	0.10296	0.003	B	0.15052	0.012	T	0.39440	-0.9614	10	0.32370	T	0.25	-14.2951	11.1318	0.48351	0.1375:0.0:0.0:0.8625	.	43	Q96PB8	LRC3B_HUMAN	A	43	ENSP00000379880:S43A;ENSP00000398184:S43A;ENSP00000406370:S43A;ENSP00000394940:S43A	ENSP00000379880:S43A	S	+	1	0	LRRC3B	26726294	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.787000	0.38704	2.371000	0.80710	0.533000	0.62120	TCT	.	.		0.438	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953	
DUSP7	1849	hgsc.bcm.edu	37	3	52084943	52084943	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:52084943C>T	ENST00000495880.1	-	3	1331	c.1148G>A	c.(1147-1149)cGg>cAg	p.R383Q	DUSP7_ENST00000296483.6_Missense_Mutation_p.R332Q			Q16829	DUS7_HUMAN	dual specificity phosphatase 7	383					inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of MAP kinase activity (GO:0043407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)	p.R332Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCCCAGCGTCCGCTCAAAGTC	0.552																																					p.R383Q		Atlas-SNP	.											DUSP7,NS,carcinoma,0,1	DUSP7	34	.	1	Substitution - Missense(1)	kidney(1)	c.G1148A						.						157.0	130.0	139.0					3																	52084943		2203	4300	6503	SO:0001583	missense	1849	exon3			AGCGTCCGCTCAA	X93921	CCDS33766.1, CCDS33766.2	3p21	2011-06-09			ENSG00000164086	ENSG00000164086		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3073	protein-coding gene	gene with protein product		602749				8626780, 9205128	Standard	NM_001947		Approved	MKP-X, PYST2	uc003dct.3	Q16829	OTTHUMG00000157819	ENST00000495880.1:c.1148G>A	chr3.hg19:g.52084943C>T	ENSP00000417183:p.Arg383Gln	304.0	0.0		234.0	47.0	NM_001947	Q2M3J7|Q8NFJ0	Missense_Mutation	SNP	ENST00000495880.1	hg19	CCDS33766.2	.	.	.	.	.	.	.	.	.	.	c	19.45	3.829829	0.71258	.	.	ENSG00000164086	ENST00000495880;ENST00000296483	D;D	0.85773	-2.03;-2.03	5.75	4.89	0.63831	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.121832	0.56097	D	0.000031	T	0.73418	0.3584	N	0.25485	0.75	0.80722	D	1	P	0.46656	0.882	B	0.33254	0.16	T	0.74542	-0.3631	10	0.37606	T	0.19	.	14.4234	0.67200	0.0:0.9285:0.0:0.0715	.	383	Q16829	DUS7_HUMAN	Q	383;332	ENSP00000417183:R383Q;ENSP00000296483:R332Q	ENSP00000296483:R332Q	R	-	2	0	DUSP7	52059983	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.083000	0.71326	1.448000	0.47680	-0.148000	0.13756	CGG	.	.		0.552	DUSP7-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349697.1	NM_001947	
BAP1	8314	hgsc.bcm.edu	37	3	52441334	52441334	+	Splice_Site	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:52441334T>A	ENST00000460680.1	-	7	909		c.e7-2		BAP1_ENST00000296288.5_Splice_Site	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)						anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGCTCGGGCCTGGGGAAAAAC	0.582			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															.	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.,1	BAP1	371	.	1	Unknown(1)	pleura(1)	c.438-2A>T						.						74.0	78.0	77.0					3																	52441334		2203	4300	6503	SO:0001630	splice_region_variant	8314	exon8			CGGGCCTGGGGAA	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.438-2A>T	chr3.hg19:g.52441334T>A		106.0	0.0		98.0	60.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Splice_Site	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675559	0.67928	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000470173	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.023	0.80512	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BAP1	52416374	1.000000	0.71417	0.984000	0.44739	0.752000	0.42762	8.005000	0.88553	2.193000	0.70182	0.533000	0.62120	.	.	.		0.582	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Intron
CADPS	8618	hgsc.bcm.edu	37	3	62522190	62522191	+	Missense_Mutation	DNP	TG	TG	AT			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:62522190_62522191TG>AT	ENST00000383710.4	-	12	2381_2382	c.2032_2033CA>AT	c.(2032-2034)CAc>ATc	p.H678I	CADPS_ENST00000357948.3_Missense_Mutation_p.H678I|CADPS_ENST00000283269.9_Missense_Mutation_p.H678I	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	678					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		GAGGGAAGCGTGGTCAAAGTTA	0.396																																					p.H678L|p.H678N		Atlas-SNP	.											.	CADPS	387	.	0			c.A2033T|c.C2032A						.																																			SO:0001583	missense	8618	exon12			GAAGCGTGGTCAA|AAGCGTGGTCAAA	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2032_2033delinsAT	chr3.hg19:g.62522190_62522191delinsAT	ENSP00000373215:p.His678Ile	211.0|210.0	0.0		135.0	62.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1																																																																																			.	.		0.396	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64640083	64640083	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:64640083C>T	ENST00000498707.1	-	8	1604	c.1262G>A	c.(1261-1263)aGt>aAt	p.S421N	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.S393N|ADAMTS9_ENST00000459780.1_Missense_Mutation_p.S421N	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	421	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ACTATCTTCACTAATAGAACA	0.398																																					p.S421N		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G1262A						.						155.0	166.0	162.0					3																	64640083		2203	4300	6503	SO:0001583	missense	56999	exon8			TCTTCACTAATAG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.1262G>A	chr3.hg19:g.64640083C>T	ENSP00000418735:p.Ser421Asn	192.0	0.0		176.0	31.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.911770	0.33721	.	.	ENSG00000163638	ENST00000295903;ENST00000498707;ENST00000459780	D;D;D	0.86164	-2.08;-2.08;-2.08	5.66	4.78	0.61160	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.105461	0.64402	D	0.000009	T	0.76227	0.3958	N	0.02960	-0.455	0.44736	D	0.997738	P;B;B;P	0.39737	0.685;0.124;0.423;0.549	P;B;B;B	0.45406	0.479;0.105;0.126;0.329	T	0.74740	-0.3563	10	0.10636	T	0.68	.	16.7235	0.85416	0.0:0.8706:0.1294:0.0	.	393;421;421;421	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	N	393;421;421	ENSP00000295903:S393N;ENSP00000418735:S421N;ENSP00000419217:S421N	ENSP00000295903:S393N	S	-	2	0	ADAMTS9	64615123	1.000000	0.71417	0.962000	0.40283	0.755000	0.42902	4.906000	0.63293	1.384000	0.46424	-0.165000	0.13383	AGT	.	.		0.398	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
HTR1F	3355	hgsc.bcm.edu	37	3	88040703	88040703	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:88040703C>T	ENST00000319595.4	+	1	858	c.804C>T	c.(802-804)ctC>ctT	p.L268L		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	268					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(8;0.147)	Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00664)	Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Ketamine(DB01221)|Methysergide(DB00247)|Mianserin(DB06148)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Zolmitriptan(DB00315)	TGAGAAGTCTCAGGTCTGAAT	0.403																																					p.L268L		Atlas-SNP	.											.	HTR1F	66	.	0			c.C804T						.						61.0	66.0	64.0					3																	88040703		2203	4300	6503	SO:0001819	synonymous_variant	3355	exon2			AAGTCTCAGGTCT	L05597	CCDS2920.1	3p12	2012-08-08	2012-02-03		ENSG00000179097	ENSG00000179097		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5292	protein-coding gene	gene with protein product		182134	"""5-hydroxytryptamine (serotonin) receptor 1F"""			8384716, 8380639	Standard	NM_000866		Approved	HTR1EL, 5-HT1F	uc003dqr.2	P30939	OTTHUMG00000159008	ENST00000319595.4:c.804C>T	chr3.hg19:g.88040703C>T		59.0	0.0		50.0	8.0	NM_000866		Silent	SNP	ENST00000319595.4	hg19	CCDS2920.1																																																																																			.	.		0.403	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866	
STX19	415117	hgsc.bcm.edu	37	3	93733261	93733261	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:93733261A>C	ENST00000315099.2	-	2	1109	c.853T>G	c.(853-855)Tgt>Ggt	p.C285G	ARL13B_ENST00000303097.7_Intron|ARL13B_ENST00000486562.1_Intron|ARL13B_ENST00000539730.1_Intron|ARL13B_ENST00000394222.3_Intron|ARL13B_ENST00000471138.1_Intron|ARL13B_ENST00000535334.1_Intron	NM_001001850.2	NP_001001850.1	Q8N4C7	STX19_HUMAN	syntaxin 19	285	Cys-rich.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(4)|prostate(1)	9						CAGCACCAACAACACAGTACT	0.318																																					p.C285G		Atlas-SNP	.											.	STX19	19	.	0			c.T853G						.						49.0	47.0	48.0					3																	93733261		2203	4299	6502	SO:0001583	missense	415117	exon2			ACCAACAACACAG	AF461456	CCDS33793.1	3q11	2005-12-30			ENSG00000178750	ENSG00000178750			19300	protein-coding gene	gene with protein product							Standard	NM_001001850		Approved	MGC21382	uc003drh.1	Q8N4C7	OTTHUMG00000159013	ENST00000315099.2:c.853T>G	chr3.hg19:g.93733261A>C	ENSP00000320679:p.Cys285Gly	46.0	0.0		62.0	4.0	NM_001001850		Missense_Mutation	SNP	ENST00000315099.2	hg19	CCDS33793.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.841483	0.51057	.	.	ENSG00000178750	ENST00000315099	T	0.52057	0.68	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.70509	0.3232	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.75258	-0.3381	10	0.72032	D	0.01	-11.8478	15.7642	0.78114	1.0:0.0:0.0:0.0	.	285	Q8N4C7	STX19_HUMAN	G	285	ENSP00000320679:C285G	ENSP00000320679:C285G	C	-	1	0	STX19	95215951	1.000000	0.71417	0.997000	0.53966	0.924000	0.55760	8.678000	0.91211	2.260000	0.74910	0.528000	0.53228	TGT	.	.		0.318	STX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352909.1	NM_001001850	
MYH15	22989	hgsc.bcm.edu	37	3	108178291	108178291	+	Missense_Mutation	SNP	G	G	T	rs372985354		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:108178291G>T	ENST00000273353.3	-	19	2054	c.1998C>A	c.(1996-1998)aaC>aaA	p.N666K	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	666	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						ATTTATTCAGGTTTTCCTAAA	0.328																																					p.N666K		Atlas-SNP	.											.	MYH15	223	.	0			c.C1998A						.						91.0	84.0	86.0					3																	108178291		1830	4079	5909	SO:0001583	missense	22989	exon19			ATTCAGGTTTTCC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1998C>A	chr3.hg19:g.108178291G>T	ENSP00000273353:p.Asn666Lys	61.0	0.0		71.0	6.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.746075	0.69418	.	.	ENSG00000144821	ENST00000273353	T	0.71817	-0.6	5.67	0.301	0.15781	Myosin head, motor domain (2);	.	.	.	.	T	0.79902	0.4526	H	0.95294	3.65	0.33015	D	0.528001	P	0.45957	0.869	P	0.49561	0.615	T	0.80612	-0.1305	9	0.87932	D	0	.	4.0982	0.10002	0.532:0.0:0.2831:0.1848	.	666	Q9Y2K3	MYH15_HUMAN	K	666	ENSP00000273353:N666K	ENSP00000273353:N666K	N	-	3	2	MYH15	109660981	0.997000	0.39634	0.990000	0.47175	0.974000	0.67602	0.654000	0.24918	0.344000	0.23847	0.655000	0.94253	AAC	.	.		0.328	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
MORC1	27136	hgsc.bcm.edu	37	3	108833252	108833252	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:108833252G>A	ENST00000483760.1	-	2	141	c.98C>T	c.(97-99)gCt>gTt	p.A33V	MORC1_ENST00000232603.5_Missense_Mutation_p.A33V					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						CAGCAATTCAGCCAGTGCTCC	0.348																																					p.A33V		Atlas-SNP	.											.	MORC1	211	.	0			c.C98T						.						101.0	98.0	99.0					3																	108833252		2203	4300	6503	SO:0001583	missense	27136	exon2			AATTCAGCCAGTG	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.98C>T	chr3.hg19:g.108833252G>A	ENSP00000417282:p.Ala33Val	109.0	0.0		93.0	12.0	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.3	4.265123	0.80358	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	D;D	0.95307	-3.67;-3.67	4.51	4.51	0.55191	ATPase-like, ATP-binding domain (3);	0.000000	0.46145	D	0.000312	D	0.96623	0.8898	M	0.75264	2.295	0.42169	D	0.991635	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96872	0.9640	10	0.87932	D	0	-14.6246	12.8941	0.58089	0.0:0.0:1.0:0.0	.	33;33	E7ERX1;Q86VD1	.;MORC1_HUMAN	V	33	ENSP00000232603:A33V;ENSP00000417282:A33V	ENSP00000232603:A33V	A	-	2	0	MORC1	110315942	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.459000	0.60102	2.478000	0.83669	0.563000	0.77884	GCT	.	.		0.348	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
KIAA1407	57577	hgsc.bcm.edu	37	3	113720448	113720448	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:113720448C>A	ENST00000295878.3	-	13	2303	c.2157G>T	c.(2155-2157)aaG>aaT	p.K719N	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	719										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TAACCATTTTCTTCAGTCTCT	0.448																																					p.K719N		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G2157T						.						267.0	246.0	253.0					3																	113720448		2203	4300	6503	SO:0001583	missense	57577	exon13			CATTTTCTTCAGT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2157G>T	chr3.hg19:g.113720448C>A	ENSP00000295878:p.Lys719Asn	323.0	0.0		330.0	45.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.179453	0.38511	.	.	ENSG00000163617	ENST00000295878	T	0.32988	1.43	5.19	4.32	0.51571	.	0.424673	0.27841	N	0.017626	T	0.37625	0.1010	M	0.63428	1.95	0.80722	D	1	D	0.53462	0.96	P	0.50537	0.643	T	0.19224	-1.0312	10	0.51188	T	0.08	.	8.1568	0.31173	0.0:0.8225:0.0:0.1775	.	719	Q8NCU4	K1407_HUMAN	N	719	ENSP00000295878:K719N	ENSP00000295878:K719N	K	-	3	2	KIAA1407	115203138	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	1.561000	0.36342	1.557000	0.49525	0.650000	0.86243	AAG	.	.		0.448	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
C3orf30	152405	hgsc.bcm.edu	37	3	118867060	118867060	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:118867060T>C	ENST00000295622.1	+	2	1472	c.1432T>C	c.(1432-1434)Tat>Cat	p.Y478H	RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000354673.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	478										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		AGGAAAGGGTTATCATATACG	0.368																																					p.Y478H		Atlas-SNP	.											.	C3orf30	64	.	0			c.T1432C						.						84.0	90.0	88.0					3																	118867060		2203	4300	6503	SO:0001583	missense	152405	exon2			AAGGGTTATCATA	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1432T>C	chr3.hg19:g.118867060T>C	ENSP00000295622:p.Tyr478His	98.0	0.0		134.0	18.0	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	hg19	CCDS2984.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.769112	0.31320	.	.	ENSG00000163424	ENST00000295622;ENST00000470341	T	0.12672	2.66	3.71	1.33	0.21861	.	1.417150	0.04833	N	0.439075	T	0.18635	0.0447	L	0.36672	1.1	0.09310	N	1	P;D	0.59767	0.845;0.986	B;P	0.53861	0.41;0.736	T	0.17868	-1.0355	10	0.34782	T	0.22	0.0439	5.2338	0.15436	0.0:0.2404:0.0:0.7596	.	478;478	E9PFE5;Q96M34	.;CC030_HUMAN	H	478	ENSP00000295622:Y478H	ENSP00000295622:Y478H	Y	+	1	0	C3orf30	120349750	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.027000	0.13621	0.281000	0.22233	0.533000	0.62120	TAT	.	.		0.368	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
DNAJB8	165721	hgsc.bcm.edu	37	3	128181553	128181553	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:128181553A>C	ENST00000469083.1	-	2	3093	c.536T>G	c.(535-537)tTc>tGc	p.F179C	DNAJB8_ENST00000319153.3_Missense_Mutation_p.F179C|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	179	Ser-rich.				chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CACCGACTTGAACCCCGAGCT	0.617																																					p.F179C		Atlas-SNP	.											.	DNAJB8	34	.	0			c.T536G						.						84.0	81.0	82.0					3																	128181553		2203	4300	6503	SO:0001583	missense	165721	exon3			GACTTGAACCCCG		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"""Heat shock proteins / DNAJ (HSP40)"""	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.536T>G	chr3.hg19:g.128181553A>C	ENSP00000417418:p.Phe179Cys	136.0	0.0		171.0	22.0	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	hg19	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217198	0.39201	.	.	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.52754	0.65;0.65	4.75	3.44	0.39384	.	0.840609	0.10715	N	0.642473	T	0.60117	0.2244	M	0.85945	2.785	0.53688	D	0.999976	D	0.59767	0.986	P	0.49708	0.62	T	0.64210	-0.6461	10	0.49607	T	0.09	.	10.4522	0.44528	0.8439:0.0:0.0:0.1561	.	179	Q8NHS0	DNJB8_HUMAN	C	179	ENSP00000417418:F179C;ENSP00000316053:F179C	ENSP00000316053:F179C	F	-	2	0	DNAJB8	129664243	0.996000	0.38824	0.992000	0.48379	0.165000	0.22458	2.423000	0.44705	1.772000	0.52199	0.459000	0.35465	TTC	.	.		0.617	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
CEP70	80321	hgsc.bcm.edu	37	3	138256157	138256157	+	Silent	SNP	C	C	A	rs372060625		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:138256157C>A	ENST00000264982.3	-	7	764	c.498G>T	c.(496-498)acG>acT	p.T166T	CEP70_ENST00000481834.1_Silent_p.T166T|CEP70_ENST00000542237.1_Silent_p.T146T|CEP70_ENST00000464035.1_Silent_p.T166T|CEP70_ENST00000489254.1_Silent_p.T14T|CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000484888.1_Silent_p.T166T	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	166					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.T166T(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						CTTCTTGCTCCGTTCGTTTTT	0.343																																					p.T166T		Atlas-SNP	.											CEP70,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CEP70	51	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G498T						.						117.0	105.0	109.0					3																	138256157		2202	4300	6502	SO:0001819	synonymous_variant	80321	exon7			TTGCTCCGTTCGT	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.498G>T	chr3.hg19:g.138256157C>A		97.0	0.0		92.0	8.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Silent	SNP	ENST00000264982.3	hg19	CCDS3102.1																																																																																			.	.		0.343	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
GRK7	131890	hgsc.bcm.edu	37	3	141497352	141497352	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:141497352A>T	ENST00000264952.2	+	1	363	c.226A>T	c.(226-228)Aca>Tca	p.T76S		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	76	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CTTCCTAGCCACAGTGCCCAC	0.657																																					p.T76S		Atlas-SNP	.											.	GRK7	65	.	0			c.A226T						.						26.0	25.0	25.0					3																	141497352		2201	4292	6493	SO:0001583	missense	131890	exon1			CTAGCCACAGTGC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.226A>T	chr3.hg19:g.141497352A>T	ENSP00000264952:p.Thr76Ser	97.0	0.0		82.0	11.0	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	hg19	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	A	5.777	0.327664	0.10956	.	.	ENSG00000114124	ENST00000264952	T	0.02258	4.37	4.5	2.02	0.26589	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.277794	0.36665	N	0.002479	T	0.02230	0.0069	L	0.47716	1.5	0.31971	N	0.607198	B	0.18461	0.028	B	0.15052	0.012	T	0.31308	-0.9948	10	0.24483	T	0.36	-6.5237	6.0404	0.19730	0.7748:0.0:0.0804:0.1448	.	76	Q8WTQ7	GRK7_HUMAN	S	76	ENSP00000264952:T76S	ENSP00000264952:T76S	T	+	1	0	GRK7	142980042	0.989000	0.36119	0.551000	0.28230	0.123000	0.20343	1.878000	0.39608	0.113000	0.18004	0.533000	0.62120	ACA	.	.		0.657	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
IGSF10	285313	hgsc.bcm.edu	37	3	151161336	151161336	+	Missense_Mutation	SNP	G	G	T	rs367812916	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:151161336G>T	ENST00000282466.3	-	5	5398	c.5399C>A	c.(5398-5400)aCg>aAg	p.T1800K	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1800	Ig-like C2-type 4.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCCGTCAACCGTCACCACAGC	0.507																																					p.T1800K		Atlas-SNP	.											.	IGSF10	279	.	0			c.C5399A						.						101.0	89.0	93.0					3																	151161336		2203	4300	6503	SO:0001583	missense	285313	exon5			TCAACCGTCACCA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5399C>A	chr3.hg19:g.151161336G>T	ENSP00000282466:p.Thr1800Lys	357.0	0.0		348.0	58.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.481930	0.00163	.	.	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.66815	-0.23	5.26	3.29	0.37713	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.135403	0.32769	N	0.005673	T	0.44561	0.1299	N	0.24115	0.695	0.26731	N	0.970595	B	0.12013	0.005	B	0.19946	0.027	T	0.18808	-1.0325	9	.	.	.	.	2.5263	0.04692	0.1013:0.1253:0.3843:0.3892	.	1800	Q6WRI0	IGS10_HUMAN	K	1800;427	ENSP00000282466:T1800K	.	T	-	2	0	IGSF10	152644026	0.074000	0.21230	0.366000	0.25914	0.026000	0.11368	2.357000	0.44125	0.558000	0.29135	-0.186000	0.12905	ACG	.	.		0.507	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
SLC33A1	9197	hgsc.bcm.edu	37	3	155571758	155571758	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:155571758C>T	ENST00000392845.3	-	1	409	c.29G>A	c.(28-30)aGc>aAc	p.S10N	SLC33A1_ENST00000359479.3_Missense_Mutation_p.S10N|SLC33A1_ENST00000460729.1_5'Flank			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	10					acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTGCCGGCTGCTGTCCTTGTG	0.612																																					p.S10N		Atlas-SNP	.											.	SLC33A1	57	.	0			c.G29A						.						25.0	30.0	28.0					3																	155571758		2187	4268	6455	SO:0001583	missense	9197	exon1			CGGCTGCTGTCCT	D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"""Solute carriers"""	95	protein-coding gene	gene with protein product		603690	"""acetyl-Coenzyme A transporter"", ""spastic paraplegia 42 (autosomal dominant)"""	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.29G>A	chr3.hg19:g.155571758C>T	ENSP00000376587:p.Ser10Asn	188.0	0.0		177.0	79.0	NM_004733	B2R5Q2|D3DNK4	Missense_Mutation	SNP	ENST00000392845.3	hg19	CCDS3173.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.777797	0.31502	.	.	ENSG00000169359	ENST00000392845;ENST00000359479	T;T	0.72615	-0.67;-0.67	4.95	-5.36	0.02689	Major facilitator superfamily domain, general substrate transporter (1);	0.631198	0.18395	N	0.142532	T	0.51890	0.1701	N	0.24115	0.695	0.24318	N	0.99506	B	0.02656	0.0	B	0.04013	0.001	T	0.12656	-1.0539	10	0.19147	T	0.46	0.0017	18.1138	0.89543	0.0:0.9078:0.0:0.0922	.	10	O00400	ACATN_HUMAN	N	10	ENSP00000376587:S10N;ENSP00000352456:S10N	ENSP00000352456:S10N	S	-	2	0	SLC33A1	157054452	0.830000	0.29337	0.620000	0.29132	0.833000	0.47200	-0.557000	0.05985	-1.339000	0.02230	-0.355000	0.07637	AGC	.	.		0.612	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3	NM_004733	
FNDC3B	64778	hgsc.bcm.edu	37	3	172048416	172048416	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:172048416A>T	ENST00000336824.4	+	13	1564	c.1465A>T	c.(1465-1467)Aca>Tca	p.T489S	FNDC3B_ENST00000416957.1_Missense_Mutation_p.T489S|FNDC3B_ENST00000415807.2_Missense_Mutation_p.T489S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	489	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGCTGGCATCACATGGGTCAC	0.478																																					p.T489S		Atlas-SNP	.											.	FNDC3B	118	.	0			c.A1465T						.						133.0	110.0	118.0					3																	172048416		2203	4300	6503	SO:0001583	missense	64778	exon13			GGCATCACATGGG	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1465A>T	chr3.hg19:g.172048416A>T	ENSP00000338523:p.Thr489Ser	197.0	0.0		218.0	38.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.453217	0.43531	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.59502	0.26;0.26;0.26	5.12	5.12	0.69794	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.048827	0.85682	D	0.000000	T	0.45013	0.1321	N	0.17082	0.46	0.80722	D	1	B;B	0.16396	0.008;0.017	B;B	0.28305	0.005;0.088	T	0.34527	-0.9825	10	0.32370	T	0.25	-15.0524	15.2444	0.73497	1.0:0.0:0.0:0.0	.	489;489	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	S	489	ENSP00000411242:T489S;ENSP00000338523:T489S;ENSP00000389094:T489S	ENSP00000338523:T489S	T	+	1	0	FNDC3B	173531110	1.000000	0.71417	0.999000	0.59377	0.697000	0.40408	6.621000	0.74228	2.078000	0.62432	0.533000	0.62120	ACA	.	.		0.478	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
GNB4	59345	hgsc.bcm.edu	37	3	179119095	179119095	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:179119095C>G	ENST00000232564.3	-	10	1215	c.929G>C	c.(928-930)gGt>gCt	p.G310A	AC007620.3_ENST00000598857.1_RNA|AC007620.3_ENST00000600539.1_RNA|AC007620.3_ENST00000495081.2_RNA|GNB4_ENST00000468623.1_Missense_Mutation_p.G310A	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	310					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			GTTGTCATGACCAGCAAGGAC	0.383																																					p.G310A	Melanoma(105;1405 1491 7265 20440 33721)	Atlas-SNP	.											.	GNB4	37	.	0			c.G929C						.						62.0	57.0	58.0					3																	179119095		2203	4300	6503	SO:0001583	missense	59345	exon10			TCATGACCAGCAA	AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"""WD repeat domain containing"""	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.929G>C	chr3.hg19:g.179119095C>G	ENSP00000232564:p.Gly310Ala	241.0	0.0		228.0	31.0	NM_021629	B3KMH5|D3DNR8	Missense_Mutation	SNP	ENST00000232564.3	hg19	CCDS3230.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446597	0.63178	.	.	ENSG00000114450	ENST00000232564;ENST00000466899;ENST00000468623	T;T	0.67698	-0.28;-0.28	4.92	4.92	0.64577	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78735	0.4330	L	0.50993	1.605	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.80103	-0.1522	10	0.59425	D	0.04	-12.3924	18.5626	0.91105	0.0:1.0:0.0:0.0	.	310	Q9HAV0	GBB4_HUMAN	A	310;160;310	ENSP00000232564:G310A;ENSP00000419693:G310A	ENSP00000232564:G310A	G	-	2	0	GNB4	180601789	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.702000	0.84576	2.436000	0.82500	0.644000	0.83932	GGT	.	.		0.383	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629	
MCCC1	56922	hgsc.bcm.edu	37	3	182788806	182788806	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr3:182788806T>A	ENST00000265594.4	-	7	888	c.742A>T	c.(742-744)Aag>Tag	p.K248*	MCCC1_ENST00000492597.1_Nonsense_Mutation_p.K139*|MCCC1_ENST00000539926.1_Nonsense_Mutation_p.K113*	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	248	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	TCTACAAACTTCTCGATCAGC	0.338																																					p.K248X		Atlas-SNP	.											.	MCCC1	87	.	0			c.A742T						.						89.0	83.0	85.0					3																	182788806		2203	4300	6503	SO:0001587	stop_gained	56922	exon7			CAAACTTCTCGAT	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.742A>T	chr3.hg19:g.182788806T>A	ENSP00000265594:p.Lys248*	150.0	0.0		181.0	26.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Nonsense_Mutation	SNP	ENST00000265594.4	hg19	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	T	36	5.743537	0.96873	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585;ENST00000541636	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.0863	0.81056	0.0:0.0:0.0:1.0	.	.	.	.	X	248;139;98;113;201;201;139	.	ENSP00000265594:K248X	K	-	1	0	MCCC1	184271500	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	7.567000	0.82357	2.251000	0.74343	0.528000	0.53228	AAG	.	.		0.338	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
ZNF518B	85460	hgsc.bcm.edu	37	4	10445461	10445461	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:10445461C>T	ENST00000326756.3	-	3	2930	c.2492G>A	c.(2491-2493)gGg>gAg	p.G831E		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	831					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						ATCTATTGGCCCCCTTTCACT	0.463																																					p.G831E		Atlas-SNP	.											.	ZNF518B	116	.	0			c.G2492A						.						91.0	89.0	90.0					4																	10445461		2203	4300	6503	SO:0001583	missense	85460	exon3			ATTGGCCCCCTTT	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.2492G>A	chr4.hg19:g.10445461C>T	ENSP00000317614:p.Gly831Glu	127.0	0.0		136.0	27.0	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	hg19	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	C	11.04	1.521364	0.27211	.	.	ENSG00000178163	ENST00000326756	T	0.01406	4.93	6.02	0.754	0.18410	.	0.625953	0.15390	N	0.264864	T	0.01092	0.0036	L	0.33485	1.01	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49322	-0.8952	10	0.02654	T	1	-8.3179	7.3401	0.26632	0.0:0.4118:0.0:0.5882	.	831	Q9C0D4	Z518B_HUMAN	E	831	ENSP00000317614:G831E	ENSP00000317614:G831E	G	-	2	0	ZNF518B	10054559	0.001000	0.12720	0.001000	0.08648	0.143000	0.21401	0.838000	0.27572	0.160000	0.19432	-0.140000	0.14226	GGG	.	.		0.463	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
FAM114A1	92689	hgsc.bcm.edu	37	4	38910313	38910313	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:38910313A>G	ENST00000358869.2	+	7	934	c.758A>G	c.(757-759)aAg>aGg	p.K253R	FAM114A1_ENST00000515037.1_Missense_Mutation_p.K46R	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	253						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						AAGCGGACCAAGACGCTCATG	0.388																																					p.K253R		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A758G						.						81.0	78.0	79.0					4																	38910313		2203	4300	6503	SO:0001583	missense	92689	exon7			GGACCAAGACGCT		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.758A>G	chr4.hg19:g.38910313A>G	ENSP00000351740:p.Lys253Arg	141.0	0.0		147.0	22.0	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	hg19	CCDS3447.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.009511	0.93346	.	.	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.42900	0.96;0.96	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.53965	0.1829	L	0.37697	1.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.43523	-0.9386	10	0.17832	T	0.49	-26.8338	16.8222	0.85835	1.0:0.0:0.0:0.0	.	253	Q8IWE2	NXP20_HUMAN	R	46;253;46	ENSP00000424115:K46R;ENSP00000351740:K253R	ENSP00000347569:K46R	K	+	2	0	FAM114A1	38586708	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.388	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
GABRA4	2557	hgsc.bcm.edu	37	4	46967002	46967002	+	Silent	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:46967002A>T	ENST00000264318.3	-	8	2101	c.1119T>A	c.(1117-1119)ccT>ccA	p.P373P		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	373					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	GAGGGGCTTCAGGATGCTTCT	0.408																																					p.P373P	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.T1119A						.						80.0	86.0	84.0					4																	46967002		2202	4299	6501	SO:0001819	synonymous_variant	2557	exon8			GGCTTCAGGATGC		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1119T>A	chr4.hg19:g.46967002A>T		128.0	0.0		115.0	12.0	NM_000809	Q8IYR7	Silent	SNP	ENST00000264318.3	hg19	CCDS3473.1																																																																																			.	.		0.408	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
FRYL	285527	hgsc.bcm.edu	37	4	48607809	48607809	+	Silent	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:48607809T>A	ENST00000503238.1	-	8	782	c.783A>T	c.(781-783)atA>atT	p.I261I	FRYL_ENST00000506685.1_5'UTR|FRYL_ENST00000507711.1_Silent_p.I261I|FRYL_ENST00000537810.1_Silent_p.I261I|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Silent_p.I261I			O94915	FRYL_HUMAN	FRY-like	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GTGCATGTTTTATATCTTTAT	0.313																																					p.I261I		Atlas-SNP	.											.	FRYL	242	.	0			c.A783T						.						110.0	113.0	112.0					4																	48607809		1824	4090	5914	SO:0001819	synonymous_variant	285527	exon11			ATGTTTTATATCT	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.783A>T	chr4.hg19:g.48607809T>A		149.0	0.0		142.0	32.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.		0.313	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
LPHN3	23284	hgsc.bcm.edu	37	4	62800605	62800605	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:62800605T>A	ENST00000514591.1	+	13	2285	c.1956T>A	c.(1954-1956)aaT>aaA	p.N652K	LPHN3_ENST00000512091.2_Missense_Mutation_p.N652K|LPHN3_ENST00000511324.1_Missense_Mutation_p.N720K|LPHN3_ENST00000504896.1_Missense_Mutation_p.N652K|LPHN3_ENST00000514157.1_Missense_Mutation_p.N652K|LPHN3_ENST00000506746.1_Missense_Mutation_p.N720K|LPHN3_ENST00000509896.1_Missense_Mutation_p.N720K|LPHN3_ENST00000506700.1_Missense_Mutation_p.N652K|LPHN3_ENST00000514996.1_Missense_Mutation_p.N652K|LPHN3_ENST00000508693.1_Missense_Mutation_p.N720K|LPHN3_ENST00000508946.1_Missense_Mutation_p.N652K|LPHN3_ENST00000506720.1_Missense_Mutation_p.N720K|LPHN3_ENST00000507164.1_Missense_Mutation_p.N720K|LPHN3_ENST00000507625.1_Missense_Mutation_p.N720K|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000545650.1_Missense_Mutation_p.N652K			Q9HAR2	LPHN3_HUMAN	latrophilin 3	639					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AAGCTTTGAATGCATGGAGAG	0.478																																					p.N652K		Atlas-SNP	.											.	LPHN3	800	.	0			c.T1956A						.						86.0	89.0	88.0					4																	62800605		2058	4215	6273	SO:0001583	missense	23284	exon11			TTTGAATGCATGG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1956T>A	chr4.hg19:g.62800605T>A	ENSP00000422533:p.Asn652Lys	210.0	0.0		238.0	65.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.289|4.289	0.052855|0.052855	0.08291|0.08291	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000502815|ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.08634	.|3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07;3.07	5.43|5.43	3.01|3.01	0.34805|0.34805	.|Domain of unknown function DUF3497 (1);	.|0.276650	.|0.42172	.|D	.|0.000742	T|T	0.02304|0.02304	0.0071|0.0071	N|N	0.01576|0.01576	-0.805|-0.805	0.39293|0.39293	D|D	0.964778|0.964778	.|B;B;B	.|0.11235	.|0.002;0.003;0.004	.|B;B;B	.|0.11329	.|0.006;0.006;0.002	T|T	0.41070|0.41070	-0.9529|-0.9529	5|10	.|0.10636	.|T	.|0.68	.|.	4.8759|4.8759	0.13656|0.13656	0.1267:0.2102:0.0:0.6631|0.1267:0.2102:0.0:0.6631	.|.	.|652;639;652	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	S|K	110|652;652;720;720;652;639;652;639;652;720;720;720;652;652;652;720;720;652	.|ENSP00000423388:N652K;ENSP00000422533:N652K;ENSP00000423787:N720K;ENSP00000425033:N720K;ENSP00000424120:N652K;ENSP00000439831:N652K;ENSP00000421476:N720K;ENSP00000424030:N720K;ENSP00000421372:N720K;ENSP00000425201:N652K;ENSP00000423434:N652K;ENSP00000421627:N652K;ENSP00000420931:N720K;ENSP00000425884:N720K;ENSP00000424258:N652K	.|ENSP00000280009:N652K	C|N	+|+	1|3	0|2	LPHN3|LPHN3	62483200|62483200	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.965000|0.965000	0.64279|0.64279	0.175000|0.175000	0.16762|0.16762	0.511000|0.511000	0.28236|0.28236	-0.263000|-0.263000	0.10527|0.10527	TGC|AAT	.	.		0.478	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
ARHGAP24	83478	hgsc.bcm.edu	37	4	86852134	86852134	+	Intron	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:86852134A>T	ENST00000395184.1	+	4	857				ARHGAP24_ENST00000503995.1_Intron|ARHGAP24_ENST00000264343.4_Silent_p.S17S|ARHGAP24_ENST00000395183.2_Intron	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24						activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CCTTAGCCTCAACTCCTTTCA	0.438																																					p.S17S		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A51T						.						82.0	88.0	86.0					4																	86852134		2203	4300	6503	SO:0001627	intron_variant	83478	exon1			AGCCTCAACTCCT	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.391+7211A>T	chr4.hg19:g.86852134A>T		159.0	0.0		96.0	21.0	NM_031305	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	hg19	CCDS34025.1																																																																																			.	.		0.438	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
SEC24B	10427	hgsc.bcm.edu	37	4	110442311	110442311	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:110442311C>T	ENST00000265175.5	+	13	2339	c.2284C>T	c.(2284-2286)Cta>Tta	p.L762L	SEC24B_ENST00000504968.2_Silent_p.L792L|SEC24B_ENST00000399100.2_Silent_p.L727L	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	762					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		ACTTGTGAATCTATATGAAAG	0.244																																					p.L762L		Atlas-SNP	.											.	SEC24B	186	.	0			c.C2284T						.						62.0	58.0	59.0					4																	110442311		1782	4042	5824	SO:0001819	synonymous_variant	10427	exon13			GTGAATCTATATG	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.2284C>T	chr4.hg19:g.110442311C>T		112.0	0.0		62.0	13.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	hg19	CCDS47124.1																																																																																			.	.		0.244	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
USP53	54532	hgsc.bcm.edu	37	4	120192951	120192951	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:120192951A>T	ENST00000274030.6	+	16	3115	c.1936A>T	c.(1936-1938)Atg>Ttg	p.M646L	USP53_ENST00000450251.1_Missense_Mutation_p.M646L	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						TGAAGATGAAATGAAGCAGGA	0.363																																					p.M646L		Atlas-SNP	.											.	USP53	69	.	0			c.A1936T						.						117.0	105.0	109.0					4																	120192951		1838	4092	5930	SO:0001583	missense	54532	exon15			GATGAAATGAAGC	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1936A>T	chr4.hg19:g.120192951A>T	ENSP00000274030:p.Met646Leu	132.0	0.0		101.0	16.0	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	hg19	CCDS43265.1	.	.	.	.	.	.	.	.	.	.	A	7.268	0.606516	0.14002	.	.	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.40225	1.04;1.04	5.58	-3.41	0.04839	.	1.734410	0.02229	N	0.064775	T	0.25082	0.0609	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.11916	-1.0568	10	0.11485	T	0.65	1.203	6.2006	0.20573	0.3925:0.2442:0.3634:0.0	.	646	Q70EK8	UBP53_HUMAN	L	646	ENSP00000274030:M646L;ENSP00000409906:M646L	ENSP00000274030:M646L	M	+	1	0	USP53	120412399	0.434000	0.25570	0.486000	0.27416	0.980000	0.70556	0.359000	0.20233	-0.191000	0.10448	-0.376000	0.06991	ATG	.	.		0.363	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
GRIA2	2891	hgsc.bcm.edu	37	4	158257592	158257592	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:158257592T>A	ENST00000264426.9	+	11	1816	c.1537T>A	c.(1537-1539)Tca>Aca	p.S513T	GRIA2_ENST00000449365.1_Missense_Mutation_p.S466T|GRIA2_ENST00000296526.7_Missense_Mutation_p.S513T|GRIA2_ENST00000507898.1_Missense_Mutation_p.S466T|GRIA2_ENST00000393815.2_Missense_Mutation_p.S466T	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	513					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GATTGACTTCTCAAAGCCCTT	0.408																																					p.S513T		Atlas-SNP	.											.	GRIA2	358	.	0			c.T1537A						.						168.0	167.0	167.0					4																	158257592		2203	4300	6503	SO:0001583	missense	2891	exon11			GACTTCTCAAAGC		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1537T>A	chr4.hg19:g.158257592T>A	ENSP00000264426:p.Ser513Thr	164.0	0.0		144.0	45.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.493758	0.64186	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.46	5.46	0.80206	Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.42017	0.1184	N	0.05554	-0.025	0.80722	D	1	P;B;D	0.54964	0.92;0.292;0.969	B;B;D	0.63381	0.444;0.097;0.914	T	0.44667	-0.9313	10	0.31617	T	0.26	.	15.8205	0.78638	0.0:0.0:0.0:1.0	.	513;513;466	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	T	466;466;513;513;466	ENSP00000426845:S466T;ENSP00000377403:S466T;ENSP00000296526:S513T;ENSP00000264426:S513T;ENSP00000389837:S466T	ENSP00000264426:S513T	S	+	1	0	GRIA2	158477042	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.196000	0.70406	0.533000	0.62120	TCA	.	.		0.408	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
NAF1	92345	hgsc.bcm.edu	37	4	164061471	164061471	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:164061471T>C	ENST00000274054.2	-	5	975	c.782A>G	c.(781-783)cAc>cGc	p.H261R	NAF1_ENST00000509434.1_5'UTR|NAF1_ENST00000422287.2_Missense_Mutation_p.H261R	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	261					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				ACTCTCAATGTGATCTGAAGA	0.299																																					p.H261R		Atlas-SNP	.											.	NAF1	69	.	0			c.A782G						.						84.0	92.0	90.0					4																	164061471		2203	4292	6495	SO:0001583	missense	92345	exon5			TCAATGTGATCTG		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.782A>G	chr4.hg19:g.164061471T>C	ENSP00000274054:p.His261Arg	52.0	0.0		55.0	10.0	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	hg19	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311775	0.81358	.	.	ENSG00000145414	ENST00000422287;ENST00000274054	T;T	0.32515	1.48;1.45	5.68	5.68	0.88126	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.235594	0.43747	D	0.000528	T	0.47002	0.1422	M	0.65975	2.015	0.46458	D	0.999053	P;D	0.54047	0.897;0.964	P;P	0.57057	0.498;0.812	T	0.33317	-0.9873	10	0.21540	T	0.41	-15.0885	15.1134	0.72380	0.0:0.0:0.0:1.0	.	261;261	E9PAZ2;Q96HR8	.;NAF1_HUMAN	R	261	ENSP00000408963:H261R;ENSP00000274054:H261R	ENSP00000274054:H261R	H	-	2	0	NAF1	164280921	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.880000	0.75578	2.175000	0.68902	0.533000	0.62120	CAC	.	.		0.299	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	
TLL1	7092	hgsc.bcm.edu	37	4	166976353	166976353	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:166976353T>C	ENST00000061240.2	+	13	2297	c.1650T>C	c.(1648-1650)aaT>aaC	p.N550N	RNA5SP170_ENST00000517150.1_RNA|TLL1_ENST00000507499.1_Silent_p.N573N	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	550	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		CTACCTCCAATACTTTGTGGA	0.378																																					p.N550N		Atlas-SNP	.											.	TLL1	194	.	0			c.T1650C						.						122.0	119.0	120.0					4																	166976353		2203	4300	6503	SO:0001819	synonymous_variant	7092	exon13			CTCCAATACTTTG	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.1650T>C	chr4.hg19:g.166976353T>C		112.0	0.0		69.0	14.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	hg19	CCDS3811.1																																																																																			.	.		0.378	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
ASB5	140458	hgsc.bcm.edu	37	4	177190077	177190077	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:177190077T>C	ENST00000296525.3	-	1	296	c.183A>G	c.(181-183)gtA>gtG	p.V61V		NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	61					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GTCCTTGGGTTACTCCATAAA	0.393																																					p.V61V		Atlas-SNP	.											.	ASB5	88	.	0			c.A183G						.						105.0	92.0	96.0					4																	177190077		2203	4300	6503	SO:0001819	synonymous_variant	140458	exon1			TTGGGTTACTCCA	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"""Ankyrin repeat domain containing"""	17180	protein-coding gene	gene with protein product		615050	"""ankyrin repeat and SOCS box-containing 5"""				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.183A>G	chr4.hg19:g.177190077T>C		120.0	0.0		91.0	14.0	NM_080874	Q8N7B5	Silent	SNP	ENST00000296525.3	hg19	CCDS3827.1																																																																																			.	.		0.393	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1		
CCDC110	256309	hgsc.bcm.edu	37	4	186366663	186366663	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:186366663T>A	ENST00000307588.3	-	7	2570	c.2495A>T	c.(2494-2496)cAt>cTt	p.H832L	C4orf47_ENST00000378850.4_Intron|CCDC110_ENST00000393540.3_Missense_Mutation_p.H795L	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	832						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		ATCCTAATGATGCTTGAGAGT	0.308																																					p.H832L		Atlas-SNP	.											.	CCDC110	78	.	0			c.A2495T						.						94.0	94.0	94.0					4																	186366663		2203	4300	6503	SO:0001583	missense	256309	exon7			TAATGATGCTTGA	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.2495A>T	chr4.hg19:g.186366663T>A	ENSP00000306776:p.His832Leu	33.0	0.0		31.0	7.0	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	hg19	CCDS3843.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.012950	0.54468	.	.	ENSG00000168491	ENST00000393540;ENST00000307588	T;T	0.07021	3.23;3.24	3.11	-1.6	0.08426	.	2.526390	0.02211	N	0.063204	T	0.08980	0.0222	L	0.40543	1.245	0.09310	N	1	B;B	0.21606	0.058;0.058	B;B	0.17098	0.017;0.017	T	0.41342	-0.9514	10	0.87932	D	0	9.5423	7.001	0.24809	0.0:0.4395:0.0:0.5605	.	795;832	Q8TBZ0-2;Q8TBZ0	.;CC110_HUMAN	L	795;832	ENSP00000377172:H795L;ENSP00000306776:H832L	ENSP00000306776:H832L	H	-	2	0	CCDC110	186603657	0.000000	0.05858	0.000000	0.03702	0.402000	0.30811	-1.131000	0.03238	-0.389000	0.07786	0.383000	0.25322	CAT	.	.		0.308	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
MTNR1A	4543	hgsc.bcm.edu	37	4	187455096	187455096	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr4:187455096C>T	ENST00000307161.5	-	2	1001	c.800G>A	c.(799-801)aGc>aAc	p.S267N	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	267					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	AGGCACCATGCTGGCGGGGTC	0.502																																					p.S267N		Atlas-SNP	.											.	MTNR1A	46	.	0			c.G800A						.						73.0	79.0	77.0					4																	187455096		2203	4300	6503	SO:0001583	missense	4543	exon2			ACCATGCTGGCGG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.800G>A	chr4.hg19:g.187455096C>T	ENSP00000302811:p.Ser267Asn	113.0	0.0		129.0	32.0	NM_005958	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	hg19	CCDS3848.1	.	.	.	.	.	.	.	.	.	.	C	0.029	-1.347024	0.01266	.	.	ENSG00000168412	ENST00000307161	T	0.71934	-0.61	4.71	-3.51	0.04696	GPCR, rhodopsin-like superfamily (1);	1.129860	0.06353	N	0.710224	T	0.59115	0.2170	L	0.42581	1.335	0.09310	N	1	B	0.02656	0.0	B	0.12837	0.008	T	0.41270	-0.9518	10	0.23302	T	0.38	-4.4854	9.5902	0.39541	0.0:0.2529:0.4968:0.2503	.	267	P48039	MTR1A_HUMAN	N	267	ENSP00000302811:S267N	ENSP00000302811:S267N	S	-	2	0	MTNR1A	187692090	0.000000	0.05858	0.009000	0.14445	0.004000	0.04260	-0.404000	0.07205	-0.907000	0.03862	-1.224000	0.01588	AGC	.	.		0.502	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
ADCY2	108	hgsc.bcm.edu	37	5	7743819	7743819	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:7743819T>C	ENST00000338316.4	+	15	1999	c.1910T>C	c.(1909-1911)cTc>cCc	p.L637P	ADCY2_ENST00000537121.1_Missense_Mutation_p.L457P|RP11-711G10.1_ENST00000514105.2_RNA	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	637					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GCTGCGTTTCTCTTGCTGGCC	0.483																																					p.L637P		Atlas-SNP	.											.	ADCY2	337	.	0			c.T1910C						.						373.0	332.0	346.0					5																	7743819		2203	4300	6503	SO:0001583	missense	108	exon15			CGTTTCTCTTGCT	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1910T>C	chr5.hg19:g.7743819T>C	ENSP00000342952:p.Leu637Pro	260.0	0.0		250.0	47.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	T	9.737	1.163866	0.21538	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;D	0.83419	-1.24;-1.72	5.48	5.48	0.80851	.	0.064498	0.64402	D	0.000011	D	0.86167	0.5868	M	0.71581	2.175	0.58432	D	0.999999	P;B	0.45474	0.859;0.003	P;B	0.49708	0.62;0.006	D	0.87327	0.2322	10	0.59425	D	0.04	.	13.3916	0.60827	0.0:0.0:0.0:1.0	.	457;637	B7Z2C1;Q08462	.;ADCY2_HUMAN	P	637;470;457	ENSP00000342952:L637P;ENSP00000444803:L457P	ENSP00000342952:L637P	L	+	2	0	ADCY2	7796819	0.999000	0.42202	0.298000	0.25002	0.266000	0.26442	5.187000	0.65087	2.213000	0.71641	0.454000	0.30748	CTC	.	.		0.483	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
ANKRA2	57763	hgsc.bcm.edu	37	5	72857022	72857022	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:72857022T>C	ENST00000296785.3	-	3	1039	c.381A>G	c.(379-381)aaA>aaG	p.K127K		NM_023039.4	NP_075526.1	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2	127						cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	low-density lipoprotein particle binding (GO:0030169)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		Lung NSC(167;0.0378)|Ovarian(174;0.0908)		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)		TGGTTGACTGTTTTATGGGTG	0.398																																					p.K127K		Atlas-SNP	.											.	ANKRA2	23	.	0			c.A381G						.						311.0	279.0	290.0					5																	72857022		2203	4300	6503	SO:0001819	synonymous_variant	57763	exon3			TGACTGTTTTATG	AA442702	CCDS4020.1	5q12-q13	2013-01-10			ENSG00000164331	ENSG00000164331		"""Ankyrin repeat domain containing"""	13208	protein-coding gene	gene with protein product		605787				10965114	Standard	NM_023039		Approved		uc003kcu.2	Q9H9E1	OTTHUMG00000102030	ENST00000296785.3:c.381A>G	chr5.hg19:g.72857022T>C		216.0	0.0		241.0	25.0	NM_023039		Silent	SNP	ENST00000296785.3	hg19	CCDS4020.1																																																																																			.	.		0.398	ANKRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219814.2	NM_023039	
AP3B1	8546	hgsc.bcm.edu	37	5	77409598	77409598	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:77409598T>C	ENST00000255194.6	-	19	2402	c.2227A>G	c.(2227-2229)Aac>Gac	p.N743D	AP3B1_ENST00000519295.1_Missense_Mutation_p.N694D	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	743	Glu/Ser-rich.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GCTTTTGAGTTCCTCTTGGCT	0.433									Hermansky-Pudlak syndrome																												p.N743D		Atlas-SNP	.											.	AP3B1	94	.	0			c.A2227G						.						190.0	174.0	180.0					5																	77409598		2203	4300	6503	SO:0001583	missense	8546	exon19	Familial Cancer Database	HPS, HPS1-8	TTGAGTTCCTCTT	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2227A>G	chr5.hg19:g.77409598T>C	ENSP00000255194:p.Asn743Asp	84.0	0.0		66.0	16.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	3.780	-0.045885	0.07452	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.13538	2.58;2.58	5.92	4.75	0.60458	.	1.063530	0.07119	N	0.843528	T	0.10294	0.0252	N	0.22421	0.69	0.09310	N	1	B	0.19817	0.039	B	0.16722	0.016	T	0.37641	-0.9697	10	0.08381	T	0.77	-3.3181	10.549	0.45077	0.0:0.0728:0.0:0.9272	.	743	O00203	AP3B1_HUMAN	D	743;694;743	ENSP00000255194:N743D;ENSP00000430597:N694D	ENSP00000255194:N743D	N	-	1	0	AP3B1	77445354	0.017000	0.18338	0.004000	0.12327	0.755000	0.42902	2.013000	0.40942	1.066000	0.40716	0.459000	0.35465	AAC	.	.		0.433	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
MCTP1	79772	hgsc.bcm.edu	37	5	94114816	94114816	+	Splice_Site	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:94114816T>A	ENST00000515393.1	-	19	2608	c.2609A>T	c.(2608-2610)aAg>aTg	p.K870M	MCTP1_ENST00000312216.8_Splice_Site_p.K649M|MCTP1_ENST00000429576.2_Splice_Site_p.K563M|MCTP1_ENST00000505078.1_Splice_Site_p.K386M|MCTP1_ENST00000514040.1_5'UTR	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	870					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		GATAATTACCTTGTCATCTTT	0.423																																					p.K870M		Atlas-SNP	.											.	MCTP1	110	.	0			c.A2609T						.						184.0	142.0	156.0					5																	94114816		2203	4300	6503	SO:0001630	splice_region_variant	79772	exon19			ATTACCTTGTCAT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2610+1A>T	chr5.hg19:g.94114816T>A		186.0	0.0		234.0	36.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Missense_Mutation	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084013	0.76642	.	.	ENSG00000175471	ENST00000515393;ENST00000429576;ENST00000505078;ENST00000312216;ENST00000508509	T;T;T;T;T	0.78924	-1.22;-1.04;-0.18;-1.11;-0.93	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.87989	0.6317	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.988	D	0.89320	0.3639	10	0.72032	D	0.01	-16.3989	15.7739	0.78193	0.0:0.0:0.0:1.0	.	870;563;649	Q6DN14;Q6DN14-3;Q6DN14-2	MCTP1_HUMAN;.;.	M	870;563;386;649;590	ENSP00000424126:K870M;ENSP00000391639:K563M;ENSP00000426417:K386M;ENSP00000308957:K649M;ENSP00000423410:K590M	ENSP00000308957:K649M	K	-	2	0	MCTP1	94140572	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.165000	0.77544	2.367000	0.80283	0.528000	0.53228	AAG	.	.		0.423	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	Missense_Mutation
FAM81B	153643	hgsc.bcm.edu	37	5	94749823	94749823	+	Missense_Mutation	SNP	G	G	T	rs202064996		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:94749823G>T	ENST00000283357.5	+	4	512	c.466G>T	c.(466-468)Gcc>Tcc	p.A156S		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	156						nucleus (GO:0005634)		p.A156T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		GGAATCGCTCGCCAGGAAGTT	0.458																																					p.A156S		Atlas-SNP	.											FAM81B,NS,carcinoma,0,1	FAM81B	51	.	1	Substitution - Missense(1)	large_intestine(1)	c.G466T						.						94.0	95.0	95.0					5																	94749823		1977	4164	6141	SO:0001583	missense	153643	exon4			TCGCTCGCCAGGA		CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.466G>T	chr5.hg19:g.94749823G>T	ENSP00000283357:p.Ala156Ser	158.0	0.0		189.0	36.0	NM_152548		Missense_Mutation	SNP	ENST00000283357.5	hg19	CCDS43341.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399513	0.62177	.	.	ENSG00000153347	ENST00000283357	T	0.21932	1.98	5.53	3.72	0.42706	.	0.057016	0.64402	D	0.000002	T	0.37999	0.1024	M	0.66939	2.045	0.34388	D	0.693884	D	0.71674	0.998	P	0.61533	0.89	T	0.50039	-0.8874	10	0.48119	T	0.1	-9.6175	11.8194	0.52230	0.1296:0.0:0.8704:0.0	.	156	Q96LP2	FA81B_HUMAN	S	156	ENSP00000283357:A156S	ENSP00000283357:A156S	A	+	1	0	FAM81B	94775579	1.000000	0.71417	0.985000	0.45067	0.379000	0.30106	3.689000	0.54706	2.602000	0.87976	0.650000	0.86243	GCC	.	G|1.000;A|0.000		0.458	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548	
CHD1	1105	hgsc.bcm.edu	37	5	98212136	98212136	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:98212136T>C	ENST00000284049.3	-	23	3513	c.3364A>G	c.(3364-3366)Aat>Gat	p.N1122D		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1122					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	CCTTTAATATTCTCCCGAGGA	0.403																																					p.N1122D		Atlas-SNP	.											.	CHD1	137	.	0			c.A3364G						.						216.0	217.0	216.0					5																	98212136		2203	4300	6503	SO:0001583	missense	1105	exon23			TAATATTCTCCCG	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.3364A>G	chr5.hg19:g.98212136T>C	ENSP00000284049:p.Asn1122Asp	96.0	0.0		107.0	28.0	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.272766	0.40194	.	.	ENSG00000153922	ENST00000284049	D	0.89485	-2.52	5.14	5.14	0.70334	.	0.209202	0.22250	U	0.062567	D	0.85340	0.5674	L	0.48642	1.525	0.58432	D	0.999999	P	0.38863	0.65	B	0.39660	0.306	T	0.82575	-0.0389	10	0.12430	T	0.62	.	15.2607	0.73621	0.0:0.0:0.0:1.0	.	1122	O14646	CHD1_HUMAN	D	1122	ENSP00000284049:N1122D	ENSP00000284049:N1122D	N	-	1	0	CHD1	98240036	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.955000	0.70306	2.058000	0.61347	0.528000	0.53228	AAT	.	.		0.403	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
SEMA6A	57556	hgsc.bcm.edu	37	5	115811300	115811300	+	Splice_Site	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:115811300C>G	ENST00000343348.6	-	16	2437		c.e16-1		CTB-118N6.3_ENST00000507558.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA|SEMA6A_ENST00000257414.8_Splice_Site|SEMA6A_ENST00000282394.6_Splice_Site|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000510263.1_Splice_Site	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A						apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		AAAAGTCAGTCTTTTAAAAAA	0.383																																					.		Atlas-SNP	.											.	SEMA6A	93	.	0			c.1650-1G>C						.						50.0	46.0	47.0					5																	115811300		1874	4107	5981	SO:0001630	splice_region_variant	57556	exon17			GTCAGTCTTTTAA	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.1650-1G>C	chr5.hg19:g.115811300C>G		70.0	0.0		80.0	8.0	NM_020796	Q9P2H9	Splice_Site	SNP	ENST00000343348.6	hg19	CCDS47256.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.570226	0.86542	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000515129;ENST00000282394;ENST00000510263	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4745	0.99168	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA6A	115839199	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	7.242000	0.78210	2.941000	0.99782	0.655000	0.94253	.	.	.		0.383	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	Intron
ZNF608	57507	hgsc.bcm.edu	37	5	123983011	123983011	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:123983011A>G	ENST00000306315.5	-	4	3501	c.3066T>C	c.(3064-3066)agT>agC	p.S1022S	ZNF608_ENST00000513985.1_5'Flank|ZNF608_ENST00000504926.1_Silent_p.S595S	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1022							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		GCGTGCTCCCACTATTTCCAG	0.468																																					p.S1022S		Atlas-SNP	.											.	ZNF608	117	.	0			c.T3066C						.						166.0	159.0	161.0					5																	123983011		2203	4300	6503	SO:0001819	synonymous_variant	57507	exon4			GCTCCCACTATTT	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"""Zinc fingers, C2H2-type"""	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.3066T>C	chr5.hg19:g.123983011A>G		161.0	0.0		170.0	31.0	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	hg19	CCDS34219.1																																																																																			.	.		0.468	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
JADE2	23338	hgsc.bcm.edu	37	5	133914456	133914456	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:133914456C>T	ENST00000282605.4	+	12	2040	c.1954C>T	c.(1954-1956)Cca>Tca	p.P652S	PHF15_ENST00000395003.1_Missense_Mutation_p.P608S|PHF15_ENST00000361895.2_Missense_Mutation_p.P609S|PHF15_ENST00000402835.1_3'UTR																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAAACCACCACCACCACCACC	0.662																																					p.P608S		Atlas-SNP	.											.	PHF15	60	.	0			c.C1822T						.						38.0	41.0	40.0					5																	133914456		2203	4299	6502	SO:0001583	missense	23338	exon11			CCACCACCACCAC																												ENST00000282605.4:c.1954C>T	chr5.hg19:g.133914456C>T	ENSP00000282605:p.Pro652Ser	92.0	0.0		74.0	19.0	NM_015288		Missense_Mutation	SNP	ENST00000282605.4	hg19		.	.	.	.	.	.	.	.	.	.	c	1.629	-0.519539	0.04171	.	.	ENSG00000043143	ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000395003	T;T;T	0.40476	1.03;1.05;1.05	2.62	2.62	0.31277	.	1.120060	0.06720	N	0.774630	T	0.16171	0.0389	N	0.02011	-0.69	0.22693	N	0.998845	B;B;P	0.41673	0.421;0.231;0.759	B;B;B	0.37267	0.109;0.037;0.245	T	0.02020	-1.1228	10	0.07813	T	0.8	.	9.2958	0.37815	0.0:1.0:0.0:0.0	.	608;609;668	Q9NQC1;D3DQA3;B3KPL2	JADE2_HUMAN;.;.	S	668;652;609;609;608	ENSP00000282605:P652S;ENSP00000354425:P609S;ENSP00000378451:P608S	ENSP00000282605:P652S	P	+	1	0	PHF15	133942355	0.025000	0.19082	0.137000	0.22149	0.184000	0.23303	0.399000	0.20916	1.401000	0.46761	0.306000	0.20318	CCA	.	.		0.662	PHF15-003	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251170.1		
DDX46	9879	hgsc.bcm.edu	37	5	134121190	134121190	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:134121190C>G	ENST00000354283.4	+	11	1513	c.1378C>G	c.(1378-1380)Cag>Gag	p.Q460E	DDX46_ENST00000509178.1_3'UTR|DDX46_ENST00000452510.2_Missense_Mutation_p.Q460E			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	460	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACTGGCTTTACAGATTACTAA	0.398																																					p.Q460E	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.C1378G						.						153.0	154.0	154.0					5																	134121190		2203	4300	6503	SO:0001583	missense	9879	exon11			GCTTTACAGATTA		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"""DEAD-boxes"""	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1378C>G	chr5.hg19:g.134121190C>G	ENSP00000346236:p.Gln460Glu	88.0	0.0		134.0	11.0	NM_014829	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.671964	0.88348	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	D;D	0.81996	-1.56;-1.56	5.79	5.79	0.91817	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95943	0.8679	H	0.99740	4.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97669	1.0165	10	0.87932	D	0	-18.3815	20.0281	0.97530	0.0:1.0:0.0:0.0	.	460	Q7L014	DDX46_HUMAN	E	460	ENSP00000416534:Q460E;ENSP00000346236:Q460E	ENSP00000346236:Q460E	Q	+	1	0	DDX46	134149089	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.805000	0.86005	2.727000	0.93392	0.655000	0.94253	CAG	.	.		0.398	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829	
WNT8A	7478	hgsc.bcm.edu	37	5	137426301	137426301	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:137426301G>C	ENST00000398754.1	+	6	600	c.595G>C	c.(595-597)Gct>Cct	p.A199P	WNT8A_ENST00000506684.1_Missense_Mutation_p.A217P	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	199					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GCTGCAGCTGGCTGAATTCCG	0.522																																					p.A199P		Atlas-SNP	.											.	WNT8A	36	.	0			c.G595C						.						47.0	46.0	46.0					5																	137426301		1937	4144	6081	SO:0001583	missense	7478	exon6			CAGCTGGCTGAAT	AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"""Wingless-type MMTV integration sites"""	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.595G>C	chr5.hg19:g.137426301G>C	ENSP00000381739:p.Ala199Pro	124.0	0.0		144.0	17.0	NM_058244	Q96S51	Missense_Mutation	SNP	ENST00000398754.1	hg19	CCDS43368.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.570448	0.28003	.	.	ENSG00000061492	ENST00000506684;ENST00000504809;ENST00000398754	T;T;T	0.74842	-0.88;-0.88;-0.88	4.89	4.89	0.63831	.	0.168053	0.51477	D	0.000084	T	0.58119	0.2100	N	0.04820	-0.15	0.80722	D	1	B;B;P	0.40250	0.18;0.18;0.709	B;B;B	0.42593	0.174;0.174;0.392	T	0.58109	-0.7694	10	0.12103	T	0.63	.	18.2498	0.89998	0.0:0.0:1.0:0.0	.	217;217;199	D6RF47;D6RF94;Q9H1J5	.;.;WNT8A_HUMAN	P	217;217;199	ENSP00000426653:A217P;ENSP00000424809:A217P;ENSP00000381739:A199P	ENSP00000354726:A199P	A	+	1	0	WNT8A	137454200	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.214000	0.42853	2.537000	0.85549	0.557000	0.71058	GCT	.	.		0.522	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244	
PSD2	84249	hgsc.bcm.edu	37	5	139219614	139219614	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:139219614G>A	ENST00000274710.3	+	14	2176	c.1971G>A	c.(1969-1971)gaG>gaA	p.E657E		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	657					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTTGCAGGAGGAGCAACTGC	0.547																																					p.E657E		Atlas-SNP	.											.	PSD2	88	.	0			c.G1971A						.						82.0	76.0	78.0					5																	139219614		2203	4300	6503	SO:0001819	synonymous_variant	84249	exon14			GCAGGAGGAGCAA	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"""Pleckstrin homology (PH) domain containing"""	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1971G>A	chr5.hg19:g.139219614G>A		173.0	0.0		159.0	18.0	NM_032289	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	hg19	CCDS4216.1																																																																																			.	.		0.547	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289	
NRG2	9542	hgsc.bcm.edu	37	5	139239488	139239488	+	Intron	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:139239488C>T	ENST00000361474.1	-	6	1414				NRG2_ENST00000541337.1_Intron|NRG2_ENST00000545385.1_Intron|NRG2_ENST00000358522.3_Missense_Mutation_p.G394E|NRG2_ENST00000289422.7_Missense_Mutation_p.G400E|NRG2_ENST00000340391.3_Intron|NRG2_ENST00000289409.4_Intron|NRG2_ENST00000394770.1_Intron	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2						embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAATTCAAATCCAAGGTGCTC	0.552																																					p.G400E		Atlas-SNP	.											.	NRG2	69	.	0			c.G1199A						.						47.0	51.0	50.0					5																	139239488		1938	4157	6095	SO:0001627	intron_variant	9542	exon6			TCAAATCCAAGGT		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.1190-4125G>A	chr5.hg19:g.139239488C>T		213.0	0.0		244.0	32.0	NM_013982		Missense_Mutation	SNP	ENST00000361474.1	hg19	CCDS4217.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.92|17.92	3.507888|3.507888	0.64410|0.64410	.|.	.|.	ENSG00000158458|ENSG00000158458	ENST00000544729|ENST00000289422;ENST00000358522	.|T;T	.|0.73681	.|-0.63;-0.77	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|.	.|.	.|.	.|.	T|T	0.57125|0.57125	0.2032|0.2032	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|B;P	.|0.39696	.|0.007;0.683	.|B;B	.|0.34385	.|0.001;0.181	T|T	0.63985|0.63985	-0.6513|-0.6513	6|9	0.87932|0.46703	D|T	0|0.11	.|.	19.0293|19.0293	0.92948|0.92948	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|394;400	.|O14511-4;O14511-3	.|.;.	N|E	328|400;394	.|ENSP00000289422:G400E;ENSP00000351323:G394E	ENSP00000444943:D328N|ENSP00000289422:G400E	D|G	-|-	1|2	0|0	NRG2|NRG2	139219672|139219672	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.900000|0.900000	0.52787|0.52787	7.484000|7.484000	0.81180|0.81180	2.509000|2.509000	0.84616|0.84616	0.313000|0.313000	0.20887|0.20887	GAT|GGA	.	.		0.552	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982	
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711003	140711003	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:140711003T>C	ENST00000517417.1	+	1	752	c.752T>C	c.(751-753)gTc>gCc	p.V251A	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.V251A	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	251	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATATAAATGTCCCCGAAAAC	0.488																																					p.V251A		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.T752C						.						65.0	65.0	65.0					5																	140711003		2203	4300	6503	SO:0001583	missense	56114	exon1			TAAATGTCCCCGA	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.752T>C	chr5.hg19:g.140711003T>C	ENSP00000431083:p.Val251Ala	65.0	0.0		62.0	14.0	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	hg19	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	T	12.06	1.825319	0.32237	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.58210	0.35;0.35	4.2	4.2	0.49525	Cadherin (4);Cadherin-like (1);	0.000000	0.44483	D	0.000456	T	0.76751	0.4031	M	0.93898	3.47	0.09310	N	1	D;P	0.67145	0.996;0.932	D;P	0.65233	0.933;0.718	T	0.72541	-0.4262	10	0.87932	D	0	.	13.4192	0.60987	0.0:0.0:0.0:1.0	.	251;251	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	A	251	ENSP00000431083:V251A;ENSP00000367345:V251A	ENSP00000367345:V251A	V	+	2	0	PCDHGA1	140691187	0.527000	0.26306	0.073000	0.20177	0.016000	0.09150	4.106000	0.57804	1.905000	0.55150	0.533000	0.62120	GTC	.	.		0.488	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
PCDH1	5097	hgsc.bcm.edu	37	5	141248811	141248811	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:141248811T>A	ENST00000394536.3	-	2	365	c.226A>T	c.(226-228)Agc>Tgc	p.S76C	PCDH1_ENST00000536585.1_Missense_Mutation_p.S54C|PCDH1_ENST00000287008.3_Missense_Mutation_p.S76C|PCDH1_ENST00000503492.1_Missense_Mutation_p.S76C|PCDH1_ENST00000456271.1_Missense_Mutation_p.S76C	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	76	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		GCTGCGAGGCTCCCAATGAGG	0.602																																					p.S76C	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.A226T						.						40.0	39.0	40.0					5																	141248811		2203	4300	6503	SO:0001583	missense	5097	exon2			CGAGGCTCCCAAT	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.226A>T	chr5.hg19:g.141248811T>A	ENSP00000378043:p.Ser76Cys	121.0	0.0		102.0	6.0	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	hg19	CCDS43375.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146111	0.57044	.	.	ENSG00000156453	ENST00000503492;ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585;ENST00000514773	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	4.21	4.21	0.49690	Cadherin, N-terminal (1);Cadherin (2);	0.000000	0.64402	D	0.000007	T	0.51075	0.1653	M	0.67953	2.075	0.50171	D	0.999852	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.987	T	0.54827	-0.8235	10	0.87932	D	0	.	11.5439	0.50681	0.0:0.0:0.0:1.0	.	76;76	Q08174;Q08174-2	PCDH1_HUMAN;.	C	76;76;76;76;87;54;54	ENSP00000424667:S76C;ENSP00000287008:S76C;ENSP00000378043:S76C;ENSP00000403497:S76C;ENSP00000350122:S87C;ENSP00000438825:S54C;ENSP00000424163:S54C	ENSP00000287008:S76C	S	-	1	0	PCDH1	141228995	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	7.754000	0.85163	1.895000	0.54865	0.454000	0.30748	AGC	.	.		0.602	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420	
KCTD16	57528	hgsc.bcm.edu	37	5	143853260	143853260	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:143853260C>G	ENST00000507359.3	+	3	1961	c.870C>G	c.(868-870)tgC>tgG	p.C290W	KCTD16_ENST00000512467.1_Missense_Mutation_p.C290W	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	290					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)				large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			ACTGCGATTGCTGCTGCAAGA	0.527																																					p.C290W		Atlas-SNP	.											.	KCTD16	70	.	0			c.C870G						.						81.0	79.0	80.0					5																	143853260		2203	4300	6503	SO:0001583	missense	57528	exon4			CGATTGCTGCTGC	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"""potassium channel tetramerisation domain containing 16"""			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.870C>G	chr5.hg19:g.143853260C>G	ENSP00000426548:p.Cys290Trp	323.0	0.0		356.0	54.0	NM_020768	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	hg19	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.412415	0.42817	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.44083	0.93;0.93	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.27967	0.0689	N	0.08118	0	0.80722	D	1	P	0.45283	0.855	B	0.37780	0.258	T	0.26292	-1.0107	10	0.72032	D	0.01	.	20.04	0.97581	0.0:1.0:0.0:0.0	.	290	Q68DU8	KCD16_HUMAN	W	290	ENSP00000424151:C290W;ENSP00000426548:C290W	ENSP00000426548:C290W	C	+	3	2	KCTD16	143833453	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.758000	0.55220	2.733000	0.93635	0.655000	0.94253	TGC	.	.		0.527	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368	
SPINK6	404203	hgsc.bcm.edu	37	5	147593570	147593570	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:147593570C>T	ENST00000325630.2	+	3	435	c.179C>T	c.(178-180)gCc>gTc	p.A60V		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	60	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATAAATGTGCCTTCTGTAAG	0.428																																					p.A60V		Atlas-SNP	.											.	SPINK6	8	.	0			c.C179T						.						102.0	84.0	90.0					5																	147593570		2203	4300	6503	SO:0001583	missense	404203	exon3			AATGTGCCTTCTG	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"""Serine peptidase inhibitors, Kazal type"""	29486	protein-coding gene	gene with protein product	"""protease inhibitor H"""	615868	"""serine protease inhibitor, Kazal type 6"""			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.179C>T	chr5.hg19:g.147593570C>T	ENSP00000324870:p.Ala60Val	66.0	0.0		73.0	12.0	NM_205841	E0X656|Q8N5P0	Missense_Mutation	SNP	ENST00000325630.2	hg19	CCDS34268.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.074108	0.36566	.	.	ENSG00000178172	ENST00000325630	T	0.75154	-0.91	5.75	5.75	0.90469	Proteinase inhibitor I1, Kazal (3);	0.343853	0.30159	N	0.010270	T	0.69967	0.3170	.	.	.	0.38896	D	0.957212	B	0.31705	0.336	B	0.37833	0.259	T	0.66716	-0.5853	8	.	.	.	-2.5242	15.8177	0.78615	0.0:1.0:0.0:0.0	.	60	Q6UWN8	ISK6_HUMAN	V	60	ENSP00000324870:A60V	.	A	+	2	0	SPINK6	147573763	0.961000	0.32948	1.000000	0.80357	0.981000	0.71138	2.917000	0.48821	2.885000	0.99019	0.655000	0.94253	GCC	.	.		0.428	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841	
FAT2	2196	hgsc.bcm.edu	37	5	150945319	150945319	+	Silent	SNP	G	G	A	rs542235186	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:150945319G>A	ENST00000261800.5	-	1	3186	c.3174C>T	c.(3172-3174)gaC>gaT	p.D1058D		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1058	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACTGTCATCGTCCTGGGCAG	0.602													G|||	2	0.000399361	0.0008	0.0	5008	,	,		14351	0.0		0.0	False		,,,				2504	0.001				p.D1058D		Atlas-SNP	.											.	FAT2	465	.	0			c.C3174T						.						60.0	58.0	59.0					5																	150945319		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GTCATCGTCCTGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.3174C>T	chr5.hg19:g.150945319G>A		155.0	0.0		136.0	20.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.602	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
NMUR2	56923	hgsc.bcm.edu	37	5	151775082	151775082	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:151775082C>G	ENST00000255262.3	-	3	1040	c.875G>C	c.(874-876)aGc>aCc	p.S292T	NMUR2_ENST00000518933.1_5'UTR	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	292					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CTCCACAAAGCTGAAGAAGAG	0.473																																					p.S292T		Atlas-SNP	.											.	NMUR2	111	.	0			c.G875C						.						158.0	137.0	144.0					5																	151775082		2203	4300	6503	SO:0001583	missense	56923	exon3			ACAAAGCTGAAGA	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.875G>C	chr5.hg19:g.151775082C>G	ENSP00000255262:p.Ser292Thr	296.0	0.0		322.0	57.0	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	hg19	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.805392	0.50315	.	.	ENSG00000132911	ENST00000255262	T	0.36699	1.24	5.8	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.62986	0.2473	M	0.84585	2.705	0.54753	D	0.999982	D	0.76494	0.999	D	0.76575	0.988	T	0.67530	-0.5647	10	0.48119	T	0.1	-26.0049	13.8172	0.63299	0.0:0.9271:0.0:0.0728	.	292	Q9GZQ4	NMUR2_HUMAN	T	292	ENSP00000255262:S292T	ENSP00000255262:S292T	S	-	2	0	NMUR2	151755275	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.133000	0.77259	1.451000	0.47736	0.655000	0.94253	AGC	.	.		0.473	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167	
EBF1	1879	hgsc.bcm.edu	37	5	158250310	158250310	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:158250310T>C	ENST00000313708.6	-	8	934	c.652A>G	c.(652-654)Aca>Gca	p.T218A	EBF1_ENST00000380654.4_Missense_Mutation_p.T195A|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000517373.1_Missense_Mutation_p.T218A	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	218					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|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)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACATTGACTGTCGTAGACACC	0.438			T	HMGA2	lipoma																																p.T218A		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1	110	.	0			c.A652G						.						72.0	58.0	63.0					5																	158250310		2203	4300	6503	SO:0001583	missense	1879	exon8			TGACTGTCGTAGA	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"""early B-cell factor"""	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.652A>G	chr5.hg19:g.158250310T>C	ENSP00000322898:p.Thr218Ala	93.0	0.0		135.0	20.0	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	hg19	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.584095	0.65992	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.47869	0.89;0.83;0.9	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	M	0.62016	1.91	0.58432	D	0.999997	B;P;B;B	0.45212	0.003;0.853;0.016;0.215	B;P;B;B	0.56127	0.003;0.792;0.022;0.209	T	0.65487	-0.6156	10	0.72032	D	0.01	-4.0874	15.6488	0.77076	0.0:0.0:0.0:1.0	.	218;204;218;195	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	A	218;218;195;218	ENSP00000322898:T218A;ENSP00000370029:T195A;ENSP00000428020:T218A	ENSP00000322898:T218A	T	-	1	0	EBF1	158182888	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	8.036000	0.88901	2.069000	0.61940	0.533000	0.62120	ACA	.	.		0.438	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007	
GABRA6	2559	hgsc.bcm.edu	37	5	161116665	161116665	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:161116665A>G	ENST00000274545.5	+	6	986	c.553A>G	c.(553-555)Ata>Gta	p.I185V	GABRA6_ENST00000523217.1_Missense_Mutation_p.I175V|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	185					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AAGTGAAATCATATATACGTG	0.343										TCGA Ovarian(5;0.080)																											p.I185V		Atlas-SNP	.											.	GABRA6	139	.	0			c.A553G						.						45.0	48.0	47.0					5																	161116665		2200	4298	6498	SO:0001583	missense	2559	exon6			GAAATCATATATA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.553A>G	chr5.hg19:g.161116665A>G	ENSP00000274545:p.Ile185Val	72.0	0.0		78.0	12.0	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	A	3.400	-0.122553	0.06795	.	.	ENSG00000145863	ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.4	5.4	0.78164	Neurotransmitter-gated ion-channel ligand-binding (3);	0.049657	0.85682	D	0.000000	T	0.56934	0.2019	N	0.04686	-0.185	0.43010	D	0.994543	B	0.16603	0.018	B	0.30943	0.122	T	0.53563	-0.8421	10	0.08599	T	0.76	.	9.8755	0.41200	0.9235:0.0:0.0765:0.0	.	185	Q16445	GBRA6_HUMAN	V	185;175;132;105	ENSP00000274545:I185V;ENSP00000430527:I175V;ENSP00000430212:I132V;ENSP00000427989:I105V	ENSP00000274545:I185V	I	+	1	0	GABRA6	161049243	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	3.568000	0.53820	2.040000	0.60383	0.528000	0.53228	ATA	.	.		0.343	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
ZFP2	80108	hgsc.bcm.edu	37	5	178359572	178359572	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:178359572A>G	ENST00000361362.2	+	5	1788	c.1258A>G	c.(1258-1260)Att>Gtt	p.I420V	ZFP2_ENST00000523286.1_Missense_Mutation_p.I420V|ZFP2_ENST00000503510.2_Missense_Mutation_p.I420V|ZFP2_ENST00000520301.1_Missense_Mutation_p.I420V	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	420					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)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		AAAAGCCTTCATTAAGAATTC	0.418																																					p.I420V		Atlas-SNP	.											.	ZFP2	70	.	0			c.A1258G						.						63.0	66.0	65.0					5																	178359572		2203	4300	6503	SO:0001583	missense	80108	exon5			GCCTTCATTAAGA	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"""Zinc fingers, C2H2-type"""	26138	protein-coding gene	gene with protein product			"""zinc finger protein 2 homolog (mouse)"""				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.1258A>G	chr5.hg19:g.178359572A>G	ENSP00000354453:p.Ile420Val	50.0	0.0		52.0	7.0	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	hg19	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	a	12.02	1.811931	0.32053	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.05717	3.4;3.4;3.4;3.4	4.85	4.85	0.62838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.32719	N	0.005737	T	0.02807	0.0084	N	0.03238	-0.38	0.26509	N	0.974633	P	0.45283	0.855	B	0.38225	0.268	T	0.36672	-0.9738	10	0.51188	T	0.08	-11.7412	7.8747	0.29586	0.816:0.0:0.0:0.184	.	420	Q6ZN57	ZFP2_HUMAN	V	420	ENSP00000354453:I420V;ENSP00000430980:I420V;ENSP00000430531:I420V;ENSP00000438114:I420V	ENSP00000354453:I420V	I	+	1	0	ZFP2	178292178	0.000000	0.05858	1.000000	0.80357	0.999000	0.98932	0.602000	0.24134	2.018000	0.59344	0.533000	0.62120	ATT	.	.		0.418	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613	
FOXC1	2296	hgsc.bcm.edu	37	6	1612242	1612242	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:1612242C>T	ENST00000380874.2	+	1	1562	c.1562C>T	c.(1561-1563)tCt>tTt	p.S521F		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	521					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|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)|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)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		TTGAACAACTCTCCAGTGAAC	0.602																																					p.S521F	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C1562T						.						63.0	46.0	52.0					6																	1612242		2201	4299	6500	SO:0001583	missense	2296	exon1			ACAACTCTCCAGT	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"""Forkhead boxes"""	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1562C>T	chr6.hg19:g.1612242C>T	ENSP00000370256:p.Ser521Phe	137.0	0.0		238.0	21.0	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Missense_Mutation	SNP	ENST00000380874.2	hg19	CCDS4473.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.672562	0.67928	.	.	ENSG00000054598	ENST00000380874	D	0.82433	-1.61	3.52	3.52	0.40303	.	0.000000	0.64402	U	0.000004	D	0.83635	0.5297	L	0.39245	1.2	0.58432	D	0.999995	D	0.65815	0.995	D	0.75484	0.986	D	0.86117	0.1566	10	0.72032	D	0.01	.	14.0047	0.64456	0.0:1.0:0.0:0.0	.	521	Q12948	FOXC1_HUMAN	F	521	ENSP00000370256:S521F	ENSP00000370256:S521F	S	+	2	0	FOXC1	1557241	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	6.548000	0.73896	1.828000	0.53243	0.448000	0.29417	TCT	.	.		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1		
NRSN1	140767	hgsc.bcm.edu	37	6	24146149	24146149	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:24146149A>G	ENST00000378491.4	+	4	864	c.563A>G	c.(562-564)aAt>aGt	p.N188S		NM_080723.4	NP_542454.3			neurensin 1											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	22						AGGGTTCAAAATGTCCAGCCT	0.483																																					p.N188S		Atlas-SNP	.											.	NRSN1	31	.	0			c.A563G						.						58.0	65.0	63.0					6																	24146149		2203	4300	6503	SO:0001583	missense	140767	exon4			TTCAAAATGTCCA	AF418980	CCDS4549.1	6p22.1	2008-02-05	2006-07-04	2006-07-04	ENSG00000152954	ENSG00000152954			17881	protein-coding gene	gene with protein product			"""vesicular membrane protein p24"""	VMP		12463420	Standard	NM_080723		Approved	p24	uc010jpq.1	Q8IZ57	OTTHUMG00000016406	ENST00000378491.4:c.563A>G	chr6.hg19:g.24146149A>G	ENSP00000367752:p.Asn188Ser	78.0	0.0		119.0	14.0	NM_080723		Missense_Mutation	SNP	ENST00000378491.4	hg19	CCDS4549.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.540610	0.45280	.	.	ENSG00000152954	ENST00000378491	T	0.19250	2.16	5.35	4.19	0.49359	.	0.042896	0.85682	N	0.000000	T	0.08088	0.0202	L	0.42245	1.32	0.80722	D	1	B	0.21071	0.051	B	0.20955	0.032	T	0.07520	-1.0768	10	0.29301	T	0.29	-9.71	11.1828	0.48638	0.9276:0.0:0.0724:0.0	.	188	Q8IZ57	NRSN1_HUMAN	S	188	ENSP00000367752:N188S	ENSP00000367752:N188S	N	+	2	0	NRSN1	24254128	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	5.652000	0.67959	0.866000	0.35629	0.528000	0.53228	AAT	.	.		0.483	NRSN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043866.1	NM_080723	
POM121L2	94026	hgsc.bcm.edu	37	6	27279209	27279209	+	Silent	SNP	G	G	A	rs375438522		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:27279209G>A	ENST00000444565.1	-	1	740	c.741C>T	c.(739-741)ggC>ggT	p.G247G	POM121L2_ENST00000377451.2_Silent_p.G247G	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	247										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						AGCTGAGGGTGCCACCTCTGT	0.507																																					p.G247G		Atlas-SNP	.											.	POM121L2	61	.	0			c.C741T						.						29.0	25.0	26.0					6																	27279209		692	1591	2283	SO:0001819	synonymous_variant	94026	exon1			GAGGGTGCCACCT	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.741C>T	chr6.hg19:g.27279209G>A		74.0	0.0		100.0	7.0	NM_033482	C9J1I7	Silent	SNP	ENST00000444565.1	hg19	CCDS59497.1																																																																																			.	.		0.507	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
NEU1	4758	hgsc.bcm.edu	37	6	31827993	31827993	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:31827993T>C	ENST00000375631.4	-	5	976	c.847A>G	c.(847-849)Aac>Gac	p.N283D		NM_000434.3	NP_000425.1	Q99519	NEUR1_HUMAN	sialidase 1 (lysosomal sialidase)	283					glycosphingolipid metabolic process (GO:0006687)|lipid catabolic process (GO:0016042)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10					Oseltamivir(DB00198)	TGGTAGTTGTTCTGGTTTCGG	0.577																																					p.N283D		Atlas-SNP	.											.	NEU1	21	.	0			c.A847G						.						88.0	71.0	77.0					6																	31827993		1511	2709	4220	SO:0001583	missense	4758	exon5			AGTTGTTCTGGTT	AF040958	CCDS4723.1	6p21	2012-10-02			ENSG00000204386	ENSG00000204386	3.2.1.18		7758	protein-coding gene	gene with protein product		608272		NEU		9054950	Standard	NM_000434		Approved		uc003nxq.4	Q99519	OTTHUMG00000031284	ENST00000375631.4:c.847A>G	chr6.hg19:g.31827993T>C	ENSP00000364782:p.Asn283Asp	219.0	0.0		312.0	39.0	NM_000434		Missense_Mutation	SNP	ENST00000375631.4	hg19	CCDS4723.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.178532	0.38511	.	.	ENSG00000204386	ENST00000375631	D	0.83591	-1.74	5.1	5.1	0.69264	Neuraminidase (2);	0.047002	0.85682	D	0.000000	T	0.73377	0.3579	L	0.39245	1.2	0.45183	D	0.998191	P	0.51147	0.942	P	0.54965	0.765	T	0.71307	-0.4632	10	0.13470	T	0.59	-18.8045	8.4812	0.33043	0.1729:0.0:0.0:0.8271	.	283	Q99519	NEUR1_HUMAN	D	283	ENSP00000364782:N283D	ENSP00000364782:N283D	N	-	1	0	NEU1	31935972	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	5.374000	0.66167	2.270000	0.75569	0.460000	0.39030	AAC	.	.		0.577	NEU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076616.2		
C2	717	hgsc.bcm.edu	37	6	31911759	31911759	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:31911759G>A	ENST00000299367.5	+	14	2075	c.1799G>A	c.(1798-1800)tGt>tAt	p.C600Y	C2_ENST00000469372.1_Missense_Mutation_p.C354Y|C2_ENST00000452323.2_Missense_Mutation_p.C386Y|CFB_ENST00000477310.1_Missense_Mutation_p.C371Y|CFB_ENST00000425368.2_5'Flank|C2_ENST00000442278.2_Missense_Mutation_p.C468Y|CFB_ENST00000556679.1_Missense_Mutation_p.C447Y|CFB_ENST00000456570.1_Missense_Mutation_p.C447Y|C2_ENST00000468407.1_3'UTR	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	600	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)		GGCAGCACCTGTAGGGACCAT	0.612																																					p.C600Y		Atlas-SNP	.											.	C2	50	.	0			c.G1799A						.						55.0	55.0	55.0					6																	31911759		1509	2707	4216	SO:0001583	missense	717	exon14			GCACCTGTAGGGA		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.1799G>A	chr6.hg19:g.31911759G>A	ENSP00000299367:p.Cys600Tyr	110.0	0.0		135.0	19.0	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.3|21.3	4.122491|4.122491	0.77436|0.77436	.|.	.|.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255|ENSG00000166278	ENST00000469372;ENST00000497706;ENST00000452323;ENST00000299367;ENST00000375493;ENST00000442278;ENST00000556679;ENST00000456570;ENST00000477310|ENST00000383177	T;T;T;T;T;T;T;T|.	0.35048|.	1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33|.	5.21|5.21	5.21|5.21	0.72293|0.72293	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);|.	0.000000|.	0.41194|.	D|.	0.000935|.	T|T	0.75824|0.75824	0.3902|0.3902	M|M	0.88512|0.88512	2.96|2.96	0.39187|0.39187	D|D	0.962896|0.962896	D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D|.	0.97110|.	1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0|.	T|T	0.80605|0.80605	-0.1308|-0.1308	10|5	0.87932|.	D|.	0|.	-14.3006|-14.3006	14.2644|14.2644	0.66107|0.66107	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	447;571;386;354;468;285;468;600;387|.	B4E1Z4;B4DV48;B4DPF3;B4DQI1;E9PFN7;F8VNY6;B4DV20;P06681;E9PDZ0|.	.;.;.;.;.;.;.;CO2_HUMAN;.|.	Y|I	354;387;386;600;285;468;447;447;371|374	ENSP00000418923:C354Y;ENSP00000417482:C387Y;ENSP00000392322:C386Y;ENSP00000299367:C600Y;ENSP00000395683:C468Y;ENSP00000451848:C447Y;ENSP00000410815:C447Y;ENSP00000418996:C371Y|.	ENSP00000299367:C600Y|.	C|V	+|+	2|1	0|0	CFB;C2;XXbac-BPG116M5.17|C2	32019738|32019738	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.978000|0.978000	0.69477|0.69477	5.559000|5.559000	0.67326|0.67326	2.453000|2.453000	0.82957|0.82957	0.563000|0.563000	0.77884|0.77884	TGT|GTA	.	.		0.612	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9		
NOTCH4	4855	hgsc.bcm.edu	37	6	32188291	32188291	+	Silent	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:32188291T>A	ENST00000375023.3	-	6	1188	c.1050A>T	c.(1048-1050)acA>acT	p.T350T		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	350	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CCTCACAGCTTGTGCCGCCCC	0.617																																					p.T350T		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A1050T						.						101.0	101.0	101.0					6																	32188291		1511	2709	4220	SO:0001819	synonymous_variant	4855	exon6			ACAGCTTGTGCCG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.1050A>T	chr6.hg19:g.32188291T>A		60.0	0.0		125.0	15.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.		0.617	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
KCTD20	222658	hgsc.bcm.edu	37	6	36449534	36449534	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:36449534A>G	ENST00000373731.2	+	6	1245	c.854A>G	c.(853-855)cAa>cGa	p.Q285R	KCTD20_ENST00000544295.1_Missense_Mutation_p.Q39R|KCTD20_ENST00000536244.1_Missense_Mutation_p.Q140R|KCTD20_ENST00000449081.2_Missense_Mutation_p.Q119R|KCTD20_ENST00000474988.1_3'UTR	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	285					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						GAATATTCCCAAAGTAGGAGC	0.478																																					p.Q285R		Atlas-SNP	.											.	KCTD20	37	.	0			c.A854G						.						78.0	73.0	75.0					6																	36449534		2203	4300	6503	SO:0001583	missense	222658	exon6			ATTCCCAAAGTAG	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"""chromosome 6 open reading frame 69"", ""potassium channel tetramerisation domain containing 20"""	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.854A>G	chr6.hg19:g.36449534A>G	ENSP00000362836:p.Gln285Arg	101.0	0.0		170.0	23.0	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	hg19	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018039	0.75275	.	.	ENSG00000112078	ENST00000373731;ENST00000544295;ENST00000449081;ENST00000536244	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.88108	0.6348	M	0.61703	1.905	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.968	D	0.88993	0.3416	10	0.62326	D	0.03	-19.6228	16.5764	0.84681	1.0:0.0:0.0:0.0	.	119;285	Q7Z5Y7-2;Q7Z5Y7	.;KCD20_HUMAN	R	285;39;119;140	ENSP00000362836:Q285R;ENSP00000440150:Q39R;ENSP00000412205:Q119R;ENSP00000439118:Q140R	ENSP00000362836:Q285R	Q	+	2	0	KCTD20	36557512	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.371000	0.80710	0.533000	0.62120	CAA	.	.		0.478	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562	
CPNE5	57699	hgsc.bcm.edu	37	6	36730726	36730726	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:36730726C>T	ENST00000244751.2	-	12	1447	c.823G>A	c.(823-825)Gcc>Acc	p.A275T		NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	275						extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						TGCCCACGGGCCAGCTCCCGG	0.587																																					p.A275T		Atlas-SNP	.											.	CPNE5	56	.	0			c.G823A						.						146.0	116.0	126.0					6																	36730726		2203	4300	6503	SO:0001583	missense	57699	exon12			CACGGGCCAGCTC	H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.823G>A	chr6.hg19:g.36730726C>T	ENSP00000244751:p.Ala275Thr	123.0	0.0		166.0	46.0	NM_020939	Q7Z6C8	Missense_Mutation	SNP	ENST00000244751.2	hg19	CCDS4825.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.057349	0.36277	.	.	ENSG00000124772	ENST00000244751	T	0.39406	1.08	5.36	5.36	0.76844	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.166115	0.51477	D	0.000082	T	0.10294	0.0252	N	0.04880	-0.145	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.14200	-1.0481	10	0.18276	T	0.48	.	11.9785	0.53107	0.1732:0.8268:0.0:0.0	.	275	Q9HCH3	CPNE5_HUMAN	T	275	ENSP00000244751:A275T	ENSP00000244751:A275T	A	-	1	0	CPNE5	36838704	0.859000	0.29813	1.000000	0.80357	0.982000	0.71751	0.336000	0.19823	2.693000	0.91896	0.313000	0.20887	GCC	.	.		0.587	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939	
MDGA1	266727	hgsc.bcm.edu	37	6	37606362	37606362	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:37606362T>C	ENST00000434837.3	-	15	3796	c.2618A>G	c.(2617-2619)aAt>aGt	p.N873S	MDGA1_ENST00000297153.7_Missense_Mutation_p.N877S|MDGA1_ENST00000505425.1_Missense_Mutation_p.N873S	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	873	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CTGCCACACATTGCCCTTATT	0.652																																					p.N873S		Atlas-SNP	.											.	MDGA1	104	.	0			c.A2618G						.						51.0	57.0	55.0					6																	37606362		2046	4181	6227	SO:0001583	missense	266727	exon15			CACACATTGCCCT	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.2618A>G	chr6.hg19:g.37606362T>C	ENSP00000402584:p.Asn873Ser	73.0	0.0		109.0	9.0	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	T	19.73	3.881862	0.72294	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.02050	4.48;4.48;4.48	5.04	5.04	0.67666	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.234553	0.28600	N	0.014779	T	0.01730	0.0055	L	0.43598	1.365	0.25207	N	0.990003	D;P	0.54964	0.969;0.625	P;B	0.47673	0.554;0.353	T	0.43589	-0.9382	10	0.56958	D	0.05	.	13.0768	0.59091	0.0:0.0:0.0:1.0	.	873;873	Q8NFP4-2;Q8NFP4	.;MDGA1_HUMAN	S	873;877;873	ENSP00000402584:N873S;ENSP00000297153:N877S;ENSP00000422042:N873S	ENSP00000297153:N877S	N	-	2	0	MDGA1	37714340	0.975000	0.34042	0.999000	0.59377	0.997000	0.91878	2.341000	0.43983	2.017000	0.59298	0.529000	0.55759	AAT	.	.		0.652	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
TREML4	285852	hgsc.bcm.edu	37	6	41196565	41196565	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:41196565T>C	ENST00000341495.2	+	2	281	c.177T>C	c.(175-177)tcT>tcC	p.S59S	TREML4_ENST00000448827.2_Silent_p.S59S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	59	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					AGCAGACATCTCCAAGTCGGT	0.522																																					p.S59S		Atlas-SNP	.											.	TREML4	25	.	0			c.T177C						.						90.0	84.0	86.0					6																	41196565		2203	4300	6503	SO:0001819	synonymous_variant	285852	exon2			GACATCTCCAAGT	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"""Immunoglobulin superfamily / V-set domain containing"""	30807	protein-coding gene	gene with protein product	"""TREM like transcript 4"""	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.177T>C	chr6.hg19:g.41196565T>C		80.0	0.0		125.0	17.0	NM_198153	B7ZL92	Silent	SNP	ENST00000341495.2	hg19	CCDS34446.1																																																																																			.	.		0.522	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
RSPH9	221421	hgsc.bcm.edu	37	6	43623341	43623341	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:43623341C>G	ENST00000372163.4	+	3	489	c.436C>G	c.(436-438)Cag>Gag	p.Q146E	RSPH9_ENST00000372165.4_Intron	NM_152732.4	NP_689945.2	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog (Chlamydomonas)	146					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)				NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						TGTCATTGACCAGATTGACAA	0.607									Kartagener syndrome																												p.Q146E		Atlas-SNP	.											.	RSPH9	60	.	0			c.C436G						.						133.0	132.0	132.0					6																	43623341		2203	4300	6503	SO:0001583	missense	221421	exon3	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATTGACCAGATTG	AK055407	CCDS4905.1, CCDS55005.1	6p21.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000172426	ENSG00000172426			21057	protein-coding gene	gene with protein product		612648	"""mitochondrial ribosomal protein S18A-like 1"", ""chromosome 6 open reading frame 206"""	MRPS18AL1, C6orf206		19200523	Standard	NM_152732		Approved	FLJ30845, CILD12	uc003ovx.2	Q9H1X1	OTTHUMG00000014746	ENST00000372163.4:c.436C>G	chr6.hg19:g.43623341C>G	ENSP00000361236:p.Gln146Glu	69.0	0.0		114.0	9.0	NM_152732	A8K5T4|Q96NH9	Missense_Mutation	SNP	ENST00000372163.4	hg19	CCDS4905.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.69|14.69	2.610405|2.610405	0.46527|0.46527	.|.	.|.	ENSG00000172426|ENSG00000172426	ENST00000417236|ENST00000372163;ENST00000372154	.|T	.|0.39997	.|1.05	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	.|.	.|.	.|.	.|.	T|T	0.20941|0.20941	0.0504|0.0504	L|L	0.40543|0.40543	1.245|1.245	0.35723|0.35723	D|D	0.817357|0.817357	.|P	.|0.50369	.|0.934	.|P	.|0.45167	.|0.472	T|T	0.02813|0.02813	-1.1107|-1.1107	5|9	.|0.10111	.|T	.|0.7	.|.	12.2605|12.2605	0.54647|0.54647	0.1697:0.8303:0.0:0.0|0.1697:0.8303:0.0:0.0	.|.	.|146	.|Q9H1X1	.|RSPH9_HUMAN	R|E	70|146;114	.|ENSP00000361236:Q146E	.|ENSP00000361227:Q114E	P|Q	+|+	2|1	0|0	RSPH9|RSPH9	43731319|43731319	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	2.918000|2.918000	0.48829|0.48829	2.672000|2.672000	0.90937|0.90937	0.591000|0.591000	0.81541|0.81541	CCA|CAG	.	.		0.607	RSPH9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040690.1	NM_152732	
GPR116	221395	hgsc.bcm.edu	37	6	46823751	46823751	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:46823751A>G	ENST00000283296.7	-	20	4209	c.3921T>C	c.(3919-3921)tcT>tcC	p.S1307S	GPR116_ENST00000545669.1_Silent_p.S736S|GPR116_ENST00000265417.7_Silent_p.S1307S|GPR116_ENST00000362015.4_Silent_p.S1287S|GPR116_ENST00000456426.2_Silent_p.S1165S	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	1307					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			TTGATATTGGAGAACTCATAG	0.423																																					p.S1307S	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.T3921C						.						56.0	50.0	52.0					6																	46823751		2203	4296	6499	SO:0001819	synonymous_variant	221395	exon20			TATTGGAGAACTC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.3921T>C	chr6.hg19:g.46823751A>G		380.0	0.0		547.0	75.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	hg19	CCDS4919.1																																																																																			.	.		0.423	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
PKHD1	5314	hgsc.bcm.edu	37	6	51609291	51609291	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:51609291T>C	ENST00000371117.3	-	60	10323	c.10048A>G	c.(10048-10050)Aga>Gga	p.R3350G	PKHD1_ENST00000340994.4_Missense_Mutation_p.R3350G	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3350					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGATATTTTCTTGGACTTGCA	0.423																																					p.R3350G		Atlas-SNP	.											.	PKHD1	927	.	0			c.A10048G						.						91.0	89.0	89.0					6																	51609291		2203	4300	6503	SO:0001583	missense	5314	exon60			ATTTTCTTGGACT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10048A>G	chr6.hg19:g.51609291T>C	ENSP00000360158:p.Arg3350Gly	132.0	0.0		176.0	25.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.488143	0.26686	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87966	-2.11;-2.32	5.21	2.81	0.32909	.	0.573790	0.17845	N	0.160070	T	0.66982	0.2845	L	0.41824	1.3	0.18873	N	0.999988	B;B;B	0.14438	0.003;0.01;0.001	B;B;B	0.12156	0.002;0.007;0.002	T	0.60637	-0.7224	10	0.51188	T	0.08	.	7.7127	0.28688	0.0:0.1666:0.0:0.8334	.	3350;3350;3350	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	G	3350	ENSP00000360158:R3350G;ENSP00000341097:R3350G	ENSP00000341097:R3350G	R	-	1	2	PKHD1	51717250	0.976000	0.34144	0.193000	0.23327	0.673000	0.39480	2.284000	0.43478	0.410000	0.25675	0.528000	0.53228	AGA	.	.		0.423	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PKHD1	5314	hgsc.bcm.edu	37	6	51917941	51917941	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:51917941G>A	ENST00000371117.3	-	21	2348	c.2073C>T	c.(2071-2073)ctC>ctT	p.L691L	PKHD1_ENST00000340994.4_Silent_p.L691L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	691					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGGCCAGAGGGAGAAGGTTGA	0.522																																					p.L691L		Atlas-SNP	.											.	PKHD1	927	.	0			c.C2073T						.						74.0	75.0	75.0					6																	51917941		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon21			CAGAGGGAGAAGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2073C>T	chr6.hg19:g.51917941G>A		86.0	0.0		142.0	13.0	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.		0.522	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
LGSN	51557	hgsc.bcm.edu	37	6	63990576	63990576	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:63990576T>A	ENST00000370657.4	-	4	913	c.880A>T	c.(880-882)Agg>Tgg	p.R294W	LGSN_ENST00000370658.5_Intron			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	294					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTATATTTCCTTGCCACTTCT	0.413																																					p.R294W		Atlas-SNP	.											.	LGSN	82	.	0			c.A880T						.						58.0	57.0	57.0					6																	63990576		2203	4300	6503	SO:0001583	missense	51557	exon4			ATTTCCTTGCCAC	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"""glutamate-ammonia ligase (glutamine synthetase) domain containing 1"""	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.880A>T	chr6.hg19:g.63990576T>A	ENSP00000359691:p.Arg294Trp	104.0	0.0		145.0	17.0	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	hg19	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258331	0.39896	.	.	ENSG00000146166	ENST00000370657	D	0.86769	-2.17	5.62	4.44	0.53790	Glutamine synthetase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.083576	0.85682	D	0.000000	D	0.85596	0.5733	M	0.68593	2.085	0.80722	D	1	P	0.40197	0.706	P	0.48815	0.591	D	0.86624	0.1881	10	0.87932	D	0	-25.0044	12.1	0.53778	0.0:0.0:0.1438:0.8562	.	294	Q5TDP6	LGSN_HUMAN	W	294	ENSP00000359691:R294W	ENSP00000359691:R294W	R	-	1	2	LGSN	64048535	1.000000	0.71417	0.981000	0.43875	0.007000	0.05969	4.968000	0.63728	0.936000	0.37367	0.533000	0.62120	AGG	.	.		0.413	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571	
COL12A1	1303	hgsc.bcm.edu	37	6	75884975	75884975	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:75884975A>G	ENST00000322507.8	-	13	2798	c.2489T>C	c.(2488-2490)aTg>aCg	p.M830T	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.M830T|COL12A1_ENST00000416123.2_Missense_Mutation_p.M830T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	830	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						AGATAATTTCATAGTAGACGT	0.413																																					p.M830T		Atlas-SNP	.											.	COL12A1	385	.	0			c.T2489C						.						125.0	118.0	120.0					6																	75884975		1864	4083	5947	SO:0001583	missense	1303	exon13			AATTTCATAGTAG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2489T>C	chr6.hg19:g.75884975A>G	ENSP00000325146:p.Met830Thr	166.0	0.0		172.0	31.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.869910	0.51588	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.53640	0.61;0.61;0.61	5.79	5.79	0.91817	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.148812	0.48286	D	0.000196	T	0.36358	0.0964	M	0.62266	1.93	0.47153	D	0.999338	B	0.20887	0.049	B	0.23150	0.044	T	0.36696	-0.9737	10	0.72032	D	0.01	.	16.1267	0.81400	1.0:0.0:0.0:0.0	.	830	Q99715	COCA1_HUMAN	T	830	ENSP00000325146:M830T;ENSP00000412864:M830T;ENSP00000421216:M830T	ENSP00000325146:M830T	M	-	2	0	COL12A1	75941695	1.000000	0.71417	0.996000	0.52242	0.771000	0.43674	8.962000	0.93254	2.205000	0.71048	0.455000	0.32223	ATG	.	.		0.413	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90581017	90581017	+	RNA	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:90581017C>T	ENST00000551025.1	+	0	7239									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GAAATGATGACCGGGAAATTT	0.368																																					p.D1934D	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.C5802T						.						74.0	71.0	72.0					6																	90581017		1798	4066	5864			9994	exon9			TGATGACCGGGAA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90581017C>T		161.0	0.0		121.0	23.0	NM_001137667		Silent	SNP	ENST00000551025.1	hg19																																																																																				.	.		0.368	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
POU3F2	5454	hgsc.bcm.edu	37	6	99283906	99283907	+	Nonsense_Mutation	DNP	CC	CC	AA			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:99283906_99283907CC>AA	ENST00000328345.5	+	1	1327_1328	c.1157_1158CC>AA	c.(1156-1158)tCC>tAA	p.S386*		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	386					astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		GAGATCACCTCCCTCGCGGACA	0.579																																					p.S386Y|p.S386S		Atlas-SNP	.											.	POU3F2	33	.	0			c.C1157A|c.C1158A						.																																			SO:0001587	stop_gained	5454	exon1			TCACCTCCCTCGC|CACCTCCCTCGCG	Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"""Homeoboxes / POU class"""	9215	protein-coding gene	gene with protein product		600494	"""POU domain class 3, transcription factor 2"""	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	Exception_encountered	chr6.hg19:g.99283906_99283907delinsAA	ENSP00000329170:p.Ser386*	78.0	0.0		129.0|126.0	48.0|46.0	NM_005604	Q14960|Q86V54|Q9UJL0	Missense_Mutation|Silent	SNP	ENST00000328345.5	hg19	CCDS5040.1																																																																																			.	.		0.579	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2		
ASCC3	10973	hgsc.bcm.edu	37	6	100960788	100960788	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:100960788T>A	ENST00000369162.2	-	40	6426	c.6082A>T	c.(6082-6084)Aat>Tat	p.N2028Y		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	2028	SEC63 2.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GATAAGAAATTCCATGCCTAA	0.343																																					p.N2028Y		Atlas-SNP	.											.	ASCC3	205	.	0			c.A6082T						.						62.0	55.0	57.0					6																	100960788		2203	4300	6503	SO:0001583	missense	10973	exon40			AGAAATTCCATGC	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.6082A>T	chr6.hg19:g.100960788T>A	ENSP00000358159:p.Asn2028Tyr	74.0	0.0		118.0	17.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.300595	0.60195	.	.	ENSG00000112249	ENST00000369162	T	0.61392	0.11	5.74	5.74	0.90152	Sec63 domain (3);	0.335977	0.32578	N	0.005906	T	0.63010	0.2475	M	0.77820	2.39	0.80722	D	1	P	0.48834	0.916	P	0.54431	0.752	T	0.69993	-0.4994	10	0.72032	D	0.01	.	12.5418	0.56174	0.0:0.0:0.1388:0.8612	.	2028	Q8N3C0	HELC1_HUMAN	Y	2028	ENSP00000358159:N2028Y	ENSP00000358159:N2028Y	N	-	1	0	ASCC3	101067509	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.136000	0.42121	2.198000	0.70561	0.533000	0.62120	AAT	.	.		0.343	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
AIM1	202	hgsc.bcm.edu	37	6	106987360	106987360	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:106987360G>A	ENST00000369066.3	+	7	4064	c.3577G>A	c.(3577-3579)Gat>Aat	p.D1193N	AIM1_ENST00000535438.1_5'Flank	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GTCCTTCTGGGATACAGAAGA	0.443																																					p.D1193N		Atlas-SNP	.											.	AIM1	161	.	0			c.G3577A						.						141.0	134.0	137.0					6																	106987360		2203	4300	6503	SO:0001583	missense	202	exon7			TTCTGGGATACAG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3577G>A	chr6.hg19:g.106987360G>A	ENSP00000358062:p.Asp1193Asn	133.0	0.0		176.0	22.0	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.357776	0.41801	.	.	ENSG00000112297	ENST00000369066	T	0.75589	-0.95	5.66	1.95	0.26073	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.521950	0.23966	N	0.042805	T	0.19485	0.0468	N	0.00707	-1.245	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.05289	-1.0894	10	0.20519	T	0.43	.	8.5611	0.33511	0.357:0.0:0.643:0.0	.	1193	Q9Y4K1	AIM1_HUMAN	N	1193	ENSP00000358062:D1193N	ENSP00000358062:D1193N	D	+	1	0	AIM1	107094053	1.000000	0.71417	0.684000	0.30055	0.964000	0.63967	3.315000	0.51951	0.342000	0.23796	0.655000	0.94253	GAT	.	.		0.443	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
OSTM1	28962	hgsc.bcm.edu	37	6	108372335	108372335	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:108372335T>A	ENST00000193322.3	-	4	768	c.683A>T	c.(682-684)tAc>tTc	p.Y228F		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	228					ion transmembrane transport (GO:0034220)|osteoclast differentiation (GO:0030316)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		CAGAGTTTTGTATGCTTCACG	0.348																																					p.Y228F	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											.	OSTM1	22	.	0			c.A683T						.						155.0	138.0	144.0					6																	108372335		2202	4300	6502	SO:0001583	missense	28962	exon4			GTTTTGTATGCTT	AF533891	CCDS5062.1	6q21	2014-06-17			ENSG00000081087	ENSG00000081087			21652	protein-coding gene	gene with protein product	"""CLCN7 accessory beta subunit"""	607649				12627228, 21527911	Standard	NM_014028		Approved	HSPC019, GL	uc003psd.3	Q86WC4	OTTHUMG00000015317	ENST00000193322.3:c.683A>T	chr6.hg19:g.108372335T>A	ENSP00000193322:p.Tyr228Phe	172.0	0.0		228.0	31.0	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	hg19	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	t	25.8	4.678364	0.88542	.	.	ENSG00000081087	ENST00000193322;ENST00000440575	T	0.61392	0.11	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.72260	0.3438	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77075	-0.2722	10	0.87932	D	0	-7.8843	16.1376	0.81497	0.0:0.0:0.0:1.0	.	228	Q86WC4	OSTM1_HUMAN	F	228;81	ENSP00000193322:Y228F	ENSP00000193322:Y228F	Y	-	2	0	OSTM1	108479028	1.000000	0.71417	0.430000	0.26722	0.937000	0.57800	6.767000	0.74975	2.212000	0.71576	0.533000	0.62120	TAC	.	.		0.348	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028	
RFX6	222546	hgsc.bcm.edu	37	6	117248312	117248312	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:117248312C>T	ENST00000332958.2	+	17	2024	c.2008C>T	c.(2008-2010)Cca>Tca	p.P670S		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	670					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AAGTGTGGGCCCAGTACTGTC	0.527																																					p.P670S		Atlas-SNP	.											.	RFX6	141	.	0			c.C2008T						.						142.0	133.0	136.0					6																	117248312		2203	4300	6503	SO:0001583	missense	222546	exon17			GTGGGCCCAGTAC	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.2008C>T	chr6.hg19:g.117248312C>T	ENSP00000332208:p.Pro670Ser	146.0	0.0		195.0	15.0	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.334435	0.24253	.	.	ENSG00000185002	ENST00000332958	T	0.55760	0.5	5.68	1.69	0.24217	.	0.558936	0.20589	N	0.089387	T	0.11239	0.0274	N	0.12182	0.205	0.09310	N	0.999995	B	0.09022	0.002	B	0.08055	0.003	T	0.27331	-1.0077	10	0.35671	T	0.21	-1.9504	4.6315	0.12504	0.1296:0.6161:0.1186:0.1356	.	670	Q8HWS3	RFX6_HUMAN	S	670	ENSP00000332208:P670S	ENSP00000332208:P670S	P	+	1	0	RFX6	117355005	0.291000	0.24352	0.020000	0.16555	0.957000	0.61999	1.187000	0.32090	0.018000	0.15052	0.655000	0.94253	CCA	.	.		0.527	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
RNF146	81847	hgsc.bcm.edu	37	6	127607830	127607830	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:127607830C>T	ENST00000368314.1	+	3	496	c.72C>T	c.(70-72)tcC>tcT	p.S24S	RNF146_ENST00000489534.1_3'UTR|RNF146_ENST00000356799.2_3'UTR|RNF146_ENST00000608991.1_Silent_p.S23S|RNF146_ENST00000610153.1_Silent_p.S24S|RNF146_ENST00000309649.3_Silent_p.S23S|RNF146_ENST00000476956.1_3'UTR|RNF146_ENST00000477776.1_3'UTR|RNF146_ENST00000480444.1_3'UTR	NM_001242850.1|NM_001242851.1	NP_001229779.1|NP_001229780.1	Q9NTX7	RN146_HUMAN	ring finger protein 146	24					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly-ADP-D-ribose binding (GO:0072572)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(226;0.0407)|all cancers(137;0.2)		CGAACGAGTCCTGTTCTAATA	0.403																																					p.S24S		Atlas-SNP	.											.	RNF146	31	.	0			c.C72T						.						189.0	153.0	165.0					6																	127607830		2203	4300	6503	SO:0001819	synonymous_variant	81847	exon3			CGAGTCCTGTTCT	AK027558	CCDS5136.1, CCDS56449.1	6q22.1-q22.33	2008-02-05			ENSG00000118518	ENSG00000118518		"""RING-type (C3HC4) zinc fingers"""	21336	protein-coding gene	gene with protein product		612137					Standard	NM_001242844		Approved	DKFZp434O1427, dactylidin, dJ351K20.1	uc021zes.1	Q9NTX7	OTTHUMG00000015522	ENST00000368314.1:c.72C>T	chr6.hg19:g.127607830C>T		207.0	0.0		326.0	34.0	NM_001242850	E1P572|Q6FIB2|Q7L8H4|Q96K03|Q96T06|Q9NTX6	Silent	SNP	ENST00000368314.1	hg19	CCDS56449.1																																																																																			.	.		0.403	RNF146-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042112.1	NM_030963	
KIAA1244	57221	hgsc.bcm.edu	37	6	138655566	138655566	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:138655566C>T	ENST00000251691.4	+	33	5749	c.5583C>T	c.(5581-5583)gaC>gaT	p.D1861D		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AGGATGAAGACATCTTTGAGG	0.562																																					p.D1861D		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C5583T						.						30.0	29.0	29.0					6																	138655566		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon33			TGAAGACATCTTT	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.5583C>T	chr6.hg19:g.138655566C>T		79.0	0.0		106.0	11.0	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.562	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
GRM1	2911	hgsc.bcm.edu	37	6	146755591	146755591	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:146755591C>T	ENST00000282753.1	+	8	3479	c.3244C>T	c.(3244-3246)Ctg>Ttg	p.L1082L	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000361719.2_Silent_p.L1082L|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000492807.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1082					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCCGCTGCAGCTGAGCACCTT	0.692																																					p.L1082L		Atlas-SNP	.											.	GRM1	419	.	0			c.C3244T						.						47.0	52.0	50.0					6																	146755591		2201	4300	6501	SO:0001819	synonymous_variant	2911	exon9			CTGCAGCTGAGCA	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3244C>T	chr6.hg19:g.146755591C>T		41.0	0.0		44.0	5.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	hg19	CCDS5209.1																																																																																			.	.		0.692	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
SASH1	23328	hgsc.bcm.edu	37	6	148841002	148841002	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:148841002G>A	ENST00000367467.3	+	10	1657	c.1182G>A	c.(1180-1182)aaG>aaA	p.K394K		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	394					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GGGAGATGAAGAAGGGTCTCG	0.567																																					p.K394K		Atlas-SNP	.											.	SASH1	123	.	0			c.G1182A						.						13.0	15.0	15.0					6																	148841002		2199	4295	6494	SO:0001819	synonymous_variant	23328	exon10			GATGAAGAAGGGT	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1182G>A	chr6.hg19:g.148841002G>A		19.0	0.0		22.0	7.0	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	hg19	CCDS5212.1																																																																																			.	.		0.567	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
SYNE1	23345	hgsc.bcm.edu	37	6	152740828	152740828	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:152740828T>C	ENST00000367255.5	-	40	5898	c.5297A>G	c.(5296-5298)gAa>gGa	p.E1766G	SYNE1_ENST00000423061.1_Missense_Mutation_p.E1773G|SYNE1_ENST00000341594.5_Missense_Mutation_p.E1803G|SYNE1_ENST00000448038.1_Missense_Mutation_p.E1773G|SYNE1_ENST00000265368.4_Missense_Mutation_p.E1766G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1766					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTGCTGGTGTTCAGCAACCAC	0.348										HNSCC(10;0.0054)																											p.E1773G		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A5318G						.						78.0	77.0	78.0					6																	152740828		2203	4300	6503	SO:0001583	missense	23345	exon40			TGGTGTTCAGCAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.5297A>G	chr6.hg19:g.152740828T>C	ENSP00000356224:p.Glu1766Gly	140.0	0.0		165.0	15.0	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	12.96	2.093332	0.36952	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	5.21	5.21	0.72293	.	0.091701	0.47093	D	0.000256	T	0.40670	0.1126	L	0.54323	1.7	0.80722	D	1	D;P;P;D	0.59767	0.986;0.839;0.839;0.982	P;B;B;P	0.56751	0.494;0.218;0.218;0.805	T	0.38373	-0.9664	10	0.66056	D	0.02	.	15.382	0.74664	0.0:0.0:0.0:1.0	.	1749;1766;1766;1773	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	G	1766;1773;1766;1773;1803	ENSP00000356224:E1766G;ENSP00000396024:E1773G;ENSP00000265368:E1766G;ENSP00000390975:E1773G;ENSP00000341887:E1803G	ENSP00000265368:E1766G	E	-	2	0	SYNE1	152782521	1.000000	0.71417	0.777000	0.31699	0.723000	0.41478	6.047000	0.71038	2.097000	0.63578	0.528000	0.53228	GAA	.	.		0.348	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
PLG	5340	hgsc.bcm.edu	37	6	161137785	161137785	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:161137785C>T	ENST00000308192.9	+	7	840	c.777C>T	c.(775-777)atC>atT	p.I259I		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	259	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	TTTGTGACATCCCCCGCTGCA	0.517																																					p.I259I		Atlas-SNP	.											.	PLG	150	.	0			c.C777T						.						65.0	61.0	62.0					6																	161137785		2203	4300	6503	SO:0001819	synonymous_variant	5340	exon7			TGACATCCCCCGC	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.777C>T	chr6.hg19:g.161137785C>T		76.0	0.0		112.0	6.0	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	hg19	CCDS5279.1																																																																																			.	.		0.517	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
C6orf118	168090	hgsc.bcm.edu	37	6	165715083	165715083	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:165715083G>A	ENST00000230301.8	-	2	748	c.728C>T	c.(727-729)gCg>gTg	p.A243V	C6orf118_ENST00000543069.1_Missense_Mutation_p.A139V	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	243										breast(1)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)		CTCGTGGCCCGCGGCCGCCTT	0.607																																					p.A243V		Atlas-SNP	.											C6orf118,NS,carcinoma,0,1	C6orf118	116	.	0			c.C728T						.						51.0	53.0	52.0					6																	165715083		2203	4300	6503	SO:0001583	missense	168090	exon2			TGGCCCGCGGCCG		CCDS5288.1	6q27	2012-02-06			ENSG00000112539	ENSG00000112539			21233	protein-coding gene	gene with protein product							Standard	NM_144980		Approved	MGC23884, bA85G2.1	uc003qum.4	Q5T5N4	OTTHUMG00000015984	ENST00000230301.8:c.728C>T	chr6.hg19:g.165715083G>A	ENSP00000230301:p.Ala243Val	109.0	0.0		122.0	14.0	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	hg19	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	G	7.212	0.595566	0.13875	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.14266	2.52;2.52	4.92	-9.85	0.00476	.	3.383220	0.00839	N	0.001730	T	0.00724	0.0024	N	0.00841	-1.15	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33803	-0.9854	10	0.28530	T	0.3	0.9594	2.604	0.04873	0.117:0.1644:0.326:0.3926	.	243	Q5T5N4	CF118_HUMAN	V	243;139	ENSP00000230301:A243V;ENSP00000439288:A139V	ENSP00000230301:A243V	A	-	2	0	C6orf118	165635073	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.152000	0.01288	-3.367000	0.00178	-2.617000	0.00157	GCG	.	.		0.607	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
GPR31	2853	hgsc.bcm.edu	37	6	167570796	167570796	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr6:167570796A>T	ENST00000366834.1	-	1	1021	c.524T>A	c.(523-525)aTc>aAc	p.I175N		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	175					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		CTGCCAGATGATGCTGAAGGA	0.582																																					p.I175N		Atlas-SNP	.											.	GPR31	44	.	0			c.T524A						.						91.0	98.0	96.0					6																	167570796		2203	4300	6503	SO:0001583	missense	2853	exon1			CAGATGATGCTGA	U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"""GPCR / Class A : Orphans"""	4486	protein-coding gene	gene with protein product	"""hydroxyeicosatetraenoic (HETE) acid receptor 1"", ""12-(S)-HETE acid receptor"""	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.524T>A	chr6.hg19:g.167570796A>T	ENSP00000355799:p.Ile175Asn	80.0	0.0		95.0	6.0	NM_005299	B0M0K2|Q4VBL3|Q9NQ20	Missense_Mutation	SNP	ENST00000366834.1	hg19	CCDS5299.1	.	.	.	.	.	.	.	.	.	.	A	0.030	-1.342818	0.01277	.	.	ENSG00000120436	ENST00000366834	T	0.37058	1.22	3.51	-7.01	0.01594	GPCR, rhodopsin-like superfamily (1);	2.652600	0.02280	U	0.069294	T	0.07052	0.0179	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.10382	-1.0632	10	0.56958	D	0.05	-6.3835	1.4616	0.02397	0.1533:0.2113:0.3534:0.282	.	175	O00270	GPR31_HUMAN	N	175	ENSP00000355799:I175N	ENSP00000355799:I175N	I	-	2	0	GPR31	167490786	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-1.680000	0.01939	-1.692000	0.01428	-0.981000	0.02577	ATC	.	.		0.582	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299	
PKD1L1	168507	hgsc.bcm.edu	37	7	47933628	47933628	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:47933628C>T	ENST00000289672.2	-	15	2350	c.2300G>A	c.(2299-2301)aGc>aAc	p.S767N		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	767	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACAGTAGTTGCTGTACACCAC	0.572																																					p.S767N		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G2300A						.						90.0	68.0	75.0					7																	47933628		2203	4300	6503	SO:0001583	missense	168507	exon15			TAGTTGCTGTACA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2300G>A	chr7.hg19:g.47933628C>T	ENSP00000289672:p.Ser767Asn	86.0	0.0		66.0	6.0	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	c	17.73	3.460343	0.63401	.	.	ENSG00000158683	ENST00000289672	T	0.69806	-0.43	5.23	4.35	0.52113	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.104209	0.42682	D	0.000675	T	0.78604	0.4309	M	0.63843	1.955	0.25786	N	0.984675	D	0.89917	1.0	D	0.91635	0.999	T	0.71724	-0.4506	10	0.54805	T	0.06	-11.3743	13.6843	0.62506	0.0:0.8439:0.1561:0.0	.	767	Q8TDX9	PK1L1_HUMAN	N	767	ENSP00000289672:S767N	ENSP00000289672:S767N	S	-	2	0	PKD1L1	47900153	1.000000	0.71417	0.179000	0.23059	0.558000	0.35554	3.411000	0.52672	1.197000	0.43143	0.543000	0.68304	AGC	.	.		0.572	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
CCDC132	55610	hgsc.bcm.edu	37	7	92905597	92905597	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:92905597C>A	ENST00000305866.5	+	12	1050	c.922C>A	c.(922-924)Caa>Aaa	p.Q308K	CCDC132_ENST00000317751.6_Missense_Mutation_p.Q39K|CCDC132_ENST00000541136.1_Missense_Mutation_p.Q119K|CCDC132_ENST00000544910.1_Missense_Mutation_p.Q278K|CCDC132_ENST00000251739.5_Missense_Mutation_p.Q308K|CCDC132_ENST00000535481.1_Intron	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	308						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.Q308*(2)		endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			CCAAAAGCTGCAATATAAGGA	0.343																																					p.Q308K		Atlas-SNP	.											CCDC132_ENST00000305866,NS,carcinoma,-1,2	CCDC132	136	.	2	Substitution - Nonsense(2)	lung(2)	c.C922A						.						144.0	136.0	139.0					7																	92905597		2203	4300	6503	SO:0001583	missense	55610	exon12			AAGCTGCAATATA	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.922C>A	chr7.hg19:g.92905597C>A	ENSP00000307666:p.Gln308Lys	113.0	0.0		122.0	27.0	NM_024553	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.70|11.70	1.715847|1.715847	0.30413|0.30413	.|.	.|.	ENSG00000004766|ENSG00000004766	ENST00000458707|ENST00000251739;ENST00000305866;ENST00000544910;ENST00000541136;ENST00000317751	.|T	.|0.43688	.|0.94	5.6|5.6	5.6|5.6	0.85130|0.85130	.|Vacuolar protein sorting-associated protein 54 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.40015	.|0.1100	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.33266	.|0.135;0.08;0.404	.|B;B;B	.|0.29440	.|0.051;0.058;0.102	.|T	.|0.42899	.|-0.9424	.|10	.|0.02654	.|T	.|1	-30.2354|-30.2354	19.9884|19.9884	0.97356|0.97356	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|278;308;308	.|F5H5U7;Q96JG6;Q96JG6-2	.|.;CC132_HUMAN;.	X|K	94|308;308;278;119;39	.|ENSP00000325582:Q39K	.|ENSP00000251739:Q308K	C|Q	+|+	3|1	2|0	CCDC132|CCDC132	92743533|92743533	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.770000|7.770000	0.85390|0.85390	2.809000|2.809000	0.96659|0.96659	0.655000|0.655000	0.94253|0.94253	TGC|CAA	.	.		0.343	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
DYNC1I1	1780	hgsc.bcm.edu	37	7	95614244	95614244	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:95614244A>G	ENST00000324972.6	+	8	942	c.749A>G	c.(748-750)gAc>gGc	p.D250G	DYNC1I1_ENST00000537881.1_Missense_Mutation_p.D213G|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.D233G|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.D230G|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.D233G|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.D213G	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	250					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			GAAGATTCCGACATCTTTTTT	0.393																																					p.D250G		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.A749G						.						111.0	114.0	113.0					7																	95614244		2203	4299	6502	SO:0001583	missense	1780	exon8			ATTCCGACATCTT	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2963	protein-coding gene	gene with protein product		603772	"""dynein, cytoplasmic, intermediate polypeptide 1"""	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.749A>G	chr7.hg19:g.95614244A>G	ENSP00000320130:p.Asp250Gly	73.0	0.0		70.0	12.0	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.826322	0.90955	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.79454	-1.1;-1.04;-1.27;-1.04;-1.05;-1.1	4.95	4.95	0.65309	WD40 repeat-like-containing domain (1);	0.049011	0.85682	D	0.000000	D	0.82490	0.5048	M	0.79926	2.475	0.80722	D	1	B;B;B;B;B	0.28178	0.029;0.014;0.049;0.008;0.202	B;B;B;B;B	0.38842	0.047;0.101;0.101;0.047;0.283	D	0.83531	0.0091	10	0.66056	D	0.02	-17.9527	15.0944	0.72223	1.0:0.0:0.0:0.0	.	233;230;233;250;213	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	G	233;250;213;230;213;233	ENSP00000392337:D233G;ENSP00000320130:D250G;ENSP00000438377:D213G;ENSP00000398118:D230G;ENSP00000352348:D213G;ENSP00000412444:D233G	ENSP00000320130:D250G	D	+	2	0	DYNC1I1	95452180	1.000000	0.71417	0.993000	0.49108	0.973000	0.67179	7.312000	0.78968	2.209000	0.71365	0.533000	0.62120	GAC	.	.		0.393	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411	
IFRD1	3475	hgsc.bcm.edu	37	7	112102235	112102235	+	Splice_Site	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:112102235G>A	ENST00000403825.3	+	7	1058		c.e7+1		IFRD1_ENST00000005558.4_Splice_Site|IFRD1_ENST00000535603.1_Splice_Site	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1						adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						AGCTTGAGATGTATGTATTTT	0.338																																					.		Atlas-SNP	.											.	IFRD1	46	.	0			c.647+1G>A						.						94.0	94.0	94.0					7																	112102235		2203	4300	6503	SO:0001630	splice_region_variant	3475	exon7			TGAGATGTATGTA	Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.797+1G>A	chr7.hg19:g.112102235G>A		67.0	0.0		71.0	8.0	NM_001197080	B7Z5G1|O75234|Q5U013|Q9BVE4	Splice_Site	SNP	ENST00000403825.3	hg19	CCDS34736.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.530375	0.64860	.	.	ENSG00000006652	ENST00000005558;ENST00000403825;ENST00000536259;ENST00000535603;ENST00000421296	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8426	0.96695	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IFRD1	111889471	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.914000	0.69964	2.775000	0.95449	0.655000	0.94253	.	.	.		0.338	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	Intron
NOS3	4846	hgsc.bcm.edu	37	7	150698351	150698351	+	Silent	SNP	C	C	T	rs534664057		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:150698351C>T	ENST00000484524.1	+	10	1266	c.1266C>T	c.(1264-1266)gcC>gcT	p.A422A	NOS3_ENST00000461406.1_Silent_p.A216A|NOS3_ENST00000297494.3_Silent_p.A422A|NOS3_ENST00000467517.1_Silent_p.A422A	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACCACCACGCCGCCACGGCCT	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		16148	0.0		0.0	False		,,,				2504	0.001				p.A422A		Atlas-SNP	.											.	NOS3	131	.	0			c.C1266T						.						73.0	77.0	76.0					7																	150698351		2203	4300	6503	SO:0001819	synonymous_variant	4846	exon10			CCACGCCGCCACG		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1266C>T	chr7.hg19:g.150698351C>T		88.0	0.0		96.0	18.0	NM_001160111	Q495E5	Silent	SNP	ENST00000484524.1	hg19	CCDS55182.1																																																																																			.	.		0.637	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603	
SLC4A2	6522	hgsc.bcm.edu	37	7	150773389	150773389	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr7:150773389G>A	ENST00000485713.1	+	23	4701	c.3661G>A	c.(3661-3663)Gca>Aca	p.A1221T	SLC4A2_ENST00000392826.2_Missense_Mutation_p.A1212T|SLC4A2_ENST00000461735.1_Missense_Mutation_p.A1207T|SLC4A2_ENST00000413384.2_Missense_Mutation_p.A1221T|RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000489884.1_5'Flank|SLC4A2_ENST00000310317.5_Missense_Mutation_p.A1139T	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	1221	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCTAACGAGGCAGAGCCGGT	0.632																																					p.A1221T		Atlas-SNP	.											.	SLC4A2	98	.	0			c.G3661A						.						60.0	51.0	54.0					7																	150773389		2202	4300	6502	SO:0001583	missense	6522	exon23			AACGAGGCAGAGC		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.3661G>A	chr7.hg19:g.150773389G>A	ENSP00000419412:p.Ala1221Thr	97.0	0.0		116.0	21.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.385894	0.61956	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.08	4.13	0.48395	.	0.000000	0.85682	D	0.000000	D	0.86527	0.5954	M	0.91920	3.255	0.54753	D	0.999987	B;P;B	0.36633	0.364;0.562;0.427	B;P;B	0.49829	0.236;0.623;0.418	D	0.86766	0.1970	10	0.40728	T	0.16	.	12.0057	0.53257	0.0:0.0:0.8265:0.1735	.	1212;1207;1221	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	T	1221;1221;1139;1212;1207	ENSP00000419412:A1221T;ENSP00000405600:A1221T;ENSP00000311402:A1139T;ENSP00000376571:A1212T;ENSP00000419164:A1207T	ENSP00000311402:A1139T	A	+	1	0	SLC4A2	150404322	1.000000	0.71417	0.997000	0.53966	0.898000	0.52572	6.630000	0.74272	2.361000	0.80049	0.655000	0.94253	GCA	.	.		0.632	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
CYP11B2	1585	hgsc.bcm.edu	37	8	143994784	143994784	+	Silent	SNP	G	G	A	rs200388238		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr8:143994784G>A	ENST00000323110.2	-	6	1040	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	346					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	TGGCTGCGGCGGCCAGGCTCT	0.637									Familial Hyperaldosteronism type I																												p.A346A		Atlas-SNP	.											.	CYP11B2	107	.	0			c.C1038T						.						56.0	61.0	60.0					8																	143994784		2202	4299	6501	SO:0001819	synonymous_variant	1585	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TGCGGCGGCCAGG	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1038C>T	chr8.hg19:g.143994784G>A		147.0	0.0		92.0	15.0	NM_000498	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	hg19	CCDS6393.1																																																																																			.	G|0.999;A|0.001		0.637	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
DMRT3	58524	hgsc.bcm.edu	37	9	990928	990928	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:990928C>T	ENST00000190165.2	+	2	1380	c.1342C>T	c.(1342-1344)Cag>Tag	p.Q448*		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	448					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		TGTGTCAAAGCAGTCCATTTA	0.542																																					p.Q448X		Atlas-SNP	.											.	DMRT3	83	.	0			c.C1342T						.						93.0	90.0	91.0					9																	990928		2203	4300	6503	SO:0001587	stop_gained	58524	exon2			TCAAAGCAGTCCA	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1342C>T	chr9.hg19:g.990928C>T	ENSP00000190165:p.Gln448*	165.0	0.0		139.0	19.0	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Nonsense_Mutation	SNP	ENST00000190165.2	hg19	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	C	35	5.519543	0.96416	.	.	ENSG00000064218	ENST00000190165	.	.	.	5.22	4.28	0.50868	.	0.218002	0.41396	D	0.000885	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-29.9764	15.1877	0.73016	0.1412:0.8588:0.0:0.0	.	.	.	.	X	448	.	ENSP00000190165:Q448X	Q	+	1	0	DMRT3	980928	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.542000	0.53625	2.424000	0.82194	0.655000	0.94253	CAG	.	.		0.542	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
FREM1	158326	hgsc.bcm.edu	37	9	14824891	14824891	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:14824891T>A	ENST00000380880.3	-	11	2764	c.1981A>T	c.(1981-1983)Ata>Tta	p.I661L	FREM1_ENST00000380881.4_Missense_Mutation_p.I662L|FREM1_ENST00000422223.2_Missense_Mutation_p.I661L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	661					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTCTTAGTTATATAGGCCACC	0.433																																					p.I661L		Atlas-SNP	.											.	FREM1	261	.	0			c.A1981T						.						84.0	79.0	81.0					9																	14824891		1834	4082	5916	SO:0001583	missense	158326	exon12			TAGTTATATAGGC	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.1981A>T	chr9.hg19:g.14824891T>A	ENSP00000370262:p.Ile661Leu	111.0	0.0		81.0	21.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	T	8.773	0.926378	0.18056	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.52983	0.64;0.64;0.64	5.92	2.25	0.28309	.	0.214563	0.49305	D	0.000158	T	0.24470	0.0593	N	0.17082	0.46	0.37515	D	0.917298	B	0.11235	0.004	B	0.17979	0.02	T	0.22277	-1.0221	10	0.02654	T	1	-13.0527	8.8665	0.35289	0.0:0.0781:0.3598:0.5621	.	661	Q5H8C1	FREM1_HUMAN	L	662;661;661	ENSP00000370263:I662L;ENSP00000412940:I661L;ENSP00000370262:I661L	ENSP00000370257:I664L	I	-	1	0	FREM1	14814891	1.000000	0.71417	0.995000	0.50966	0.964000	0.63967	1.878000	0.39608	0.448000	0.26722	0.533000	0.62120	ATA	.	.		0.433	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
TEK	7010	hgsc.bcm.edu	37	9	27173269	27173269	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:27173269A>G	ENST00000380036.4	+	6	1252	c.810A>G	c.(808-810)ggA>ggG	p.G270G	TEK_ENST00000406359.4_Silent_p.G270G|TEK_ENST00000519097.1_Silent_p.G166G	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	270	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	GGTGCAGTGGACAAGAGGGAT	0.483																																					p.G270G		Atlas-SNP	.											.	TEK	250	.	0			c.A810G						.						175.0	143.0	154.0					9																	27173269		2203	4300	6503	SO:0001819	synonymous_variant	7010	exon6			CAGTGGACAAGAG	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.810A>G	chr9.hg19:g.27173269A>G		245.0	0.0		234.0	44.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.483	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
SMC5	23137	hgsc.bcm.edu	37	9	72895730	72895730	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:72895730G>T	ENST00000361138.5	+	6	792	c.734G>T	c.(733-735)aGa>aTa	p.R245I		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	245					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						AGGAATGAAAGATATAAACAA	0.338																																					p.R245I		Atlas-SNP	.											.	SMC5	96	.	0			c.G734T						.						135.0	142.0	140.0					9																	72895730		2203	4300	6503	SO:0001583	missense	23137	exon6			ATGAAAGATATAA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.734G>T	chr9.hg19:g.72895730G>T	ENSP00000354957:p.Arg245Ile	31.0	0.0		35.0	5.0	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	hg19	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465506	0.84425	.	.	ENSG00000198887	ENST00000361138	T	0.80909	-1.43	5.2	5.2	0.72013	RecF/RecN/SMC (1);	0.053403	0.64402	D	0.000001	D	0.89550	0.6747	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89234	0.3579	10	0.45353	T	0.12	-15.6154	18.7238	0.91705	0.0:0.0:1.0:0.0	.	245	Q8IY18	SMC5_HUMAN	I	245	ENSP00000354957:R245I	ENSP00000354957:R245I	R	+	2	0	SMC5	72085550	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.556000	0.82233	2.441000	0.82636	0.591000	0.81541	AGA	.	.		0.338	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
SPATA31C1	441452	hgsc.bcm.edu	37	9	90535712	90535712	+	RNA	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:90535712A>T	ENST00000602681.1	+	0	1616							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGGTCGCAGGAGACTACCAAA	0.552																																					p.E297V		Atlas-SNP	.											.	.	.	.	0			c.A890T						.						79.0	75.0	76.0					9																	90535712		692	1591	2283			441452	exon4			CGCAGGAGACTAC	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"""family with sequence similarity 75, member C1"""	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		chr9.hg19:g.90535712A>T		251.0	0.0		260.0	55.0	NM_001145124		Missense_Mutation	SNP	ENST00000602681.1	hg19																																																																																				.	.		0.552	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124	
NUTM2F	54754	hgsc.bcm.edu	37	9	97082514	97082514	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:97082514A>G	ENST00000253262.4	-	5	1364	c.1344T>C	c.(1342-1344)tgT>tgC	p.C448C	NUTM2F_ENST00000335456.7_Silent_p.C433C|NUTM2F_ENST00000341207.4_Silent_p.C433C	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	448																	CTTCCTGGGAACACAGCTTGT	0.567																																					p.C448C		Atlas-SNP	.											.	FAM22F	72	.	0			c.T1344C						.						44.0	54.0	51.0					9																	97082514		1897	4108	6005	SO:0001819	synonymous_variant	54754	exon5			CTGGGAACACAGC		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1344T>C	chr9.hg19:g.97082514A>G		150.0	0.0		118.0	24.0	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Silent	SNP	ENST00000253262.4	hg19	CCDS47994.1																																																																																			.	.		0.567	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
OR13C3	138803	hgsc.bcm.edu	37	9	107298487	107298487	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:107298487A>G	ENST00000374781.2	-	1	650	c.608T>C	c.(607-609)aTt>aCt	p.I203T		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						ATGATTGATAATATTATTCCC	0.418																																					p.I203T	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.T608C						.						116.0	115.0	115.0					9																	107298487		2203	4300	6503	SO:0001583	missense	138803	exon1			TTGATAATATTAT		CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"""GPCR / Class A : Olfactory receptors"""	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.608T>C	chr9.hg19:g.107298487A>G	ENSP00000363913:p.Ile203Thr	90.0	0.0		98.0	19.0	NM_001001961	Q5VVG1|Q6IF52	Missense_Mutation	SNP	ENST00000374781.2	hg19	CCDS35089.1	.	.	.	.	.	.	.	.	.	.	A	9.459	1.092577	0.20471	.	.	ENSG00000204246	ENST00000374781	T	0.00198	8.57	4.08	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	1.087510	0.07255	U	0.866611	T	0.00109	0.0003	N	0.16201	0.385	0.09310	N	1	P	0.35821	0.523	B	0.32149	0.141	T	0.29671	-1.0004	10	0.39692	T	0.17	.	7.0004	0.24807	0.7969:0.0:0.0:0.2031	.	203	Q8NGS6	O13C3_HUMAN	T	203	ENSP00000363913:I203T	ENSP00000363913:I203T	I	-	2	0	OR13C3	106338308	0.000000	0.05858	0.986000	0.45419	0.745000	0.42441	0.188000	0.17018	1.843000	0.53566	0.482000	0.46254	ATT	.	.		0.418	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2		
MUSK	4593	hgsc.bcm.edu	37	9	113509954	113509954	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:113509954G>A	ENST00000374448.4	+	7	921	c.787G>A	c.(787-789)Gac>Aac	p.D263N	MUSK_ENST00000416899.2_Missense_Mutation_p.D263N|MUSK_ENST00000189978.5_Missense_Mutation_p.D263N	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	263	Ig-like 3.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						GAGTGTGAAAGACCGAGTGAT	0.423																																					p.D273N		Atlas-SNP	.											.	MUSK	112	.	0			c.G817A						.						179.0	167.0	170.0					9																	113509954		1921	4138	6059	SO:0001583	missense	4593	exon8			GTGAAAGACCGAG	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.787G>A	chr9.hg19:g.113509954G>A	ENSP00000363571:p.Asp263Asn	116.0	0.0		126.0	32.0	NM_001166280	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167133	0.57476	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	T	0.31510	1.49	5.78	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.049251	0.85682	D	0.000000	T	0.37210	0.0995	N	0.22421	0.69	0.80722	D	1	D;D	0.69078	0.993;0.997	D;D	0.67382	0.951;0.93	T	0.09250	-1.0683	10	0.25106	T	0.35	.	12.7894	0.57523	0.0795:0.0:0.9205:0.0	.	263;273	O15146;F5H6T2	MUSK_HUMAN;.	N	263;263;263;273;273;263	ENSP00000363571:D263N	ENSP00000189978:D263N	D	+	1	0	MUSK	112549775	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.003000	0.70701	1.446000	0.47643	0.655000	0.94253	GAC	.	.		0.423	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PTGR1	22949	hgsc.bcm.edu	37	9	114348379	114348379	+	Silent	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:114348379T>A	ENST00000407693.2	-	5	538	c.276A>T	c.(274-276)acA>acT	p.T92T	PTGR1_ENST00000238248.3_5'UTR|PTGR1_ENST00000538962.1_Silent_p.T92T|PTGR1_ENST00000309195.5_Silent_p.T92T	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	92					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						TGGAGTGCGTTGTCCAGCCTG	0.463																																					p.T92T	Ovarian(200;132 2151 7551 19220 46064)	Atlas-SNP	.											.	PTGR1	23	.	0			c.A276T						.						163.0	131.0	142.0					9																	114348379		2203	4300	6503	SO:0001819	synonymous_variant	22949	exon5			GTGCGTTGTCCAG	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"""zinc binding alcohol dehydrogenase domain containing 3"""	601274	"""leukotriene B4 12-hydroxydehydrogenase"""	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.276A>T	chr9.hg19:g.114348379T>A		264.0	0.0		219.0	41.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Silent	SNP	ENST00000407693.2	hg19	CCDS6779.1																																																																																			.	.		0.463	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2		
COL27A1	85301	hgsc.bcm.edu	37	9	116973290	116973290	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:116973290G>A	ENST00000356083.3	+	12	2742	c.2351G>A	c.(2350-2352)gGc>gAc	p.G784D	MIR455_ENST00000384993.1_RNA	NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	784	Collagen-like 3.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GGCAAGAGGGGCAAGATGGGT	0.642																																					p.G784D		Atlas-SNP	.											.	COL27A1	200	.	0			c.G2351A						.						119.0	102.0	108.0					9																	116973290		2203	4300	6503	SO:0001583	missense	85301	exon12			AGAGGGGCAAGAT	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.2351G>A	chr9.hg19:g.116973290G>A	ENSP00000348385:p.Gly784Asp	141.0	0.0		96.0	14.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.855050	0.71719	.	.	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.99619	-5.52;-6.28	5.67	5.67	0.87782	.	.	.	.	.	D	0.99822	0.9921	H	0.98629	4.285	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.85130	0.87;0.997	D	0.96851	0.9625	9	0.87932	D	0	.	17.2564	0.87057	0.0:0.0:1.0:0.0	.	784;680	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	D	784;784;680;680	ENSP00000348385:G784D;ENSP00000391328:G680D	ENSP00000348385:G784D	G	+	2	0	COL27A1	116013111	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.384000	0.97219	2.676000	0.91093	0.561000	0.74099	GGC	.	.		0.642	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
FBXW2	26190	hgsc.bcm.edu	37	9	123526906	123526906	+	Silent	SNP	C	C	T	rs377576429		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:123526906C>T	ENST00000608872.1	-	8	1483	c.1296G>A	c.(1294-1296)acG>acA	p.T432T	FBXW2_ENST00000340778.5_Silent_p.T367T|FBXW2_ENST00000493559.1_Intron	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	432					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)	p.T432T(1)		ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						AGACCAAGCCCGTGTCATTGT	0.567																																					p.T432T		Atlas-SNP	.											.	FBXW2	34	.	1	Substitution - coding silent(1)	lung(1)	c.G1296A						.	C		0,4338		0,0,2169	143.0	155.0	151.0		1296	-5.2	0.7	9		151	4,8512		0,4,4254	no	coding-synonymous	FBXW2	NM_012164.3		0,4,6423	TT,TC,CC		0.047,0.0,0.0311		432/455	123526906	4,12850	2169	4258	6427	SO:0001819	synonymous_variant	26190	exon8			CAAGCCCGTGTCA	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13608	protein-coding gene	gene with protein product		609071	"""F-box and WD-40 domain protein 2"""			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1296G>A	chr9.hg19:g.123526906C>T		202.0	0.0		201.0	39.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Silent	SNP	ENST00000608872.1	hg19	CCDS43872.1																																																																																			.	.		0.567	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2		
NR6A1	2649	hgsc.bcm.edu	37	9	127284984	127284984	+	Nonstop_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:127284984T>C	ENST00000487099.2	-	10	1600	c.1443A>G	c.(1441-1443)tgA>tgG	p.*481W	NR6A1_ENST00000344523.4_Nonstop_Mutation_p.*480W|NR6A1_ENST00000416460.2_Nonstop_Mutation_p.*476W|NR6A1_ENST00000373584.3_Nonstop_Mutation_p.*477W	NM_001278546.1	NP_001265475.1	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1	0					cell proliferation (GO:0008283)|gamete generation (GO:0007276)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	17						CTGGAACAGGTCATTCCTTGC	0.592																																					p.X481W	Esophageal Squamous(192;272 2884 6208 20560)	Atlas-SNP	.											.	NR6A1	38	.	0			c.A1443G						.						48.0	34.0	39.0					9																	127284984		2202	4298	6500	SO:0001578	stop_lost	2649	exon10			AACAGGTCATTCC	U64876	CCDS35137.1, CCDS55340.1, CCDS65127.1	9q33.3	2014-01-21			ENSG00000148200	ENSG00000148200		"""Nuclear hormone receptors"""	7985	protein-coding gene	gene with protein product		602778		GCNF		9134503, 8982251	Standard	NM_001489		Approved	GCNF1, RTR, CT150	uc004bor.1	Q15406	OTTHUMG00000020661	ENST00000487099.2:c.1443A>G	chr9.hg19:g.127284984T>C	ENSP00000420267:p.*481Cysext*66	42.0	0.0		33.0	4.0	NM_033334	O00551|O00603|Q5T6F4|Q8NHQ0|Q92898|Q99802	Missense_Mutation	SNP	ENST00000487099.2	hg19	CCDS35137.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.864714	0.71949	.	.	ENSG00000148200	ENST00000487099;ENST00000373584;ENST00000416460;ENST00000344523	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2214	0.73313	0.0:0.0:0.0:1.0	.	.	.	.	W	481;477;476;480	.	.	X	-	3	0	NR6A1	126324805	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.412000	0.66392	2.168000	0.68352	0.533000	0.62120	TGA	.	.		0.592	NR6A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054043.4		
USP20	10868	hgsc.bcm.edu	37	9	132632035	132632035	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:132632035T>C	ENST00000315480.4	+	14	1635	c.1477T>C	c.(1477-1479)Tac>Cac	p.Y493H	USP20_ENST00000372429.3_Missense_Mutation_p.Y493H|USP20_ENST00000358355.1_Missense_Mutation_p.Y493H			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	493	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				TTCAGCCATCTACCAGAATGT	0.597																																					p.Y493H		Atlas-SNP	.											.	USP20	186	.	0			c.T1477C						.						69.0	71.0	71.0					9																	132632035		1949	4135	6084	SO:0001583	missense	10868	exon14			GCCATCTACCAGA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1477T>C	chr9.hg19:g.132632035T>C	ENSP00000313811:p.Tyr493His	260.0	0.0		176.0	8.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	T	4.693	0.128839	0.08981	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.02863	4.13;4.13;4.13	4.84	4.84	0.62591	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.394499	0.28665	N	0.014553	T	0.00906	0.0030	N	0.00599	-1.345	0.46798	D	0.999202	B	0.06786	0.001	B	0.06405	0.002	T	0.48305	-0.9047	10	0.07175	T	0.84	.	8.6795	0.34201	0.0:0.0853:0.0:0.9147	.	493	Q9Y2K6	UBP20_HUMAN	H	493	ENSP00000361506:Y493H;ENSP00000313811:Y493H;ENSP00000351122:Y493H	ENSP00000313811:Y493H	Y	+	1	0	USP20	131671856	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.358000	0.66064	2.165000	0.68154	0.533000	0.62120	TAC	.	.		0.597	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
NUP214	8021	hgsc.bcm.edu	37	9	134038560	134038560	+	Splice_Site	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:134038560G>A	ENST00000359428.5	+	19	2867	c.2723G>A	c.(2722-2724)aGt>aAt	p.S908N	RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000586662.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|NUP214_ENST00000411637.2_Splice_Site_p.S898N|RP11-544A12.4_ENST00000592466.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|NUP214_ENST00000451030.1_Splice_Site_p.S909N|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000589128.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000589095.1_RNA|RP11-544A12.4_ENST00000417798.2_RNA|RP11-544A12.4_ENST00000588325.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	908	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		AGCATTCACAGGTGTGGAGAG	0.483			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.S908N	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G2723A						.						79.0	75.0	76.0					9																	134038560		2203	4300	6503	SO:0001630	splice_region_variant	8021	exon19			TTCACAGGTGTGG	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.2723+1G>A	chr9.hg19:g.134038560G>A		103.0	0.0		95.0	17.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030341	0.54790	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	T;T;T	0.35605	1.3;1.32;1.31	5.6	5.6	0.85130	.	0.147968	0.31233	N	0.008012	T	0.31482	0.0798	N	0.08118	0	0.80722	D	1	P;D;B;P	0.53312	0.672;0.959;0.057;0.928	B;P;B;P	0.50659	0.412;0.647;0.013;0.647	T	0.27191	-1.0081	10	0.59425	D	0.04	-8.2165	16.757	0.85502	0.0:0.0:1.0:0.0	.	897;502;898;908	P35658-2;Q5JUP9;P35658-4;P35658	.;.;.;NU214_HUMAN	N	908;898;909;897;502;337	ENSP00000352400:S908N;ENSP00000396576:S898N;ENSP00000405014:S909N	ENSP00000352400:S908N	S	+	2	0	NUP214	133028381	1.000000	0.71417	0.970000	0.41538	0.375000	0.29983	5.485000	0.66850	2.636000	0.89361	0.467000	0.42956	AGT	.	.		0.483	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	Missense_Mutation
SEC16A	9919	hgsc.bcm.edu	37	9	139361447	139361447	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:139361447A>G	ENST00000371706.3	-	4	3390	c.3357T>C	c.(3355-3357)taT>taC	p.Y1119Y	SEC16A_ENST00000313050.7_Silent_p.Y1297Y|SEC16A_ENST00000431893.2_Silent_p.Y1119Y|SEC16A_ENST00000290037.6_Silent_p.Y1119Y			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1119	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		TGTATGCGTCATACTCTGCAT	0.607																																					p.Y1297Y		Atlas-SNP	.											.	SEC16A	249	.	0			c.T3891C						.						74.0	79.0	78.0					9																	139361447		2003	4160	6163	SO:0001819	synonymous_variant	9919	exon6			TGCGTCATACTCT	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.3357T>C	chr9.hg19:g.139361447A>G		48.0	0.0		62.0	14.0	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	hg19																																																																																				.	.		0.607	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
CUBN	8029	hgsc.bcm.edu	37	10	16967302	16967302	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:16967302A>T	ENST00000377833.4	-	43	6649	c.6584T>A	c.(6583-6585)tTt>tAt	p.F2195Y		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2195	CUB 15. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATCAGAAATAAACTGAACAAA	0.388																																					p.F2195Y		Atlas-SNP	.											.	CUBN	515	.	0			c.T6584A						.						69.0	70.0	69.0					10																	16967302		2203	4300	6503	SO:0001583	missense	8029	exon43			GAAATAAACTGAA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.6584T>A	chr10.hg19:g.16967302A>T	ENSP00000367064:p.Phe2195Tyr	260.0	0.0		298.0	48.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.325243	0.81580	.	.	ENSG00000107611	ENST00000377833	T	0.30182	1.54	5.32	5.32	0.75619	CUB (5);	0.000000	0.48286	D	0.000191	T	0.62660	0.2446	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.69636	-0.5092	10	0.51188	T	0.08	.	15.4412	0.75184	1.0:0.0:0.0:0.0	.	2195	O60494	CUBN_HUMAN	Y	2195	ENSP00000367064:F2195Y	ENSP00000367064:F2195Y	F	-	2	0	CUBN	17007308	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	8.494000	0.90477	2.241000	0.73720	0.533000	0.62120	TTT	.	.		0.388	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
GPR158	57512	hgsc.bcm.edu	37	10	25887663	25887663	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:25887663G>T	ENST00000376351.3	+	11	3467	c.3108G>T	c.(3106-3108)atG>atT	p.M1036I	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1036					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.M1036I(1)|p.M1036_E1037>IK(1)		breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CTTCTGAAATGGAGAAAAACC	0.463																																					p.M1036I		Atlas-SNP	.											GPR158,NS,carcinoma,0,1	GPR158	255	.	2	Substitution - Missense(1)|Complex - compound substitution(1)	lung(2)	c.G3108T						.						72.0	70.0	71.0					10																	25887663		2203	4300	6503	SO:0001583	missense	57512	exon11			TGAAATGGAGAAA	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3108G>T	chr10.hg19:g.25887663G>T	ENSP00000365529:p.Met1036Ile	88.0	0.0		110.0	31.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	6.532	0.466459	0.12402	.	.	ENSG00000151025	ENST00000376351	T	0.28454	1.61	5.27	1.02	0.19986	.	0.582024	0.17324	N	0.178381	T	0.19485	0.0468	L	0.36672	1.1	0.22684	N	0.998852	B	0.02656	0.0	B	0.09377	0.004	T	0.13926	-1.0491	10	0.40728	T	0.16	.	4.7247	0.12935	0.3964:0.272:0.3316:0.0	.	1036	Q5T848	GP158_HUMAN	I	1036	ENSP00000365529:M1036I	ENSP00000365529:M1036I	M	+	3	0	GPR158	25927669	0.062000	0.20869	1.000000	0.80357	0.983000	0.72400	-0.120000	0.10660	0.593000	0.29745	0.655000	0.94253	ATG	.	.		0.463	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37507997	37507997	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:37507997C>T	ENST00000602533.1	+	34	3288	c.3189C>T	c.(3187-3189)gcC>gcT	p.A1063A	ANKRD30A_ENST00000361713.1_Silent_p.A1063A|ANKRD30A_ENST00000374660.1_Silent_p.A1182A			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1119					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TGGAAATAGCCACACTGAAAC	0.313																																					p.A1063A		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.C3189T						.						61.0	60.0	61.0					10																	37507997		1812	4062	5874	SO:0001819	synonymous_variant	91074	exon34			AATAGCCACACTG	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3189C>T	chr10.hg19:g.37507997C>T		174.0	0.0		203.0	65.0	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	hg19																																																																																				.	.		0.313	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
PCDH15	65217	hgsc.bcm.edu	37	10	55600110	55600110	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:55600110T>C	ENST00000320301.6	-	29	4347	c.3953A>G	c.(3952-3954)aAc>aGc	p.N1318S	PCDH15_ENST00000395432.2_Missense_Mutation_p.N1281S|PCDH15_ENST00000373965.2_Missense_Mutation_p.N1325S|PCDH15_ENST00000395438.1_Missense_Mutation_p.N1318S|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.N1325S|PCDH15_ENST00000395430.1_Missense_Mutation_p.N1318S|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Missense_Mutation_p.N1247S|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.N929S|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.N1296S|PCDH15_ENST00000361849.3_Missense_Mutation_p.N1318S|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000414778.1_Missense_Mutation_p.N1323S	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1318					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GATGGCTCTGTTGGTTTGGGG	0.428										HNSCC(58;0.16)																											p.N1323S		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A3968G						.						159.0	151.0	153.0					10																	55600110		2203	4300	6503	SO:0001583	missense	65217	exon30			GCTCTGTTGGTTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3953A>G	chr10.hg19:g.55600110T>C	ENSP00000322604:p.Asn1318Ser	142.0	0.0		186.0	30.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.456328	0.84317	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.61392	0.3;0.34;0.24;0.26;0.25;0.14;0.13;0.18;0.13;0.11;0.11	5.43	5.43	0.79202	.	.	.	.	.	T	0.67878	0.2940	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.997;1.0;0.999;0.998;0.999;1.0;0.997;0.997;0.998;0.998;0.997;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D	0.85130	0.989;0.997;0.97;0.952;0.997;0.997;0.989;0.995;0.952;0.952;0.995;0.997;0.97	T	0.70204	-0.4936	9	0.59425	D	0.04	.	15.4284	0.75072	0.0:0.0:0.0:1.0	.	1296;1318;1318;1323;1247;1281;1318;1318;1325;1325;1318;1323;1318	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	S	1325;1323;1318;1318;929;1325;1281;1318;1296;1318;1318;1323;1247	ENSP00000363076:N1325S;ENSP00000410304:N1323S;ENSP00000378826:N1318S;ENSP00000386693:N929S;ENSP00000378832:N1325S;ENSP00000378820:N1281S;ENSP00000354950:N1318S;ENSP00000378821:N1296S;ENSP00000322604:N1318S;ENSP00000378818:N1318S;ENSP00000412628:N1247S	ENSP00000322604:N1318S	N	-	2	0	PCDH15	55270116	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.986000	0.88173	2.182000	0.69389	0.472000	0.43445	AAC	.	.		0.428	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
CCSER2	54462	hgsc.bcm.edu	37	10	86131874	86131874	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:86131874G>C	ENST00000224756.8	+	2	1251	c.1066G>C	c.(1066-1068)Gct>Cct	p.A356P	CCSER2_ENST00000372088.2_Missense_Mutation_p.A356P|CCSER2_ENST00000359979.4_Missense_Mutation_p.A356P	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	356					microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											TACAGTTTTGGCTAAGGACAG	0.373																																					p.A356P		Atlas-SNP	.											.	CCSER2	7	.	0			c.G1066C						.						104.0	103.0	103.0					10																	86131874		2203	4300	6503	SO:0001583	missense	54462	exon2			GTTTTGGCTAAGG		CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"""KIAA1128"", ""family with sequence similarity 190, member B"""	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.1066G>C	chr10.hg19:g.86131874G>C	ENSP00000224756:p.Ala356Pro	104.0	0.0		142.0	23.0	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Missense_Mutation	SNP	ENST00000224756.8	hg19	CCDS31235.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.437135	0.25900	.	.	ENSG00000107771	ENST00000359979;ENST00000224756;ENST00000372088	T;T;T	0.55588	0.51;1.86;1.86	5.73	-0.0679	0.13758	.	0.578352	0.16610	N	0.206949	T	0.41488	0.1161	L	0.44542	1.39	0.09310	N	1	P;B;P	0.46220	0.874;0.437;0.874	B;B;P	0.44990	0.369;0.189;0.466	T	0.27640	-1.0068	10	0.52906	T	0.07	-1.1022	3.7258	0.08474	0.4805:0.0:0.3444:0.1751	.	356;356;356	Q9H7U1-3;Q9H7U1;Q9H7U1-2	.;F190B_HUMAN;.	P	356	ENSP00000353068:A356P;ENSP00000224756:A356P;ENSP00000361160:A356P	ENSP00000224756:A356P	A	+	1	0	FAM190B	86121854	0.000000	0.05858	0.003000	0.11579	0.878000	0.50629	-0.266000	0.08631	0.381000	0.24851	-0.136000	0.14681	GCT	.	.		0.373	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999	
OPN4	94233	hgsc.bcm.edu	37	10	88419162	88419162	+	Missense_Mutation	SNP	T	T	C	rs34344653		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:88419162T>C	ENST00000241891.5	+	5	904	c.737T>C	c.(736-738)cTc>cCc	p.L246P	OPN4_ENST00000372071.2_Missense_Mutation_p.L257P	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	246					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						GTGTTCTTCCTCCCTCTGCTT	0.592																																					p.L257P		Atlas-SNP	.											.	OPN4	61	.	0			c.T770C						.						260.0	190.0	214.0					10																	88419162		2203	4300	6503	SO:0001583	missense	94233	exon6			TCTTCCTCCCTCT	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	ENST00000241891.5:c.737T>C	chr10.hg19:g.88419162T>C	ENSP00000241891:p.Leu246Pro	101.0	0.0		148.0	26.0	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369293	0.82463	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.45668	0.89;0.89;0.89	5.15	5.15	0.70609	GPCR, rhodopsin-like superfamily (1);	0.156406	0.39083	N	0.001476	T	0.66096	0.2755	M	0.81614	2.55	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.72982	0.979;0.961;0.943	T	0.71971	-0.4431	10	0.87932	D	0	.	14.9869	0.71356	0.0:0.0:0.0:1.0	.	257;246;257	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	P	257;246;257	ENSP00000361141:L257P;ENSP00000241891:L246P;ENSP00000393132:L257P	ENSP00000241891:L246P	L	+	2	0	OPN4	88409142	1.000000	0.71417	0.834000	0.33040	0.928000	0.56348	6.172000	0.71932	1.942000	0.56320	0.533000	0.62120	CTC	.	.		0.592	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
BMPR1A	657	hgsc.bcm.edu	37	10	88649933	88649933	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:88649933G>A	ENST00000372037.3	+	4	719	c.182G>A	c.(181-183)tGc>tAc	p.C61Y	RNU1-19P_ENST00000363306.1_RNA	NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	61					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						TTTTTAAAGTGCTATTGCTCA	0.403			"""Mis, N, F"""			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2																												p.C61Y	Ovarian(190;603 2086 22044 30335 47971)	Atlas-SNP	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"""bone morphogenetic protein receptor, type IA"""		E	.	BMPR1A	118	.	0			c.G182A						.						165.0	151.0	156.0					10																	88649933		2203	4300	6503	SO:0001583	missense	657	exon4	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	TAAAGTGCTATTG	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"""CD molecules"""	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.182G>A	chr10.hg19:g.88649933G>A	ENSP00000361107:p.Cys61Tyr	243.0	0.0		275.0	34.0	NM_004329	A8K6U9|Q8NEN8	Missense_Mutation	SNP	ENST00000372037.3	hg19	CCDS7378.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.805747	0.90623	.	.	ENSG00000107779	ENST00000224764;ENST00000372037	D	0.99940	-8.4	6.01	6.01	0.97437	TGF-beta receptor/activin receptor, type I/II (1);	0.000000	0.85682	D	0.000000	D	0.99951	0.9979	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96378	0.9279	10	0.87932	D	0	.	20.5211	0.99222	0.0:0.0:1.0:0.0	.	61	P36894	BMR1A_HUMAN	Y	61	ENSP00000361107:C61Y	ENSP00000224764:C61Y	C	+	2	0	BMPR1A	88639913	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.065000	0.93941	2.861000	0.98227	0.650000	0.86243	TGC	.	.		0.403	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329	
IFIT2	3433	hgsc.bcm.edu	37	10	91066441	91066441	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:91066441C>T	ENST00000371826.3	+	2	897	c.728C>T	c.(727-729)gCc>gTc	p.A243V	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	243					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				TTGGAGAAAGCCCCAGGTGTA	0.438																																					p.A243V		Atlas-SNP	.											.	IFIT2	39	.	0			c.C728T						.						78.0	78.0	78.0					10																	91066441		1981	4180	6161	SO:0001583	missense	3433	exon2			AGAAAGCCCCAGG	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"""Tetratricopeptide (TTC) repeat domain containing"""	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.728C>T	chr10.hg19:g.91066441C>T	ENSP00000360891:p.Ala243Val	129.0	0.0		137.0	12.0	NM_001547	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	hg19	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	C	8.312	0.822276	0.16678	.	.	ENSG00000119922	ENST00000371826	T	0.38240	1.15	4.58	-2.38	0.06622	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.684102	0.13110	U	0.413079	T	0.26412	0.0645	M	0.62723	1.935	0.09310	N	0.999999	B	0.12630	0.006	B	0.15052	0.012	T	0.25882	-1.0119	10	0.33940	T	0.23	-0.2574	1.7187	0.02907	0.1298:0.3984:0.2394:0.2324	.	243	P09913	IFIT2_HUMAN	V	243	ENSP00000360891:A243V	ENSP00000360891:A243V	A	+	2	0	IFIT2	91056421	0.002000	0.14202	0.012000	0.15200	0.069000	0.16628	0.167000	0.16602	-0.421000	0.07416	0.655000	0.94253	GCC	.	.		0.438	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547	
PLCE1	51196	hgsc.bcm.edu	37	10	95791760	95791760	+	Silent	SNP	G	G	A	rs573916830	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:95791760G>A	ENST00000371380.3	+	1	1192	c.957G>A	c.(955-957)aaG>aaA	p.K319K	PLCE1_ENST00000260766.3_Silent_p.K319K			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	319					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				AAAGCAAAAAGGAGCGATCCA	0.388																																					p.K319K		Atlas-SNP	.											.	PLCE1	543	.	0			c.G957A						.						114.0	112.0	113.0					10																	95791760		1853	4088	5941	SO:0001819	synonymous_variant	51196	exon2			CAAAAAGGAGCGA		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.957G>A	chr10.hg19:g.95791760G>A		110.0	0.0		134.0	13.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	hg19	CCDS41552.1																																																																																			.	.		0.388	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
SLK	9748	hgsc.bcm.edu	37	10	105763103	105763103	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:105763103A>G	ENST00000369755.3	+	9	2712	c.2167A>G	c.(2167-2169)Aaa>Gaa	p.K723E	SLK_ENST00000335753.4_Missense_Mutation_p.K723E	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	723					apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TGGAGAAAATAAAGAAGAAAT	0.373																																					p.K723E	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A2167G						.						48.0	51.0	50.0					10																	105763103		2203	4300	6503	SO:0001583	missense	9748	exon9			GAAAATAAAGAAG		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.2167A>G	chr10.hg19:g.105763103A>G	ENSP00000358770:p.Lys723Glu	40.0	0.0		40.0	12.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	8.487	0.861211	0.17178	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.70045	-0.45;-0.45	5.71	5.71	0.89125	Protein kinase-like domain (1);	0.382752	0.29348	N	0.012408	T	0.62196	0.2408	M	0.63428	1.95	0.45108	D	0.99812	B;B	0.19583	0.037;0.022	B;B	0.19148	0.024;0.011	T	0.58624	-0.7604	10	0.31617	T	0.26	.	11.086	0.48086	0.9281:0.0:0.0719:0.0	.	723;723	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	E	723	ENSP00000336824:K723E;ENSP00000358770:K723E	ENSP00000336824:K723E	K	+	1	0	SLK	105753093	1.000000	0.71417	0.994000	0.49952	0.092000	0.18411	4.782000	0.62396	2.184000	0.69523	0.454000	0.30748	AAA	.	.		0.373	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
CFAP43	80217	hgsc.bcm.edu	37	10	105952057	105952057	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:105952057A>G	ENST00000278064.2	-	12	1564	c.1239T>C	c.(1237-1239)taT>taC	p.Y413Y	WDR96_ENST00000357060.3_Silent_p.Y482Y|WDR96_ENST00000428666.1_Silent_p.Y483Y																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTTGCTGATCATAACTAGAAA	0.363																																					p.Y482Y		Atlas-SNP	.											.	WDR96	183	.	0			c.T1446C						.						97.0	94.0	95.0					10																	105952057		2202	4299	6501	SO:0001819	synonymous_variant	80217	exon12			CTGATCATAACTA																												ENST00000278064.2:c.1239T>C	chr10.hg19:g.105952057A>G		69.0	0.0		75.0	19.0	NM_025145		Silent	SNP	ENST00000278064.2	hg19																																																																																				.	.		0.363	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1		
EDRF1	26098	hgsc.bcm.edu	37	10	127434413	127434413	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:127434413A>G	ENST00000356792.4	+	19	2960	c.2728A>G	c.(2728-2730)Atg>Gtg	p.M910V	RP11-383C5.7_ENST00000594025.1_RNA|RP11-383C5.7_ENST00000449436.1_RNA|RP11-383C5.7_ENST00000593871.1_RNA|RP11-383C5.7_ENST00000601363.1_RNA|RP11-383C5.7_ENST00000602030.1_RNA|C10orf137_ENST00000337623.3_Missense_Mutation_p.M876V|RP11-383C5.7_ENST00000600784.1_RNA	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		910					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GGGAAGGCTCATGCGGATTTG	0.428																																					p.M910V		Atlas-SNP	.											.	C10orf137	153	.	0			c.A2728G						.						118.0	116.0	117.0					10																	127434413		2203	4300	6503	SO:0001583	missense	26098	exon19			AGGCTCATGCGGA																												ENST00000356792.4:c.2728A>G	chr10.hg19:g.127434413A>G	ENSP00000349244:p.Met910Val	128.0	0.0		166.0	50.0	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	hg19	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.980803	0.53827	.	.	ENSG00000107938	ENST00000356792;ENST00000337623	T;T	0.75589	-0.95;-0.95	5.6	5.6	0.85130	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.84880	0.5570	M	0.71871	2.18	0.80722	D	1	D;D;P	0.71674	0.982;0.998;0.917	D;D;D	0.70016	0.961;0.967;0.915	D	0.85902	0.1435	10	0.54805	T	0.06	.	15.8023	0.78463	1.0:0.0:0.0:0.0	.	910;257;876	Q3B7T1;Q5VZQ1;Q3B7T1-5	EDRF1_HUMAN;.;.	V	910;876	ENSP00000349244:M910V;ENSP00000336727:M876V	ENSP00000336727:M876V	M	+	1	0	C10orf137	127424403	1.000000	0.71417	0.998000	0.56505	0.073000	0.16967	8.962000	0.93254	2.137000	0.66172	0.533000	0.62120	ATG	.	.		0.428	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1		
KNDC1	85442	hgsc.bcm.edu	37	10	135038187	135038187	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:135038187G>A	ENST00000304613.3	+	30	5064	c.5043G>A	c.(5041-5043)caG>caA	p.Q1681Q	KNDC1_ENST00000368572.2_Silent_p.Q1683Q			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1681	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TGGTGAGCCAGGTGCACGCGT	0.612																																					p.Q1681Q		Atlas-SNP	.											.	KNDC1	155	.	0			c.G5043A						.						86.0	70.0	75.0					10																	135038187		2203	4300	6503	SO:0001819	synonymous_variant	85442	exon30			GAGCCAGGTGCAC	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.5043G>A	chr10.hg19:g.135038187G>A		207.0	0.0		307.0	37.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	hg19	CCDS7674.1																																																																																			.	.		0.612	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
ECHS1	1892	hgsc.bcm.edu	37	10	135179489	135179489	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:135179489C>G	ENST00000368547.3	-	6	1085	c.730G>C	c.(730-732)Gtg>Ctg	p.V244L		NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	244					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		CCTGCATTCACTGATTCTTTG	0.483																																					p.V244L	GBM(132;1720 1771 5373 10277 21402)	Atlas-SNP	.											.	ECHS1	31	.	0			c.G730C						.						212.0	176.0	188.0					10																	135179489		2202	4300	6502	SO:0001583	missense	1892	exon6			CATTCACTGATTC		CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"""enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"""			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.730G>C	chr10.hg19:g.135179489C>G	ENSP00000357535:p.Val244Leu	101.0	0.0		100.0	18.0	NM_004092	O00739|Q5VWY1|Q96H54	Missense_Mutation	SNP	ENST00000368547.3	hg19	CCDS7681.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760004	0.69763	.	.	ENSG00000127884	ENST00000368547	T	0.67698	-0.28	5.39	5.39	0.77823	Crontonase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63604	0.2525	L	0.34521	1.04	0.80722	D	1	B	0.28233	0.204	B	0.38755	0.281	T	0.65076	-0.6256	10	0.72032	D	0.01	.	15.0604	0.71947	0.0:1.0:0.0:0.0	.	244	P30084	ECHM_HUMAN	L	244	ENSP00000357535:V244L	ENSP00000357535:V244L	V	-	1	0	ECHS1	135029479	0.999000	0.42202	0.993000	0.49108	0.944000	0.59088	4.484000	0.60271	2.701000	0.92244	0.555000	0.69702	GTG	.	.		0.483	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1		
ODF3	113746	hgsc.bcm.edu	37	11	198506	198506	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:198506C>A	ENST00000325113.4	+	5	772	c.455C>A	c.(454-456)aCc>aAc	p.T152N	BET1L_ENST00000410108.1_Intron|ODF3_ENST00000525282.1_Missense_Mutation_p.T152N	NM_053280.3	NP_444510.2	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3	152					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	outer dense fiber (GO:0001520)				biliary_tract(1)|breast(1)|kidney(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)	9		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		GGGCCCAATACCGTCGGCAAG	0.662																																					p.T152N		Atlas-SNP	.											.	ODF3	27	.	0			c.C455A						.						56.0	56.0	56.0					11																	198506		2203	4300	6503	SO:0001583	missense	113746	exon5			CCAATACCGTCGG	AB067774	CCDS7688.1, CCDS65981.1	11p15.5	2010-04-23			ENSG00000177947	ENSG00000177947			19905	protein-coding gene	gene with protein product	"""cancer/testis antigen 135"""	608356				11870087	Standard	NM_001286136		Approved	SHIPPO1, hSHIPPO, CT135	uc001lob.3	Q96PU9	OTTHUMG00000119073	ENST00000325113.4:c.455C>A	chr11.hg19:g.198506C>A	ENSP00000325868:p.Thr152Asn	171.0	0.0		159.0	23.0	NM_053280	B7ZLT0|Q69YX0	Missense_Mutation	SNP	ENST00000325113.4	hg19	CCDS7688.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.845103	0.71603	.	.	ENSG00000177947	ENST00000325113;ENST00000540150;ENST00000525282	T;T	0.32272	1.48;1.46	4.87	4.87	0.63330	.	0.127854	0.35407	N	0.003240	T	0.35508	0.0934	N	0.19112	0.55	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.68483	0.939;0.958	T	0.06075	-1.0847	10	0.15952	T	0.53	-21.333	13.5189	0.61555	0.0:1.0:0.0:0.0	.	152;152	B7ZLT0;Q96PU9	.;ODF3A_HUMAN	N	152;69;152	ENSP00000325868:T152N;ENSP00000436588:T152N	ENSP00000325868:T152N	T	+	2	0	ODF3	188506	0.002000	0.14202	0.732000	0.30844	0.854000	0.48673	1.682000	0.37628	2.227000	0.72691	0.561000	0.74099	ACC	.	.		0.662	ODF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239287.1		
PHRF1	57661	hgsc.bcm.edu	37	11	611702	611702	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:611702C>A	ENST00000264555.5	+	18	5003	c.4875C>A	c.(4873-4875)gaC>gaA	p.D1625E	PHRF1_ENST00000413872.2_Missense_Mutation_p.D1623E|PHRF1_ENST00000416188.2_Missense_Mutation_p.D1624E|PHRF1_ENST00000533464.1_Missense_Mutation_p.D1621E	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1625					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CGTACGTGGACAAGTACAGGC	0.617																																					p.D1624E		Atlas-SNP	.											.	PHRF1	188	.	0			c.C4872A						.						55.0	61.0	59.0					11																	611702		2138	4264	6402	SO:0001583	missense	57661	exon18			CGTGGACAAGTAC	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4875C>A	chr11.hg19:g.611702C>A	ENSP00000264555:p.Asp1625Glu	66.0	0.0		81.0	9.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	C	10.15	1.271567	0.23221	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03	4.58	-0.252	0.12999	.	0.201391	0.24920	N	0.034546	T	0.47303	0.1438	L	0.42245	1.32	0.32907	D	0.514006	B;B;B;B	0.31548	0.15;0.328;0.099;0.06	B;B;B;B	0.37015	0.046;0.239;0.069;0.031	T	0.42816	-0.9429	10	0.30854	T	0.27	-32.3459	2.791	0.05388	0.153:0.3802:0.3095:0.1572	.	1621;1623;1624;1625	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	E	1625;1623;1624;1621	ENSP00000264555:D1625E;ENSP00000388589:D1623E;ENSP00000410626:D1624E;ENSP00000431870:D1621E	ENSP00000264555:D1625E	D	+	3	2	PHRF1	601702	0.974000	0.33945	0.992000	0.48379	0.174000	0.22865	0.139000	0.16036	-0.053000	0.13289	-1.134000	0.01955	GAC	.	.		0.617	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
MUC2	4583	hgsc.bcm.edu	37	11	1081136	1081136	+	Missense_Mutation	SNP	G	G	A	rs555224884		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:1081136G>A	ENST00000441003.2	+	11	1459	c.1432G>A	c.(1432-1434)Gtg>Atg	p.V478M	MUC2_ENST00000359061.5_Missense_Mutation_p.V478M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	478	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCTGCCCCACGTGACCGGTGA	0.652													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16186	0.0		0.0	False		,,,				2504	0.0				p.V478M		Atlas-SNP	.											.	MUC2	614	.	0			c.G1432A						.						33.0	38.0	36.0					11																	1081136		1979	4161	6140	SO:0001583	missense	4583	exon11			CCCCACGTGACCG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1432G>A	chr11.hg19:g.1081136G>A	ENSP00000415183:p.Val478Met	96.0	0.0		143.0	27.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	14.51	2.558420	0.45590	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.59906	0.23;0.23	3.64	1.6	0.23607	.	1.376200	0.05521	U	0.562127	T	0.65091	0.2658	M	0.62723	1.935	0.21697	N	0.999588	P	0.48764	0.915	P	0.53760	0.734	T	0.54289	-0.8316	10	0.33940	T	0.23	.	8.1327	0.31037	0.0988:0.1638:0.7374:0.0	.	478	E7EUV1	.	M	478	ENSP00000415183:V478M;ENSP00000351956:V478M	ENSP00000351956:V478M	V	+	1	0	MUC2	1071136	0.221000	0.23642	0.987000	0.45799	0.798000	0.45092	1.379000	0.34340	1.878000	0.54408	0.491000	0.48974	GTG	.	.		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1629511	1629511	+	Silent	SNP	G	G	A	rs371318576		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:1629511G>A	ENST00000399685.1	-	1	182	c.105C>T	c.(103-105)tgC>tgT	p.C35C		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	35	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		CAGGTACACAGCAGCCGGAGC	0.677																																					p.C35C		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C105T						.	G		1,4397		0,1,2198	59.0	77.0	71.0		105	1.4	1.0	11		71	0,8590		0,0,4295	no	coding-synonymous	KRTAP5-3	NM_001012708.2		0,1,6493	AA,AG,GG		0.0,0.0227,0.0077		35/239	1629511	1,12987	2199	4295	6494	SO:0001819	synonymous_variant	387266	exon1			TACACAGCAGCCG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"""Keratin associated proteins"""	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.105C>T	chr11.hg19:g.1629511G>A		49.0	0.0		42.0	10.0	NM_001012708	Q6PL44|Q701N3	Silent	SNP	ENST00000399685.1	hg19	CCDS41591.1																																																																																			.	.		0.677	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
TNNT3	7140	hgsc.bcm.edu	37	11	1955022	1955023	+	Silent	DNP	CC	CC	AA	rs193178655		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:1955022_1955023CC>AA	ENST00000397301.1	+	11	284_285	c.276_277CC>AA	c.(274-279)gcCCgg>gcAAgg	p.92_93AR>AR	TNNT3_ENST00000446240.1_Silent_p.62_63AR>AR|TNNT3_ENST00000381561.4_Silent_p.84_85AR>AR|TNNT3_ENST00000397304.2_Silent_p.62_63AR>AR|TNNT3_ENST00000360603.3_Silent_p.75_76AR>AR|TNNT3_ENST00000381548.3_Silent_p.83_84AR>AR|TNNT3_ENST00000381549.3_Silent_p.73_74AR>AR|TNNT3_ENST00000381589.3_Silent_p.79_80AR>AR|TNNT3_ENST00000278317.6_Silent_p.81_82AR>AR|TNNT3_ENST00000381579.3_Silent_p.73_74AR>AR|TNNT3_ENST00000381558.1_Silent_p.73_74AR>AR			P45378	TNNT3_HUMAN	troponin T type 3 (skeletal, fast)	92					ATP catabolic process (GO:0006200)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)|regulation of striated muscle contraction (GO:0006942)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium-dependent protein binding (GO:0048306)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		ACTTTGAAGCCCGGAAGAAGGA	0.604																																					p.A81A|p.R82R		Atlas-SNP	.											.	TNNT3	68	.	0			c.C243A|c.C244A						.																																			SO:0001819	synonymous_variant	7140	exon10			TGAAGCCCGGAAG|GAAGCCCGGAAGA	M21984	CCDS7727.1, CCDS41594.1, CCDS41595.1, CCDS41596.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130595	ENSG00000130595			11950	protein-coding gene	gene with protein product	"""troponin-T3, skeletal, fast"""	600692	"""troponin T3, skeletal, fast"""			8172653	Standard	NM_001042782		Approved	AMCD2B, DA2B, FSSV, DKFZp779M2348	uc001lup.4	P45378	OTTHUMG00000012475	Exception_encountered	chr11.hg19:g.1955022_1955023delinsAA		178.0|177.0	0.0		218.0|219.0	26.0|25.0	NM_006757	A8MQ76|A8MSW1|B3KPX3|B7WP64|B7ZL26|B7ZVV9|Q12975|Q12976|Q12977|Q12978|Q17RG9|Q6FH29|Q6N056|Q86TH6	Silent	SNP	ENST00000397301.1	hg19																																																																																				.	.|C|1.000;T|0.000		0.604	TNNT3-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000142920.3	NM_006757	
INS-IGF2	723961	hgsc.bcm.edu	37	11	2170519	2170519	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:2170519T>A	ENST00000397270.1	-	3	302	c.244A>T	c.(244-246)Aca>Tca	p.T82S	IGF2-AS_ENST00000381361.3_RNA|INS-IGF2_ENST00000481781.1_5'UTR|IGF2-AS_ENST00000381363.4_RNA|IGF2-AS_ENST00000445504.2_RNA|IGF2_ENST00000300632.5_5'UTR	NM_001042376.2	NP_001035835.1	F8WCM5	INSR2_HUMAN	INS-IGF2 readthrough	82						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		all_epithelial(84;0.00018)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.0832)|Lung(200;0.156)		GCCCTGGCTGTGGCGTCCAGA	0.587																																					p.T82S		Atlas-SNP	.											.	INS-IGF2	8	.	0			c.A244T						.						75.0	85.0	82.0					11																	2170519		2036	4167	6203	SO:0001583	missense	723961	exon3			TGGCTGTGGCGTC	DQ104205	CCDS41598.1	11p15.5	2011-03-23			ENSG00000129965	ENSG00000129965			33527	other	readthrough						16531418	Standard	NM_001042376		Approved		uc001lvm.3	F8WCM5	OTTHUMG00000166213	ENST00000397270.1:c.244A>T	chr11.hg19:g.2170519T>A	ENSP00000380440:p.Thr82Ser	60.0	0.0		62.0	11.0	NM_001042376	Q1WM24	Missense_Mutation	SNP	ENST00000397270.1	hg19	CCDS41598.1	.	.	.	.	.	.	.	.	.	.	T	10.58	1.391123	0.25118	.	.	ENSG00000129965	ENST00000397270	D	0.95412	-3.7	3.26	-5.09	0.02920	.	0.526148	0.12594	U	0.455347	D	0.90304	0.6967	L	0.43152	1.355	0.09310	N	1	B	0.16396	0.017	B	0.16289	0.015	T	0.79254	-0.1879	10	0.72032	D	0.01	-6.1421	7.8832	0.29635	0.1511:0.0:0.6126:0.2362	.	82	F8WCM5	.	S	82	ENSP00000380440:T82S	ENSP00000348986:T82S	T	-	1	0	INS-IGF2	2127095	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	-1.544000	0.02192	-1.047000	0.03242	0.454000	0.30748	ACA	.	.		0.587	INS-IGF2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000388404.1	NM_001042376.2	
TSSC4	10078	hgsc.bcm.edu	37	11	2424378	2424378	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:2424378A>C	ENST00000333256.6	+	3	958	c.515A>C	c.(514-516)gAg>gCg	p.E172A	TSSC4_ENST00000467308.1_3'UTR|TSSC4_ENST00000380996.5_Missense_Mutation_p.E108A|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000451491.2_Missense_Mutation_p.E172A|TSSC4_ENST00000380992.1_Splice_Site_p.E108A			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	172										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGTGACCGAGGTCAGCGAG	0.667																																					p.E172A		Atlas-SNP	.											.	TSSC4	19	.	0			c.A515C						.						28.0	28.0	28.0					11																	2424378		2201	4298	6499	SO:0001583	missense	10078	exon2			TGACCGAGGTCAG	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.515A>C	chr11.hg19:g.2424378A>C	ENSP00000331087:p.Glu172Ala	99.0	0.0		90.0	9.0	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	hg19	CCDS7735.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.126501	0.56721	.	.	ENSG00000184281	ENST00000380996;ENST00000333256;ENST00000380992;ENST00000437110;ENST00000440813;ENST00000496468;ENST00000451491	T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69	3.52	3.52	0.40303	.	0.144148	0.44902	U	0.000419	T	0.66277	0.2773	M	0.77103	2.36	0.50813	D	0.999895	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	T	0.70988	-0.4722	10	0.72032	D	0.01	-19.9944	11.6947	0.51536	1.0:0.0:0.0:0.0	.	172;108	Q9Y5U2;Q9Y5U2-2	TSSC4_HUMAN;.	A	108;172;108;172;108;172;172	ENSP00000370384:E108A;ENSP00000331087:E172A;ENSP00000370380:E108A;ENSP00000396925:E172A;ENSP00000416937:E108A;ENSP00000435013:E172A;ENSP00000411224:E172A	ENSP00000331087:E172A	E	+	2	0	TSSC4	2380954	1.000000	0.71417	0.717000	0.30585	0.362000	0.29581	4.604000	0.61112	1.618000	0.50286	0.379000	0.24179	GAG	.	.		0.667	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706	
DNHD1	144132	hgsc.bcm.edu	37	11	6579426	6579426	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:6579426T>C	ENST00000527990.2	+	23	8901	c.8901T>C	c.(8899-8901)ccT>ccC	p.P2967P	DNHD1_ENST00000254579.6_Silent_p.P2967P			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2967					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GCAGTTTCCCTGGCCAGTACA	0.537																																					p.P2967P		Atlas-SNP	.											.	DNHD1	198	.	0			c.T8901C						.						68.0	59.0	62.0					11																	6579426		692	1591	2283	SO:0001819	synonymous_variant	144132	exon25			TTTCCCTGGCCAG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8901T>C	chr11.hg19:g.6579426T>C		147.0	0.0		137.0	69.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
OR10A5	144124	hgsc.bcm.edu	37	11	6867579	6867579	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:6867579T>C	ENST00000299454.4	+	1	697	c.666T>C	c.(664-666)atT>atC	p.I222I	OR10A5_ENST00000379831.2_Silent_p.I226I			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	222					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ATACTCGCATTGCTGCTGCTA	0.473																																					p.I222I	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											.	OR10A5	48	.	0			c.T666C						.						289.0	236.0	254.0					11																	6867579		2201	4296	6497	SO:0001819	synonymous_variant	144124	exon1			TCGCATTGCTGCT	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"""GPCR / Class A : Olfactory receptors"""	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.666T>C	chr11.hg19:g.6867579T>C		445.0	0.0		452.0	54.0	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	hg19	CCDS7773.1																																																																																			.	.		0.473	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168	
SYT9	143425	hgsc.bcm.edu	37	11	7334640	7334640	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:7334640G>A	ENST00000318881.6	+	3	749	c.512G>A	c.(511-513)cGa>cAa	p.R171Q	SYT9_ENST00000396716.2_Missense_Mutation_p.R139Q	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	171					positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		AATTCAATCCGAAGACAACTC	0.388																																					p.R171Q		Atlas-SNP	.											.	SYT9	91	.	0			c.G512A						.						44.0	42.0	43.0					11																	7334640		2201	4296	6497	SO:0001583	missense	143425	exon3			CAATCCGAAGACA	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"""Synaptotagmins"""	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.512G>A	chr11.hg19:g.7334640G>A	ENSP00000324419:p.Arg171Gln	95.0	0.0		126.0	25.0	NM_175733		Missense_Mutation	SNP	ENST00000318881.6	hg19	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.623302	0.87460	.	.	ENSG00000170743	ENST00000396716;ENST00000318881	T;T	0.56103	0.48;0.5	5.85	5.85	0.93711	.	0.000000	0.56097	D	0.000029	T	0.49745	0.1575	L	0.50333	1.59	0.58432	D	0.999998	B	0.23650	0.089	B	0.23716	0.048	T	0.34700	-0.9818	10	0.25106	T	0.35	.	18.0311	0.89285	0.0:0.0:1.0:0.0	.	171	Q86SS6	SYT9_HUMAN	Q	139;171	ENSP00000379944:R139Q;ENSP00000324419:R171Q	ENSP00000324419:R171Q	R	+	2	0	SYT9	7291216	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.814000	0.86154	2.932000	0.99384	0.643000	0.83706	CGA	.	.		0.388	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733	
COMMD9	29099	hgsc.bcm.edu	37	11	36296268	36296268	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:36296268C>T	ENST00000263401.5	-	6	527	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	LINC00610_ENST00000355500.1_lincRNA|COMMD9_ENST00000452374.2_Missense_Mutation_p.V129M|COMMD9_ENST00000533308.1_5'Flank|COMMD9_ENST00000532705.1_Missense_Mutation_p.R159H	NM_014186.3	NP_054905.2	Q9P000	COMD9_HUMAN	COMM domain containing 9	171	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	5	all_lung(20;0.211)	all_hematologic(20;0.107)				CTCAGCTCCACGGTGACAGCT	0.547																																					p.V171M		Atlas-SNP	.											.	COMMD9	21	.	0			c.G511A						.						165.0	135.0	145.0					11																	36296268		2202	4298	6500	SO:0001583	missense	29099	exon6			GCTCCACGGTGAC	AY542164	CCDS7900.1, CCDS44571.1	11p13	2008-02-05			ENSG00000110442	ENSG00000110442			25014	protein-coding gene	gene with protein product		612299				15799966	Standard	NM_014186		Approved	HSPC166, FLJ31106	uc001mwn.4	Q9P000	OTTHUMG00000166333	ENST00000263401.5:c.511G>A	chr11.hg19:g.36296268C>T	ENSP00000263401:p.Val171Met	248.0	0.0		345.0	173.0	NM_014186	E9PAN2|Q96FI2|Q9H0R0	Missense_Mutation	SNP	ENST00000263401.5	hg19	CCDS7900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.65|13.65	2.301182|2.301182	0.40694|0.40694	.|.	.|.	ENSG00000110442|ENSG00000110442	ENST00000532705|ENST00000263401;ENST00000452374	.|T;T	.|0.09723	.|2.95;2.95	5.66|5.66	-8.51|-8.51	0.00923|0.00923	.|COMM domain (1);	.|0.383306	.|0.33772	.|N	.|0.004574	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.10916|0.10916	0.065|0.065	0.18873|0.18873	N|N	0.999989|0.999989	.|P;B	.|0.48230	.|0.907;0.031	.|B;B	.|0.32022	.|0.139;0.018	T|T	0.24870|0.24870	-1.0148|-1.0148	6|10	0.87932|0.27082	D|T	0|0.32	-16.116|-16.116	16.1983|16.1983	0.82046|0.82046	0.0:0.5707:0.0:0.4293|0.0:0.5707:0.0:0.4293	.|.	.|129;171	.|Q9P000-2;Q9P000	.|.;COMD9_HUMAN	H|M	159|171;129	.|ENSP00000263401:V171M;ENSP00000392510:V129M	ENSP00000435599:R159H|ENSP00000263401:V171M	R|V	-|-	2|1	0|0	COMMD9|COMMD9	36252844|36252844	0.001000|0.001000	0.12720|0.12720	0.443000|0.443000	0.26883|0.26883	0.938000|0.938000	0.57974|0.57974	-0.637000|-0.637000	0.05459|0.05459	-1.794000|-1.794000	0.01256|0.01256	-0.290000|-0.290000	0.09829|0.09829	CGT|GTG	.	.		0.547	COMMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389196.1	NM_014186	
RAG1	5896	hgsc.bcm.edu	37	11	36596385	36596385	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:36596385A>T	ENST00000299440.5	+	2	1643	c.1531A>T	c.(1531-1533)Aag>Tag	p.K511*		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	511					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GAATGCTGAGAAGGTACTTCT	0.502									Familial Hemophagocytic Lymphohistiocytosis																												p.K511X	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A1531T						.						120.0	113.0	115.0					11																	36596385		2202	4298	6500	SO:0001587	stop_gained	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCTGAGAAGGTAC	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.1531A>T	chr11.hg19:g.36596385A>T	ENSP00000299440:p.Lys511*	152.0	0.0		205.0	41.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Nonsense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	A	34	5.298417	0.95574	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7965	0.78416	1.0:0.0:0.0:0.0	.	.	.	.	X	511	.	ENSP00000299440:K511X	K	+	1	0	RAG1	36552961	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	8.962000	0.93254	2.140000	0.66376	0.529000	0.55759	AAG	.	.		0.502	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
RAG2	5897	hgsc.bcm.edu	37	11	36614459	36614459	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:36614459G>T	ENST00000311485.3	-	2	1421	c.1260C>A	c.(1258-1260)tgC>tgA	p.C420*	C11orf74_ENST00000446510.2_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	420					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				CACAAGTAGGGCAGCATGTAA	0.443									Familial Hemophagocytic Lymphohistiocytosis																												p.C420X		Atlas-SNP	.											.	RAG2	92	.	0			c.C1260A						.						147.0	133.0	138.0					11																	36614459		2202	4298	6500	SO:0001587	stop_gained	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AGTAGGGCAGCAT	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.1260C>A	chr11.hg19:g.36614459G>T	ENSP00000308620:p.Cys420*	113.0	0.0		104.0	14.0	NM_001243785	A8K9E9|Q8TBL4	Nonsense_Mutation	SNP	ENST00000311485.3	hg19	CCDS7903.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.576484	0.86645	.	.	ENSG00000175097	ENST00000311485	.	.	.	5.23	0.144	0.14824	.	0.048134	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.072	8.5692	0.33558	0.6253:0.0:0.3747:0.0	.	.	.	.	X	420	.	ENSP00000308620:C420X	C	-	3	2	RAG2	36571035	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	0.778000	0.26732	0.053000	0.16036	0.650000	0.86243	TGC	.	.		0.443	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536	
TP53I11	9537	hgsc.bcm.edu	37	11	44958391	44958391	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:44958391G>T	ENST00000533940.1	-	8	901	c.297C>A	c.(295-297)agC>agA	p.S99R	TP53I11_ENST00000525680.1_Missense_Mutation_p.S99R|TP53I11_ENST00000531928.2_Missense_Mutation_p.S99R|TP53I11_ENST00000308212.5_Missense_Mutation_p.S99R|TP53I11_ENST00000395648.3_Missense_Mutation_p.S99R|TP53I11_ENST00000531130.2_5'UTR	NM_001258320.1	NP_001245249.1	O14683	P5I11_HUMAN	tumor protein p53 inducible protein 11	99					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5						TGGGGGTCTTGCTGGTCACCT	0.687											OREG0020923	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S99R		Atlas-SNP	.											.	TP53I11	17	.	0			c.C297A						.						30.0	30.0	30.0					11																	44958391		2203	4297	6500	SO:0001583	missense	9537	exon5			GGTCTTGCTGGTC	AF010315	CCDS7911.1	11p11.2	2005-09-22				ENSG00000175274			16842	protein-coding gene	gene with protein product						9305847	Standard	NM_006034		Approved	PIG11	uc001myk.3	O14683		ENST00000533940.1:c.297C>A	chr11.hg19:g.44958391G>T	ENSP00000436152:p.Ser99Arg	80.0	0.0	115	97.0	4.0	NM_001258324	Q3ZCS0	Missense_Mutation	SNP	ENST00000533940.1	hg19	CCDS7911.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744191	0.69418	.	.	ENSG00000175274	ENST00000395648;ENST00000308212;ENST00000308220;ENST00000533940;ENST00000525680;ENST00000528473	.	.	.	4.96	3.05	0.35203	.	.	.	.	.	T	0.45577	0.1349	L	0.59436	1.845	0.42510	D	0.992965	P;B	0.42203	0.773;0.062	B;B	0.37304	0.246;0.075	T	0.47548	-0.9109	8	0.48119	T	0.1	-0.4843	10.0393	0.42148	0.2226:0.0:0.7774:0.0	.	46;99	Q8N8U5;O14683	.;P5I11_HUMAN	R	99;99;46;99;99;99	.	ENSP00000309532:S99R	S	-	3	2	TP53I11	44914967	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	2.144000	0.42197	1.087000	0.41251	0.561000	0.74099	AGC	.	.		0.687	TP53I11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389909.1	NM_006034	
MADD	8567	hgsc.bcm.edu	37	11	47315515	47315515	+	Missense_Mutation	SNP	G	G	A	rs375878509		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:47315515G>A	ENST00000311027.5	+	22	3662	c.3497G>A	c.(3496-3498)aGc>aAc	p.S1166N	MADD_ENST00000342922.4_Missense_Mutation_p.S1128N|MADD_ENST00000406482.1_Missense_Mutation_p.S1085N|MADD_ENST00000405573.2_5'UTR|MADD_ENST00000402799.1_Missense_Mutation_p.S1085N|MADD_ENST00000395336.3_Missense_Mutation_p.S1166N|MADD_ENST00000395344.3_Missense_Mutation_p.S1085N|MADD_ENST00000402192.2_Missense_Mutation_p.S1128N|MADD_ENST00000407859.3_Missense_Mutation_p.S1105N|MADD_ENST00000349238.3_Missense_Mutation_p.S1148N	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		AGTGGTGTGAGCCTGACGTCT	0.428																																					p.S1166N		Atlas-SNP	.											.	MADD	172	.	0			c.G3497A						.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	0,4402		0,0,2201	152.0	140.0	144.0		3254,3254,3497,3383,3314,3254,3443,3254,3497,3383	5.6	1.0	11		144	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	MADD	NM_001135943.1,NM_001135944.1,NM_003682.3,NM_130470.2,NM_130471.2,NM_130472.2,NM_130473.2,NM_130474.2,NM_130475.2,NM_130476.2	46,46,46,46,46,46,46,46,46,46	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1085/1545,1085/1542,1166/1648,1128/1589,1105/1566,1085/1546,1148/1609,1085/1480,1166/1582,1128/1588	47315515	1,12997	2201	4298	6499	SO:0001583	missense	8567	exon22			GTGTGAGCCTGAC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.3497G>A	chr11.hg19:g.47315515G>A	ENSP00000310933:p.Ser1166Asn	128.0	0.0		132.0	32.0	NM_130475		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.987413	0.93106	0.0	1.16E-4	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.08458	3.33;3.13;3.13;3.34;3.22;3.14;3.09;3.22;3.33	5.56	5.56	0.83823	.	0.039078	0.85682	D	0.000000	T	0.16214	0.0390	L	0.32530	0.975	0.80722	D	1	P;P;P;P;P;P;P;P;P;P	0.48911	0.839;0.745;0.917;0.835;0.9;0.9;0.855;0.915;0.864;0.855	B;B;P;P;P;P;P;P;P;P	0.54460	0.445;0.445;0.753;0.648;0.648;0.648;0.697;0.697;0.571;0.697	T	0.01051	-1.1468	10	0.36615	T	0.2	-16.3602	19.5211	0.95185	0.0:0.0:1.0:0.0	.	1085;1085;1166;1085;1085;1085;1148;1105;1166;1128	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	N	1128;1085;1085;1085;1148;1166;1105;1085;1166;1128	ENSP00000343902:S1128N;ENSP00000385585:S1085N;ENSP00000384435:S1085N;ENSP00000304505:S1148N;ENSP00000310933:S1166N;ENSP00000384204:S1105N;ENSP00000378753:S1085N;ENSP00000378745:S1166N;ENSP00000384287:S1128N	ENSP00000310933:S1166N	S	+	2	0	MADD	47272091	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.598000	0.82745	2.589000	0.87451	0.655000	0.94253	AGC	.	.		0.428	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
SPI1	6688	hgsc.bcm.edu	37	11	47376978	47376978	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:47376978G>C	ENST00000378538.3	-	5	835	c.613C>G	c.(613-615)Cac>Gac	p.H205D	MYBPC3_ENST00000256993.4_5'Flank|MYBPC3_ENST00000545968.1_5'Flank|SPI1_ENST00000533030.1_3'UTR|MYBPC3_ENST00000399249.2_5'Flank|SPI1_ENST00000227163.4_Missense_Mutation_p.H206D	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	205					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|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 distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		GCCTCCTTGTGCTTGGACGAG	0.617																																					p.H206D		Atlas-SNP	.											.	SPI1	21	.	0			c.C616G						.						96.0	83.0	87.0					11																	47376978		2201	4298	6499	SO:0001583	missense	6688	exon5			CCTTGTGCTTGGA	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"""hematopoietic transcription factor PU.1"", ""31 kDa transforming protein"""	165170	"""spleen focus forming virus (SFFV) proviral integration oncogene"""			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.613C>G	chr11.hg19:g.47376978G>C	ENSP00000367799:p.His205Asp	117.0	0.0		109.0	19.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	g	22.0	4.226466	0.79576	.	.	ENSG00000066336	ENST00000378538;ENST00000227163	T;T	0.10099	2.91;2.91	4.23	3.31	0.37934	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.13500	0.0327	N	0.17345	0.48	0.80722	D	1	D;D	0.69078	0.992;0.997	D;D	0.66351	0.943;0.932	T	0.10291	-1.0636	10	0.10111	T	0.7	-18.2234	12.2235	0.54447	0.0845:0.0:0.9155:0.0	.	205;206	P17947;P17947-2	SPI1_HUMAN;.	D	205;206	ENSP00000367799:H205D;ENSP00000227163:H206D	ENSP00000227163:H206D	H	-	1	0	SPI1	47333554	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.542000	0.82095	0.896000	0.36366	0.479000	0.44913	CAC	.	.		0.617	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120	
OR4A5	81318	hgsc.bcm.edu	37	11	51412084	51412084	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:51412084G>A	ENST00000319760.6	-	1	364	c.312C>T	c.(310-312)ttC>ttT	p.F104F		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CCCCACCAAAGAAATGGTCTA	0.448																																					p.F104F		Atlas-SNP	.											OR4A5,NS,carcinoma,0,1	OR4A5	116	.	0			c.C312T						.						66.0	67.0	67.0					11																	51412084		2201	4296	6497	SO:0001819	synonymous_variant	81318	exon1			ACCAAAGAAATGG	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.312C>T	chr11.hg19:g.51412084G>A		276.0	0.0		250.0	36.0	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	hg19	CCDS31497.1																																																																																			.	.		0.448	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
OR5D18	219438	hgsc.bcm.edu	37	11	55587463	55587463	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:55587463G>A	ENST00000333976.4	+	1	378	c.358G>A	c.(358-360)Gcc>Acc	p.A120T		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				AGCTGTGATGGCCTATGACCG	0.453																																					p.A120T		Atlas-SNP	.											OR5D18,right_upper_lobe,carcinoma,0,1	OR5D18	121	.	0			c.G358A						.						167.0	162.0	164.0					11																	55587463		2200	4296	6496	SO:0001583	missense	219438	exon1			GTGATGGCCTATG	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.358G>A	chr11.hg19:g.55587463G>A	ENSP00000335025:p.Ala120Thr	288.0	1.0		338.0	70.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	hg19	CCDS31510.1	.	.	.	.	.	.	.	.	.	.	.	20.7	4.036021	0.75617	.	.	ENSG00000186119	ENST00000333976	T	0.54071	0.59	4.84	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39210	N	0.001428	T	0.68869	0.3048	H	0.96365	3.81	0.35287	D	0.781833	P	0.50369	0.934	P	0.44696	0.458	D	0.84873	0.0826	10	0.87932	D	0	-38.6253	13.543	0.61686	0.0:0.0:0.8427:0.1573	.	120	Q8NGL1	OR5DI_HUMAN	T	120	ENSP00000335025:A120T	ENSP00000335025:A120T	A	+	1	0	OR5D18	55344039	1.000000	0.71417	0.996000	0.52242	0.870000	0.49936	3.767000	0.55288	1.190000	0.43042	0.560000	0.71715	GCC	.	.		0.453	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
AHNAK	79026	hgsc.bcm.edu	37	11	62290481	62290481	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:62290481T>C	ENST00000378024.4	-	5	11682	c.11408A>G	c.(11407-11409)aAg>aGg	p.K3803R	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3803					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTTGGGCATCTTCAGGTGCCA	0.522																																					p.K3803R		Atlas-SNP	.											.	AHNAK	532	.	0			c.A11408G						.						255.0	262.0	260.0					11																	62290481		2202	4299	6501	SO:0001583	missense	79026	exon5			GGCATCTTCAGGT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11408A>G	chr11.hg19:g.62290481T>C	ENSP00000367263:p.Lys3803Arg	140.0	0.0		209.0	41.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	12.17	1.856915	0.32791	.	.	ENSG00000124942	ENST00000378024	T	0.01538	4.79	4.61	3.48	0.39840	.	0.000000	0.42964	D	0.000635	T	0.06005	0.0156	H	0.95539	3.685	0.36755	D	0.882988	B	0.19073	0.033	B	0.19946	0.027	T	0.01472	-1.1346	10	0.35671	T	0.21	.	9.8977	0.41329	0.0:0.0829:0.0:0.9171	.	3803	Q09666	AHNK_HUMAN	R	3803	ENSP00000367263:K3803R	ENSP00000367263:K3803R	K	-	2	0	AHNAK	62047057	0.970000	0.33590	1.000000	0.80357	0.979000	0.70002	1.794000	0.38774	0.743000	0.32719	0.444000	0.29173	AAG	.	.		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
KCNK7	10089	hgsc.bcm.edu	37	11	65365896	65365896	+	5'Flank	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:65365896T>C	ENST00000340313.4	-	0	0				KCNK7_ENST00000394217.2_5'Flank|KCNK7_ENST00000342202.4_5'Flank|MAP3K11_ENST00000534432.1_5'Flank|MAP3K11_ENST00000309100.3_Missense_Mutation_p.T804A|MAP3K11_ENST00000530153.1_Missense_Mutation_p.T547A|MAP3K11_ENST00000532507.1_Missense_Mutation_p.T220A|KCNK7_ENST00000394216.2_5'Flank	NM_033347.1	NP_203133.1	Q9Y2U2	KCNK7_HUMAN	potassium channel, subfamily K, member 7						potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|liver(1)|lung(1)	3						GGGAACAAGGTCCAGGGTGCT	0.667																																					p.T804A		Atlas-SNP	.											.	MAP3K11	67	.	0			c.A2410G						.						43.0	41.0	41.0					11																	65365896		2201	4297	6498	SO:0001631	upstream_gene_variant	4296	exon10			ACAAGGTCCAGGG	AF110522	CCDS8106.1, CCDS31608.1, CCDS41673.1	11q13	2012-03-07			ENSG00000173338	ENSG00000173338		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6282	protein-coding gene	gene with protein product		603940				10206991, 11256078, 16382106	Standard	NM_033347		Approved	K2p7.1	uc001oes.3	Q9Y2U2	OTTHUMG00000166528		chr11.hg19:g.65365896T>C	Exception_encountered	36.0	0.0		42.0	5.0	NM_002419	Q3SYI2|Q9Y2U3|Q9Y2U4	Missense_Mutation	SNP	ENST00000340313.4	hg19	CCDS31608.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760226	0.69763	.	.	ENSG00000173327	ENST00000309100;ENST00000532507;ENST00000530153	T;T	0.75938	-0.87;-0.98	5.3	4.09	0.47781	.	0.078766	0.49916	D	0.000129	T	0.58538	0.2129	N	0.22421	0.69	0.30055	N	0.811426	B;B	0.24768	0.111;0.023	B;B	0.27170	0.077;0.009	T	0.56842	-0.7912	10	0.40728	T	0.16	.	7.9927	0.30250	0.1818:0.0:0.0:0.8182	.	293;804	B3KQY4;Q16584	.;M3K11_HUMAN	A	804;220;547	ENSP00000309597:T804A;ENSP00000433886:T547A	ENSP00000309597:T804A	T	-	1	0	MAP3K11	65122472	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.632000	0.37102	2.126000	0.65437	0.533000	0.62120	ACC	.	.		0.667	KCNK7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390206.1	NM_005714	
RBM14	10432	hgsc.bcm.edu	37	11	66392861	66392861	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:66392861G>A	ENST00000310137.4	+	2	1653	c.1514G>A	c.(1513-1515)gGg>gAg	p.G505E	RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000409738.4_Intron|RBM4_ENST00000503028.2_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM4_ENST00000514361.3_Intron|RBM14-RBM4_ENST00000500635.2_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	505	Ala-rich.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GCAGCCTACGGGGCCCAACCT	0.627																																					p.G505E		Atlas-SNP	.											RBM14,colon,carcinoma,0,1	RBM14	59	.	0			c.G1514A						.						45.0	44.0	44.0					11																	66392861		2200	4295	6495	SO:0001583	missense	10432	exon2			CCTACGGGGCCCA	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"""RNA binding motif (RRM) containing"""	14219	protein-coding gene	gene with protein product	"""coactivator activator"", ""SYT interacting protein"""	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.1514G>A	chr11.hg19:g.66392861G>A	ENSP00000311747:p.Gly505Glu	59.0	0.0		69.0	11.0	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.244440	0.39697	.	.	ENSG00000239306	ENST00000310137	D	0.84370	-1.84	5.75	5.75	0.90469	.	0.173489	0.49916	D	0.000127	D	0.86847	0.6031	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.88458	0.3053	10	0.87932	D	0	-3.9247	15.4418	0.75190	0.0:0.0:1.0:0.0	.	505	Q96PK6	RBM14_HUMAN	E	505	ENSP00000311747:G505E	ENSP00000311747:G505E	G	+	2	0	RBM14	66149437	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.738000	0.47401	2.720000	0.93068	0.655000	0.94253	GGG	.	.		0.627	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328	
TMEM135	65084	hgsc.bcm.edu	37	11	86782616	86782616	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:86782616G>A	ENST00000305494.5	+	3	360	c.321G>A	c.(319-321)ctG>ctA	p.L107L	TMEM135_ENST00000532959.1_Intron|TMEM135_ENST00000355734.4_Silent_p.L107L|TMEM135_ENST00000340353.7_Silent_p.L107L|TMEM135_ENST00000535167.1_5'UTR	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	107					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GTGCCGCTCTGCCAGCATCTT	0.373																																					p.L107L		Atlas-SNP	.											.	TMEM135	40	.	0			c.G321A						.						69.0	73.0	72.0					11																	86782616		2201	4299	6500	SO:0001819	synonymous_variant	65084	exon3			CGCTCTGCCAGCA	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.321G>A	chr11.hg19:g.86782616G>A		73.0	0.0		62.0	7.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	hg19	CCDS8280.1																																																																																			.	.		0.373	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918	
NAALAD2	10003	hgsc.bcm.edu	37	11	89896533	89896533	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:89896533C>G	ENST00000534061.1	+	10	1361	c.1131C>G	c.(1129-1131)gaC>gaG	p.D377E	NAALAD2_ENST00000525171.1_Missense_Mutation_p.D284E|NAALAD2_ENST00000375944.3_Intron|NAALAD2_ENST00000321955.4_Missense_Mutation_p.D344E	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	377	NAALADase.				neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)	p.D377E(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GAGCTATTGACCCAACCAGTG	0.413																																					p.D377E		Atlas-SNP	.											NAALAD2,NS,carcinoma,0,1	NAALAD2	113	.	1	Substitution - Missense(1)	lung(1)	c.C1131G						.						118.0	126.0	123.0					11																	89896533		2201	4299	6500	SO:0001583	missense	10003	exon10			TATTGACCCAACC	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase III"""	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1131C>G	chr11.hg19:g.89896533C>G	ENSP00000432481:p.Asp377Glu	67.0	1.0		74.0	10.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	hg19	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761927	0.49468	.	.	ENSG00000077616	ENST00000534061;ENST00000321955;ENST00000525171	D;D;D	0.90844	-2.74;-2.74;-2.74	5.51	2.53	0.30540	Peptidase M28 (1);	0.000000	0.85682	D	0.000000	D	0.95014	0.8386	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.93788	0.7090	9	.	.	.	-20.3126	7.9396	0.29950	0.0:0.6005:0.0:0.3995	.	377;284	Q9Y3Q0;E9PKX5	NALD2_HUMAN;.	E	377;344;284	ENSP00000432481:D377E;ENSP00000320083:D344E;ENSP00000435249:D284E	.	D	+	3	2	NAALAD2	89536181	0.980000	0.34600	1.000000	0.80357	0.996000	0.88848	0.098000	0.15189	0.755000	0.32990	0.591000	0.81541	GAC	.	.		0.413	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467	
MMP1	4312	hgsc.bcm.edu	37	11	102662135	102662135	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:102662135C>T	ENST00000315274.6	-	8	1192	c.1125G>A	c.(1123-1125)aaG>aaA	p.K375K	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	375					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	CATCGATATGCTTCACAGTTC	0.453																																					p.K375K		Atlas-SNP	.											.	MMP1	74	.	0			c.G1125A						.						233.0	221.0	225.0					11																	102662135		2203	4299	6502	SO:0001819	synonymous_variant	4312	exon8			GATATGCTTCACA	X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"""Endogenous ligands"""	7155	protein-coding gene	gene with protein product		120353	"""matrix metalloproteinase 1 (interstitial collagenase)"""	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.1125G>A	chr11.hg19:g.102662135C>T		135.0	0.0		149.0	23.0	NM_002421	P08156	Silent	SNP	ENST00000315274.6	hg19	CCDS8322.1																																																																																			.	.		0.453	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421	
ALG9	79796	hgsc.bcm.edu	37	11	111740961	111740961	+	3'UTR	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:111740961C>T	ENST00000524880.1	-	0	1256				ALG9_ENST00000531154.1_5'UTR|ALG9_ENST00000527377.1_5'Flank|ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000398006.2_5'UTR			Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)|dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		CTACTGGCTCCCAGTAGTTGA	0.403																																					p.W88X		Atlas-SNP	.											.	ALG9	77	.	0			c.G264A						.						74.0	73.0	73.0					11																	111740961		1837	4102	5939	SO:0001624	3_prime_UTR_variant	79796	exon3			TGGCTCCCAGTAG		CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	2.4.1.259, 2.4.1.261	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	15672	protein-coding gene	gene with protein product	"""dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"", ""dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"", ""dol-P-Man dependent alpha-1,2-mannosyltransferase"""	606941	"""disrupted in bipolar affective disorder 1"", ""asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)"", ""asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"""	DIBD1		12030331, 15148656	Standard	NM_024740		Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000524880.1:c.*94G>A	chr11.hg19:g.111740961C>T		97.0	0.0		113.0	20.0	NM_001077690	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Nonsense_Mutation	SNP	ENST00000524880.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.68	2.308016	0.40895	.	.	ENSG00000086848	ENST00000428306	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7951	18.9101	0.92479	0.0:1.0:0.0:0.0	.	.	.	.	X	321	.	ENSP00000387627:W321X	W	-	3	0	ALG9	111246171	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	7.336000	0.79245	2.539000	0.85634	0.655000	0.94253	TGG	.	.		0.403	ALG9-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000413376.1	NM_024740	
KMT2A	4297	hgsc.bcm.edu	37	11	118374789	118374789	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:118374789G>A	ENST00000389506.5	+	27	8173	c.8173G>A	c.(8173-8175)Gag>Aag	p.E2725K	KMT2A_ENST00000534358.1_Missense_Mutation_p.E2728K|KMT2A_ENST00000354520.4_Missense_Mutation_p.E2687K			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2725					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGATGGGACAGAGAGTGATAC	0.423																																					p.E2728K		Atlas-SNP	.											.	MLL	548	.	0			c.G8182A						.						65.0	61.0	62.0					11																	118374789		2200	4296	6496	SO:0001583	missense	4297	exon27			GGGACAGAGAGTG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.8173G>A	chr11.hg19:g.118374789G>A	ENSP00000374157:p.Glu2725Lys	109.0	0.0		127.0	26.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250792	0.59212	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.87966	-2.32;-2.32;-2.27	5.65	5.65	0.86999	.	0.049407	0.85682	D	0.000000	D	0.93015	0.7777	M	0.67569	2.06	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	D	0.92890	0.6330	10	0.87932	D	0	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	2728;2725	E9PQG7;Q03164	.;MLL1_HUMAN	K	2728;2725;2687;1635	ENSP00000436786:E2728K;ENSP00000374157:E2725K;ENSP00000346516:E2687K	ENSP00000346516:E2687K	E	+	1	0	MLL	117879999	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.144000	0.94629	2.941000	0.99782	0.655000	0.94253	GAG	.	.		0.423	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
BLID	414899	hgsc.bcm.edu	37	11	121986461	121986461	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:121986461G>T	ENST00000560104.1	-	1	462	c.170C>A	c.(169-171)cCt>cAt	p.P57H		NM_001001786.2	NP_001001786.2	Q8IZY5	BLID_HUMAN	BH3-like motif containing, cell death inducer	57					apoptotic process (GO:0006915)	mitochondrion (GO:0005739)				NS(1)|large_intestine(4)|lung(6)|pancreas(1)	12		Breast(109;0.0164)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;2.08e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.101)		AGGCAACATAGGTTCTTTGTT	0.502											OREG0021435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P57H		Atlas-SNP	.											.	BLID	20	.	0			c.C170A						.						141.0	141.0	141.0					11																	121986461		2202	4299	6501	SO:0001583	missense	414899	exon1			AACATAGGTTCTT	AF303179	CCDS31693.1	11q24.1	2007-06-22				ENSG00000259571			33495	protein-coding gene	gene with protein product	"""breast cancer cell 2"""	608853				15069058, 17220890	Standard	NM_001001786		Approved	BRCC2	uc001pyf.3	Q8IZY5		ENST00000560104.1:c.170C>A	chr11.hg19:g.121986461G>T	ENSP00000453153:p.Pro57His	162.0	0.0	1515	183.0	29.0	NM_001001786	A1L416	Missense_Mutation	SNP	ENST00000560104.1	hg19	CCDS31693.1	.	.	.	.	.	.	.	.	.	.	G	8.767	0.924959	0.18056	.	.	ENSG00000258606;ENSG00000258574	ENST00000553434;ENST00000556841	.	.	.	3.92	1.85	0.25348	.	.	.	.	.	T	0.17238	0.0414	N	0.08118	0	0.09310	N	1	B	0.20261	0.043	B	0.21546	0.035	T	0.21724	-1.0237	8	0.87932	D	0	.	2.5933	0.04847	0.1789:0.0:0.5378:0.2833	.	57	Q8IZY5	BLID_HUMAN	H	57	.	ENSP00000448995:P57H	P	-	2	0	BLID;AP001924.1	121491671	0.007000	0.16637	0.002000	0.10522	0.022000	0.10575	0.717000	0.25851	0.494000	0.27859	-0.293000	0.09583	CCT	.	.		0.502	BLID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387656.1	NM_001001786	
OPCML	4978	hgsc.bcm.edu	37	11	132306092	132306092	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr11:132306092T>C	ENST00000331898.7	-	6	1403	c.825A>G	c.(823-825)aaA>aaG	p.K275K	OPCML_ENST00000524381.1_Silent_p.K268K|OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000374778.4_Silent_p.K234K|OPCML_ENST00000541867.1_Silent_p.K275K	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	275	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		ACATGCGGCCTTTGTTTTCAA	0.458																																					p.K275K		Atlas-SNP	.											.	OPCML	166	.	0			c.A825G						.						159.0	145.0	150.0					11																	132306092		2201	4297	6498	SO:0001819	synonymous_variant	4978	exon6			GCGGCCTTTGTTT	BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"""Immunoglobulin superfamily / I-set domain containing"""	8143	protein-coding gene	gene with protein product	"""IgLON family member 1"""	600632	"""opioid-binding protein/cell adhesion molecule-like"""			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.825A>G	chr11.hg19:g.132306092T>C		125.0	0.0		146.0	21.0	NM_002545	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Silent	SNP	ENST00000331898.7	hg19	CCDS8492.1																																																																																			.	.		0.458	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393	
A2M	2	hgsc.bcm.edu	37	12	9258835	9258835	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:9258835C>T	ENST00000318602.7	-	10	1408	c.1101G>A	c.(1099-1101)ggG>ggA	p.G367G		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	367					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	ACTCCACCTGCCCAAAGAAGG	0.408																																					p.G367G		Atlas-SNP	.											.	A2M	180	.	0			c.G1101A						.						134.0	126.0	128.0					12																	9258835		1880	4107	5987	SO:0001819	synonymous_variant	2	exon10			CACCTGCCCAAAG	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.1101G>A	chr12.hg19:g.9258835C>T		82.0	0.0		107.0	12.0	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	hg19	CCDS44827.1																																																																																			.	.		0.408	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
TMEM52B	120939	hgsc.bcm.edu	37	12	10339065	10339065	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:10339065T>C	ENST00000381923.2	+	5	588	c.184T>C	c.(184-186)Tcc>Ccc	p.S62P	TMEM52B_ENST00000298530.3_Missense_Mutation_p.S42P|TMEM52B_ENST00000536952.1_Missense_Mutation_p.S62P			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	62						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TGGCCTGACGTCCCTGTGCTT	0.597																																					p.S42P		Atlas-SNP	.											.	.	.	.	0			c.T124C						.						106.0	89.0	95.0					12																	10339065		2203	4300	6503	SO:0001583	missense	120939	exon3			CTGACGTCCCTGT	AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 59"""	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.184T>C	chr12.hg19:g.10339065T>C	ENSP00000371348:p.Ser62Pro	125.0	0.0		152.0	24.0	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.10	2.732160	0.48939	.	.	ENSG00000165685	ENST00000381923;ENST00000298530;ENST00000543484;ENST00000536952	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	5.45	4.29	0.51040	.	0.278907	0.31404	N	0.007708	T	0.47078	0.1426	M	0.62723	1.935	0.09310	N	0.999991	D;D	0.57571	0.98;0.98	P;P	0.55303	0.773;0.698	T	0.39035	-0.9633	10	0.59425	D	0.04	-16.9785	9.589	0.39534	0.1699:0.0:0.0:0.8301	.	62;42	Q4KMG9;Q4KMG9-2	CL059_HUMAN;.	P	62;42;62;62	ENSP00000371348:S62P;ENSP00000298530:S42P;ENSP00000445582:S62P;ENSP00000446102:S62P	ENSP00000298530:S42P	S	+	1	0	C12orf59	10230332	0.460000	0.25776	0.041000	0.18516	0.316000	0.28119	3.312000	0.51927	1.041000	0.40125	0.528000	0.53228	TCC	.	.		0.597	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022	
PLBD1	79887	hgsc.bcm.edu	37	12	14706133	14706133	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:14706133G>C	ENST00000240617.5	-	2	981	c.329C>G	c.(328-330)aCt>aGt	p.T110S	RN7SKP134_ENST00000363960.1_RNA	NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	110					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						TTACGGGGCAGTGAGGTAACC	0.532																																					p.T110S		Atlas-SNP	.											.	PLBD1	36	.	0			c.C329G						.						68.0	59.0	62.0					12																	14706133		2203	4300	6503	SO:0001583	missense	79887	exon2			GGGGCAGTGAGGT	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"""PLB homolog 1 (Dictyostelium)"""					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.329C>G	chr12.hg19:g.14706133G>C	ENSP00000240617:p.Thr110Ser	100.0	0.0		137.0	13.0	NM_024829	A8K4E9|Q9BVV3|Q9H625	Missense_Mutation	SNP	ENST00000240617.5	hg19	CCDS31751.1	.	.	.	.	.	.	.	.	.	.	G	32	5.122416	0.94429	.	.	ENSG00000121316	ENST00000240617;ENST00000540572	T;T	0.21734	1.99;1.99	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.33033	-0.9884	10	0.87932	D	0	-21.8403	19.0599	0.93085	0.0:0.0:1.0:0.0	.	110	Q6P4A8	PLBL1_HUMAN	S	110;63	ENSP00000240617:T110S;ENSP00000438367:T63S	ENSP00000240617:T110S	T	-	2	0	PLBD1	14597400	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.506000	0.90518	2.941000	0.99782	0.655000	0.94253	ACT	.	.		0.532	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18552717	18552717	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:18552717C>T	ENST00000266497.5	+	14	2166	c.2128C>T	c.(2128-2130)Cat>Tat	p.H710Y	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.H751Y|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.H710Y			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	710	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTCAGAAATGCATACCATTTT	0.408																																					p.H710Y		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C2128T						.						87.0	86.0	86.0					12																	18552717		1850	4095	5945	SO:0001583	missense	5288	exon15			GAAATGCATACCA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2128C>T	chr12.hg19:g.18552717C>T	ENSP00000266497:p.His710Tyr	100.0	0.0		84.0	4.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	C	1.214	-0.628771	0.03610	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.61158	0.13;0.13;0.13	5.08	3.13	0.36017	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.255174	0.32970	N	0.005432	T	0.22820	0.0551	N	0.05230	-0.09	0.33701	D	0.614569	B;B;B	0.29955	0.263;0.222;0.15	B;B;B	0.26770	0.073;0.044;0.041	T	0.32613	-0.9900	10	0.02654	T	1	-8.4714	1.4909	0.02456	0.1841:0.4398:0.2092:0.1669	.	750;751;710	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	Y	710;710;751	ENSP00000404845:H710Y;ENSP00000266497:H710Y;ENSP00000445381:H751Y	ENSP00000266497:H710Y	H	+	1	0	PIK3C2G	18443984	1.000000	0.71417	0.971000	0.41717	0.803000	0.45373	1.742000	0.38248	1.330000	0.45394	0.585000	0.79938	CAT	.	.		0.408	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
BICD1	636	hgsc.bcm.edu	37	12	32260378	32260378	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:32260378G>A	ENST00000281474.5	+	1	216	c.113G>A	c.(112-114)gGg>gAg	p.G38E	RP11-843B15.2_ENST00000551974.1_RNA|BICD1_ENST00000548411.1_Missense_Mutation_p.G38E|BICD1_ENST00000551086.1_Missense_Mutation_p.G38E|BICD1_ENST00000551848.1_Missense_Mutation_p.G38E|BICD1_ENST00000550207.1_Missense_Mutation_p.G38E	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	38					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GCCGAGTACGGGCTGGTGGTG	0.547																																					p.G38E		Atlas-SNP	.											.	BICD1	89	.	0			c.G113A						.						73.0	63.0	66.0					12																	32260378		2203	4300	6503	SO:0001583	missense	636	exon1			AGTACGGGCTGGT	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.113G>A	chr12.hg19:g.32260378G>A	ENSP00000281474:p.Gly38Glu	139.0	0.0		125.0	11.0	NM_001714	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	hg19	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	G	33	5.197433	0.94960	.	.	ENSG00000151746	ENST00000551848;ENST00000550207;ENST00000548411;ENST00000281474;ENST00000551086	T;T;T;T;T	0.75477	1.27;1.27;-0.9;-0.94;1.27	4.01	4.01	0.46588	.	0.000000	0.64402	D	0.000010	D	0.84973	0.5591	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.83652	0.0156	10	0.24483	T	0.36	.	16.2917	0.82756	0.0:0.0:1.0:0.0	.	38;38	F8W113;Q96G01	.;BICD1_HUMAN	E	38	ENSP00000448933:G38E;ENSP00000447663:G38E;ENSP00000446793:G38E;ENSP00000281474:G38E;ENSP00000447238:G38E	ENSP00000281474:G38E	G	+	2	0	BICD1	32151645	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.971000	0.93419	2.067000	0.61834	0.561000	0.74099	GGG	.	.		0.547	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
TUBA1A	7846	hgsc.bcm.edu	37	12	49578875	49578875	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:49578875A>G	ENST00000295766.5	-	4	1753	c.1274T>C	c.(1273-1275)aTg>aCg	p.M425T	TUBA1A_ENST00000550767.1_Missense_Mutation_p.M390T|TUBA1A_ENST00000301071.7_Missense_Mutation_p.M425T	NM_001270399.1	NP_001257328.1	Q71U36	TBA1A_HUMAN	tubulin, alpha 1a	425					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			stomach(1)|upper_aerodigestive_tract(1)	2					Albendazole(DB00518)|Mebendazole(DB00643)|Vinblastine(DB00570)	AAGGGCAGCCATGTCCTCACG	0.493																																					p.M425T	Pancreas(111;782 2307 24613 44561)|NSCLC(165;1667 2752 9496 39006)|Ovarian(19;24 776 10875 37451)	Atlas-SNP	.											.	TUBA1A	32	.	0			c.T1274C						.						167.0	163.0	164.0					12																	49578875		2203	4300	6503	SO:0001583	missense	7846	exon4			GCAGCCATGTCCT	AF141347	CCDS8781.1, CCDS58226.1, CCDS58227.1	12q13.12	2007-02-07						"""Tubulins"""	20766	protein-coding gene	gene with protein product	"""tubulin, alpha, brain-specific"""	602529				11504633, 3839072	Standard	NM_006009		Approved	TUBA3, B-ALPHA-1, FLJ25113	uc010smg.1	Q71U36	OTTHUMG00000169511	ENST00000295766.5:c.1274T>C	chr12.hg19:g.49578875A>G	ENSP00000439020:p.Met425Thr	348.0	0.0		336.0	90.0	NM_001270399	A8K0B8|G3V1U9|P04687|P05209	Missense_Mutation	SNP	ENST00000295766.5	hg19	CCDS58227.1	.	.	.	.	.	.	.	.	.	.	a	9.610	1.131008	0.21041	.	.	ENSG00000167552	ENST00000301071;ENST00000552597;ENST00000548405;ENST00000295766;ENST00000550767	D;D;D	0.83914	-1.78;-1.78;-1.78	5.51	5.51	0.81932	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83147	0.5191	M	0.76433	2.335	0.80722	D	1	B	0.02656	0.0	B	0.15870	0.014	T	0.81116	-0.1079	10	0.87932	D	0	.	14.6291	0.68643	1.0:0.0:0.0:0.0	.	425	Q71U36	TBA1A_HUMAN	T	425;156;272;425;390	ENSP00000301071:M425T;ENSP00000439020:M425T;ENSP00000446637:M390T	ENSP00000439020:M425T	M	-	2	0	TUBA1A	47865142	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.879000	0.92398	2.088000	0.63022	0.533000	0.62120	ATG	.	.		0.493	TUBA1A-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404547.2	NM_006009	
HELB	92797	hgsc.bcm.edu	37	12	66704296	66704296	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:66704296A>T	ENST00000247815.4	+	4	1647	c.1588A>T	c.(1588-1590)Aag>Tag	p.K530*		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	530					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		AGAGGCGGACAAGGCTATAGA	0.423																																					p.K530X		Atlas-SNP	.											.	HELB	90	.	0			c.A1588T						.						125.0	134.0	131.0					12																	66704296		2203	4300	6503	SO:0001587	stop_gained	92797	exon4			GCGGACAAGGCTA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1588A>T	chr12.hg19:g.66704296A>T	ENSP00000247815:p.Lys530*	101.0	0.0		144.0	18.0	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Nonsense_Mutation	SNP	ENST00000247815.4	hg19	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.197075	0.79015	.	.	ENSG00000127311	ENST00000247815	.	.	.	6.04	3.63	0.41609	.	0.237672	0.41500	D	0.000878	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.5058	2.2931	0.04144	0.6062:0.1353:0.1293:0.1292	.	.	.	.	X	530	.	.	K	+	1	0	HELB	64990563	0.386000	0.25180	0.469000	0.27204	0.083000	0.17756	1.723000	0.38053	0.492000	0.27815	0.459000	0.35465	AAG	.	.		0.423	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
TRHDE	29953	hgsc.bcm.edu	37	12	72936136	72936136	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:72936136A>G	ENST00000261180.4	+	7	1749	c.1653A>G	c.(1651-1653)caA>caG	p.Q551Q		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	551					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						GGGGTTTGCAAGTAAGTAAAA	0.318																																					p.Q551Q		Atlas-SNP	.											.	TRHDE	194	.	0			c.A1653G						.						99.0	97.0	98.0					12																	72936136		2203	4299	6502	SO:0001630	splice_region_variant	29953	exon7			TTTGCAAGTAAGT	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"""pyroglutamyl-peptidase II"", ""pyroglutamyl aminopeptidase II"", ""TRH-specific aminopeptidase"""	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.1653+1A>G	chr12.hg19:g.72936136A>G		26.0	0.0		35.0	9.0	NM_013381	A5PL19|Q6UWJ4	Silent	SNP	ENST00000261180.4	hg19	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.906348	0.33628	.	.	ENSG00000072657	ENST00000547300	.	.	.	5.25	4.09	0.47781	.	.	.	.	.	T	0.62368	0.2422	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59343	-0.7472	4	.	.	.	.	11.2667	0.49114	0.9276:0.0:0.0724:0.0	.	.	.	.	G	139	.	.	R	+	1	2	TRHDE	71222403	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	3.790000	0.55461	0.928000	0.37168	0.459000	0.35465	AGA	.	.		0.318	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381	Silent
PTPRQ	374462	hgsc.bcm.edu	37	12	81014030	81014030	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:81014030A>G	ENST00000266688.5	+	37	5475	c.5475A>G	c.(5473-5475)acA>acG	p.T1825T				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1871					regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						CTCCATGTACAGAAGGAAAGA	0.373																																					p.T1657T		Atlas-SNP	.											.	PTPRQ	119	.	0			c.A4971G						.						152.0	117.0	128.0					12																	81014030		692	1590	2282	SO:0001819	synonymous_variant	374462	exon29			ATGTACAGAAGGA	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.5475A>G	chr12.hg19:g.81014030A>G		175.0	0.0		189.0	53.0	NM_001145026		Silent	SNP	ENST00000266688.5	hg19		.	.	.	.	.	.	.	.	.	.	A	8.173	0.792023	0.16258	.	.	ENSG00000139304	ENST00000532722	.	.	.	5.29	-2.68	0.06041	.	.	.	.	.	T	0.49729	0.1574	.	.	.	0.43688	D	0.996138	.	.	.	.	.	.	T	0.43343	-0.9397	4	.	.	.	.	6.1526	0.20320	0.4049:0.2491:0.346:0.0	.	.	.	.	R	1526	.	.	Q	+	2	0	PTPRQ	79538161	0.319000	0.24607	0.806000	0.32338	0.987000	0.75469	0.506000	0.22658	-0.404000	0.07610	0.454000	0.30748	CAG	.	.		0.373	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
NR2C1	7181	hgsc.bcm.edu	37	12	95422248	95422248	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:95422248T>C	ENST00000333003.5	-	12	1776	c.1446A>G	c.(1444-1446)ctA>ctG	p.L482L	NR2C1_ENST00000545833.1_5'UTR	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	482					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						AAAACTCCTGTAGTTTGAAGA	0.318																																					p.L482L		Atlas-SNP	.											.	NR2C1	56	.	0			c.A1446G						.						132.0	120.0	124.0					12																	95422248		2203	4300	6503	SO:0001819	synonymous_variant	7181	exon12			CTCCTGTAGTTTG	M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"""Nuclear hormone receptors"""	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.1446A>G	chr12.hg19:g.95422248T>C		63.0	0.0		64.0	6.0	NM_003297	A8K5K4|Q15625|Q15626	Silent	SNP	ENST00000333003.5	hg19	CCDS9051.1																																																																																			.	.		0.318	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297	
CMKLR1	1240	hgsc.bcm.edu	37	12	108686719	108686719	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:108686719A>T	ENST00000312143.7	-	3	384	c.21T>A	c.(19-21)gaT>gaA	p.D7E	CMKLR1_ENST00000412676.1_Missense_Mutation_p.D7E|CMKLR1_ENST00000397688.2_Missense_Mutation_p.D5E|CMKLR1_ENST00000552995.1_Missense_Mutation_p.D5E|CMKLR1_ENST00000550402.1_Missense_Mutation_p.D7E	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	7					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						AAGTGTTGTAATCTTCATCCT	0.453																																					p.D7E		Atlas-SNP	.											.	CMKLR1	67	.	0			c.T21A						.						57.0	53.0	55.0					12																	108686719		1921	4137	6058	SO:0001583	missense	1240	exon3			GTTGTAATCTTCA	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.21T>A	chr12.hg19:g.108686719A>T	ENSP00000311733:p.Asp7Glu	136.0	0.0		119.0	6.0	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Missense_Mutation	SNP	ENST00000312143.7	hg19	CCDS44965.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.359097	0.41801	.	.	ENSG00000174600	ENST00000312143;ENST00000412676;ENST00000397688;ENST00000552995;ENST00000550402;ENST00000550573;ENST00000549466	T;T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.34;-0.34;-0.35;1.24;1.25	5.26	-3.64	0.04515	.	2.205920	0.02384	U	0.079066	T	0.51261	0.1664	L	0.59436	1.845	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39035	-0.9633	10	0.02654	T	1	.	0.4293	0.00468	0.3752:0.13:0.2427:0.2521	.	7	Q99788	CML1_HUMAN	E	7;7;5;5;7;7;7	ENSP00000311733:D7E;ENSP00000401293:D7E;ENSP00000380803:D5E;ENSP00000447579:D5E;ENSP00000449716:D7E;ENSP00000448925:D7E;ENSP00000448362:D7E	ENSP00000311733:D7E	D	-	3	2	CMKLR1	107210849	0.005000	0.15991	0.001000	0.08648	0.203000	0.24098	-0.209000	0.09358	-1.005000	0.03417	-0.378000	0.06908	GAT	.	.		0.453	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
TRPV4	59341	hgsc.bcm.edu	37	12	110230527	110230527	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:110230527C>A	ENST00000418703.2	-	10	1848	c.1754G>T	c.(1753-1755)gGc>gTc	p.G585V	TRPV4_ENST00000346520.2_Missense_Mutation_p.G525V|TRPV4_ENST00000544971.1_Missense_Mutation_p.G478V|TRPV4_ENST00000536838.1_Missense_Mutation_p.G551V|TRPV4_ENST00000541794.1_Missense_Mutation_p.G538V|TRPV4_ENST00000392719.2_Missense_Mutation_p.G538V|TRPV4_ENST00000261740.2_Missense_Mutation_p.G585V|TRPV4_ENST00000537083.1_Missense_Mutation_p.G525V	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	585					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						ATTCATCCAGCCCAGGACCAG	0.587																																					p.G585V		Atlas-SNP	.											.	TRPV4	88	.	0			c.G1754T						.						89.0	70.0	77.0					12																	110230527		2203	4300	6503	SO:0001583	missense	59341	exon11			ATCCAGCCCAGGA	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.1754G>T	chr12.hg19:g.110230527C>A	ENSP00000406191:p.Gly585Val	123.0	0.0		155.0	17.0	NM_021625	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Missense_Mutation	SNP	ENST00000418703.2	hg19	CCDS9134.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055045	0.93793	.	.	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000392719;ENST00000346520;ENST00000544971;ENST00000537083;ENST00000541794;ENST00000536838	D;D;D;D;D;D;D;D	0.98437	-4.93;-4.93;-4.93;-4.93;-4.93;-4.93;-4.93;-4.93	6.06	6.06	0.98353	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99146	0.9705	M	0.89095	3.005	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.997;0.995	D	0.99406	1.0929	10	0.59425	D	0.04	-1.2413	19.6125	0.95613	0.0:1.0:0.0:0.0	.	525;585;478;538;551	Q9HBA0-2;Q9HBA0;Q9HBA0-6;Q9HBA0-4;Q9HBA0-5	.;TRPV4_HUMAN;.;.;.	V	585;585;538;525;478;525;538;551	ENSP00000406191:G585V;ENSP00000261740:G585V;ENSP00000376480:G538V;ENSP00000319003:G525V;ENSP00000443611:G478V;ENSP00000442738:G525V;ENSP00000442167:G538V;ENSP00000444336:G551V	ENSP00000261740:G585V	G	-	2	0	TRPV4	108714910	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.879000	0.98667	0.650000	0.86243	GGC	.	.		0.587	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
RBM19	9904	hgsc.bcm.edu	37	12	114296692	114296692	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:114296692C>T	ENST00000545145.2	-	22	2646	c.2568G>A	c.(2566-2568)ggG>ggA	p.G856G	RBM19_ENST00000261741.5_Silent_p.G856G|RBM19_ENST00000392561.3_Silent_p.G856G	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	856	RRM 6. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCTTCAACTCCCCAAAGGTGC	0.527																																					p.G856G		Atlas-SNP	.											.	RBM19	117	.	0			c.G2568A						.						86.0	83.0	84.0					12																	114296692		2203	4300	6503	SO:0001819	synonymous_variant	9904	exon22			CAACTCCCCAAAG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.2568G>A	chr12.hg19:g.114296692C>T		99.0	0.0		88.0	31.0	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	hg19	CCDS9172.1																																																																																			.	.		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
HIP1R	9026	hgsc.bcm.edu	37	12	123338690	123338690	+	Silent	SNP	C	C	T	rs35154568		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:123338690C>T	ENST00000253083.4	+	8	803	c.678C>T	c.(676-678)ctC>ctT	p.L226L		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	226					receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GCAGCCACCTCTACCACTACA	0.582																																					p.L226L		Atlas-SNP	.											.	HIP1R	68	.	0			c.C678T						.						117.0	103.0	108.0					12																	123338690		2203	4300	6503	SO:0001819	synonymous_variant	9026	exon8			CCACCTCTACCAC	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.678C>T	chr12.hg19:g.123338690C>T		88.0	0.0		61.0	5.0	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Silent	SNP	ENST00000253083.4	hg19	CCDS31922.1																																																																																			.	.		0.582	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	
TMEM132D	121256	hgsc.bcm.edu	37	12	129559407	129559407	+	Missense_Mutation	SNP	C	C	G	rs577207277		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr12:129559407C>G	ENST00000422113.2	-	9	2639	c.2313G>C	c.(2311-2313)atG>atC	p.M771I	TMEM132D_ENST00000389441.4_Missense_Mutation_p.M309I	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	771					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CACTAATAACCATTTCCACCT	0.468																																					p.M771I		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G2313C						.						153.0	134.0	141.0					12																	129559407		2203	4300	6503	SO:0001583	missense	121256	exon9			AATAACCATTTCC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2313G>C	chr12.hg19:g.129559407C>G	ENSP00000408581:p.Met771Ile	251.0	0.0		269.0	14.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.804071	0.50315	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.13778	2.56;2.56	4.2	4.2	0.49525	.	0.110120	0.56097	D	0.000021	T	0.21145	0.0509	M	0.79805	2.47	0.50171	D	0.999852	P;P	0.40834	0.631;0.73	B;B	0.40506	0.31;0.331	T	0.03840	-1.0999	9	.	.	.	-46.7885	12.7483	0.57293	0.0:0.8344:0.1656:0.0	.	771;309	Q14C87;Q14C87-2	T132D_HUMAN;.	I	309;771	ENSP00000374092:M309I;ENSP00000408581:M771I	.	M	-	3	0	TMEM132D	128125360	1.000000	0.71417	0.596000	0.28811	0.475000	0.33008	3.701000	0.54793	2.033000	0.60031	0.462000	0.41574	ATG	.	.		0.468	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
AMER2	219287	hgsc.bcm.edu	37	13	25743926	25743926	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:25743926C>G	ENST00000515384.1	-	1	2499	c.1832G>C	c.(1831-1833)aGc>aCc	p.S611T	AMER2_ENST00000381853.3_Missense_Mutation_p.S492T|AMER2_ENST00000357816.2_Missense_Mutation_p.S492T			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	611					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										GTGCTTGATGCTAATAGGGAT	0.547																																					p.S611T		Atlas-SNP	.											.	.	.	.	0			c.G1832C						.						196.0	169.0	178.0					13																	25743926		2203	4300	6503	SO:0001583	missense	219287	exon1			TTGATGCTAATAG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"""-"""	26360	protein-coding gene	gene with protein product		614659	"""family with sequence similarity 123A"""	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1832G>C	chr13.hg19:g.25743926C>G	ENSP00000426528:p.Ser611Thr	366.0	0.0		257.0	59.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507438	0.85282	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.50813	0.81;0.81;0.73	5.97	5.97	0.96955	.	0.105202	0.64402	D	0.000001	T	0.59609	0.2206	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.994;0.997	T	0.60885	-0.7174	10	0.66056	D	0.02	-18.8671	19.4162	0.94700	0.0:1.0:0.0:0.0	.	611;492	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	T	492;492;611	ENSP00000350469:S492T;ENSP00000371277:S492T;ENSP00000426528:S611T	ENSP00000350469:S492T	S	-	2	0	FAM123A	24641926	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.080000	0.76837	2.837000	0.97791	0.655000	0.94253	AGC	.	.		0.547	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704	
FLT1	2321	hgsc.bcm.edu	37	13	28942739	28942739	+	Intron	SNP	T	T	C	rs371573097|rs558386334	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:28942739T>C	ENST00000282397.4	-	15	2368				FLT1_ENST00000541932.1_Silent_p.S726S	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	atgatgacgatgatgatgatg	0.343																																					p.S726S		Atlas-SNP	.											.	FLT1	393	.	0			c.A2178G						.						289.0	303.0	299.0					13																	28942739		692	1591	2283	SO:0001627	intron_variant	2321	exon15			TGACGATGATGAT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2117-10917A>G	chr13.hg19:g.28942739T>C		54.0	0.0		99.0	10.0	NM_001160030	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.		0.343	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
KLF12	11278	hgsc.bcm.edu	37	13	74387348	74387348	+	Silent	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:74387348G>T	ENST00000377669.2	-	4	773	c.747C>A	c.(745-747)acC>acA	p.T249T	KLF12_ENST00000377666.4_Silent_p.T249T|KLF12_ENST00000472022.1_5'UTR	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	249					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		CGCTATCTAAGGTCACATTTG	0.433																																					p.T249T		Atlas-SNP	.											.	KLF12	42	.	0			c.C747A						.						239.0	205.0	216.0					13																	74387348		2203	4300	6503	SO:0001819	synonymous_variant	11278	exon5			ATCTAAGGTCACA	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6346	protein-coding gene	gene with protein product	"""KLF12 zinc finger transcriptional repressor"", ""AP-2rep transcription factor"", ""AP-2 repressor"""	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.747C>A	chr13.hg19:g.74387348G>T		222.0	0.0		170.0	38.0	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Silent	SNP	ENST00000377669.2	hg19	CCDS9449.1																																																																																			.	.		0.433	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249	
MYO16	23026	hgsc.bcm.edu	37	13	109792700	109792700	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr13:109792700G>A	ENST00000357550.2	+	31	4115	c.4074G>A	c.(4072-4074)aaG>aaA	p.K1358K	MYO16_ENST00000356711.2_Silent_p.K1358K	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CCAACACCAAGCTCAGCGGCT	0.701																																					p.K1380K		Atlas-SNP	.											.	MYO16	285	.	0			c.G4140A						.						38.0	32.0	34.0					13																	109792700		2198	4283	6481	SO:0001819	synonymous_variant	23026	exon32			CACCAAGCTCAGC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4074G>A	chr13.hg19:g.109792700G>A		8.0	0.0		6.0	4.0	NM_001198950		Silent	SNP	ENST00000357550.2	hg19	CCDS32008.1																																																																																			.	.		0.701	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
ACTR10	55860	hgsc.bcm.edu	37	14	58690343	58690343	+	Missense_Mutation	SNP	G	G	A	rs372667907		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:58690343G>A	ENST00000254286.4	+	9	718	c.638G>A	c.(637-639)cGt>cAt	p.R213H		NM_018477.2	NP_060947.1	Q9NZ32	ARP10_HUMAN	actin-related protein 10 homolog (S. cerevisiae)	213					microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|dynactin complex (GO:0005869)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	13						CTTAAAGCGCGTACTTGCTTT	0.333																																					p.R213H		Atlas-SNP	.											.	ACTR10	33	.	0			c.G638A						.	G	HIS/ARG	0,4404		0,0,2202	77.0	77.0	77.0		638	5.7	1.0	14		77	2,8598	2.2+/-6.3	0,2,4298	no	missense	ACTR10	NM_018477.2	29	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	213/418	58690343	2,13002	2202	4300	6502	SO:0001583	missense	55860	exon9			AAGCGCGTACTTG	AF220190	CCDS32090.1	14q23.1	2014-08-08			ENSG00000131966	ENSG00000131966			17372	protein-coding gene	gene with protein product						12857853	Standard	NM_018477		Approved	HARP11, ACTR11, Arp11	uc001xdf.3	Q9NZ32	OTTHUMG00000171049	ENST00000254286.4:c.638G>A	chr14.hg19:g.58690343G>A	ENSP00000254286:p.Arg213His	65.0	0.0		65.0	20.0	NM_018477	Q9H9Y5|Q9NWY2	Missense_Mutation	SNP	ENST00000254286.4	hg19	CCDS32090.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034221	0.75617	0.0	2.33E-4	ENSG00000131966	ENST00000543474;ENST00000254286	D	0.94650	-3.48	5.74	5.74	0.90152	.	0.105394	0.64402	D	0.000004	D	0.97219	0.9091	M	0.86864	2.845	0.80722	D	1	D;D	0.69078	0.995;0.997	P;P	0.59012	0.791;0.85	D	0.97628	1.0140	10	0.87932	D	0	-26.2586	18.9079	0.92471	0.0:0.0:1.0:0.0	.	213;213	Q53H79;Q9NZ32	.;ARP10_HUMAN	H	213	ENSP00000254286:R213H	ENSP00000254286:R213H	R	+	2	0	ACTR10	57760096	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	8.926000	0.92839	2.702000	0.92279	0.655000	0.94253	CGT	.	.		0.333	ACTR10-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411405.1		
RTN1	6252	hgsc.bcm.edu	37	14	60074189	60074189	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:60074189C>T	ENST00000267484.5	-	4	2122	c.1787G>A	c.(1786-1788)cGg>cAg	p.R596Q	RTN1_ENST00000395090.1_Missense_Mutation_p.R13Q|RTN1_ENST00000557422.1_5'UTR|RTN1_ENST00000342503.4_Missense_Mutation_p.R28Q	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	596	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		CTTGATGTCCCGCCAATACAA	0.602																																					p.R596Q		Atlas-SNP	.											.	RTN1	139	.	0			c.G1787A						.						31.0	31.0	31.0					14																	60074189		2203	4300	6503	SO:0001583	missense	6252	exon4			ATGTCCCGCCAAT	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"""neuroendocrine-specific protein"""	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1787G>A	chr14.hg19:g.60074189C>T	ENSP00000267484:p.Arg596Gln	190.0	0.0		134.0	23.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	37	6.022003	0.97211	.	.	ENSG00000139970	ENST00000432103;ENST00000267484;ENST00000395090;ENST00000342503;ENST00000433623	T;T;T	0.54866	0.55;0.55;0.55	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.77890	0.4198	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.995	T	0.79676	-0.1704	10	0.87932	D	0	.	20.4777	0.99188	0.0:1.0:0.0:0.0	.	13;596;28	A8MT72;Q16799;Q16799-3	.;RTN1_HUMAN;.	Q	176;596;13;28;522	ENSP00000267484:R596Q;ENSP00000378525:R13Q;ENSP00000340716:R28Q	ENSP00000267484:R596Q	R	-	2	0	RTN1	59143942	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.840000	0.97914	0.655000	0.94253	CGG	.	.		0.602	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2		
PAPLN	89932	hgsc.bcm.edu	37	14	73721644	73721644	+	Silent	SNP	G	G	A	rs369082075		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:73721644G>A	ENST00000554301.1	+	13	1708	c.1545G>A	c.(1543-1545)ccG>ccA	p.P515P	PAPLN_ENST00000340738.5_Silent_p.P488P|PAPLN_ENST00000381166.3_Silent_p.P515P|PAPLN_ENST00000427855.1_Silent_p.P515P|PAPLN_ENST00000555445.1_Silent_p.P515P			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	515	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		CCATTGGGCCGCCCAGCCACT	0.642																																					p.P488P		Atlas-SNP	.											PAPLN_ENST00000427855,NS,carcinoma,0,2	PAPLN	180	.	0			c.G1464A						.	G		1,4405	2.1+/-5.4	0,1,2202	36.0	37.0	37.0		1464	-9.4	0.0	14		37	0,8600		0,0,4300	no	coding-synonymous	PAPLN	NM_173462.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		488/1252	73721644	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	89932	exon13			TGGGCCGCCCAGC	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1545G>A	chr14.hg19:g.73721644G>A		35.0	1.0		37.0	14.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	hg19																																																																																				.	.		0.642	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
SEL1L	6400	hgsc.bcm.edu	37	14	81955626	81955626	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:81955626C>A	ENST00000336735.4	-	14	1481	c.1365G>T	c.(1363-1365)atG>atT	p.M455I		NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	455	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		AGAGGTAGGCCATTCCAAGCC	0.423																																					p.M455I		Atlas-SNP	.											.	SEL1L	67	.	0			c.G1365T						.						98.0	90.0	93.0					14																	81955626		2203	4300	6503	SO:0001583	missense	6400	exon14			GTAGGCCATTCCA		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"""sel-1 suppressor of lin-12-like 1 (C. elegans)"""	602329	"""sel-1 (suppressor of lin-12, C.elegans)-like"""			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.1365G>T	chr14.hg19:g.81955626C>A	ENSP00000337053:p.Met455Ile	160.0	0.0		182.0	25.0	NM_005065	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	hg19	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.298139	0.60086	.	.	ENSG00000071537	ENST00000336735	T	0.49432	0.78	5.6	5.6	0.85130	Tetratricopeptide-like helical (1);	0.039238	0.85682	D	0.000000	T	0.29914	0.0748	N	0.04994	-0.135	0.80722	D	1	B	0.18310	0.027	B	0.22880	0.042	T	0.11155	-1.0599	10	0.19590	T	0.45	.	17.7997	0.88583	0.0:1.0:0.0:0.0	.	455	Q9UBV2	SE1L1_HUMAN	I	455	ENSP00000337053:M455I	ENSP00000337053:M455I	M	-	3	0	SEL1L	81025379	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.793000	0.75130	2.640000	0.89533	0.655000	0.94253	ATG	.	.		0.423	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	
EML5	161436	hgsc.bcm.edu	37	14	89202777	89202777	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:89202777T>A	ENST00000380664.5	-	7	979	c.980A>T	c.(979-981)gAa>gTa	p.E327V	EML5_ENST00000554922.1_Missense_Mutation_p.E327V|EML5_ENST00000352093.5_Missense_Mutation_p.E327V			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	327						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						TGCCCAAAGTTCACCTTCACA	0.398																																					p.E327V		Atlas-SNP	.											.	EML5	141	.	0			c.A980T						.						211.0	205.0	207.0					14																	89202777		1926	4124	6050	SO:0001583	missense	161436	exon7			CAAAGTTCACCTT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.980A>T	chr14.hg19:g.89202777T>A	ENSP00000370039:p.Glu327Val	185.0	0.0		185.0	38.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.471295	0.84533	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.60171	0.21;0.21;0.21	5.06	5.06	0.68205	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.121386	0.53938	D	0.000042	T	0.72914	0.3520	M	0.68593	2.085	0.58432	D	0.999998	D	0.71674	0.998	D	0.70016	0.967	T	0.74774	-0.3551	10	0.51188	T	0.08	-27.7062	14.9672	0.71204	0.0:0.0:0.0:1.0	.	327	Q05BV3	EMAL5_HUMAN	V	327	ENSP00000451998:E327V;ENSP00000298315:E327V;ENSP00000370039:E327V	ENSP00000298315:E327V	E	-	2	0	EML5	88272530	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.525000	0.81892	2.128000	0.65567	0.482000	0.46254	GAA	.	.		0.398	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
KCNK13	56659	hgsc.bcm.edu	37	14	90651207	90651207	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:90651207C>T	ENST00000282146.4	+	2	1528	c.1087C>T	c.(1087-1089)Ctg>Ttg	p.L363L		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	363					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				GTTGGCCATCCTGCAGAAGCA	0.617																																					p.L363L		Atlas-SNP	.											.	KCNK13	76	.	0			c.C1087T						.						29.0	31.0	31.0					14																	90651207		2200	4299	6499	SO:0001819	synonymous_variant	56659	exon2			GCCATCCTGCAGA	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.1087C>T	chr14.hg19:g.90651207C>T		169.0	0.0		163.0	26.0	NM_022054	B5TJL8|Q96E79	Silent	SNP	ENST00000282146.4	hg19	CCDS9889.1																																																																																			.	.		0.617	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054	
RTL1	388015	hgsc.bcm.edu	37	14	101350875	101350875	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:101350875G>A	ENST00000534062.1	-	1	309	c.251C>T	c.(250-252)cCa>cTa	p.P84L	MIR432_ENST00000606207.1_RNA|MIR433_ENST00000384837.1_RNA|MIR127_ENST00000384876.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	84					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TTCCTTACGTGGGCCACTGGA	0.572																																					p.P84L		Atlas-SNP	.											.	RTL1	120	.	0			c.C251T						.						82.0	72.0	75.0					14																	101350875		1568	3582	5150	SO:0001583	missense	388015	exon1			TTACGTGGGCCAC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.251C>T	chr14.hg19:g.101350875G>A	ENSP00000435342:p.Pro84Leu	119.0	0.0		103.0	16.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.770758	0.49680	.	.	ENSG00000254656	ENST00000534062	T	0.42131	0.98	3.54	2.63	0.31362	.	.	.	.	.	T	0.43100	0.1232	N	0.24115	0.695	0.33458	D	0.584537	D	0.69078	0.997	P	0.61328	0.887	T	0.55560	-0.8122	9	0.87932	D	0	.	8.2736	0.31860	0.0:0.0:0.7636:0.2364	.	84	E9PKS8	.	L	84	ENSP00000435342:P84L	ENSP00000435342:P84L	P	-	2	0	RTL1	100420628	0.994000	0.37717	0.984000	0.44739	0.957000	0.61999	2.134000	0.42102	1.038000	0.40049	0.561000	0.74099	CCA	.	.		0.572	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414859	105414859	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr14:105414859T>C	ENST00000333244.5	-	7	7048	c.6929A>G	c.(6928-6930)gAc>gGc	p.D2310G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2310						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCAGTCACGTCCTTGTCGGC	0.607																																					p.D2310G		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A6929G						.						199.0	215.0	210.0					14																	105414859		2036	4201	6237	SO:0001583	missense	113146	exon7			GTCACGTCCTTGT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.6929A>G	chr14.hg19:g.105414859T>C	ENSP00000353114:p.Asp2310Gly	159.0	0.0		122.0	28.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	11.15	1.553352	0.27739	.	.	ENSG00000185567	ENST00000333244	T	0.01279	5.06	3.54	1.12	0.20585	.	.	.	.	.	T	0.02047	0.0064	M	0.71871	2.18	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.45585	-0.9251	9	0.20046	T	0.44	.	6.1488	0.20301	0.0:0.2236:0.0:0.7764	.	2310	Q8IVF2	AHNK2_HUMAN	G	2310	ENSP00000353114:D2310G	ENSP00000353114:D2310G	D	-	2	0	AHNAK2	104485904	0.013000	0.17824	0.067000	0.19924	0.005000	0.04900	1.221000	0.32503	0.255000	0.21593	-0.760000	0.03462	GAC	.	.		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NPAP1	23742	hgsc.bcm.edu	37	15	24921553	24921553	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:24921553T>C	ENST00000329468.2	+	1	1013	c.539T>C	c.(538-540)cTt>cCt	p.L180P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	180					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.L180H(1)									AGGACCCCCCTTAGCAGCGGA	0.607																																					p.L180P		Atlas-SNP	.											C15orf2,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.T539C						.						47.0	40.0	42.0					15																	24921553		2203	4300	6503	SO:0001583	missense	23742	exon1			CCCCCCTTAGCAG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.539T>C	chr15.hg19:g.24921553T>C	ENSP00000333735:p.Leu180Pro	85.0	0.0		97.0	15.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	10.21	1.286474	0.23478	.	.	ENSG00000185823	ENST00000329468	T	0.11821	2.74	2.03	-2.41	0.06562	.	5.007880	0.00589	N	0.000348	T	0.14743	0.0356	L	0.29908	0.895	0.09310	N	1	D	0.54772	0.968	P	0.55749	0.783	T	0.15492	-1.0435	10	0.23302	T	0.38	.	0.011	0.00001	0.3043:0.1978:0.1893:0.3085	.	180	Q9NZP6	CO002_HUMAN	P	180	ENSP00000333735:L180P	ENSP00000333735:L180P	L	+	2	0	C15orf2	22472646	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.233000	0.01204	-0.601000	0.05783	0.352000	0.21897	CTT	.	.		0.607	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
GABRB3	2562	hgsc.bcm.edu	37	15	26793135	26793135	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:26793135T>C	ENST00000311550.5	-	9	1338	c.1227A>G	c.(1225-1227)cgA>cgG	p.R409R	GABRB3_ENST00000400188.3_Silent_p.R338R|GABRB3_ENST00000299267.4_Silent_p.R409R|GABRB3_ENST00000545868.1_Silent_p.R324R|GABRB3_ENST00000541819.2_Silent_p.R465R	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	409					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CATGCCCTTCTCGAGGCATGC	0.488																																					p.R409R		Atlas-SNP	.											.	GABRB3	338	.	0			c.A1227G						.						84.0	75.0	78.0					15																	26793135		2203	4300	6503	SO:0001819	synonymous_variant	2562	exon9			CCCTTCTCGAGGC		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1227A>G	chr15.hg19:g.26793135T>C		167.0	0.0		174.0	37.0	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	hg19	CCDS10019.1																																																																																			.	.		0.488	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
CHRM5	1133	hgsc.bcm.edu	37	15	34356472	34356472	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:34356472A>G	ENST00000383263.5	+	3	2224	c.1554A>G	c.(1552-1554)aaA>aaG	p.K518K	CHRM5_ENST00000557872.1_Silent_p.K518K	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	518					adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	AAAAGAAAAAAGTGGAAGAGA	0.463																																					p.K518K		Atlas-SNP	.											.	CHRM5	59	.	0			c.A1554G						.						56.0	62.0	60.0					15																	34356472		2201	4298	6499	SO:0001819	synonymous_variant	1133	exon3			GAAAAAAGTGGAA		CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1954	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 5"""	118496					Standard	NM_012125		Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.1554A>G	chr15.hg19:g.34356472A>G		99.0	0.0		103.0	11.0	NM_012125	Q96RG7	Silent	SNP	ENST00000383263.5	hg19	CCDS10031.1																																																																																			.	.		0.463	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251521.2		
CASC5	57082	hgsc.bcm.edu	37	15	40920293	40920293	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:40920293A>G	ENST00000346991.5	+	12	5870	c.5480A>G	c.(5479-5481)gAt>gGt	p.D1827G	CASC5_ENST00000399668.2_Missense_Mutation_p.D1801G			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1827					acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ACTGAAGAGGATATAGATAAA	0.358																																					p.D1827G		Atlas-SNP	.											.	CASC5	269	.	0			c.A5480G						.						84.0	87.0	86.0					15																	40920293		1819	4084	5903	SO:0001583	missense	57082	exon12			AAGAGGATATAGA	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5480A>G	chr15.hg19:g.40920293A>G	ENSP00000335463:p.Asp1827Gly	113.0	0.0		89.0	17.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.14|11.14	1.550390|1.550390	0.27739|0.27739	.|.	.|.	ENSG00000137812|ENSG00000137812	ENST00000346991;ENST00000399668|ENST00000532406	T;T|.	0.05580|.	3.42;3.42|.	5.49|5.49	3.15|3.15	0.36227|0.36227	.|.	0.842583|.	0.10359|.	N|.	0.684210|.	T|T	0.35799|0.35799	0.0944|0.0944	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	B;B|.	0.29646|.	0.253;0.253|.	B;B|.	0.25291|.	0.059;0.059|.	T|T	0.22138|0.22138	-1.0225|-1.0225	10|5	0.33940|.	T|.	0.23|.	.|.	6.819|6.819	0.23847|0.23847	0.6374:0.2864:0.0762:0.0|0.6374:0.2864:0.0762:0.0	.|.	1801;1827|.	Q8NG31-2;Q8NG31|.	.;CASC5_HUMAN|.	G|V	1827;1801|8	ENSP00000335463:D1827G;ENSP00000382576:D1801G|.	ENSP00000335463:D1827G|.	D|I	+|+	2|1	0|0	CASC5|CASC5	38707585|38707585	0.000000|0.000000	0.05858|0.05858	0.122000|0.122000	0.21767|0.21767	0.983000|0.983000	0.72400|0.72400	0.589000|0.589000	0.23939|0.23939	0.373000|0.373000	0.24621|0.24621	0.529000|0.529000	0.55759|0.55759	GAT|ATA	.	.		0.358	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
SPINT1	6692	hgsc.bcm.edu	37	15	41137074	41137074	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:41137074C>T	ENST00000344051.4	+	2	556	c.322C>T	c.(322-324)Cgc>Tgc	p.R108C	RP11-532F12.5_ENST00000568525.1_RNA|RP11-532F12.5_ENST00000564302.1_RNA|SPINT1_ENST00000431806.1_Missense_Mutation_p.R108C|RP11-532F12.5_ENST00000565315.1_RNA|RP11-532F12.5_ENST00000568419.1_RNA|SPINT1_ENST00000562057.1_Missense_Mutation_p.R108C			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	108	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCAGCCCGACCGCGGGGAGGA	0.657																																					p.R108C		Atlas-SNP	.											.	SPINT1	28	.	0			c.C322T						.						32.0	31.0	31.0					15																	41137074		2203	4299	6502	SO:0001583	missense	6692	exon2			CCCGACCGCGGGG		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"""serine protease inhibitor, Kunitz type 1"""				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.322C>T	chr15.hg19:g.41137074C>T	ENSP00000342098:p.Arg108Cys	80.0	0.0		70.0	9.0	NM_181642	Q7Z7D2	Missense_Mutation	SNP	ENST00000344051.4	hg19	CCDS10067.1	.	.	.	.	.	.	.	.	.	.	C	17.70	3.453648	0.63290	.	.	ENSG00000166145	ENST00000344051;ENST00000536281;ENST00000431806	T;T	0.23348	1.91;1.91	4.98	3.1	0.35709	Seven cysteines (1);Seven cysteines, N-terminal (2);	0.853113	0.10682	N	0.646338	T	0.25121	0.0610	L	0.29908	0.895	0.09310	N	1	D;D;D	0.57571	0.975;0.98;0.975	P;P;P	0.52856	0.594;0.711;0.594	T	0.12967	-1.0527	10	0.56958	D	0.05	-7.0573	2.8482	0.05550	0.1646:0.148:0.5449:0.1426	.	108;108;108	B2RBU9;O43278-2;O43278	.;.;SPIT1_HUMAN	C	108;75;108	ENSP00000342098:R108C;ENSP00000409935:R108C	ENSP00000342098:R108C	R	+	1	0	SPINT1	38924366	0.003000	0.15002	0.858000	0.33744	0.838000	0.47535	0.608000	0.24223	0.621000	0.30232	0.563000	0.77884	CGC	.	.		0.657	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710	
INO80	54617	hgsc.bcm.edu	37	15	41337196	41337196	+	Missense_Mutation	SNP	T	T	A	rs115089447	byFrequency	TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:41337196T>A	ENST00000361937.3	-	24	3237	c.2813A>T	c.(2812-2814)gAg>gTg	p.E938V	INO80_ENST00000401393.3_Missense_Mutation_p.E938V			Q9ULG1	INO80_HUMAN	INO80 complex subunit	938	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTGGTGGCTCTCCCCTTCTGG	0.502																																					p.E938V		Atlas-SNP	.											.	INO80	122	.	0			c.A2813T						.						97.0	99.0	98.0					15																	41337196		2203	4300	6503	SO:0001583	missense	54617	exon24			TGGCTCTCCCCTT	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.2813A>T	chr15.hg19:g.41337196T>A	ENSP00000355205:p.Glu938Val	63.0	0.0		66.0	14.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.358497	0.41801	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.91464	-2.85;-2.85	4.95	1.29	0.21616	.	0.587060	0.19449	N	0.113990	T	0.78792	0.4339	N	0.14661	0.345	0.34448	D	0.700379	B	0.26445	0.149	B	0.21708	0.036	T	0.71761	-0.4495	10	0.38643	T	0.18	.	6.5731	0.22549	0.0:0.1395:0.1301:0.7304	.	938	Q9ULG1	INO80_HUMAN	V	938	ENSP00000355205:E938V;ENSP00000384686:E938V	ENSP00000355205:E938V	E	-	2	0	INO80	39124488	0.756000	0.28383	0.846000	0.33378	0.928000	0.56348	1.139000	0.31504	0.113000	0.18004	0.459000	0.35465	GAG	.	T|0.989;C|0.011		0.502	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553	
FBN1	2200	hgsc.bcm.edu	37	15	48719788	48719788	+	Nonsense_Mutation	SNP	G	G	A	rs397515848		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:48719788G>A	ENST00000316623.5	-	58	7635	c.7180C>T	c.(7180-7182)Cga>Tga	p.R2394*		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2394					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		ATGAATCCTCGGCCATGGGGA	0.463																																					p.R2394X		Atlas-SNP	.											.	FBN1	310	.	0			c.C7180T	GRCh37	CM993162	FBN1	M		.						79.0	77.0	78.0					15																	48719788		2198	4296	6494	SO:0001587	stop_gained	2200	exon58			ATCCTCGGCCATG	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.7180C>T	chr15.hg19:g.48719788G>A	ENSP00000325527:p.Arg2394*	124.0	0.0		137.0	12.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Nonsense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	50	17.109795	0.99879	.	.	ENSG00000166147	ENST00000316623	.	.	.	5.44	4.51	0.55191	.	0.206926	0.42053	D	0.000769	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	13.249	0.60041	0.0:0.0:0.7113:0.2887	.	.	.	.	X	2394	.	ENSP00000325527:R2394X	R	-	1	2	FBN1	46507080	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.625000	0.67770	1.412000	0.46977	0.650000	0.86243	CGA	.	.		0.463	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
RFX7	64864	hgsc.bcm.edu	37	15	56394441	56394441	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:56394441T>C	ENST00000559447.2	-	6	509	c.238A>G	c.(238-240)Agt>Ggt	p.S80G	RFX7_ENST00000423270.1_Missense_Mutation_p.S177G|RFX7_ENST00000317318.6_Missense_Mutation_p.S177G|RFX7_ENST00000422057.1_Missense_Mutation_p.S80G			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	80					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CTTAGTCCACTGTAGCAATAT	0.313																																					p.S177G		Atlas-SNP	.											.	RFX7	170	.	0			c.A529G						.						61.0	59.0	60.0					15																	56394441		1787	4060	5847	SO:0001583	missense	64864	exon6			GTCCACTGTAGCA			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.238A>G	chr15.hg19:g.56394441T>C	ENSP00000453281:p.Ser80Gly	54.0	0.0		47.0	10.0	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.47	3.397234	0.62177	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	D;D;D	0.82803	-1.65;-1.65;-1.65	5.89	5.89	0.94794	Winged helix-turn-helix transcription repressor DNA-binding (1);	1.215880	0.05610	N	0.578026	T	0.81029	0.4738	L	0.39020	1.185	0.58432	D	0.999999	B	0.22683	0.073	B	0.20184	0.028	T	0.59434	-0.7455	10	0.54805	T	0.06	0.236	15.4882	0.75584	0.0:0.0:0.0:1.0	.	80	Q2KHR2	RFX7_HUMAN	G	80;177;177	ENSP00000387504:S80G;ENSP00000313299:S177G;ENSP00000397644:S177G	ENSP00000313299:S177G	S	-	1	0	RFX7	54181733	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.250000	0.74265	0.477000	0.44152	AGT	.	.		0.313	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
VPS13C	54832	hgsc.bcm.edu	37	15	62219327	62219327	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:62219327G>A	ENST00000261517.5	-	52	6552	c.6479C>T	c.(6478-6480)cCt>cTt	p.P2160L	VPS13C_ENST00000395896.4_Missense_Mutation_p.P2160L|VPS13C_ENST00000249837.3_Missense_Mutation_p.P2117L|VPS13C_ENST00000395898.3_Missense_Mutation_p.P2117L	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TCTGAGAAAAGGGCAAGCGAG	0.428																																					p.P2160L		Atlas-SNP	.											.	VPS13C	506	.	0			c.C6479T						.						123.0	120.0	121.0					15																	62219327		2203	4300	6503	SO:0001583	missense	54832	exon52			AGAAAAGGGCAAG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6479C>T	chr15.hg19:g.62219327G>A	ENSP00000261517:p.Pro2160Leu	142.0	0.0		117.0	17.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128849	0.94473	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.61980	0.06;0.06;0.06	5.41	5.41	0.78517	.	0.179966	0.49916	D	0.000129	T	0.74129	0.3676	M	0.76574	2.34	0.80722	D	1	B;P;B;P	0.47191	0.112;0.891;0.38;0.825	B;P;B;P	0.52159	0.197;0.691;0.197;0.493	T	0.73260	-0.4039	10	0.39692	T	0.17	.	19.5612	0.95373	0.0:0.0:1.0:0.0	.	2117;2160;2117;2160	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	L	2117;2160;2160;2160	ENSP00000249837:P2117L;ENSP00000261517:P2160L;ENSP00000379233:P2160L	ENSP00000249837:P2117L	P	-	2	0	VPS13C	60006619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.173000	0.94815	2.687000	0.91594	0.655000	0.94253	CCT	.	.		0.428	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
HEXA	3073	hgsc.bcm.edu	37	15	72643535	72643535	+	Missense_Mutation	SNP	T	T	A	rs121907976		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:72643535T>A	ENST00000268097.5	-	6	1114	c.611A>T	c.(610-612)cAt>cTt	p.H204L	RP11-106M3.3_ENST00000570175.1_RNA|HEXA_ENST00000457859.2_Missense_Mutation_p.H12L|HEXA_ENST00000567159.1_Missense_Mutation_p.H204L|RP11-106M3.2_ENST00000379915.4_RNA|HEXA_ENST00000566304.1_Missense_Mutation_p.H215L|HEXA_ENST00000429918.2_Missense_Mutation_p.H31L	NM_000520.4	NP_000511.2	P06865	HEXA_HUMAN	hexosaminidase A (alpha polypeptide)	204			H -> R (in GM2G1; infantile).		carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	24						ATCTACCAGATGCCAGTGGAA	0.453																																					p.H204L		Atlas-SNP	.											.	HEXA	48	.	0			c.A611T	GRCh37	CM930394	HEXA	M	rs121907976	.						174.0	145.0	155.0					15																	72643535		2199	4297	6496	SO:0001583	missense	3073	exon6			ACCAGATGCCAGT	M13520	CCDS10243.1	15q24.1	2012-10-02			ENSG00000213614	ENSG00000213614	3.2.1.52		4878	protein-coding gene	gene with protein product	"""Tay Sachs disease"", ""GM2 gangliosidosis"""	606869				2952641, 3013851	Standard	NM_000520		Approved		uc002aun.4	P06865	OTTHUMG00000133445	ENST00000268097.5:c.611A>T	chr15.hg19:g.72643535T>A	ENSP00000268097:p.His204Leu	116.0	0.0		174.0	24.0	NM_000520	B4DKE7|E7ENH7|Q53HS8|Q6AI32	Missense_Mutation	SNP	ENST00000268097.5	hg19	CCDS10243.1	.	.	.	.	.	.	.	.	.	.	T	34	5.303095	0.95601	.	.	ENSG00000213614	ENST00000268097;ENST00000457859;ENST00000429918	D;D;D	0.98602	-5.02;-5.02;-5.02	5.78	5.78	0.91487	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);Glycoside hydrolase, family 20 (1);	0.000000	0.85682	D	0.000000	D	0.99560	0.9842	H	0.99881	4.885	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.97392	0.9990	10	0.87932	D	0	-24.6736	16.1109	0.81263	0.0:0.0:0.0:1.0	.	31;215;31;84;204	E9PGL4;B4DVA7;B4DVL8;Q9BVJ8;P06865	.;.;.;.;HEXA_HUMAN	L	204;12;31	ENSP00000268097:H204L;ENSP00000398026:H12L;ENSP00000416187:H31L	ENSP00000268097:H204L	H	-	2	0	HEXA	70430589	1.000000	0.71417	0.946000	0.38457	0.996000	0.88848	7.940000	0.87693	2.185000	0.69588	0.533000	0.62120	CAT	.	.		0.453	HEXA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257317.2	NM_000520	
IQGAP1	8826	hgsc.bcm.edu	37	15	91043276	91043276	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:91043276A>C	ENST00000268182.5	+	38	5034	c.4910A>C	c.(4909-4911)gAt>gCt	p.D1637A	IQGAP1_ENST00000560738.1_Missense_Mutation_p.D1065A	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1637	C2.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AAATTATTTGATAGAGCTAAA	0.368																																					p.D1637A		Atlas-SNP	.											.	IQGAP1	140	.	0			c.A4910C						.						95.0	88.0	90.0					15																	91043276		2198	4298	6496	SO:0001583	missense	8826	exon38			TATTTGATAGAGC	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.4910A>C	chr15.hg19:g.91043276A>C	ENSP00000268182:p.Asp1637Ala	76.0	0.0		69.0	5.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.148846	0.78001	.	.	ENSG00000140575	ENST00000268182	T	0.03181	4.02	5.7	5.7	0.88788	.	0.051090	0.85682	D	0.000000	T	0.18509	0.0444	M	0.85197	2.74	0.80722	D	1	D;D	0.57899	0.981;0.961	P;P	0.60012	0.867;0.778	T	0.00346	-1.1800	10	0.72032	D	0.01	-22.2177	15.1546	0.72730	1.0:0.0:0.0:0.0	.	258;1637	B4DNP4;P46940	.;IQGA1_HUMAN	A	1637	ENSP00000268182:D1637A	ENSP00000268182:D1637A	D	+	2	0	IQGAP1	88844280	1.000000	0.71417	0.987000	0.45799	0.524000	0.34500	9.173000	0.94815	2.180000	0.69256	0.454000	0.30748	GAT	.	.		0.368	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870	
IGF1R	3480	hgsc.bcm.edu	37	15	99451929	99451929	+	Silent	SNP	C	C	T	rs542546475		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:99451929C>T	ENST00000268035.6	+	6	1874	c.1263C>T	c.(1261-1263)taC>taT	p.Y421Y	IGF1R_ENST00000558762.1_Silent_p.Y421Y	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	421					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.Y421Y(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ACTCCTTCTACGTCCTCGACA	0.507													C|||	1	0.000199681	0.0	0.0014	5008	,	,		22331	0.0		0.0	False		,,,				2504	0.0				p.Y421Y		Atlas-SNP	.											IGF1R,colon,carcinoma,0,1	IGF1R	147	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1263T						.						107.0	91.0	96.0					15																	99451929		2197	4297	6494	SO:0001819	synonymous_variant	3480	exon6			CTTCTACGTCCTC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1263C>T	chr15.hg19:g.99451929C>T		195.0	0.0		190.0	15.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	hg19	CCDS10378.1																																																																																			.	.		0.507	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
LRRK1	79705	hgsc.bcm.edu	37	15	101592136	101592136	+	Silent	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr15:101592136T>A	ENST00000388948.3	+	24	4019	c.3660T>A	c.(3658-3660)ccT>ccA	p.P1220P	RP11-505E24.3_ENST00000558979.1_RNA|LRRK1_ENST00000284395.5_Silent_p.P1217P|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AGCTGGTCCCTGAACTGTTCA	0.637																																					p.P1220P		Atlas-SNP	.											.	LRRK1	310	.	0			c.T3660A						.						43.0	49.0	47.0					15																	101592136		2021	4180	6201	SO:0001819	synonymous_variant	79705	exon24			GGTCCCTGAACTG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.3660T>A	chr15.hg19:g.101592136T>A		134.0	0.0		108.0	10.0	NM_024652		Silent	SNP	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.		0.637	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
NUP93	9688	hgsc.bcm.edu	37	16	56872968	56872968	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:56872968A>T	ENST00000308159.5	+	19	2244	c.2123A>T	c.(2122-2124)gAt>gTt	p.D708V	NUP93_ENST00000564887.1_Missense_Mutation_p.D585V|NUP93_ENST00000542526.1_Missense_Mutation_p.D585V|NUP93_ENST00000569842.1_Missense_Mutation_p.D708V	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	708					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GGTCATATTGATAGAGCTTTT	0.363																																					p.D708V	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.A2123T						.						173.0	158.0	163.0					16																	56872968		2198	4300	6498	SO:0001583	missense	9688	exon19			ATATTGATAGAGC	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.2123A>T	chr16.hg19:g.56872968A>T	ENSP00000310668:p.Asp708Val	201.0	0.0		223.0	54.0	NM_014669	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	hg19	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	A	18.11	3.550717	0.65311	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	T;T	0.44881	0.91;0.91	6.14	6.14	0.99180	.	0.080378	0.85682	D	0.000000	T	0.37156	0.0993	L	0.35487	1.065	0.80722	D	1	B	0.20052	0.041	B	0.26416	0.069	T	0.09509	-1.0671	10	0.31617	T	0.26	-14.8164	16.806	0.85666	1.0:0.0:0.0:0.0	.	708	Q8N1F7	NUP93_HUMAN	V	708;585	ENSP00000310668:D708V;ENSP00000440235:D585V	ENSP00000310668:D708V	D	+	2	0	NUP93	55430469	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.813000	0.91963	2.367000	0.80283	0.529000	0.55759	GAT	.	.		0.363	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76513378	76513378	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:76513378A>G	ENST00000476707.1	+	11	1973	c.1834A>G	c.(1834-1836)Ata>Gta	p.I612V	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.I560V|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.I536V|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.I608V			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	609	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GTTTTACTATATAGATTCAGA	0.343																																					p.I536V		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.A1606G						.						120.0	129.0	126.0					16																	76513378		2198	4296	6494	SO:0001583	missense	85445	exon11			TACTATATAGATT	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1834A>G	chr16.hg19:g.76513378A>G	ENSP00000417628:p.Ile612Val	195.0	0.0		171.0	26.0	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.56	1.974835	0.34848	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.57	0.815	0.18763	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (3);	0.157455	0.29087	N	0.013190	T	0.23210	0.0561	.	.	.	0.39091	D	0.961107	B;B;B;B	0.12630	0.006;0.006;0.006;0.001	B;B;B;B	0.21151	0.02;0.02;0.033;0.005	T	0.06972	-1.0797	9	0.44086	T	0.13	.	9.5427	0.39262	0.731:0.0:0.269:0.0	.	536;612;584;609	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	V	608;560;536;612	ENSP00000306893:I608V;ENSP00000439733:I560V;ENSP00000418741:I536V;ENSP00000417628:I612V	ENSP00000306893:I608V	I	+	1	0	CNTNAP4	75070879	0.867000	0.29959	0.934000	0.37439	0.964000	0.63967	1.676000	0.37565	-0.046000	0.13446	0.528000	0.53228	ATA	.	.		0.343	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77398168	77398168	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:77398168T>C	ENST00000282849.5	-	5	1307	c.889A>G	c.(889-891)Acc>Gcc	p.T297A		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	297	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ACCACGAGGGTTTCCACATTG	0.493																																					p.T297A		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.A889G						.						132.0	120.0	124.0					16																	77398168		2198	4300	6498	SO:0001583	missense	170692	exon5			CGAGGGTTTCCAC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.889A>G	chr16.hg19:g.77398168T>C	ENSP00000282849:p.Thr297Ala	222.0	0.0		218.0	51.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678734	0.68042	.	.	ENSG00000140873	ENST00000282849	T	0.62639	0.01	5.17	5.17	0.71159	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.71736	0.3375	L	0.41710	1.295	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74624	-0.3603	10	0.72032	D	0.01	.	14.3522	0.66711	0.0:0.0:0.0:1.0	.	297	Q8TE60	ATS18_HUMAN	A	297	ENSP00000282849:T297A	ENSP00000282849:T297A	T	-	1	0	ADAMTS18	75955669	1.000000	0.71417	0.805000	0.32314	0.301000	0.27625	7.477000	0.81069	2.170000	0.68504	0.482000	0.46254	ACC	.	.		0.493	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
VAT1L	57687	hgsc.bcm.edu	37	16	77859180	77859180	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:77859180C>T	ENST00000302536.2	+	3	554	c.401C>T	c.(400-402)gCc>gTc	p.A134V		NM_020927.1	NP_065978.1	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport 1-like	134							oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(10)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24						AATTACAATGCCTGGGCAGAG	0.522																																					p.A134V		Atlas-SNP	.											.	VAT1L	68	.	0			c.C401T						.						137.0	120.0	125.0					16																	77859180		2198	4300	6498	SO:0001583	missense	57687	exon3			ACAATGCCTGGGC	AB046796	CCDS32492.1	16q23.1	2014-09-09	2013-08-23		ENSG00000171724	ENSG00000171724			29315	protein-coding gene	gene with protein product			"""vesicle amine transport protein 1 homolog (T. californica)-like"""			10997877	Standard	NM_020927		Approved	KIAA1576	uc002ffg.1	Q9HCJ6	OTTHUMG00000176845	ENST00000302536.2:c.401C>T	chr16.hg19:g.77859180C>T	ENSP00000303129:p.Ala134Val	292.0	0.0		250.0	43.0	NM_020927	Q8IYW8	Missense_Mutation	SNP	ENST00000302536.2	hg19	CCDS32492.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280932	0.95489	.	.	ENSG00000171724	ENST00000302536	T	0.46063	0.88	6.03	6.03	0.97812	GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.63283	0.2498	L	0.54908	1.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60219	-0.7306	10	0.56958	D	0.05	-9.4193	20.1519	0.98089	0.0:1.0:0.0:0.0	.	134	Q9HCJ6	VAT1L_HUMAN	V	134	ENSP00000303129:A134V	ENSP00000303129:A134V	A	+	2	0	VAT1L	76416681	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	GCC	.	.		0.522	VAT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434010.1	NM_020927	
ZC3H18	124245	hgsc.bcm.edu	37	16	88643755	88643755	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:88643755A>C	ENST00000301011.5	+	2	424	c.224A>C	c.(223-225)gAg>gCg	p.E75A	ZC3H18_ENST00000452588.2_Missense_Mutation_p.E75A	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	75						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CGGGCAAGTGAGCCTAAATCC	0.637																																					p.E75A	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.A224C						.						37.0	39.0	38.0					16																	88643755		2197	4300	6497	SO:0001583	missense	124245	exon2			CAAGTGAGCCTAA	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.224A>C	chr16.hg19:g.88643755A>C	ENSP00000301011:p.Glu75Ala	83.0	0.0		52.0	9.0	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	A	9.529	1.110385	0.20714	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588;ENST00000545404	T;T	0.33865	1.4;1.39	4.36	4.36	0.52297	.	0.122077	0.56097	D	0.000040	T	0.32164	0.0820	L	0.44542	1.39	0.30475	N	0.772884	P;P;P	0.45474	0.859;0.859;0.859	B;B;B	0.41917	0.37;0.37;0.37	T	0.26677	-1.0096	10	0.31617	T	0.26	-23.6357	13.55	0.61726	1.0:0.0:0.0:0.0	.	75;75;75	E7ERS3;B4DTK7;Q86VM9	.;.;ZCH18_HUMAN	A	75	ENSP00000301011:E75A;ENSP00000416951:E75A	ENSP00000289509:E75A	E	+	2	0	ZC3H18	87171256	0.989000	0.36119	0.991000	0.47740	0.007000	0.05969	4.375000	0.59549	1.582000	0.49881	0.459000	0.35465	GAG	.	.		0.637	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	
PELP1	27043	hgsc.bcm.edu	37	17	4576104	4576104	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:4576104C>T	ENST00000574876.1	-	16	2199	c.2182G>A	c.(2182-2184)Gag>Aag	p.E728K	PELP1_ENST00000301396.4_Missense_Mutation_p.E872K|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000436683.2_Missense_Mutation_p.E581K|PELP1_ENST00000269230.7_Missense_Mutation_p.E638K|PELP1_ENST00000572293.1_Missense_Mutation_p.E778K			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	728	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CGGTGGTTCTCAGGGCCAGGA	0.627																																					p.E728K		Atlas-SNP	.											.	PELP1	102	.	0			c.G2182A						.						24.0	27.0	26.0					17																	4576104		1906	4114	6020	SO:0001583	missense	27043	exon16			GGTTCTCAGGGCC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2182G>A	chr17.hg19:g.4576104C>T	ENSP00000461625:p.Glu728Lys	78.0	0.0		64.0	26.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	hg19	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995978	0.35226	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.56776	0.44;0.64;1.07	5.4	5.4	0.78164	.	0.436543	0.21440	N	0.074508	T	0.32585	0.0834	N	0.24115	0.695	0.32589	N	0.527431	P;P	0.43231	0.664;0.801	B;B	0.38500	0.275;0.275	T	0.31613	-0.9937	10	0.06891	T	0.86	-21.713	10.1651	0.42875	0.0:0.9095:0.0:0.0905	.	581;728	E7EV54;Q8IZL8	.;PELP1_HUMAN	K	872;638;581	ENSP00000301396:E872K;ENSP00000269230:E638K;ENSP00000416231:E581K	ENSP00000269230:E638K	E	-	1	0	AC091153.1	4522853	0.906000	0.30813	1.000000	0.80357	0.948000	0.59901	0.897000	0.28390	2.526000	0.85167	0.561000	0.74099	GAG	.	.		0.627	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
PELP1	27043	hgsc.bcm.edu	37	17	4576404	4576404	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:4576404C>T	ENST00000574876.1	-	16	1899	c.1882G>A	c.(1882-1884)Gct>Act	p.A628T	PELP1_ENST00000301396.4_Missense_Mutation_p.A772T|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000436683.2_Missense_Mutation_p.A481T|PELP1_ENST00000269230.7_Missense_Mutation_p.A540T|PELP1_ENST00000572293.1_Missense_Mutation_p.A678T			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	628					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GTCAGAGCAGCACAGGTCACC	0.602																																					p.A628T		Atlas-SNP	.											.	PELP1	102	.	0			c.G1882A						.						22.0	25.0	24.0					17																	4576404		1958	4123	6081	SO:0001583	missense	27043	exon16			GAGCAGCACAGGT		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.1882G>A	chr17.hg19:g.4576404C>T	ENSP00000461625:p.Ala628Thr	83.0	0.0		74.0	25.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	hg19	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049441	0.36181	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.51817	0.94;0.69;1.58	5.92	4.94	0.65067	Uncharacterised domain NUC202 (1);	0.326300	0.33092	N	0.005282	T	0.21921	0.0528	N	0.01874	-0.695	0.34443	D	0.699862	P;P	0.36683	0.565;0.565	B;B	0.37015	0.239;0.239	T	0.34453	-0.9828	10	0.15952	T	0.53	-14.3778	12.6748	0.56887	0.1642:0.8357:0.0:0.0	.	481;628	E7EV54;Q8IZL8	.;PELP1_HUMAN	T	772;540;481	ENSP00000301396:A772T;ENSP00000269230:A540T;ENSP00000416231:A481T	ENSP00000269230:A540T	A	-	1	0	AC091153.1	4523153	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.864000	0.39469	1.483000	0.48342	0.655000	0.94253	GCT	.	.		0.602	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
GP1BA	2811	hgsc.bcm.edu	37	17	4837033	4837033	+	Silent	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:4837033C>A	ENST00000329125.5	+	2	1209	c.1134C>A	c.(1132-1134)tcC>tcA	p.S378S		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	378	Pro/Thr-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						CTCCAAAATCCACTACTGAAC	0.557																																					p.S378S		Atlas-SNP	.											.	GP1BA	53	.	0			c.C1134A						.						134.0	141.0	139.0					17																	4837033		1949	4142	6091	SO:0001819	synonymous_variant	2811	exon2			AAAATCCACTACT		CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.1134C>A	chr17.hg19:g.4837033C>A		105.0	0.0		130.0	59.0	NM_000173	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Silent	SNP	ENST00000329125.5	hg19	CCDS54068.1																																																																																			.	.		0.557	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
DNAH2	146754	hgsc.bcm.edu	37	17	7720031	7720031	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:7720031C>T	ENST00000572933.1	+	64	11332	c.9872C>T	c.(9871-9873)gCc>gTc	p.A3291V	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3291V			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3291					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GGCGAGAAGGCCAGATGGGAG	0.567																																					p.A3291V		Atlas-SNP	.											DNAH2,NS,carcinoma,0,1	DNAH2	498	.	0			c.C9872T						.						150.0	127.0	135.0					17																	7720031		2203	4300	6503	SO:0001583	missense	146754	exon63			AGAAGGCCAGATG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.9872C>T	chr17.hg19:g.7720031C>T	ENSP00000458355:p.Ala3291Val	134.0	1.0		88.0	27.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576394	0.28092	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.69175	-0.38	4.45	4.45	0.53987	Dynein heavy chain, coiled coil stalk (1);	0.208171	0.42294	D	0.000737	T	0.35068	0.0919	N	0.01438	-0.865	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.29610	-1.0006	10	0.16896	T	0.51	.	10.6403	0.45590	0.0:0.9059:0.0:0.0941	.	3252;3291	Q9P225-2;Q9P225	.;DYH2_HUMAN	V	3252;3291	ENSP00000373825:A3291V	ENSP00000353818:A3252V	A	+	2	0	DNAH2	7660756	1.000000	0.71417	1.000000	0.80357	0.593000	0.36681	2.897000	0.48664	2.469000	0.83416	0.462000	0.41574	GCC	.	.		0.567	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
MYOCD	93649	hgsc.bcm.edu	37	17	12666558	12666558	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:12666558A>G	ENST00000343344.4	+	13	2414	c.2414A>G	c.(2413-2415)gAg>gGg	p.E805G	MYOCD_ENST00000425538.1_Missense_Mutation_p.E853G|RP11-1090M7.1_ENST00000584772.1_RNA			Q8IZQ8	MYCD_HUMAN	myocardin	805					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|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 transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		GACAGTGATGAGCATCTTGAA	0.498																																					p.E853G		Atlas-SNP	.											.	MYOCD	291	.	0			c.A2558G						.						98.0	97.0	97.0					17																	12666558		2203	4300	6503	SO:0001583	missense	93649	exon14			GTGATGAGCATCT	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.2414A>G	chr17.hg19:g.12666558A>G	ENSP00000341835:p.Glu805Gly	155.0	0.0		194.0	124.0	NM_001146312	Q5UBU5|Q8N7Q1	Missense_Mutation	SNP	ENST00000343344.4	hg19	CCDS11163.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.097201	0.56075	.	.	ENSG00000141052	ENST00000395982;ENST00000425538;ENST00000343344;ENST00000443061	T;T	0.42513	0.98;0.97	5.78	5.78	0.91487	.	0.494651	0.23720	N	0.045231	T	0.30978	0.0782	L	0.39898	1.24	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.15263	-1.0443	10	0.23891	T	0.37	-34.3016	7.5161	0.27602	0.846:0.0:0.154:0.0	.	529;853;805	E9PEP9;Q8IZQ8-3;Q8IZQ8	.;.;MYCD_HUMAN	G	529;853;805;515	ENSP00000341835:E805G;ENSP00000400148:E515G	ENSP00000341835:E805G	E	+	2	0	MYOCD	12607283	0.446000	0.25665	0.994000	0.49952	0.968000	0.65278	2.469000	0.45110	2.333000	0.79357	0.533000	0.62120	GAG	.	.		0.498	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604	
ADORA2B	136	hgsc.bcm.edu	37	17	15878262	15878262	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:15878262A>G	ENST00000304222.2	+	2	937	c.605A>G	c.(604-606)tAc>tGc	p.Y202C	ZSWIM7_ENST00000399280.2_5'Flank	NM_000676.2	NP_000667.1	P29275	AA2BR_HUMAN	adenosine A2b receptor	202					activation of adenylate cyclase activity (GO:0007190)|activation of MAPK activity (GO:0000187)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular defense response (GO:0006968)|cellular response to extracellular stimulus (GO:0031668)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)|JNK cascade (GO:0007254)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to non-antigenic stimulus (GO:0002882)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation vascular endothelial growth factor production (GO:0010575)|relaxation of vascular smooth muscle (GO:0060087)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			breast(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)	9				UCEC - Uterine corpus endometrioid carcinoma (92;0.0855)	Adenosine(DB00640)|Defibrotide(DB04932)|Enprofylline(DB00824)|Theophylline(DB00277)	CTGGTGATCTACATTAAGATC	0.512																																					p.Y202C		Atlas-SNP	.											.	ADORA2B	23	.	0			c.A605G						.						115.0	103.0	107.0					17																	15878262		2203	4300	6503	SO:0001583	missense	136	exon2			TGATCTACATTAA	M97759	CCDS11173.1	17p12	2012-08-08			ENSG00000170425	ENSG00000170425		"""GPCR / Class A : Adenosine receptors"""	264	protein-coding gene	gene with protein product		600446				7558011	Standard	NM_000676		Approved		uc002gpd.1	P29275	OTTHUMG00000059140	ENST00000304222.2:c.605A>G	chr17.hg19:g.15878262A>G	ENSP00000304501:p.Tyr202Cys	189.0	1.0		165.0	102.0	NM_000676		Missense_Mutation	SNP	ENST00000304222.2	hg19	CCDS11173.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106533	0.77096	.	.	ENSG00000170425	ENST00000304222	T	0.60548	0.18	5.59	5.59	0.84812	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83385	0.5243	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88748	0.3248	10	0.87932	D	0	-15.0911	14.9373	0.70967	1.0:0.0:0.0:0.0	.	202	P29275	AA2BR_HUMAN	C	202	ENSP00000304501:Y202C	ENSP00000304501:Y202C	Y	+	2	0	ADORA2B	15818987	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.128000	0.65567	0.460000	0.39030	TAC	.	.		0.512	ADORA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131032.1		
MIEF2	125170	hgsc.bcm.edu	37	17	18167688	18167688	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:18167688G>A	ENST00000323019.4	+	4	1186	c.975G>A	c.(973-975)ctG>ctA	p.L325L	MIEF2_ENST00000395704.4_3'UTR|MIEF2_ENST00000395706.2_Silent_p.L336L	NM_001144900.1|NM_139162.3	NP_001138372.1|NP_631901.2	Q96C03	MID49_HUMAN	mitochondrial elongation factor 2	325					mitochondrion organization (GO:0007005)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein targeting to membrane (GO:0090314)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)											TGGAGGGGCTGGCGGGGAACC	0.682																																					p.L336L		Atlas-SNP	.											.	SMCR7	20	.	0			c.G1008A						.						47.0	55.0	52.0					17																	18167688		2203	4296	6499	SO:0001819	synonymous_variant	125170	exon4			GGGGCTGGCGGGG	BC014973	CCDS11193.1, CCDS45624.1, CCDS45625.1	17p11.2	2013-09-23	2013-09-23	2013-09-23	ENSG00000177427	ENSG00000177427			17920	protein-coding gene	gene with protein product		615498	"""Smith-Magenis syndrome chromosome region, candidate 7"""	SMCR7		11997338, 21508961	Standard	NM_001144900		Approved	MGC23130, MiD49	uc010vxq.2	Q96C03	OTTHUMG00000059392	ENST00000323019.4:c.975G>A	chr17.hg19:g.18167688G>A		8.0	0.0		14.0	12.0	NM_148886	J3KPT3|Q6ZRD4|Q96N07	Silent	SNP	ENST00000323019.4	hg19	CCDS11193.1																																																																																			.	.		0.682	MIEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132060.2	NM_139162	
ARL5C	390790	hgsc.bcm.edu	37	17	37321340	37321340	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:37321340G>A	ENST00000269586.7	-	2	98	c.99C>T	c.(97-99)ctC>ctT	p.L33L	ARL5C_ENST00000444555.1_Silent_p.L33L|ARL5C_ENST00000583123.1_5'UTR	NM_001143968.1	NP_001137440.1	A6NH57	ARL5C_HUMAN	ADP-ribosylation factor-like 5C	33					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)										ACAACCGGTAGAGAATGGTGG	0.597											OREG0024370	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L33L		Atlas-SNP	.											.	ARL5C	3	.	0			c.C99T						.						183.0	162.0	169.0					17																	37321340		692	1591	2283	SO:0001819	synonymous_variant	390790	exon2			CCGGTAGAGAATG		CCDS45664.1	17q12	2014-05-09	2005-11-08	2005-11-08	ENSG00000141748	ENSG00000141748		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31111	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 12"""	ARL12			Standard	NM_001143968		Approved		uc010wea.2	A6NH57		ENST00000269586.7:c.99C>T	chr17.hg19:g.37321340G>A		156.0	0.0	869	153.0	16.0	NM_001143968		Silent	SNP	ENST00000269586.7	hg19	CCDS45664.1																																																																																			.	.		0.597	ARL5C-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444566.1	NM_001143968	
CCR7	1236	hgsc.bcm.edu	37	17	38711491	38711491	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:38711491T>C	ENST00000246657.2	-	3	702	c.640A>G	c.(640-642)Aca>Gca	p.T214A	CCR7_ENST00000579344.1_Missense_Mutation_p.T208A	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	214					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				ACATGCTCTGTGATGAGAGAG	0.557																																					p.T214A		Atlas-SNP	.											.	CCR7	31	.	0			c.A640G						.						76.0	67.0	70.0					17																	38711491		2203	4300	6503	SO:0001583	missense	1236	exon3			GCTCTGTGATGAG		CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.640A>G	chr17.hg19:g.38711491T>C	ENSP00000246657:p.Thr214Ala	135.0	0.0		205.0	28.0	NM_001838		Missense_Mutation	SNP	ENST00000246657.2	hg19	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	T	5.552	0.286694	0.10513	.	.	ENSG00000126353	ENST00000246657	T	0.36340	1.26	5.31	1.69	0.24217	GPCR, rhodopsin-like superfamily (1);	0.684502	0.14082	N	0.342628	T	0.18551	0.0445	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.13407	0.009	T	0.21280	-1.0250	10	0.25106	T	0.35	.	2.8001	0.05412	0.1484:0.0963:0.4532:0.3021	.	214	P32248	CCR7_HUMAN	A	214	ENSP00000246657:T214A	ENSP00000246657:T214A	T	-	1	0	CCR7	35965017	0.002000	0.14202	0.001000	0.08648	0.916000	0.54674	0.523000	0.22925	0.089000	0.17243	0.459000	0.35465	ACA	.	.		0.557	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1		
KRT27	342574	hgsc.bcm.edu	37	17	38938637	38938637	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:38938637C>T	ENST00000301656.3	-	1	149	c.109G>A	c.(109-111)Ggt>Agt	p.G37S		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CCTGGCACACCGCATGTGTTT	0.607																																					p.G37S		Atlas-SNP	.											.	KRT27	41	.	0			c.G109A						.						64.0	59.0	61.0					17																	38938637		2203	4300	6503	SO:0001583	missense	342574	exon1			GCACACCGCATGT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.109G>A	chr17.hg19:g.38938637C>T	ENSP00000301656:p.Gly37Ser	117.0	0.0		145.0	13.0	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.451376	0.26074	.	.	ENSG00000171446	ENST00000301656	D	0.85013	-1.93	4.92	-3.33	0.04958	.	0.845034	0.10518	N	0.665346	T	0.72684	0.3491	L	0.34521	1.04	0.18873	N	0.999985	B	0.09022	0.002	B	0.06405	0.002	T	0.55250	-0.8170	10	0.17832	T	0.49	.	9.2104	0.37316	0.0:0.5159:0.0968:0.3874	.	37	Q7Z3Y8	K1C27_HUMAN	S	37	ENSP00000301656:G37S	ENSP00000301656:G37S	G	-	1	0	KRT27	36192163	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.477000	0.06583	-0.383000	0.07858	-1.063000	0.02288	GGT	.	.		0.607	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
ACE	1636	hgsc.bcm.edu	37	17	61573828	61573828	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:61573828C>T	ENST00000290866.4	+	23	3478	c.3454C>T	c.(3454-3456)Ctg>Ttg	p.L1152L	ACE_ENST00000290863.6_Silent_p.L578L|ACE_ENST00000490216.2_Silent_p.L578L|ACE_ENST00000577647.1_Silent_p.L578L|ACE_ENST00000413513.3_Intron|ACE_ENST00000428043.1_Intron|ACE_ENST00000421982.2_Intron	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1152	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	CACGGGCCCCCTGCACAAGTG	0.642																																					p.L1152L		Atlas-SNP	.											.	ACE	187	.	0			c.C3454T						.						69.0	67.0	68.0					17																	61573828		2203	4300	6503	SO:0001819	synonymous_variant	1636	exon23			GGCCCCCTGCACA	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.3454C>T	chr17.hg19:g.61573828C>T		339.0	1.0		335.0	202.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	hg19	CCDS11637.1																																																																																			.	.		0.642	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
KCNJ2	3759	hgsc.bcm.edu	37	17	68171825	68171825	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:68171825C>T	ENST00000243457.3	+	2	1028	c.645C>T	c.(643-645)ggC>ggT	p.G215G	KCNJ2_ENST00000535240.1_Silent_p.G215G	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	215					cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|magnesium ion transport (GO:0015693)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of resting membrane potential (GO:0060075)|regulation of skeletal muscle contraction via regulation of action potential (GO:0014861)|relaxation of cardiac muscle (GO:0055119)|relaxation of skeletal muscle (GO:0090076)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of membrane (GO:0031224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(13)|skin(1)|urinary_tract(1)	25	Breast(10;1.64e-08)					GGCGAGTGGGCAATCTTCGGA	0.478																																					p.G215G		Atlas-SNP	.											.	KCNJ2	74	.	0			c.C645T						.						114.0	100.0	105.0					17																	68171825		2203	4300	6503	SO:0001819	synonymous_variant	3759	exon2			AGTGGGCAATCTT	AF011904	CCDS11688.1	17q24.3	2014-09-17				ENSG00000123700		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6263	protein-coding gene	gene with protein product		600681				7696590, 11240146, 16382105	Standard	NM_000891		Approved	Kir2.1, IRK1, LQT7	uc002jir.3	P63252		ENST00000243457.3:c.645C>T	chr17.hg19:g.68171825C>T		102.0	0.0		144.0	22.0	NM_000891	O15110|P48049	Silent	SNP	ENST00000243457.3	hg19	CCDS11688.1																																																																																			.	.		0.478	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891	
DNAI2	64446	hgsc.bcm.edu	37	17	72285791	72285791	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:72285791A>G	ENST00000311014.6	+	5	593	c.526A>G	c.(526-528)Agg>Ggg	p.R176G	DNAI2_ENST00000582036.1_Missense_Mutation_p.R176G|DNAI2_ENST00000446837.2_Missense_Mutation_p.R176G|DNAI2_ENST00000579490.1_Missense_Mutation_p.R233G|DNAI2_ENST00000307504.5_Missense_Mutation_p.R33G			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	176					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CGATGGCAACAGGAAGTTGGC	0.597									Kartagener syndrome																												p.R176G		Atlas-SNP	.											.	DNAI2	102	.	0			c.A526G						.						64.0	61.0	62.0					17																	72285791		2203	4300	6503	SO:0001583	missense	64446	exon5	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGCAACAGGAAGT	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.526A>G	chr17.hg19:g.72285791A>G	ENSP00000308312:p.Arg176Gly	98.0	0.0		125.0	83.0	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	hg19	CCDS11697.1	.	.	.	.	.	.	.	.	.	.	A	9.036	0.988394	0.18966	.	.	ENSG00000171595	ENST00000311014;ENST00000307504;ENST00000446837	T;T;T	0.71461	-0.57;-0.57;-0.57	5.01	-1.01	0.10169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.620678	0.17566	N	0.169629	T	0.61185	0.2327	L	0.46741	1.465	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49624	-0.8920	10	0.23302	T	0.38	-28.5779	16.2683	0.82601	0.4592:0.5408:0.0:0.0	.	176	Q9GZS0	DNAI2_HUMAN	G	176;33;176	ENSP00000308312:R176G;ENSP00000302929:R33G;ENSP00000400252:R176G	ENSP00000302929:R33G	R	+	1	2	DNAI2	69797386	0.037000	0.19845	0.981000	0.43875	0.882000	0.50991	0.262000	0.18460	-0.053000	0.13289	0.260000	0.18958	AGG	.	.		0.597	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
ST6GALNAC2	10610	hgsc.bcm.edu	37	17	74569415	74569415	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:74569415C>T	ENST00000225276.5	-	4	711	c.392G>A	c.(391-393)gGc>gAc	p.G131D	ST6GALNAC2_ENST00000586520.1_5'UTR|RP11-666A8.9_ENST00000588104.1_RNA	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	131					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						ACTCTCTGAGCCGTTCAGAAG	0.647																																					p.G131D		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.G392A						.						24.0	22.0	23.0					17																	74569415		2199	4298	6497	SO:0001583	missense	10610	exon4			TCTGAGCCGTTCA	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"""Sialyltransferases"""	10867	protein-coding gene	gene with protein product		610137	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"", ""sialyltransferase-like 1"""	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.392G>A	chr17.hg19:g.74569415C>T	ENSP00000225276:p.Gly131Asp	52.0	0.0		46.0	9.0	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	hg19	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	C	3.794	-0.043111	0.07452	.	.	ENSG00000070731	ENST00000225276	T	0.29142	1.58	4.77	-1.48	0.08745	.	1.506000	0.03537	N	0.223268	T	0.18718	0.0449	L	0.27944	0.81	0.09310	N	1	B	0.14012	0.009	B	0.13407	0.009	T	0.15122	-1.0448	10	0.10902	T	0.67	-0.9537	5.3608	0.16087	0.0:0.3063:0.1658:0.5279	.	131	Q9UJ37	SIA7B_HUMAN	D	131	ENSP00000225276:G131D	ENSP00000225276:G131D	G	-	2	0	ST6GALNAC2	72081010	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.158000	0.03153	0.079000	0.16929	0.591000	0.81541	GGC	.	.		0.647	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456	
MFSD11	79157	hgsc.bcm.edu	37	17	74774280	74774280	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr17:74774280C>A	ENST00000588460.1	+	13	3238	c.1196C>A	c.(1195-1197)gCa>gAa	p.A399E	MFSD11_ENST00000590514.1_Missense_Mutation_p.A399E|MFSD11_ENST00000590070.1_3'UTR|MFSD11_ENST00000593181.1_Missense_Mutation_p.A347E|MFSD11_ENST00000355954.3_Missense_Mutation_p.A347E|MFSD11_ENST00000586622.1_Missense_Mutation_p.A399E|MFSD11_ENST00000336509.4_Missense_Mutation_p.A399E	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	399						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TCTATTTGCGCAGCCGTGGCA	0.493																																					p.A399E		Atlas-SNP	.											.	MFSD11	47	.	0			c.C1196A						.						164.0	149.0	154.0					17																	74774280		2203	4300	6503	SO:0001583	missense	79157	exon13			TTTGCGCAGCCGT	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.1196C>A	chr17.hg19:g.74774280C>A	ENSP00000464932:p.Ala399Glu	203.0	0.0		285.0	31.0	NM_001242532	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	C	36	5.697421	0.96802	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	D;D	0.82167	-1.58;-1.58	6.07	6.07	0.98685	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.91573	0.7338	M	0.85630	2.765	0.80722	D	1	D;D	0.61080	0.989;0.988	P;P	0.61003	0.858;0.882	D	0.91194	0.4986	10	0.54805	T	0.06	-20.4795	20.2544	0.98414	0.0:1.0:0.0:0.0	.	347;399	O43934-2;O43934	.;MFS11_HUMAN	E	399;347	ENSP00000337240:A399E;ENSP00000348225:A347E	ENSP00000337240:A399E	A	+	2	0	MFSD11	72285875	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.711000	0.84669	2.885000	0.99019	0.655000	0.94253	GCA	.	.		0.493	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311	
ANKRD12	23253	hgsc.bcm.edu	37	18	9254383	9254383	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr18:9254383A>G	ENST00000262126.4	+	9	1358	c.1118A>G	c.(1117-1119)aAg>aGg	p.K373R	ANKRD12_ENST00000383440.2_Missense_Mutation_p.K350R|ANKRD12_ENST00000400020.3_Missense_Mutation_p.K350R	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	373						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GAAATTAATAAGATGATTGAT	0.348																																					p.K373R		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A1118G						.						96.0	100.0	98.0					18																	9254383		2203	4300	6503	SO:0001583	missense	23253	exon9			TTAATAAGATGAT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.1118A>G	chr18.hg19:g.9254383A>G	ENSP00000262126:p.Lys373Arg	105.0	0.0		95.0	10.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.854741	0.32791	.	.	ENSG00000101745	ENST00000383440;ENST00000546007;ENST00000262126;ENST00000359158	T;T	0.06142	3.44;3.34	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.09862	0.0242	M	0.64997	1.995	0.80722	D	1	B;B	0.25048	0.117;0.071	B;B	0.23018	0.043;0.019	T	0.10042	-1.0647	10	0.25751	T	0.34	-28.0808	15.8893	0.79279	1.0:0.0:0.0:0.0	.	350;373	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	R	350;350;373;80	ENSP00000372932:K350R;ENSP00000262126:K373R	ENSP00000262126:K373R	K	+	2	0	ANKRD12	9244383	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.162000	0.77515	2.153000	0.67306	0.528000	0.53228	AAG	.	.		0.348	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
TRAPPC8	22878	hgsc.bcm.edu	37	18	29511372	29511372	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr18:29511372T>A	ENST00000283351.4	-	2	607	c.272A>T	c.(271-273)gAt>gTt	p.D91V	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.D37V|TRAPPC8_ENST00000584876.1_5'UTR|TRAPPC8_ENST00000582513.1_Missense_Mutation_p.D91V	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	91					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.D91V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGAAACAACATCATTCAAAAG	0.408																																					p.D91V		Atlas-SNP	.											TRAPPC8,NS,carcinoma,0,1	TRAPPC8	126	.	1	Substitution - Missense(1)	kidney(1)	c.A272T						.						160.0	156.0	157.0					18																	29511372		2203	4300	6503	SO:0001583	missense	22878	exon2			ACAACATCATTCA	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.272A>T	chr18.hg19:g.29511372T>A	ENSP00000283351:p.Asp91Val	165.0	0.0		129.0	18.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.628068	0.46944	.	.	ENSG00000153339	ENST00000283351	T	0.09350	2.99	5.98	5.98	0.97165	.	0.068910	0.64402	D	0.000009	T	0.18964	0.0455	L	0.46157	1.445	0.80722	D	1	P;P	0.52577	0.954;0.919	P;P	0.50754	0.649;0.536	T	0.00349	-1.1798	10	0.39692	T	0.17	.	16.4696	0.84102	0.0:0.0:0.0:1.0	.	91;91	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	V	91	ENSP00000283351:D91V	ENSP00000283351:D91V	D	-	2	0	TRAPPC8	27765370	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.922000	0.75811	2.289000	0.77006	0.482000	0.46254	GAT	.	.		0.408	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
TCEB3B	51224	hgsc.bcm.edu	37	18	44560523	44560523	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr18:44560523A>T	ENST00000332567.4	-	1	1465	c.1113T>A	c.(1111-1113)gaT>gaA	p.D371E	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	371					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CCTCAGCCATATCTACCTCCT	0.512																																					p.D371E		Atlas-SNP	.											.	TCEB3B	141	.	0			c.T1113A						.						84.0	81.0	82.0					18																	44560523		2203	4300	6503	SO:0001583	missense	51224	exon1			AGCCATATCTACC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1113T>A	chr18.hg19:g.44560523A>T	ENSP00000331302:p.Asp371Glu	98.0	0.0		58.0	10.0	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	hg19	CCDS11932.1	.	.	.	.	.	.	.	.	.	.	A	2.337	-0.352039	0.05173	.	.	ENSG00000206181	ENST00000332567	T	0.05199	3.48	1.67	-3.23	0.05109	.	0.233910	0.22976	U	0.053375	T	0.02193	0.0068	N	0.16656	0.425	0.09310	N	1	P	0.36959	0.575	B	0.30782	0.12	T	0.47711	-0.9096	10	0.12766	T	0.61	.	3.5575	0.07870	0.3184:0.4564:0.0:0.2251	.	371	Q8IYF1	ELOA2_HUMAN	E	371	ENSP00000331302:D371E	ENSP00000331302:D371E	D	-	3	2	TCEB3B	42814521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.910000	0.04054	-0.848000	0.04163	-1.600000	0.00815	GAT	.	.		0.512	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
FEM1A	55527	hgsc.bcm.edu	37	19	4793795	4793795	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:4793795G>A	ENST00000269856.3	+	1	2068	c.1929G>A	c.(1927-1929)gcG>gcA	p.A643A	AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA|AC005523.2_ENST00000601192.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	643					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		AGTGCCTTGCGGCCCGGGCCC	0.592																																					p.A643A		Atlas-SNP	.											FEM1A,colon,carcinoma,0,1	FEM1A	41	.	0			c.G1929A						.						31.0	29.0	29.0					19																	4793795		2203	4300	6503	SO:0001819	synonymous_variant	55527	exon1			CCTTGCGGCCCGG	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"""Ankyrin repeat domain containing"""	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1929G>A	chr19.hg19:g.4793795G>A		42.0	0.0		67.0	11.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	hg19	CCDS12135.1																																																																																			.	.		0.592	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1		
CATSPERD	257062	hgsc.bcm.edu	37	19	5766134	5766134	+	Silent	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:5766134C>G	ENST00000381624.3	+	17	1588	c.1527C>G	c.(1525-1527)ggC>ggG	p.G509G	CATSPERD_ENST00000381614.2_Silent_p.G167G|CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	509					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											TTTCAGTTGGCTGCGACCTGG	0.537																																					p.G509G		Atlas-SNP	.											.	.	.	.	0			c.C1527G						.						119.0	111.0	113.0					19																	5766134		1980	4155	6135	SO:0001819	synonymous_variant	257062	exon17			AGTTGGCTGCGAC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.1527C>G	chr19.hg19:g.5766134C>G		124.0	0.0		157.0	22.0	NM_152784	Q6ZRP1	Silent	SNP	ENST00000381624.3	hg19	CCDS12149.2																																																																																			.	.		0.537	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
MUC16	94025	hgsc.bcm.edu	37	19	9056445	9056445	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:9056445G>A	ENST00000397910.4	-	3	31204	c.31001C>T	c.(31000-31002)tCt>tTt	p.S10334F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10336	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAGGTTGAAGAGGAGAATGG	0.517																																					p.S10334F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C31001T						.						109.0	110.0	110.0					19																	9056445		2059	4200	6259	SO:0001583	missense	94025	exon3			GTTGAAGAGGAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31001C>T	chr19.hg19:g.9056445G>A	ENSP00000381008:p.Ser10334Phe	200.0	0.0		262.0	31.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	6.711	0.499943	0.12762	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	3.2	0.979	0.19745	.	.	.	.	.	T	0.02083	0.0065	N	0.24115	0.695	.	.	.	P	0.37101	0.582	B	0.34590	0.186	T	0.41179	-0.9523	8	0.87932	D	0	.	3.6769	0.08295	0.1346:0.0:0.6105:0.2549	.	10334	B5ME49	.	F	10334	ENSP00000381008:S10334F	ENSP00000381008:S10334F	S	-	2	0	MUC16	8917445	0.012000	0.17670	0.006000	0.13384	0.151000	0.21798	0.579000	0.23788	0.327000	0.23409	0.461000	0.40582	TCT	.	.		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF426	79088	hgsc.bcm.edu	37	19	9641667	9641667	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:9641667T>C	ENST00000535489.1	-	5	738	c.402A>G	c.(400-402)atA>atG	p.I134M	ZNF426_ENST00000253115.2_Missense_Mutation_p.I134M|ZNF426_ENST00000593003.1_Missense_Mutation_p.I96M|ZNF426_ENST00000589289.1_Intron			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	134					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						TTACCAATTGTATCCCAATGG	0.368																																					p.I134M		Atlas-SNP	.											ZNF426,NS,carcinoma,0,1	ZNF426	56	.	0			c.A402G						.						101.0	96.0	98.0					19																	9641667		2203	4300	6503	SO:0001583	missense	79088	exon7			CAATTGTATCCCA	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.402A>G	chr19.hg19:g.9641667T>C	ENSP00000439017:p.Ile134Met	87.0	0.0		91.0	9.0	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	hg19	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.465268	0.01053	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.05925	3.37;3.37	1.53	-0.823	0.10815	.	.	.	.	.	T	0.02610	0.0079	N	0.04636	-0.2	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.47086	-0.9144	9	0.23302	T	0.38	.	5.8549	0.18714	0.0:0.3418:0.0:0.6582	.	121;134	Q59EH4;Q9BUY5	.;ZN426_HUMAN	M	121;134;134	ENSP00000253115:I134M;ENSP00000439017:I134M	ENSP00000253115:I134M	I	-	3	3	ZNF426	9502667	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.149000	0.03182	-0.917000	0.03813	-1.811000	0.00612	ATA	.	.		0.368	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
ZNF441	126068	hgsc.bcm.edu	37	19	11888524	11888524	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:11888524G>A	ENST00000357901.4	+	2	204	c.102G>A	c.(100-102)caG>caA	p.Q34Q	ZNF441_ENST00000454339.2_5'UTR	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	34	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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						ATGTGATGCAGGAAACCATCA	0.433																																					p.Q34Q		Atlas-SNP	.											.	ZNF441	123	.	0			c.G102A						.						150.0	125.0	132.0					19																	11888524		692	1591	2283	SO:0001819	synonymous_variant	126068	exon2			GATGCAGGAAACC	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.102G>A	chr19.hg19:g.11888524G>A		180.0	0.0		191.0	19.0	NM_152355		Silent	SNP	ENST00000357901.4	hg19	CCDS12266.2																																																																																			.	.		0.433	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355	
ZNF439	90594	hgsc.bcm.edu	37	19	11978948	11978948	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:11978948A>G	ENST00000304030.2	+	3	1264	c.1064A>G	c.(1063-1065)gAa>gGa	p.E355G	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.E219G	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	355					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						AGACCTTATGAATGTAAGACA	0.368																																					p.E355G		Atlas-SNP	.											.	ZNF439	67	.	0			c.A1064G						.						82.0	83.0	83.0					19																	11978948		2203	4300	6503	SO:0001583	missense	90594	exon3			CTTATGAATGTAA	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"""Zinc fingers, C2H2-type"", ""-"""	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.1064A>G	chr19.hg19:g.11978948A>G	ENSP00000305077:p.Glu355Gly	76.0	0.0		94.0	11.0	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	hg19	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	a	10.93	1.490582	0.26686	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.07688	3.17;3.17	0.575	0.575	0.17374	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12689	0.0308	L	0.50333	1.59	0.09310	N	0.999994	D	0.53885	0.963	P	0.53146	0.719	T	0.16748	-1.0392	9	0.66056	D	0.02	.	4.5082	0.11898	0.6646:0.3354:0.0:0.0	.	355	Q8NDP4	ZN439_HUMAN	G	219;355	ENSP00000395632:E219G;ENSP00000305077:E355G	ENSP00000305077:E355G	E	+	2	0	ZNF439	11839948	0.000000	0.05858	0.012000	0.15200	0.085000	0.17905	-0.180000	0.09754	0.485000	0.27652	0.163000	0.16589	GAA	.	.		0.368	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1		
OR7C2	26658	hgsc.bcm.edu	37	19	15052324	15052324	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:15052324A>T	ENST00000248072.3	+	1	24	c.24A>T	c.(22-24)gaA>gaT	p.E8D		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					ACCAAACAGAAGTTGGAAACT	0.483																																					p.E8D		Atlas-SNP	.											.	OR7C2	50	.	0			c.A24T						.						93.0	98.0	96.0					19																	15052324		2203	4300	6503	SO:0001583	missense	26658	exon1			AACAGAAGTTGGA	U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"""GPCR / Class A : Olfactory receptors"""	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.24A>T	chr19.hg19:g.15052324A>T	ENSP00000248072:p.Glu8Asp	89.0	0.0		131.0	14.0	NM_012377	O43881|Q6IFP9	Missense_Mutation	SNP	ENST00000248072.3	hg19	CCDS12320.1	.	.	.	.	.	.	.	.	.	.	a	7.967	0.748165	0.15710	.	.	ENSG00000127529	ENST00000248072	T	0.19669	2.13	4.01	1.88	0.25563	.	1.199010	0.06609	U	0.755311	T	0.09862	0.0242	N	0.10645	0.015	0.09310	N	1	B	0.14012	0.009	B	0.17722	0.019	T	0.38908	-0.9639	10	0.19590	T	0.45	.	3.27	0.06878	0.5348:0.0:0.1031:0.3621	.	8	O60412	OR7C2_HUMAN	D	8	ENSP00000248072:E8D	ENSP00000248072:E8D	E	+	3	2	OR7C2	14913324	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.046000	0.01409	0.223000	0.20920	0.416000	0.27883	GAA	.	.		0.483	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1		
ELL	8178	hgsc.bcm.edu	37	19	18576653	18576653	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:18576653C>T	ENST00000262809.4	-	3	330	c.259G>A	c.(259-261)Gac>Aac	p.D87N	ELL_ENST00000596124.3_5'UTR	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	87					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		TGGGGGTTGTCGCGGCCGATG	0.677			T	MLL	AL																																p.D87N		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.G259A						.						38.0	41.0	40.0					19																	18576653		2203	4300	6503	SO:0001583	missense	8178	exon3			GGTTGTCGCGGCC	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23114	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 68"""	600284	"""chromosome 19 open reading frame 17"""	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.259G>A	chr19.hg19:g.18576653C>T	ENSP00000262809:p.Asp87Asn	75.0	0.0		57.0	7.0	NM_006532		Missense_Mutation	SNP	ENST00000262809.4	hg19	CCDS12380.1	.	.	.	.	.	.	.	.	.	.	c	27.9	4.875515	0.91664	.	.	ENSG00000105656	ENST00000262809	T	0.34472	1.36	3.82	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.58666	0.2138	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.65352	-0.6189	10	0.87932	D	0	-28.1359	14.9121	0.70767	0.0:1.0:0.0:0.0	.	31;87	Q59HG4;P55199	.;ELL_HUMAN	N	87	ENSP00000262809:D87N	ENSP00000262809:D87N	D	-	1	0	ELL	18437653	1.000000	0.71417	0.936000	0.37596	0.835000	0.47333	7.364000	0.79526	1.974000	0.57490	0.479000	0.44913	GAC	.	.		0.677	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
ZNF714	148206	hgsc.bcm.edu	37	19	21299624	21299624	+	Missense_Mutation	SNP	T	T	C	rs371085101		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:21299624T>C	ENST00000596143.1	+	5	479	c.154T>C	c.(154-156)Tct>Cct	p.S52P	ZNF714_ENST00000601416.1_Missense_Mutation_p.F58S|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_Intron	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	52					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						TATGTGTTCTTCTTTTACCAG	0.313																																					p.S52P		Atlas-SNP	.											.	ZNF714	121	.	0			c.T154C						.						55.0	56.0	56.0					19																	21299624		2175	4287	6462	SO:0001583	missense	148206	exon5			TGTTCTTCTTTTA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.154T>C	chr19.hg19:g.21299624T>C	ENSP00000472368:p.Ser52Pro	79.0	0.0		76.0	42.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	4.151	0.026416	0.08054	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.601	-0.932	0.10435	.	.	.	.	.	T	0.13670	0.0331	N	0.20685	0.6	0.09310	N	1	P;B	0.41041	0.736;0.386	B;B	0.31495	0.131;0.043	T	0.12192	-1.0557	7	0.59425	D	0.04	.	.	.	.	.	52;52	Q96N38-2;A6NEM4	.;.	P	52	.	ENSP00000291770:S52P	S	+	1	0	ZNF714	21091464	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	-0.067000	0.11579	-0.412000	0.07519	0.374000	0.22700	TCT	.	.		0.313	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
CEP89	84902	hgsc.bcm.edu	37	19	33439208	33439208	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:33439208C>T	ENST00000305768.5	-	5	647	c.559G>A	c.(559-561)Ggc>Agc	p.G187S	CEP89_ENST00000590597.2_Missense_Mutation_p.G187S	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	187					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GGAGGGGAGCCTGGAAACCCA	0.338																																					p.G187S		Atlas-SNP	.											.	CEP89	82	.	0			c.G559A						.						85.0	69.0	75.0					19																	33439208		2203	4300	6503	SO:0001583	missense	84902	exon5			GGGAGCCTGGAAA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.559G>A	chr19.hg19:g.33439208C>T	ENSP00000306105:p.Gly187Ser	38.0	0.0		59.0	9.0	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	hg19	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	C	6.064	0.380213	0.11466	.	.	ENSG00000121289	ENST00000305768	T	0.27720	1.65	4.69	1.43	0.22495	.	1.749320	0.02706	N	0.112223	T	0.32071	0.0817	L	0.42245	1.32	0.09310	N	1	P;B;B	0.51537	0.946;0.026;0.361	P;B;B	0.49597	0.616;0.019;0.097	T	0.28170	-1.0052	10	0.07644	T	0.81	-0.2223	6.5477	0.22414	0.0:0.6995:0.0:0.3005	.	158;187;187	Q8WUL5;Q96ST8-3;Q96ST8	.;.;CEP89_HUMAN	S	187	ENSP00000306105:G187S	ENSP00000306105:G187S	G	-	1	0	CEP89	38131048	0.030000	0.19436	0.097000	0.21041	0.125000	0.20455	-0.140000	0.10342	0.301000	0.22738	0.655000	0.94253	GGC	.	.		0.338	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
ZFP30	22835	hgsc.bcm.edu	37	19	38127120	38127120	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:38127120T>C	ENST00000351218.2	-	6	879	c.322A>G	c.(322-324)Aga>Gga	p.R108G	ZFP30_ENST00000589018.1_Intron|ZFP30_ENST00000514101.2_Missense_Mutation_p.R108G|ZFP30_ENST00000392144.1_Missense_Mutation_p.R108G	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	108					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)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTTTTAATTCTTTCCATTACC	0.343																																					p.R108G		Atlas-SNP	.											ZFP30,colon,carcinoma,+1,1	ZFP30	68	.	0			c.A322G						.						59.0	58.0	58.0					19																	38127120		2203	4300	6503	SO:0001583	missense	22835	exon6			TAATTCTTTCCAT	AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784		"""Zinc fingers, C2H2-type"", ""-"""	29555	protein-coding gene	gene with protein product			"""zinc finger protein 30 homolog (mouse)"""			10231032	Standard	NM_014898		Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.322A>G	chr19.hg19:g.38127120T>C	ENSP00000343581:p.Arg108Gly	121.0	1.0		142.0	38.0	NM_014898	Q58EY8	Missense_Mutation	SNP	ENST00000351218.2	hg19	CCDS33005.1	.	.	.	.	.	.	.	.	.	.	T	9.031	0.987309	0.18889	.	.	ENSG00000120784	ENST00000351218;ENST00000514101;ENST00000392144;ENST00000440715	T;T;T	0.05925	3.37;3.37;3.37	3.82	2.79	0.32731	.	0.655612	0.12653	N	0.450261	T	0.04907	0.0132	N	0.25957	0.775	0.30725	N	0.747856	B;B	0.24258	0.1;0.1	B;B	0.21708	0.036;0.036	T	0.14448	-1.0472	10	0.27082	T	0.32	.	8.4974	0.33136	0.0:0.1033:0.0:0.8967	.	108;108	D3Y2A0;Q9Y2G7	.;ZFP30_HUMAN	G	108;108;108;107	ENSP00000343581:R108G;ENSP00000422930:R108G;ENSP00000375988:R108G	ENSP00000343581:R108G	R	-	1	2	ZFP30	42818960	0.995000	0.38212	0.970000	0.41538	0.875000	0.50365	1.810000	0.38932	1.725000	0.51514	0.459000	0.35465	AGA	.	.		0.343	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109601.2	NM_014898	
WDR87	83889	hgsc.bcm.edu	37	19	38382236	38382236	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:38382236G>A	ENST00000303868.5	-	5	3457	c.3233C>T	c.(3232-3234)cCc>cTc	p.P1078L	WDR87_ENST00000447313.2_Missense_Mutation_p.P1117L	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	1078										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						GCCTTTGCTGGGCTTGATGGC	0.483																																					p.P1078L		Atlas-SNP	.											.	WDR87	191	.	0			c.C3233T						.						54.0	46.0	49.0					19																	38382236		692	1591	2283	SO:0001583	missense	83889	exon5			TTGCTGGGCTTGA	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.3233C>T	chr19.hg19:g.38382236G>A	ENSP00000368025:p.Pro1078Leu	158.0	0.0		201.0	30.0	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	hg19	CCDS46063.1	.	.	.	.	.	.	.	.	.	.	G	4.136	0.023645	0.08006	.	.	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.11277	2.8;2.79	3.79	-1.47	0.08772	.	1.806640	0.03118	N	0.163369	T	0.09555	0.0235	L	0.43152	1.355	0.09310	N	1	B;B	0.23058	0.079;0.079	B;B	0.15870	0.014;0.014	T	0.37337	-0.9710	10	0.10111	T	0.7	0.0221	8.4116	0.32646	0.0:0.1308:0.4877:0.3815	.	1078;1117	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	L	1117;1078	ENSP00000405012:P1117L;ENSP00000368025:P1078L	ENSP00000368025:P1078L	P	-	2	0	WDR87	43074076	0.001000	0.12720	0.012000	0.15200	0.001000	0.01503	0.030000	0.13688	-0.563000	0.06078	-2.257000	0.00281	CCC	.	.		0.483	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
TIMM50	92609	hgsc.bcm.edu	37	19	39980382	39980382	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:39980382G>A	ENST00000607714.1	+	11	1006	c.984G>A	c.(982-984)gaG>gaA	p.E328E	TIMM50_ENST00000314349.4_Silent_p.E431E|TIMM50_ENST00000599794.1_Silent_p.E132E|TIMM50_ENST00000544017.1_Silent_p.E215E			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	328					cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCCTGGCCGAGCTCTCCAAGT	0.632																																					p.E431E		Atlas-SNP	.											.	TIMM50	37	.	0			c.G1293A						.						59.0	53.0	55.0					19																	39980382		2203	4300	6503	SO:0001819	synonymous_variant	92609	exon11			GGCCGAGCTCTCC	BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	23656	protein-coding gene	gene with protein product		607381	"""translocase of inner mitochondrial membrane 50 homolog (yeast)"""			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.984G>A	chr19.hg19:g.39980382G>A		93.0	0.0		162.0	20.0	NM_001001563	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Silent	SNP	ENST00000607714.1	hg19																																																																																				.	.		0.632	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563	
MEGF8	1954	hgsc.bcm.edu	37	19	42859978	42859978	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:42859978G>A	ENST00000251268.6	+	24	4213	c.4213G>A	c.(4213-4215)Gcc>Acc	p.A1405T	MEGF8_ENST00000334370.4_Missense_Mutation_p.A1338T	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1405	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.|EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GGTGGGCTCTGCCCGCTGTGG	0.677																																					p.A1405T		Atlas-SNP	.											MEGF8_ENST00000334370,caecum,carcinoma,0,3	MEGF8	358	.	0			c.G4213A						.						15.0	13.0	14.0					19																	42859978		2199	4294	6493	SO:0001583	missense	1954	exon24			GGCTCTGCCCGCT	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.4213G>A	chr19.hg19:g.42859978G>A	ENSP00000251268:p.Ala1405Thr	76.0	0.0		57.0	9.0	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	G	15.39	2.820255	0.50633	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.20598	2.06;2.06	4.61	4.61	0.57282	CUB (1);Epidermal growth factor-like, type 3 (1);	0.183165	0.38217	N	0.001775	T	0.16214	0.0390	N	0.08118	0	0.80722	D	1	P;D	0.60575	0.93;0.988	P;P	0.57911	0.48;0.829	T	0.08932	-1.0698	10	0.12103	T	0.63	-19.2081	7.9456	0.29985	0.0:0.1735:0.6472:0.1793	.	1405;1338	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	T	1338;1405	ENSP00000334219:A1338T;ENSP00000251268:A1405T	ENSP00000251268:A1405T	A	+	1	0	MEGF8	47551818	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.566000	0.60843	2.412000	0.81896	0.563000	0.77884	GCC	.	.		0.677	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
ZNF222	7673	hgsc.bcm.edu	37	19	44536345	44536345	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:44536345A>G	ENST00000187879.8	+	4	680	c.518A>G	c.(517-519)tAt>tGt	p.Y173C	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Missense_Mutation_p.Y213C	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	173					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GTGAAATGCTATAAGTGTGAT	0.438																																					p.Y213C		Atlas-SNP	.											.	ZNF222	90	.	0			c.A638G						.						148.0	153.0	151.0					19																	44536345		2203	4300	6503	SO:0001583	missense	7673	exon4			AATGCTATAAGTG	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"""Zinc fingers, C2H2-type"", ""-"""	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.518A>G	chr19.hg19:g.44536345A>G	ENSP00000187879:p.Tyr173Cys	200.0	0.0		267.0	30.0	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Missense_Mutation	SNP	ENST00000187879.8	hg19	CCDS33045.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.552228	0.27739	.	.	ENSG00000159885	ENST00000391960;ENST00000187879;ENST00000251272	T;T	0.20463	3.15;2.07	2.79	-0.744	0.11101	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23014	0.0556	M	0.81497	2.545	0.09310	N	1	B;B	0.15473	0.013;0.008	B;B	0.17098	0.017;0.007	T	0.37314	-0.9711	9	0.72032	D	0.01	.	3.3882	0.07280	0.4917:0.0:0.3321:0.1762	.	213;173	G5E9B9;Q9UK12	.;ZN222_HUMAN	C	213;173;119	ENSP00000375822:Y213C;ENSP00000187879:Y173C	ENSP00000187879:Y173C	Y	+	2	0	ZNF222	49228185	0.000000	0.05858	0.000000	0.03702	0.669000	0.39330	-0.672000	0.05244	-0.409000	0.07553	0.172000	0.16884	TAT	.	.		0.438	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2		
CLASRP	11129	hgsc.bcm.edu	37	19	45543521	45543521	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:45543521C>T	ENST00000221455.3	+	2	149	c.51C>T	c.(49-51)gtC>gtT	p.V17V	CLASRP_ENST00000544944.2_Silent_p.V17V|CLASRP_ENST00000391953.4_Silent_p.V17V	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	17					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						GCATGATGGTCGACTACAAGA	0.587																																					p.V17V		Atlas-SNP	.											.	CLASRP	44	.	0			c.C51T						.						139.0	110.0	120.0					19																	45543521		2203	4297	6500	SO:0001819	synonymous_variant	11129	exon2			GATGGTCGACTAC	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"""Clk4 associating SR-related protein"""		"""splicing factor, arginine/serine-rich 16"""	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.51C>T	chr19.hg19:g.45543521C>T		183.0	0.0		243.0	24.0	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	hg19	CCDS12652.2																																																																																			.	.		0.587	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056	
SYNGR4	23546	hgsc.bcm.edu	37	19	48879425	48879425	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:48879425G>A	ENST00000344846.2	+	5	805	c.555G>A	c.(553-555)atG>atA	p.M185I	SYNGR4_ENST00000601610.1_3'UTR|SYNGR4_ENST00000595322.1_3'UTR	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	185						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		AGGGTGGCATGGTGCTGACCA	0.592																																					p.M185I		Atlas-SNP	.											.	SYNGR4	31	.	0			c.G555A						.						168.0	135.0	146.0					19																	48879425		2203	4300	6503	SO:0001583	missense	23546	exon5			TGGCATGGTGCTG	AJ011733	CCDS12717.1	19q13.3	2008-07-04				ENSG00000105467			11502	protein-coding gene	gene with protein product		608373					Standard	NM_012451		Approved		uc002piz.3	O95473		ENST00000344846.2:c.555G>A	chr19.hg19:g.48879425G>A	ENSP00000344041:p.Met185Ile	148.0	0.0		188.0	28.0	NM_012451	Q3KP58	Missense_Mutation	SNP	ENST00000344846.2	hg19	CCDS12717.1	.	.	.	.	.	.	.	.	.	.	G	7.766	0.706462	0.15239	.	.	ENSG00000105467	ENST00000344846	T	0.40756	1.02	5.51	4.46	0.54185	.	0.171029	0.50627	D	0.000115	T	0.26159	0.0638	N	0.19112	0.55	0.24248	N	0.995334	B	0.09022	0.002	B	0.06405	0.002	T	0.12837	-1.0532	10	0.29301	T	0.29	-24.1945	9.5076	0.39056	0.0:0.1558:0.6826:0.1615	.	185	O95473	SNG4_HUMAN	I	185	ENSP00000344041:M185I	ENSP00000344041:M185I	M	+	3	0	SYNGR4	53571237	0.918000	0.31147	0.997000	0.53966	0.250000	0.25880	0.024000	0.13555	1.451000	0.47736	0.555000	0.69702	ATG	.	.		0.592	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1		
SIGLEC11	114132	hgsc.bcm.edu	37	19	50464033	50464033	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:50464033C>T	ENST00000447370.2	-	2	326	c.236G>A	c.(235-237)aGc>aAc	p.S79N	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Missense_Mutation_p.S79N	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	79	Ig-like V-type.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		CGTCTTTGGGCTGGTCCGTCC	0.597																																					p.S79N		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.G236A						.						49.0	43.0	45.0					19																	50464033		2202	4300	6502	SO:0001583	missense	114132	exon2			TTTGGGCTGGTCC	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.236G>A	chr19.hg19:g.50464033C>T	ENSP00000412361:p.Ser79Asn	176.0	0.0		221.0	27.0	NM_052884		Missense_Mutation	SNP	ENST00000447370.2	hg19	CCDS12790.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.006|0.006	-2.083052|-2.083052	0.00371|0.00371	.|.	.|.	ENSG00000161640|ENSG00000161640	ENST00000426971|ENST00000447370;ENST00000458019	T|T	0.47177|0.66460	0.85|-0.21	2.63|2.63	-3.85|-3.85	0.04243|0.04243	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.|2.404500	.|0.01193	.|N	.|0.007397	T|T	0.41971|0.41971	0.1182|0.1182	N|N	0.04132|0.04132	-0.27|-0.27	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.37842|0.37842	-0.9688|-0.9688	6|10	.|0.13470	.|T	.|0.59	.|.	9.7995|9.7995	0.40755|0.40755	0.0:0.64:0.0:0.36|0.0:0.64:0.0:0.36	.|.	.|79;79	.|Q96RL6-2;Q96RL6	.|.;SIG11_HUMAN	T|N	69|79	ENSP00000398891:A69T|ENSP00000412361:S79N	.|ENSP00000412361:S79N	A|S	-|-	1|2	0|0	SIGLEC11|SIGLEC11	55155845|55155845	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.396000|-2.396000	0.01052|0.01052	-1.250000|-1.250000	0.02497|0.02497	-1.456000|-1.456000	0.01031|0.01031	GCC|AGC	.	.		0.597	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884	
KLK9	284366	hgsc.bcm.edu	37	19	51506441	51506441	+	Silent	SNP	T	T	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:51506441T>G	ENST00000594211.1	-	5	679	c.679A>C	c.(679-681)Aga>Cga	p.R227R	KLK9_ENST00000376832.4_Silent_p.R227R|KLK8_ENST00000391806.2_5'Flank|KLK8_ENST00000600767.1_5'Flank|KLK8_ENST00000347619.4_5'Flank|CTB-147C22.9_ENST00000594512.1_RNA|KLK8_ENST00000320838.5_5'Flank|KLK8_ENST00000291726.7_5'Flank|KLK8_ENST00000593490.1_5'Flank|KLK9_ENST00000250366.6_Silent_p.R227R			Q9UKQ9	KLK9_HUMAN	kallikrein-related peptidase 9	227	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7		all_neural(266;0.0652)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		CGCCGGGGTCTGGAGCAGGGC	0.642																																					p.R227R		Atlas-SNP	.											.	KLK9	27	.	0			c.A679C						.						62.0	67.0	65.0					19																	51506441		2203	4300	6503	SO:0001819	synonymous_variant	284366	exon5			GGGGTCTGGAGCA	AF135026	CCDS12816.1	19q13.33	2008-02-05	2006-10-27					"""Kallikreins"""	6370	protein-coding gene	gene with protein product		605504	"""kallikrein 9"""			16800724, 16800723	Standard	NM_012315		Approved	KLK-L3	uc002pux.1	Q9UKQ9		ENST00000594211.1:c.679A>C	chr19.hg19:g.51506441T>G		65.0	0.0		79.0	9.0	NM_012315	Q6QA55	Silent	SNP	ENST00000594211.1	hg19	CCDS12816.1																																																																																			.	.		0.642	KLK9-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465226.1	NM_012315	
ZNF578	147660	hgsc.bcm.edu	37	19	53014631	53014631	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:53014631C>T	ENST00000421239.2	+	6	1241	c.997C>T	c.(997-999)Cat>Tat	p.H333Y	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		CCTTACATGCCATCATAGGTG	0.428																																					p.H333Y		Atlas-SNP	.											.	.	.	.	0			c.C997T						.						112.0	114.0	113.0					19																	53014631		2200	4300	6500	SO:0001583	missense	147660	exon6			ACATGCCATCATA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.997C>T	chr19.hg19:g.53014631C>T	ENSP00000459216:p.His333Tyr	163.0	0.0		218.0	37.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	13.74	2.327480	0.41197	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	1.48	0.22813	.	.	.	.	.	T	0.60064	0.2240	H	0.95402	3.665	0.19575	N	0.999962	D	0.54047	0.964	B	0.42798	0.398	T	0.60393	-0.7272	7	.	.	.	.	10.0458	0.42186	0.0:1.0:0.0:0.0	.	333	G3V4F6	.	Y	333	.	.	H	+	1	0	ZNF578	57706443	0.991000	0.36638	0.001000	0.08648	0.011000	0.07611	3.772000	0.55325	0.835000	0.34877	0.297000	0.19635	CAT	.	.		0.428	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
NLRP7	199713	hgsc.bcm.edu	37	19	55453072	55453072	+	Missense_Mutation	SNP	G	G	A	rs142163492		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:55453072G>A	ENST00000590030.1	-	1	48	c.8C>T	c.(7-9)tCg>tTg	p.S3L	NLRP7_ENST00000340844.2_Missense_Mutation_p.S3L|NLRP7_ENST00000592784.1_Missense_Mutation_p.S3L|NLRP7_ENST00000446217.1_Missense_Mutation_p.S31L|NLRP7_ENST00000588756.1_Missense_Mutation_p.S3L|NLRP7_ENST00000328092.5_Missense_Mutation_p.S3L|NLRP7_ENST00000448121.2_Missense_Mutation_p.S3L			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	3	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TAGCTGGGGCGATGTCATAGT	0.458																																					p.S3L		Atlas-SNP	.											.	NLRP7	411	.	0			c.C8T						.	G	LEU/SER,LEU/SER,LEU/SER	0,4406		0,0,2203	33.0	34.0	34.0		8,8,8	0.5	0.0	19	dbSNP_134	34	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	145,145,145	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign,benign	3/1038,3/1010,3/981	55453072	2,13004	2203	4300	6503	SO:0001583	missense	199713	exon2			TGGGGCGATGTCA	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.8C>T	chr19.hg19:g.55453072G>A	ENSP00000465520:p.Ser3Leu	75.0	0.0		93.0	9.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	hg19	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.664353	0.29604	0.0	2.33E-4	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.79033	-1.11;-1.11;-1.19;-1.23	1.53	0.467	0.16721	Pyrin (1);DEATH-like (1);	.	.	.	.	T	0.65217	0.2670	L	0.43152	1.355	0.09310	N	1	B;B;B;B	0.13145	0.004;0.004;0.004;0.007	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.53099	-0.8486	9	0.42905	T	0.14	.	4.1013	0.10015	0.2269:0.0:0.7731:0.0	.	31;3;3;3	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	L	3;3;3;31;3	ENSP00000329568:S3L;ENSP00000409137:S3L;ENSP00000339491:S3L;ENSP00000414273:S31L	ENSP00000329568:S3L	S	-	2	0	NLRP7	60144884	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.502000	0.22594	0.197000	0.20387	-0.657000	0.03884	TCG	.	G|1.000;A|0.000		0.458	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
FAM71E2	284418	hgsc.bcm.edu	37	19	55871144	55871144	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:55871144G>A	ENST00000424985.3	-	9	1285	c.1092C>T	c.(1090-1092)ccC>ccT	p.P364P	CTD-2105E13.6_ENST00000591954.3_5'Flank	NM_001145402.1	NP_001138874.1	Q8N5Q1	F71E2_HUMAN	family with sequence similarity 71, member E2	364	Pro-rich.									NS(1)|breast(3)|endometrium(2)|kidney(1)|skin(1)	8						CCGGGGGATAGGGAGCCAGAC	0.677																																					p.P364P		Atlas-SNP	.											.	FAM71E2	41	.	0			c.C1092T						.						28.0	37.0	34.0					19																	55871144		692	1591	2283	SO:0001819	synonymous_variant	284418	exon9			GGGATAGGGAGCC	AL834316		19q13.42	2014-04-02	2007-11-20	2007-11-20	ENSG00000180043	ENSG00000180043			25278	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 16"""	C19orf16			Standard	NM_001145402		Approved	DKFZp434G1729	uc002qkr.2	Q8N5Q1	OTTHUMG00000170357	ENST00000424985.3:c.1092C>T	chr19.hg19:g.55871144G>A		141.0	0.0		159.0	16.0	NM_001145402	Q8ND99	Silent	SNP	ENST00000424985.3	hg19																																																																																				.	.		0.677	FAM71E2-010	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000409063.4	NM_001145402	
NLRP4	147945	hgsc.bcm.edu	37	19	56369470	56369470	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:56369470G>T	ENST00000301295.6	+	3	1133	c.711G>T	c.(709-711)caG>caT	p.Q237H	NLRP4_ENST00000587891.1_Missense_Mutation_p.Q162H|NLRP4_ENST00000346986.5_Missense_Mutation_p.Q237H	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	237	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		AAGAGCTGCAGGGCGGCTTGA	0.547																																					p.Q237H		Atlas-SNP	.											.	NLRP4	331	.	0			c.G711T						.						81.0	83.0	82.0					19																	56369470		2203	4300	6503	SO:0001583	missense	147945	exon3			GCTGCAGGGCGGC	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.711G>T	chr19.hg19:g.56369470G>T	ENSP00000301295:p.Gln237His	127.0	0.0		189.0	33.0	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	hg19	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.387734	0.25031	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.78707	-1.2;-1.2	4.1	-7.69	0.01263	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.65450	0.2692	L	0.27053	0.805	0.09310	N	1	B;B;B	0.25667	0.04;0.032;0.131	B;B;B	0.33196	0.013;0.099;0.159	T	0.57831	-0.7743	9	0.48119	T	0.1	.	13.3597	0.60648	0.1834:0.1283:0.6884:0.0	.	237;162;237	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	H	237	ENSP00000301295:Q237H;ENSP00000344787:Q237H	ENSP00000301295:Q237H	Q	+	3	2	NLRP4	61061282	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.986000	0.00087	-2.061000	0.00892	-0.302000	0.09304	CAG	.	.		0.547	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
ZNF135	7694	hgsc.bcm.edu	37	19	58578913	58578913	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:58578913A>T	ENST00000313434.5	+	5	1162	c.1061A>T	c.(1060-1062)tAt>tTt	p.Y354F	ZNF135_ENST00000506786.1_Missense_Mutation_p.Y312F|RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000511556.1_Missense_Mutation_p.Y366F|ZNF135_ENST00000439855.2_Missense_Mutation_p.Y354F|ZNF135_ENST00000401053.4_Missense_Mutation_p.Y378F|ZNF135_ENST00000359978.6_Missense_Mutation_p.Y366F	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	354					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)		GAGAAACCCTATCAGTGTGGT	0.567																																					p.Y378F		Atlas-SNP	.											.	ZNF135	159	.	0			c.A1133T						.						55.0	47.0	50.0					19																	58578913		2203	4300	6503	SO:0001583	missense	7694	exon4			AACCCTATCAGTG	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.1061A>T	chr19.hg19:g.58578913A>T	ENSP00000321406:p.Tyr354Phe	138.0	0.0		188.0	26.0	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.492|6.492	0.458944|0.458944	0.12342|0.12342	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000391699|ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	.|T;T;T;T;T;T	.|0.18338	.|2.22;2.22;2.22;2.22;2.22;2.22	2.75|2.75	2.75|2.75	0.32379|0.32379	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	T|T	0.14614|0.14614	0.0353|0.0353	N|N	0.12471|0.12471	0.22|0.22	0.09310|0.09310	N|N	1|1	.|P;P;B	.|0.48294	.|0.491;0.908;0.118	.|B;P;B	.|0.53490	.|0.213;0.727;0.039	T|T	0.11717|0.11717	-1.0576|-1.0576	5|9	.|0.35671	.|T	.|0.21	.|.	6.2384|6.2384	0.20776|0.20776	0.7761:0.0:0.0:0.2239|0.7761:0.0:0.0:0.2239	.|.	.|366;354;366	.|E9PEV2;P52742;Q8N1I7	.|.;ZN135_HUMAN;.	F|F	372|366;378;366;354;354;366;312	.|ENSP00000441410:Y378F;ENSP00000369437:Y366F;ENSP00000444828:Y354F;ENSP00000321406:Y354F;ENSP00000422074:Y366F;ENSP00000427691:Y312F	.|ENSP00000321406:Y354F	I|Y	+|+	1|2	0|0	ZNF135|ZNF135	63270725|63270725	0.001000|0.001000	0.12720|0.12720	0.664000|0.664000	0.29753|0.29753	0.028000|0.028000	0.11728|0.11728	1.281000|1.281000	0.33214|0.33214	1.272000|1.272000	0.44329|0.44329	0.455000|0.455000	0.32223|0.32223	ATC|TAT	.	.		0.567	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
RRBP1	6238	hgsc.bcm.edu	37	20	17616198	17616198	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:17616198C>A	ENST00000377813.1	-	7	2752	c.2449G>T	c.(2449-2451)Gag>Tag	p.E817*	RRBP1_ENST00000246043.4_Nonsense_Mutation_p.E817*|RRBP1_ENST00000360807.4_Nonsense_Mutation_p.E384*|RRBP1_ENST00000377807.2_Nonsense_Mutation_p.E384*|RRBP1_ENST00000455029.2_Nonsense_Mutation_p.E158*			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	817					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TACTTGCTCTCCACCTGGCTC	0.647																																					p.E384X		Atlas-SNP	.											.	RRBP1	157	.	0			c.G1150T						.						66.0	58.0	61.0					20																	17616198		2203	4300	6503	SO:0001587	stop_gained	6238	exon7			TGCTCTCCACCTG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.2449G>T	chr20.hg19:g.17616198C>A	ENSP00000367044:p.Glu817*	65.0	0.0		69.0	21.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Nonsense_Mutation	SNP	ENST00000377813.1	hg19		.	.	.	.	.	.	.	.	.	.	C	41	9.068143	0.99055	.	.	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	.	.	.	5.69	5.69	0.88448	.	0.000000	0.37906	N	0.001889	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-44.1293	18.3963	0.90499	0.0:1.0:0.0:0.0	.	.	.	.	X	384;817;384;817;158	.	ENSP00000246043:E817X	E	-	1	0	RRBP1	17564198	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.798000	0.85924	2.700000	0.92200	0.561000	0.74099	GAG	.	.		0.647	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576	
THBD	7056	hgsc.bcm.edu	37	20	23028767	23028767	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:23028767G>A	ENST00000377103.2	-	1	1611	c.1375C>T	c.(1375-1377)Ccc>Tcc	p.P459S		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	459	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	AAGGTACCGGGGAGGTTGTGG	0.647																																					p.P459S		Atlas-SNP	.											.	THBD	26	.	0			c.C1375T						.						37.0	38.0	38.0					20																	23028767		2202	4300	6502	SO:0001583	missense	7056	exon1			TACCGGGGAGGTT		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"""CD molecules"""	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.1375C>T	chr20.hg19:g.23028767G>A	ENSP00000366307:p.Pro459Ser	129.0	0.0		129.0	20.0	NM_000361	Q8IV29|Q9UC32	Missense_Mutation	SNP	ENST00000377103.2	hg19	CCDS13148.1	.	.	.	.	.	.	.	.	.	.	G	9.617	1.132738	0.21041	.	.	ENSG00000178726	ENST00000377103;ENST00000503590	D	0.91577	-2.87	4.73	3.78	0.43462	EGF-like calcium-binding, conserved site (1);Epidermal growth factor-like (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.551000	0.17133	U	0.185771	D	0.87055	0.6082	M	0.74467	2.265	0.09310	N	0.999999	P	0.46784	0.884	B	0.34452	0.183	T	0.79468	-0.1791	10	0.44086	T	0.13	-5.1892	9.6227	0.39732	0.0807:0.1418:0.7775:0.0	.	459	P07204	TRBM_HUMAN	S	459;441	ENSP00000366307:P459S	ENSP00000366307:P459S	P	-	1	0	THBD	22976767	0.006000	0.16342	0.487000	0.27428	0.004000	0.04260	1.581000	0.36558	1.116000	0.41820	0.561000	0.74099	CCC	.	.		0.647	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2		
C20orf24	55969	hgsc.bcm.edu	37	20	35238002	35238002	+	Splice_Site	SNP	A	A	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:35238002A>T	ENST00000373852.5	+	3	353		c.e3-1		C20orf24_ENST00000344795.3_Splice_Site|C20orf24_ENST00000342422.3_Intron|TGIF2-C20orf24_ENST00000558530.1_Splice_Site			Q9BUV8	CT024_HUMAN	chromosome 20 open reading frame 24											breast(1)|kidney(1)|lung(2)	4	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CTGTTGCTCCAGATTCTGCCT	0.483																																					.		Atlas-SNP	.											.	C20orf24	17	.	0			c.219-2A>T						.						230.0	200.0	210.0					20																	35238002		2203	4300	6503	SO:0001630	splice_region_variant	55969	exon3			TGCTCCAGATTCT	AF112213	CCDS13279.1, CCDS13280.1, CCDS56190.1	20q11.23	2011-01-25			ENSG00000101084	ENSG00000101084			15870	protein-coding gene	gene with protein product						15178406	Standard	NM_018840		Approved	PNAS-11, RIP5		Q9BUV8	OTTHUMG00000032384	ENST00000373852.5:c.219-1A>T	chr20.hg19:g.35238002A>T		180.0	0.0		229.0	26.0	NM_001199534	E1P5U0|O00605|Q5QPG6|Q5QPG7|Q9BT03|Q9BZU7|Q9UI05	Splice_Site	SNP	ENST00000373852.5	hg19	CCDS56190.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.837778	0.32513	.	.	ENSG00000101084	ENST00000344795;ENST00000373852	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5927	0.61969	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C20orf24	34671416	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	8.864000	0.92294	2.099000	0.63709	0.533000	0.62120	.	.	.		0.483	C20orf24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079006.1	NM_018840	Intron
ZHX3	23051	hgsc.bcm.edu	37	20	39833219	39833219	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:39833219C>T	ENST00000309060.3	-	4	753	c.338G>A	c.(337-339)gGg>gAg	p.G113E	ZHX3_ENST00000559234.1_Missense_Mutation_p.G113E|ZHX3_ENST00000544979.2_Missense_Mutation_p.G113E|ZHX3_ENST00000432768.2_Missense_Mutation_p.G113E|ZHX3_ENST00000540170.1_Missense_Mutation_p.G113E|ZHX3_ENST00000560361.1_Missense_Mutation_p.G113E|ZHX3_ENST00000557816.1_Missense_Mutation_p.G113E|ZHX3_ENST00000558993.1_Missense_Mutation_p.G113E			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	113					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				AAAACTGCACCCACTGCATAC	0.488																																					p.G113E		Atlas-SNP	.											.	ZHX3	78	.	0			c.G338A						.						107.0	104.0	105.0					20																	39833219		2203	4300	6503	SO:0001583	missense	23051	exon3			CTGCACCCACTGC	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.338G>A	chr20.hg19:g.39833219C>T	ENSP00000312222:p.Gly113Glu	84.0	0.0		96.0	20.0	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	hg19	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	C	0.838	-0.742884	0.03088	.	.	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000432768;ENST00000441102;ENST00000419740	T;T;T;T;T	0.24538	1.85;3.28;3.28;3.06;1.85	6.07	2.66	0.31614	Zinc finger, C2H2-like (1);	0.633648	0.17566	N	0.169659	T	0.04998	0.0134	N	0.00408	-1.53	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.001	T	0.40270	-0.9572	10	0.02654	T	1	-5.7801	5.902	0.18972	0.0:0.1905:0.3881:0.4214	.	113;113;113;113	A8K8Q0;Q9H4I2;F5H820;F6R4Q5	.;ZHX3_HUMAN;.;.	E	113	ENSP00000312222:G113E;ENSP00000362360:G113E;ENSP00000442290:G113E;ENSP00000443783:G113E;ENSP00000415498:G113E	ENSP00000312222:G113E	G	-	2	0	ZHX3	39266633	0.046000	0.20272	0.844000	0.33320	0.909000	0.53808	1.051000	0.30417	0.248000	0.21435	-0.165000	0.13383	GGG	.	.		0.488	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
PABPC1L	80336	hgsc.bcm.edu	37	20	43566743	43566743	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:43566743C>G	ENST00000217073.2	+	13	1687	c.1687C>G	c.(1687-1689)Ctg>Gtg	p.L563V	PABPC1L_ENST00000372819.1_Missense_Mutation_p.L117V|PABPC1L_ENST00000537323.1_3'UTR|PABPC1L_ENST00000255136.3_Missense_Mutation_p.L563V|PABPC1L_ENST00000217075.2_Missense_Mutation_p.L117V|PABPC1L_ENST00000372824.1_Missense_Mutation_p.L117V|PABPC1L_ENST00000490798.1_Intron			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	563	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						CCACACCCAGCTGGCTGGCAA	0.567																																					p.L563V		Atlas-SNP	.											.	PABPC1L	59	.	0			c.C1687G						.						72.0	63.0	65.0					20																	43566743		1568	3582	5150	SO:0001583	missense	80336	exon13			ACCCAGCTGGCTG	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"""RNA binding motif (RRM) containing"""	15797	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 119"""	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.1687C>G	chr20.hg19:g.43566743C>G	ENSP00000217073:p.Leu563Val	140.0	0.0		195.0	38.0	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	hg19	CCDS42878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.68|17.68	3.449107|3.449107	0.63178|0.63178	.|.	.|.	ENSG00000101104|ENSG00000101104	ENST00000255136;ENST00000421240;ENST00000217073;ENST00000372824;ENST00000372819;ENST00000217075|ENST00000372821;ENST00000372826;ENST00000372822	T;T;T;T;T|T	0.50001|0.44083	0.76;0.76;0.76;0.76;0.76|0.93	4.72|4.72	2.74|2.74	0.32292|0.32292	Polyadenylate-binding protein/Hyperplastic disc protein (5);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.57154|0.57154	0.2034|0.2034	M|M	0.82716|0.82716	2.605|2.605	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.85130|.	0.985;0.997|.	T|T	0.61277|0.61277	-0.7095|-0.7095	10|7	0.66056|0.87932	D|D	0.02|0	.|.	8.1996|8.1996	0.31417|0.31417	0.0:0.6888:0.0:0.3112|0.0:0.6888:0.0:0.3112	.|.	563;117|.	Q4VXU2;G5E9L3|.	PAP1L_HUMAN;.|.	V|R	563;117;563;117;117;117|144;98;85	ENSP00000255136:L563V;ENSP00000217073:L563V;ENSP00000361911:L117V;ENSP00000361906:L117V;ENSP00000217075:L117V|ENSP00000361909:S85R	ENSP00000217073:L563V|ENSP00000361908:S144R	L|S	+|+	1|3	2|2	PABPC1L|PABPC1L	43000157|43000157	0.947000|0.947000	0.32204|0.32204	0.905000|0.905000	0.35620|0.35620	0.991000|0.991000	0.79684|0.79684	2.125000|2.125000	0.42016|0.42016	1.224000|1.224000	0.43551|0.43551	0.591000|0.591000	0.81541|0.81541	CTG|AGC	.	.		0.567	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2		
FAM65C	140876	hgsc.bcm.edu	37	20	49212742	49212742	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:49212742C>T	ENST00000327979.2	-	15	2248	c.1837G>A	c.(1837-1839)Gcc>Acc	p.A613T	FAM65C_ENST00000535356.1_Missense_Mutation_p.A617T|FAM65C_ENST00000045083.2_Missense_Mutation_p.A613T			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	613										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGGGCACCGGCTGTGAGTTCC	0.592																																					p.A613T		Atlas-SNP	.											.	FAM65C	87	.	0			c.G1837A						.						67.0	74.0	72.0					20																	49212742		2001	4164	6165	SO:0001583	missense	140876	exon15			CACCGGCTGTGAG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 175"", ""chromosome 20 open reading frame 176"""	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1837G>A	chr20.hg19:g.49212742C>T	ENSP00000332663:p.Ala613Thr	115.0	0.0		147.0	19.0	NM_080829	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	hg19	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	C	0.062	-1.221873	0.01530	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	D;D;D	0.82984	-1.67;-1.67;-1.67	5.24	4.3	0.51218	.	0.289381	0.25604	U	0.029529	T	0.65749	0.2721	N	0.22421	0.69	0.09310	N	0.999991	B;B	0.06786	0.0;0.001	B;B	0.10450	0.005;0.003	T	0.49762	-0.8905	10	0.02654	T	1	-16.7173	7.3535	0.26706	0.0:0.7646:0.0:0.2354	.	617;613	F5H0X2;Q96MK2	.;FA65C_HUMAN	T	613;613;617	ENSP00000332663:A613T;ENSP00000045083:A613T;ENSP00000439802:A617T	ENSP00000045083:A613T	A	-	1	0	FAM65C	48646149	0.054000	0.20591	0.889000	0.34880	0.057000	0.15508	0.723000	0.25939	1.210000	0.43336	0.561000	0.74099	GCC	.	.		0.592	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1		
SYCP2	10388	hgsc.bcm.edu	37	20	58489028	58489028	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:58489028A>G	ENST00000357552.3	-	12	1056		c.e12+1		SYCP2_ENST00000371001.2_Splice_Site			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2						female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			CATTAAGTTTACCTTCTTTTG	0.294																																					.		Atlas-SNP	.											.	SYCP2	204	.	0			c.830+2T>C						.						68.0	67.0	67.0					20																	58489028		2201	4297	6498	SO:0001630	splice_region_variant	10388	exon12			AAGTTTACCTTCT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.830+1T>C	chr20.hg19:g.58489028A>G		83.0	0.0		133.0	22.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Splice_Site	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.440185	0.63067	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8546	0.70326	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SYCP2	57922423	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	8.719000	0.91436	1.968000	0.57251	0.533000	0.62120	.	.	.		0.294	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	Intron
TCFL5	10732	hgsc.bcm.edu	37	20	61488865	61488865	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr20:61488865C>T	ENST00000335351.3	-	4	1212	c.1120G>A	c.(1120-1122)Ggc>Agc	p.G374S	TCFL5_ENST00000217162.5_Missense_Mutation_p.G326S	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	374					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					TGCCAAGCGCCTTGTGTGGCG	0.587																																					p.G374S		Atlas-SNP	.											.	TCFL5	43	.	0			c.G1120A						.						123.0	116.0	118.0					20																	61488865		2203	4300	6503	SO:0001583	missense	10732	exon4			AAGCGCCTTGTGT	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"""Basic helix-loop-helix proteins"""	11646	protein-coding gene	gene with protein product	"""HPV-16 E2 binding protein 1"""	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.1120G>A	chr20.hg19:g.61488865C>T	ENSP00000334294:p.Gly374Ser	116.0	0.0		172.0	19.0	NM_006602	O94771|Q9BYW0	Missense_Mutation	SNP	ENST00000335351.3	hg19	CCDS13506.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910245	0.52439	.	.	ENSG00000101190	ENST00000335351;ENST00000217162	T;T	0.38722	1.15;1.12	5.61	5.61	0.85477	.	0.379291	0.22531	N	0.058854	T	0.32734	0.0839	L	0.32530	0.975	0.32594	N	0.526787	P;P	0.38597	0.525;0.639	B;B	0.33454	0.164;0.122	T	0.50955	-0.8766	10	0.59425	D	0.04	-25.5413	14.8546	0.70326	0.0:0.9293:0.0:0.0707	.	326;374	F8W9A4;Q9UL49	.;TCFL5_HUMAN	S	374;326	ENSP00000334294:G374S;ENSP00000217162:G326S	ENSP00000217162:G326S	G	-	1	0	TCFL5	60959310	0.998000	0.40836	0.962000	0.40283	0.005000	0.04900	2.522000	0.45572	2.651000	0.90000	0.585000	0.79938	GGC	.	.		0.587	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602	
LIPI	149998	hgsc.bcm.edu	37	21	15579225	15579225	+	Intron	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:15579225T>C	ENST00000536861.1	-	1	46				LIPI_ENST00000344577.2_Missense_Mutation_p.H7R			Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CAAGTTATTATGTAAACATTT	0.378																																					p.H7R		Atlas-SNP	.											.	LIPI	95	.	0			c.A20G						.						97.0	100.0	99.0					21																	15579225		2203	4300	6503	SO:0001627	intron_variant	149998	exon1			TTATTATGTAAAC	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.46+3895A>G	chr21.hg19:g.15579225T>C		48.0	0.0		58.0	14.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	hg19		.	.	.	.	.	.	.	.	.	.	T	5.420	0.262683	0.10294	.	.	ENSG00000188992	ENST00000344577	D	0.87729	-2.29	2.02	-0.57	0.11753	.	.	.	.	.	T	0.73289	0.3568	.	.	.	0.09310	N	1	B	0.23540	0.087	B	0.19391	0.025	T	0.57183	-0.7855	8	0.29301	T	0.29	.	1.64	0.02750	0.2944:0.1882:0.0:0.5174	.	7	Q6XZB0-2	.	R	7	ENSP00000343331:H7R	ENSP00000343331:H7R	H	-	2	0	LIPI	14501096	0.001000	0.12720	0.007000	0.13788	0.672000	0.39443	-0.397000	0.07269	-0.143000	0.11334	0.334000	0.21626	CAT	.	.		0.378	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
TIAM1	7074	hgsc.bcm.edu	37	21	32638540	32638540	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:32638540C>A	ENST00000286827.3	-	5	1220	c.749G>T	c.(748-750)gGg>gTg	p.G250V	TIAM1_ENST00000541036.1_Missense_Mutation_p.G250V|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	250					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						AAATTTGCTCCCCGGCCCCCC	0.542																																					p.G250V		Atlas-SNP	.											.	TIAM1	522	.	0			c.G749T						.						77.0	79.0	78.0					21																	32638540		2203	4300	6503	SO:0001583	missense	7074	exon5			TTGCTCCCCGGCC		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.749G>T	chr21.hg19:g.32638540C>A	ENSP00000286827:p.Gly250Val	112.0	0.0		73.0	9.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	hg19	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.036423	0.35893	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.38401	1.15;1.14	5.4	5.4	0.78164	.	0.227987	0.43919	D	0.000519	T	0.24431	0.0592	N	0.08118	0	0.41091	D	0.985594	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.05632	-1.0873	10	0.48119	T	0.1	.	19.3745	0.94503	0.0:1.0:0.0:0.0	.	250;250;250	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	V	250;91;250	ENSP00000286827:G250V;ENSP00000441570:G250V	ENSP00000286827:G250V	G	-	2	0	TIAM1	31560411	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	3.789000	0.55454	2.803000	0.96430	0.585000	0.79938	GGG	.	.		0.542	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
AIRE	326	hgsc.bcm.edu	37	21	45709596	45709596	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:45709596G>A	ENST00000291582.5	+	6	836	c.709G>A	c.(709-711)Gaa>Aaa	p.E237K	AIRE_ENST00000329347.4_5'Flank|AIRE_ENST00000355347.4_5'Flank	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	237	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.				humoral immune response (GO:0006959)|immune response (GO:0006955)|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)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		CAGCAAGTTCGAAGACTCCGG	0.662									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy																												p.E237K		Atlas-SNP	.											AIRE,NS,carcinoma,0,1	AIRE	61	.	0			c.G709A						.						46.0	53.0	50.0					21																	45709596		2203	4298	6501	SO:0001583	missense	326	exon6	Familial Cancer Database	APECED	AAGTTCGAAGACT	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.709G>A	chr21.hg19:g.45709596G>A	ENSP00000291582:p.Glu237Lys	159.0	1.0		132.0	27.0	NM_000383	B2RP50|O43922|O43932|O75745	Missense_Mutation	SNP	ENST00000291582.5	hg19	CCDS13706.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560909	0.45590	.	.	ENSG00000160224	ENST00000291582	T	0.67865	-0.29	4.12	3.19	0.36642	SAND domain-like (2);SAND domain (3);	0.132398	0.33631	N	0.004708	T	0.77116	0.4083	M	0.67953	2.075	0.43540	D	0.995837	D	0.89917	1.0	D	0.83275	0.996	T	0.76173	-0.3056	10	0.48119	T	0.1	-42.7415	10.0972	0.42482	0.0:0.2062:0.7938:0.0	.	237	O43918	AIRE_HUMAN	K	237	ENSP00000291582:E237K	ENSP00000291582:E237K	E	+	1	0	AIRE	44534024	1.000000	0.71417	0.060000	0.19600	0.008000	0.06430	4.232000	0.58645	0.981000	0.38548	0.591000	0.81541	GAA	.	.		0.662	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
PCNT	5116	hgsc.bcm.edu	37	21	47754602	47754602	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr21:47754602G>T	ENST00000359568.5	+	3	666	c.559G>T	c.(559-561)Gtc>Ttc	p.V187F	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	187					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GATGTTCACAGTCAGTGACCA	0.507																																					p.V187F		Atlas-SNP	.											.	PCNT	283	.	0			c.G559T						.						202.0	144.0	163.0					21																	47754602		2203	4300	6503	SO:0001583	missense	5116	exon3			TTCACAGTCAGTG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.559G>T	chr21.hg19:g.47754602G>T	ENSP00000352572:p.Val187Phe	309.0	0.0		319.0	38.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	G	1.081	-0.667051	0.03428	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.02177	4.41	0.235	-0.47	0.12131	.	.	.	.	.	T	0.01254	0.0041	L	0.27053	0.805	0.09310	N	1	B;B	0.30236	0.274;0.18	B;B	0.18263	0.021;0.009	T	0.48536	-0.9027	8	0.15952	T	0.53	.	.	.	.	.	69;187	O95613-2;O95613	.;PCNT_HUMAN	F	187;174	ENSP00000352572:V187F	ENSP00000338675:V174F	V	+	1	0	PCNT	46579030	0.019000	0.18553	0.001000	0.08648	0.001000	0.01503	-1.371000	0.02573	-1.906000	0.01089	-1.922000	0.00515	GTC	.	.		0.507	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MICAL3	57553	hgsc.bcm.edu	37	22	18347690	18347690	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:18347690C>T	ENST00000441493.2	-	19	2932	c.2580G>A	c.(2578-2580)gtG>gtA	p.V860V	MICAL3_ENST00000383094.3_Silent_p.V860V|MICAL3_ENST00000400561.2_Silent_p.V860V|MICAL3_ENST00000414725.2_Silent_p.V888V|MICAL3_ENST00000444520.1_Silent_p.V860V|MICAL3_ENST00000207726.7_Silent_p.V888V|MICAL3_ENST00000429452.1_Silent_p.V984V|MICAL3_ENST00000585038.1_Silent_p.V984V	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	860					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TGGAGCTGGCCACGGCGTTGG	0.597																																					p.V984V		Atlas-SNP	.											.	MICAL3	53	.	0			c.G2952A						.						95.0	92.0	93.0					22																	18347690		1568	3582	5150	SO:0001819	synonymous_variant	57553	exon23			GCTGGCCACGGCG	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2580G>A	chr22.hg19:g.18347690C>T		129.0	0.0		148.0	29.0	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.		0.597	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
SEC14L4	284904	hgsc.bcm.edu	37	22	30899672	30899672	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:30899672C>T	ENST00000255858.7	-	2	205	c.122G>A	c.(121-123)tGg>tAg	p.W41*	SEC14L4_ENST00000540456.1_Missense_Mutation_p.G10S|SEC14L4_ENST00000381982.3_Nonsense_Mutation_p.W41*|SEC14L4_ENST00000392772.2_5'UTR	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	41						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	ACCTCGCAGCCAGCGCAGGAG	0.612																																					p.W41X		Atlas-SNP	.											.	SEC14L4	43	.	0			c.G122A						.						95.0	81.0	86.0					22																	30899672		2203	4300	6503	SO:0001587	stop_gained	284904	exon2			CGCAGCCAGCGCA	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.122G>A	chr22.hg19:g.30899672C>T	ENSP00000255858:p.Trp41*	62.0	0.0		72.0	13.0	NM_001161368	A5D6W7|A6NCV4	Nonsense_Mutation	SNP	ENST00000255858.7	hg19	CCDS13878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.1|29.1	4.980158|4.980158	0.92982|0.92982	.|.	.|.	ENSG00000133488|ENSG00000133488	ENST00000540456|ENST00000255858;ENST00000381982	T|.	0.70399|.	-0.48|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.43853|.	0.1266|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|.	0.30179|.	-0.9987|.	8|.	0.52906|0.02654	T|T	0.07|1	2.4821|2.4821	16.8641|16.8641	0.86025|0.86025	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	10|.	G3V1L4|.	.|.	S|X	10|41	ENSP00000440848:G10S|.	ENSP00000440848:G10S|ENSP00000255858:W41X	G|W	-|-	1|2	0|0	SEC14L4|SEC14L4	29229672|29229672	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.635000|0.635000	0.38103|0.38103	6.147000|6.147000	0.71783|0.71783	2.691000|2.691000	0.91804|0.91804	0.585000|0.585000	0.79938|0.79938	GGC|TGG	.	.		0.612	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
EIF3D	8664	hgsc.bcm.edu	37	22	36920731	36920731	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:36920731T>C	ENST00000216190.8	-	4	588	c.218A>G	c.(217-219)cAt>cGt	p.H73R	EIF3D_ENST00000541106.1_Intron|EIF3D_ENST00000405442.1_Missense_Mutation_p.H73R	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D											cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						ATCCTCCTCATGGAAATAAGC	0.498																																					p.H73R		Atlas-SNP	.											.	EIF3D	37	.	0			c.A218G						.						236.0	208.0	218.0					22																	36920731		2203	4300	6503	SO:0001583	missense	8664	exon4			TCCTCATGGAAAT	U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"""eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"""	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.218A>G	chr22.hg19:g.36920731T>C	ENSP00000216190:p.His73Arg	147.0	0.0		210.0	42.0	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	hg19	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.026903	0.93518	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000405442;ENST00000455547;ENST00000457241;ENST00000432675;ENST00000402116	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.83640	0.5298	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83192	-0.0083	9	0.30078	T	0.28	-40.7054	16.5582	0.84512	0.0:0.0:0.0:1.0	.	73	O15371	EIF3D_HUMAN	R	73	.	ENSP00000216190:H73R	H	-	2	0	EIF3D	35250677	1.000000	0.71417	0.976000	0.42696	0.987000	0.75469	7.755000	0.85180	2.308000	0.77769	0.533000	0.62120	CAT	.	.		0.498	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1		
TCF20	6942	hgsc.bcm.edu	37	22	42606358	42606358	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr22:42606358C>G	ENST00000359486.3	-	1	5090	c.4954G>C	c.(4954-4956)Gct>Cct	p.A1652P	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Missense_Mutation_p.A1652P	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1652					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						TCTTCCTCAGCATTGATGATT	0.488																																					p.A1652P		Atlas-SNP	.											.	TCF20	164	.	0			c.G4954C						.						134.0	135.0	134.0					22																	42606358		2203	4300	6503	SO:0001583	missense	6942	exon1			CCTCAGCATTGAT	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.4954G>C	chr22.hg19:g.42606358C>G	ENSP00000352463:p.Ala1652Pro	317.0	0.0		326.0	34.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.491245	0.64074	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.60920	0.15;0.15	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000001	T	0.76162	0.3949	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	T	0.75590	-0.3265	10	0.72032	D	0.01	-15.2709	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1652;1652	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	P	1652	ENSP00000352463:A1652P;ENSP00000335561:A1652P	ENSP00000335561:A1652P	A	-	1	0	TCF20	40936302	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.022000	0.49659	2.884000	0.98904	0.655000	0.94253	GCT	.	.		0.488	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
GPM6B	2824	hgsc.bcm.edu	37	X	13801604	13801604	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:13801604C>T	ENST00000356942.5	-	3	726	c.285G>A	c.(283-285)gcG>gcA	p.A95A	GPM6B_ENST00000493677.1_Silent_p.A109A|GPM6B_ENST00000398361.3_Silent_p.A9A|GPM6B_ENST00000454189.2_Silent_p.A76A|GPM6B_ENST00000355135.2_Silent_p.A135A|GPM6B_ENST00000316715.4_Silent_p.A135A	NM_005278.3	NP_005269.1	Q13491	GPM6B_HUMAN	glycoprotein M6B	95					cell differentiation (GO:0030154)|extracellular matrix assembly (GO:0085029)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of serotonin uptake (GO:0051612)|nervous system development (GO:0007399)|ossification (GO:0001503)|positive regulation of bone mineralization (GO:0030501)|protein transport (GO:0015031)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of focal adhesion assembly (GO:0051893)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)|pancreas(1)	6						AGAAAAAGGACGCAATTCCAT	0.423																																					p.A135A		Atlas-SNP	.											.	GPM6B	46	.	0			c.G405A						.						159.0	140.0	146.0					X																	13801604		2203	4300	6503	SO:0001819	synonymous_variant	2824	exon4			AAAGGACGCAATT		CCDS14158.1, CCDS35206.1, CCDS35207.1, CCDS48084.1	Xp22.2	2010-08-03			ENSG00000046653	ENSG00000046653			4461	protein-coding gene	gene with protein product		300051				8661015	Standard	NM_001001995		Approved	M6B, MGC17150, MGC54284	uc004cvw.3	Q13491	OTTHUMG00000021162	ENST00000356942.5:c.285G>A	chrX.hg19:g.13801604C>T		209.0	0.0		210.0	29.0	NM_001001995	O76077|Q86X43|Q8N956	Silent	SNP	ENST00000356942.5	hg19	CCDS14158.1																																																																																			.	.		0.423	GPM6B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055822.1	NM_001001995	
MOSPD2	158747	hgsc.bcm.edu	37	X	14910893	14910893	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:14910893A>G	ENST00000380492.3	+	3	216	c.128A>G	c.(127-129)gAt>gGt	p.D43G	MOSPD2_ENST00000482354.1_Missense_Mutation_p.D43G|MOSPD2_ENST00000495110.1_3'UTR	NM_001177475.1|NM_152581.3	NP_001170946.1|NP_689794.1	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	43						integral component of membrane (GO:0016021)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	Hepatocellular(33;0.183)					CTACAACAAGATGATAACTGG	0.343																																					p.D43G		Atlas-SNP	.											.	MOSPD2	46	.	0			c.A128G						.						121.0	114.0	117.0					X																	14910893		2203	4300	6503	SO:0001583	missense	158747	exon3			AACAAGATGATAA	AL834345	CCDS14162.1	Xp22.31	2006-03-16			ENSG00000130150	ENSG00000130150			28381	protein-coding gene	gene with protein product						15533722	Standard	NM_152581		Approved	MGC26706	uc004cwi.3	Q8NHP6	OTTHUMG00000021170	ENST00000380492.3:c.128A>G	chrX.hg19:g.14910893A>G	ENSP00000369860:p.Asp43Gly	179.0	0.0		177.0	25.0	NM_152581	Q8N3H2|Q8NA83	Missense_Mutation	SNP	ENST00000380492.3	hg19	CCDS14162.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.203075	0.79127	.	.	ENSG00000130150	ENST00000380492	T	0.69806	-0.43	5.3	5.3	0.74995	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.051223	0.85682	D	0.000000	T	0.80048	0.4552	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	T	0.82277	-0.0537	10	0.66056	D	0.02	.	14.3328	0.66569	1.0:0.0:0.0:0.0	.	43	Q8NHP6	MSPD2_HUMAN	G	43	ENSP00000369860:D43G	ENSP00000369860:D43G	D	+	2	0	MOSPD2	14820814	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	8.870000	0.92336	1.763000	0.52060	0.486000	0.48141	GAT	.	.		0.343	MOSPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055837.1	NM_152581	
RAI2	10742	hgsc.bcm.edu	37	X	17818831	17818831	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:17818831A>G	ENST00000545871.1	-	3	1760	c.1300T>C	c.(1300-1302)Tcc>Ccc	p.S434P	RAI2_ENST00000451717.1_Missense_Mutation_p.S434P|RAI2_ENST00000415486.3_Missense_Mutation_p.S384P|RAI2_ENST00000360011.1_Missense_Mutation_p.S434P|RAI2_ENST00000331511.1_Missense_Mutation_p.S434P	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	434					embryo development (GO:0009790)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					GCCGCCTGGGACTCGCCCACC	0.542																																					p.S434P		Atlas-SNP	.											.	RAI2	66	.	0			c.T1300C						.						120.0	118.0	119.0					X																	17818831		2203	4300	6503	SO:0001583	missense	10742	exon3			CCTGGGACTCGCC	Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.1300T>C	chrX.hg19:g.17818831A>G	ENSP00000444210:p.Ser434Pro	58.0	0.0		58.0	12.0	NM_001172739	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	hg19	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	A	11.27	1.590116	0.28357	.	.	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.50001	0.79;0.79;0.79;0.79;0.76	5.12	5.12	0.69794	.	0.149607	0.46442	D	0.000300	T	0.55449	0.1921	L	0.36672	1.1	0.46113	D	0.998877	D;D	0.67145	0.996;0.969	P;P	0.61070	0.883;0.824	T	0.59778	-0.7390	10	0.87932	D	0	-22.0114	14.0845	0.64947	1.0:0.0:0.0:0.0	.	384;434	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	P	434;434;434;434;384	ENSP00000333456:S434P;ENSP00000353106:S434P;ENSP00000444210:S434P;ENSP00000401323:S434P;ENSP00000392578:S384P	ENSP00000333456:S434P	S	-	1	0	RAI2	17728752	1.000000	0.71417	0.990000	0.47175	0.149000	0.21700	4.641000	0.61375	1.901000	0.55032	0.486000	0.48141	TCC	.	.		0.542	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785	
MAGEB6	158809	hgsc.bcm.edu	37	X	26212302	26212302	+	Silent	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:26212302C>A	ENST00000379034.1	+	2	488	c.339C>A	c.(337-339)ggC>ggA	p.G113G		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	113	Ser-rich.									breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						CACCCACTGGCTCTCCTGATG	0.537																																					p.G113G		Atlas-SNP	.											.	MAGEB6	91	.	0			c.C339A						.																																			SO:0001819	synonymous_variant	158809	exon2			CACTGGCTCTCCT	AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 4"""	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.339C>A	chrX.hg19:g.26212302C>A		192.0	0.0		215.0	59.0	NM_173523	Q6GS19|Q9H219	Silent	SNP	ENST00000379034.1	hg19	CCDS14217.1																																																																																			.	.		0.537	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523	
UBA1	7317	hgsc.bcm.edu	37	X	47062208	47062208	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:47062208A>G	ENST00000335972.6	+	11	1411	c.1228A>G	c.(1228-1230)Atg>Gtg	p.M410V	INE1_ENST00000456273.1_RNA|UBA1_ENST00000490869.1_3'UTR|UBA1_ENST00000377351.4_Missense_Mutation_p.M410V	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	410	2 approximate repeats.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CCAGGAAGTCATGAAGGTCAG	0.592																																					p.M410V		Atlas-SNP	.											.	UBA1	89	.	0			c.A1228G						.						25.0	23.0	23.0					X																	47062208		2203	4298	6501	SO:0001583	missense	7317	exon11			GAAGTCATGAAGG	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1228A>G	chrX.hg19:g.47062208A>G	ENSP00000338413:p.Met410Val	84.0	0.0		102.0	17.0	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	hg19	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	A	11.16	1.556650	0.27827	.	.	ENSG00000130985	ENST00000377351;ENST00000335972	T;T	0.60040	0.22;0.22	4.75	4.75	0.60458	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.41534	0.1163	N	0.17278	0.47	0.80722	D	1	P	0.36495	0.556	B	0.37731	0.257	T	0.32587	-0.9901	10	0.26408	T	0.33	-28.6326	12.5479	0.56210	1.0:0.0:0.0:0.0	.	410	P22314	UBA1_HUMAN	V	410	ENSP00000366568:M410V;ENSP00000338413:M410V	ENSP00000338413:M410V	M	+	1	0	UBA1	46947152	0.998000	0.40836	1.000000	0.80357	0.967000	0.64934	3.453000	0.52978	1.877000	0.54381	0.427000	0.28365	ATG	.	.		0.592	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	
CCDC22	28952	hgsc.bcm.edu	37	X	49103272	49103272	+	Silent	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:49103272C>T	ENST00000376227.3	+	7	965	c.795C>T	c.(793-795)gcC>gcT	p.A265A		NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	265										NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						TGCTTGGGGCCCCCATACAAG	0.657																																					p.A265A		Atlas-SNP	.											.	CCDC22	69	.	0			c.C795T						.						16.0	14.0	15.0					X																	49103272		2178	4270	6448	SO:0001819	synonymous_variant	28952	exon7			TGGGGCCCCCATA	BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.795C>T	chrX.hg19:g.49103272C>T		45.0	0.0		33.0	8.0	NM_014008	A8K7G1	Silent	SNP	ENST00000376227.3	hg19	CCDS14322.1																																																																																			.	.		0.657	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	
CCNB3	85417	hgsc.bcm.edu	37	X	50037910	50037910	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:50037910G>C	ENST00000376042.1	+	5	550	c.252G>C	c.(250-252)gaG>gaC	p.E84D	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.E84D			Q8WWL7	CCNB3_HUMAN	cyclin B3	84					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					CCAATAAAGAGTTTGTAAAAG	0.438																																					p.E84D		Atlas-SNP	.											.	CCNB3	367	.	0			c.G252C						.						95.0	84.0	88.0					X																	50037910		2203	4300	6503	SO:0001583	missense	85417	exon4			TAAAGAGTTTGTA	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.252G>C	chrX.hg19:g.50037910G>C	ENSP00000365210:p.Glu84Asp	213.0	0.0		191.0	38.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	hg19	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	G	9.184	1.024223	0.19433	.	.	ENSG00000147082	ENST00000376042;ENST00000396540;ENST00000276014	T;T	0.12569	2.67;2.67	3.57	1.79	0.24919	.	.	.	.	.	T	0.24275	0.0588	L	0.46157	1.445	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	T	0.08269	-1.0730	8	.	.	.	.	5.1347	0.14928	0.2813:0.0:0.7187:0.0	.	84	Q8WWL7	CCNB3_HUMAN	D	84	ENSP00000365210:E84D;ENSP00000276014:E84D	.	E	+	3	2	CCNB3	50054650	0.363000	0.24989	0.034000	0.17996	0.036000	0.12997	0.489000	0.22387	0.345000	0.23873	0.591000	0.81541	GAG	.	.		0.438	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1		
SHROOM4	57477	hgsc.bcm.edu	37	X	50345797	50345797	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:50345797A>G	ENST00000289292.7	-	7	4061	c.3778T>C	c.(3778-3780)Ttt>Ctt	p.F1260L	SHROOM4_ENST00000460112.3_Missense_Mutation_p.F1144L|SHROOM4_ENST00000376020.2_Missense_Mutation_p.F1260L			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1260	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					GGAGGCGAAAAGTGCTGAAAC	0.448																																					p.F1260L		Atlas-SNP	.											.	SHROOM4	171	.	0			c.T3778C						.						57.0	51.0	53.0					X																	50345797		2203	4300	6503	SO:0001583	missense	57477	exon7			GCGAAAAGTGCTG	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3778T>C	chrX.hg19:g.50345797A>G	ENSP00000289292:p.Phe1260Leu	152.0	0.0		92.0	19.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	A	5.736	0.320178	0.10845	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.14022	2.96;2.96;2.54	5.25	3.94	0.45596	Apx/shroom, ASD2 (2);	0.146353	0.45867	D	0.000329	T	0.06462	0.0166	N	0.14661	0.345	0.28172	N	0.928549	B	0.06786	0.001	B	0.04013	0.001	T	0.22556	-1.0213	10	0.23302	T	0.38	.	4.3338	0.11076	0.4994:0.1515:0.0:0.3492	.	1260	Q9ULL8	SHRM4_HUMAN	L	1260;1260;1144	ENSP00000289292:F1260L;ENSP00000365188:F1260L;ENSP00000421450:F1144L	ENSP00000289292:F1260L	F	-	1	0	SHROOM4	50362537	0.997000	0.39634	1.000000	0.80357	0.118000	0.20060	0.898000	0.28404	1.869000	0.54173	0.417000	0.27973	TTT	.	.		0.448	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
HUWE1	10075	hgsc.bcm.edu	37	X	53563161	53563161	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:53563161G>C	ENST00000342160.3	-	79	12935	c.12478C>G	c.(12478-12480)Ctg>Gtg	p.L4160V	HUWE1_ENST00000262854.6_Missense_Mutation_p.L4160V			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4160	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TTTTCCAGCAGATAAACCAGA	0.453																																					p.L4160V		Atlas-SNP	.											.	HUWE1	724	.	0			c.C12478G						.						184.0	127.0	146.0					X																	53563161		2203	4300	6503	SO:0001583	missense	10075	exon80			CCAGCAGATAAAC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12478C>G	chrX.hg19:g.53563161G>C	ENSP00000340648:p.Leu4160Val	294.0	0.0		253.0	56.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.795|7.795	0.712448|0.712448	0.15306|0.15306	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854|ENST00000427052;ENST00000426907	T;T|.	0.63913|.	-0.07;-0.07|.	5.57|5.57	2.79|2.79	0.32731|0.32731	HECT (4);|.	0.000000|.	0.64402|.	D|.	0.000005|.	T|T	0.58481|0.58481	0.2125|0.2125	M|M	0.64170|0.64170	1.965|1.965	0.58432|0.58432	D|D	0.999998|0.999998	B;B|.	0.26363|.	0.073;0.147|.	B;B|.	0.33339|.	0.162;0.153|.	T|T	0.53507|0.53507	-0.8429|-0.8429	10|5	0.72032|.	D|.	0.01|.	.|.	5.4803|5.4803	0.16719|0.16719	0.2399:0.0:0.611:0.1491|0.2399:0.0:0.611:0.1491	.|.	4160;4144|.	Q7Z6Z7;Q7Z6Z7-2|.	HUWE1_HUMAN;.|.	V|C	4160|3193;982	ENSP00000340648:L4160V;ENSP00000262854:L4160V|.	ENSP00000262854:L4160V|.	L|S	-|-	1|2	2|0	HUWE1|HUWE1	53579886|53579886	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.495000|0.495000	0.33615|0.33615	1.850000|1.850000	0.39328|0.39328	0.624000|0.624000	0.30286|0.30286	-0.232000|-0.232000	0.12228|0.12228	CTG|TCT	.	.		0.453	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
ITIH6	347365	hgsc.bcm.edu	37	X	54823434	54823434	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:54823434G>A	ENST00000218436.6	-	2	227	c.198C>T	c.(196-198)gcC>gcT	p.A66A		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	66	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										TGGCTTCATGGGCTTCAGCAT	0.463													G|||	1	0.000264901	0.0	0.0	3775	,	,		15237	0.0		0.0	False		,,,				2504	0.001				p.A66A		Atlas-SNP	.											.	.	.	.	0			c.C198T						.						173.0	129.0	144.0					X																	54823434		2203	4300	6503	SO:0001819	synonymous_variant	347365	exon2			TTCATGGGCTTCA	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.198C>T	chrX.hg19:g.54823434G>A		333.0	0.0		342.0	14.0	NM_198510	A6NN03	Silent	SNP	ENST00000218436.6	hg19	CCDS14361.1																																																																																			.	.		0.463	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
SPIN4	139886	hgsc.bcm.edu	37	X	62570078	62570078	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:62570078A>G	ENST00000335144.3	-	1	1140	c.621T>C	c.(619-621)caT>caC	p.H207H	SPIN4_ENST00000374884.2_Silent_p.H189H|SPIN4-AS1_ENST00000451979.1_RNA	NM_001012968.2	NP_001012986.2	Q56A73	SPIN4_HUMAN	spindlin family, member 4	207					gamete generation (GO:0007276)					endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	11						CATCTTTGGCATGCTCCACCT	0.453																																					p.H207H		Atlas-SNP	.											.	SPIN4	29	.	0			c.T621C						.						113.0	109.0	110.0					X																	62570078		1978	4141	6119	SO:0001819	synonymous_variant	139886	exon1			TTTGGCATGCTCC	AK126931	CCDS43964.1	Xq11.1	2008-02-05			ENSG00000186767	ENSG00000186767			27040	protein-coding gene	gene with protein product						12477932	Standard	NM_001012968		Approved	FLJ44984	uc004dvf.3	Q56A73	OTTHUMG00000021696	ENST00000335144.3:c.621T>C	chrX.hg19:g.62570078A>G		239.0	0.0		192.0	44.0	NM_001012968	B3KX90|Q5JUL2	Silent	SNP	ENST00000335144.3	hg19	CCDS43964.1																																																																																			.	.		0.453	SPIN4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001012968	
FOXO4	4303	hgsc.bcm.edu	37	X	70320820	70320820	+	Missense_Mutation	SNP	G	G	A	rs367715683		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:70320820G>A	ENST00000374259.3	+	2	1072	c.740G>A	c.(739-741)cGt>cAt	p.R247H	FOXO4_ENST00000341558.3_Missense_Mutation_p.R192H	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	247					cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					TCTCGAAACCGTGAAGAAGCC	0.592											OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000264901	0.0	0.0	3775	,	,		12575	0.0		0.0	False		,,,				2504	0.001				p.R247H		Atlas-SNP	.											.	FOXO4	60	.	0			c.G740A						.	G	HIS/ARG,HIS/ARG	0,3458		0,0,1444,570	33.0	33.0	33.0		575,740	1.1	0.0	X		33	1,6538		0,1,2363,1811	no	missense,missense	FOXO4	NM_001170931.1,NM_005938.3	29,29	0,1,3807,2381	AA,AG,GG,G		0.0153,0.0,0.01	probably-damaging,probably-damaging	192/451,247/506	70320820	1,9996	2014	4175	6189	SO:0001583	missense	4303	exon2			GAAACCGTGAAGA		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"""Forkhead boxes"""	7139	protein-coding gene	gene with protein product		300033	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"""	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.740G>A	chrX.hg19:g.70320820G>A	ENSP00000363377:p.Arg247His	140.0	0.0	1121	116.0	30.0	NM_005938	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Missense_Mutation	SNP	ENST00000374259.3	hg19	CCDS43969.1	.	.	.	.	.	.	.	.	.	.	G	5.289	0.238767	0.10023	0.0	1.53E-4	ENSG00000184481	ENST00000374259;ENST00000341558	D;D	0.95554	-3.52;-3.74	5.11	1.14	0.20703	.	0.942857	0.08838	N	0.886220	D	0.89687	0.6787	N	0.22421	0.69	0.09310	N	1	B;B;B	0.10296	0.0;0.003;0.0	B;B;B	0.06405	0.0;0.002;0.001	T	0.80044	-0.1547	10	0.52906	T	0.07	-14.3609	5.4224	0.16407	0.2997:0.4218:0.2784:0.0	.	247;192;247	B4DTB6;P98177-2;P98177	.;.;FOXO4_HUMAN	H	247;192	ENSP00000363377:R247H;ENSP00000342209:R192H	ENSP00000342209:R192H	R	+	2	0	FOXO4	70237545	0.002000	0.14202	0.009000	0.14445	0.731000	0.41821	0.603000	0.24149	0.191000	0.20236	0.519000	0.50382	CGT	.	.		0.592	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938	
CYSLTR1	10800	hgsc.bcm.edu	37	X	77528233	77528233	+	Silent	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:77528233T>C	ENST00000373304.3	-	3	1303	c.1011A>G	c.(1009-1011)gtA>gtG	p.V337V		NM_001282187.1|NM_001282188.1|NM_006639.3	NP_001269116.1|NP_001269117.1|NP_006630.1	Q9Y271	CLTR1_HUMAN	cysteinyl leukotriene receptor 1	337					defense response (GO:0006952)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory gaseous exchange (GO:0007585)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene receptor activity (GO:0004974)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14					Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549)	GTTTAAACTATACTTTACATA	0.308																																					p.V337V		Atlas-SNP	.											.	CYSLTR1	59	.	0			c.A1011G						.						58.0	54.0	56.0					X																	77528233		2193	4295	6488	SO:0001819	synonymous_variant	10800	exon3			AAACTATACTTTA	AF119711	CCDS14439.1	Xq13-q21	2012-08-10			ENSG00000173198	ENSG00000173198		"""GPCR / Class A : Leukotriene receptors"""	17451	protein-coding gene	gene with protein product		300201				10391245, 10462554	Standard	NM_006639		Approved	CysLT1, CysLT(1), CYSLT1R	uc004edb.3	Q9Y271	OTTHUMG00000021889	ENST00000373304.3:c.1011A>G	chrX.hg19:g.77528233T>C		166.0	0.0		122.0	22.0	NM_006639	B2R954|D3DTE4|Q5JS94|Q8IV19	Silent	SNP	ENST00000373304.3	hg19	CCDS14439.1																																																																																			.	.		0.308	CYSLTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057315.1		
CYLC1	1538	hgsc.bcm.edu	37	X	83129239	83129239	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:83129239A>G	ENST00000329312.4	+	4	1560	c.1523A>G	c.(1522-1524)gAt>gGt	p.D508G		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	508					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						TCAAAGAAAGATATCAAGAAG	0.348																																					p.D508G		Atlas-SNP	.											.	CYLC1	272	.	0			c.A1523G						.						83.0	73.0	76.0					X																	83129239		2202	4299	6501	SO:0001583	missense	1538	exon4			AGAAAGATATCAA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"""cylicin 1"""	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1523A>G	chrX.hg19:g.83129239A>G	ENSP00000331556:p.Asp508Gly	142.0	0.0		92.0	27.0	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	hg19	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	a	8.594	0.885227	0.17540	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.52754	0.65	3.16	0.613	0.17597	.	.	.	.	.	T	0.35335	0.0928	L	0.50333	1.59	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12156	0.007;0.005	T	0.27640	-1.0068	9	0.32370	T	0.25	.	2.9178	0.05759	0.5928:0.2586:0.1487:0.0	.	508;508	P35663;F5H4V5	CYLC1_HUMAN;.	G	508	ENSP00000331556:D508G	ENSP00000331556:D508G	D	+	2	0	CYLC1	83015895	0.102000	0.21896	0.000000	0.03702	0.003000	0.03518	1.542000	0.36137	0.024000	0.15214	0.486000	0.48141	GAT	.	.		0.348	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118	
PCDH11X	27328	hgsc.bcm.edu	37	X	91133861	91133861	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:91133861G>C	ENST00000373094.1	+	2	3467	c.2622G>C	c.(2620-2622)aaG>aaC	p.K874N	PCDH11X_ENST00000395337.2_Missense_Mutation_p.K874N|PCDH11X_ENST00000298274.8_Missense_Mutation_p.K874N|PCDH11X_ENST00000406881.1_Missense_Mutation_p.K874N|PCDH11X_ENST00000361655.2_Missense_Mutation_p.K874N|PCDH11X_ENST00000373097.1_Missense_Mutation_p.K874N|PCDH11X_ENST00000504220.2_Missense_Mutation_p.K874N|PCDH11X_ENST00000361724.1_Missense_Mutation_p.K874N|PCDH11X_ENST00000373088.1_Missense_Mutation_p.K874N	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	874	Poly-Lys.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						aaaagaagaagaagCATTCCC	0.398																																					p.K874N	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.G2622C						.						77.0	71.0	73.0					X																	91133861		2203	4300	6503	SO:0001583	missense	27328	exon2			GAAGAAGAAGCAT	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.2622G>C	chrX.hg19:g.91133861G>C	ENSP00000362186:p.Lys874Asn	502.0	1.0		455.0	94.0	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.224235	0.39300	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06	4.86	4.0	0.46444	Protocadherin (1);	0.121275	0.53938	D	0.000050	T	0.59115	0.2170	M	0.67953	2.075	0.39692	D	0.971066	D;D;D;D;D;D;D;D	0.71674	0.995;0.997;0.997;0.997;0.997;0.998;0.995;0.995	P;D;D;D;D;D;P;P	0.72338	0.905;0.947;0.962;0.962;0.962;0.977;0.905;0.905	T	0.60747	-0.7202	10	0.46703	T	0.11	.	11.2437	0.48985	0.0931:0.0:0.9069:0.0	.	874;874;874;874;874;874;874;874	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	N	874	ENSP00000378746:K874N;ENSP00000362186:K874N;ENSP00000362189:K874N;ENSP00000355040:K874N;ENSP00000362180:K874N;ENSP00000423762:K874N;ENSP00000355105:K874N;ENSP00000384758:K874N;ENSP00000298274:K874N	ENSP00000298274:K874N	K	+	3	2	PCDH11X	91020517	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	5.989000	0.70587	0.953000	0.37825	0.600000	0.82982	AAG	.	.		0.398	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
ARL13A	392509	hgsc.bcm.edu	37	X	100240896	100240896	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:100240896C>A	ENST00000450049.2	+	4	484	c.371C>A	c.(370-372)cCc>cAc	p.P124H		NM_001162491.1	NP_001155963.1	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13A	124					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(1)|ovary(1)	2						GCAGGGAAACCCATCTTAATG	0.443																																					p.P124H		Atlas-SNP	.											.	ARL13A	7	.	0			c.C371A						.						52.0	46.0	48.0					X																	100240896		1911	4118	6029	SO:0001583	missense	392509	exon4			GGAAACCCATCTT		CCDS55463.1	Xq22.1	2014-05-09	2005-11-18	2005-11-18	ENSG00000174225	ENSG00000174225		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31709	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 13"""	ARL13			Standard	NM_001162491		Approved		uc011mrf.2	Q5H913	OTTHUMG00000022013	ENST00000450049.2:c.371C>A	chrX.hg19:g.100240896C>A	ENSP00000398637:p.Pro124His	65.0	0.0		53.0	12.0	NM_001162490	B2RTT6|B4DX50	Missense_Mutation	SNP	ENST00000450049.2	hg19	CCDS55463.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.556021	0.65425	.	.	ENSG00000174225	ENST00000450049	D	0.85258	-1.96	4.44	4.44	0.53790	.	0.050939	0.85682	D	0.000000	D	0.94145	0.8122	H	0.96048	3.76	0.44807	D	0.997813	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94886	0.8043	10	0.72032	D	0.01	.	11.4066	0.49902	0.0:1.0:0.0:0.0	.	124;124	B2RTT6;Q5H913	.;AR13A_HUMAN	H	124	ENSP00000398637:P124H	ENSP00000398637:P124H	P	+	2	0	ARL13A	100127552	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	3.203000	0.51075	2.464000	0.83262	0.594000	0.82650	CCC	.	.		0.443	ARL13A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000057504.2	XM_373358	
NRK	203447	hgsc.bcm.edu	37	X	105179196	105179196	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:105179196A>G	ENST00000243300.9	+	21	3837	c.3534A>G	c.(3532-3534)tcA>tcG	p.S1178S	NRK_ENST00000428173.2_Silent_p.S1179S	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1178					activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						CTGAGGAATCACCTAAGCAAC	0.403										HNSCC(51;0.14)																											p.S1178S		Atlas-SNP	.											.	NRK	321	.	0			c.A3534G						.						214.0	188.0	196.0					X																	105179196		1899	4117	6016	SO:0001819	synonymous_variant	203447	exon21			GGAATCACCTAAG	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.3534A>G	chrX.hg19:g.105179196A>G		104.0	0.0		94.0	12.0	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Silent	SNP	ENST00000243300.9	hg19																																																																																				.	.		0.403	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
MORC4	79710	hgsc.bcm.edu	37	X	106185319	106185319	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:106185319C>A	ENST00000355610.4	-	16	2783	c.2509G>T	c.(2509-2511)Gct>Tct	p.A837S	MORC4_ENST00000255495.7_Missense_Mutation_p.A837S|MORC4_ENST00000535534.1_Missense_Mutation_p.A585S	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	837						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						TGGAATTCAGCTTGGCGATAA	0.443																																					p.A837S		Atlas-SNP	.											.	MORC4	155	.	0			c.G2509T						.						238.0	199.0	213.0					X																	106185319		2203	4300	6503	SO:0001583	missense	79710	exon16			ATTCAGCTTGGCG	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.2509G>T	chrX.hg19:g.106185319C>A	ENSP00000347821:p.Ala837Ser	181.0	0.0		119.0	26.0	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	hg19	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	c	18.82	3.704564	0.68615	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.53857	2.62;0.6;1.92	5.4	5.4	0.78164	.	0.206970	0.34802	N	0.003677	T	0.62502	0.2433	L	0.59436	1.845	0.33796	D	0.626066	D;D;D	0.69078	0.997;0.997;0.979	D;D;P	0.75020	0.985;0.985;0.581	T	0.62973	-0.6740	10	0.02654	T	1	-11.638	13.4865	0.61369	0.0:1.0:0.0:0.0	.	585;837;837	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	S	837;585;837	ENSP00000347821:A837S;ENSP00000440359:A585S;ENSP00000255495:A837S	ENSP00000255495:A837S	A	-	1	0	MORC4	106071975	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.282000	0.58971	2.250000	0.74265	0.455000	0.32223	GCT	.	.		0.443	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
DOCK11	139818	hgsc.bcm.edu	37	X	117752606	117752606	+	Missense_Mutation	SNP	A	A	G	rs112023398		TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:117752606A>G	ENST00000276202.7	+	31	3449	c.3386A>G	c.(3385-3387)gAc>gGc	p.D1129G	DOCK11_ENST00000276204.6_Missense_Mutation_p.D1129G	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1129					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						GCTCTTCAGGACAATTATGAG	0.363																																					p.D1129G		Atlas-SNP	.											.	DOCK11	185	.	0			c.A3386G						.						105.0	89.0	95.0					X																	117752606		2203	4297	6500	SO:0001583	missense	139818	exon31			TTCAGGACAATTA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.3386A>G	chrX.hg19:g.117752606A>G	ENSP00000276202:p.Asp1129Gly	325.0	0.0		256.0	57.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.064692	0.55432	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	D;D	0.96459	-4.02;-4.02	5.68	5.68	0.88126	.	0.181876	0.52532	D	0.000069	D	0.91901	0.7436	N	0.17312	0.475	0.44570	D	0.997535	B;B	0.34161	0.439;0.439	B;B	0.33521	0.165;0.165	D	0.91313	0.5076	10	0.40728	T	0.16	-9.5385	15.0808	0.72113	1.0:0.0:0.0:0.0	.	1129;1129	A6NIW2;Q5JSL3	.;DOC11_HUMAN	G	1129	ENSP00000276204:D1129G;ENSP00000276202:D1129G	ENSP00000276202:D1129G	D	+	2	0	DOCK11	117636634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.778000	0.55371	2.012000	0.59069	0.441000	0.28932	GAC	.	A|0.500;G|0.500		0.363	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
ZNF280C	55609	hgsc.bcm.edu	37	X	129349772	129349772	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:129349772T>A	ENST00000370978.4	-	14	1984	c.1831A>T	c.(1831-1833)Aac>Tac	p.N611Y		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	611					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						TACCTTATGTTCTTCAAAGCA	0.313																																					p.N611Y		Atlas-SNP	.											.	ZNF280C	63	.	0			c.A1831T						.						145.0	131.0	136.0					X																	129349772		2203	4300	6503	SO:0001583	missense	55609	exon14			TTATGTTCTTCAA	AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 3 (Drosophila)"""	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1831A>T	chrX.hg19:g.129349772T>A	ENSP00000360017:p.Asn611Tyr	82.0	0.0		78.0	14.0	NM_017666	A8K2V8|Q9NXR3	Missense_Mutation	SNP	ENST00000370978.4	hg19	CCDS14622.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.617575	0.46736	.	.	ENSG00000056277	ENST00000066465;ENST00000370978;ENST00000447817	T;T	0.06068	4.13;3.35	5.06	3.81	0.43845	.	.	.	.	.	T	0.18841	0.0452	M	0.72894	2.215	0.21967	N	0.999441	D;P	0.55172	0.97;0.923	P;P	0.62184	0.899;0.762	T	0.03344	-1.1046	9	0.62326	D	0.03	.	8.1169	0.30948	0.1824:0.0:0.0:0.8176	.	562;611	Q9UJJ2;Q8ND82	.;Z280C_HUMAN	Y	562;611;562	ENSP00000360017:N611Y;ENSP00000408521:N562Y	ENSP00000066465:N562Y	N	-	1	0	ZNF280C	129177453	1.000000	0.71417	0.993000	0.49108	0.422000	0.31414	2.283000	0.43470	1.689000	0.51079	0.347000	0.21830	AAC	.	.		0.313	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666	
FRMD7	90167	hgsc.bcm.edu	37	X	131212020	131212020	+	Silent	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:131212020G>A	ENST00000298542.4	-	12	2200	c.2025C>T	c.(2023-2025)gcC>gcT	p.A675A	FRMD7_ENST00000370879.1_Silent_p.A555A|FRMD7_ENST00000464296.1_Silent_p.A660A	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	675					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					GGCGGATTCTGGCCATGGGTG	0.408																																					p.A675A		Atlas-SNP	.											.	FRMD7	69	.	0			c.C2025T						.						128.0	117.0	120.0					X																	131212020		2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			GATTCTGGCCATG	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.2025C>T	chrX.hg19:g.131212020G>A		433.0	0.0		346.0	49.0	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	hg19	CCDS35397.1																																																																																			.	.		0.408	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
RBMX	27316	hgsc.bcm.edu	37	X	135957309	135957309	+	Silent	SNP	A	A	G			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:135957309A>G	ENST00000320676.7	-	8	955	c.801T>C	c.(799-801)ggT>ggC	p.G267G	RBMX_ENST00000565438.1_Silent_p.G139G|RBMX_ENST00000431446.3_Missense_Mutation_p.V159A|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000562646.1_Silent_p.G267G|RBMX_ENST00000570135.1_Silent_p.G132G	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	267					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CACGATCACGACCATATCCAT	0.388																																					p.V159A		Atlas-SNP	.											.	RBMX	149	.	0			c.T476C						.						169.0	162.0	164.0					X																	135957309		2203	4300	6503	SO:0001819	synonymous_variant	27316	exon6			ATCACGACCATAT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.801T>C	chrX.hg19:g.135957309A>G		183.0	0.0		141.0	23.0	NM_001164803	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	hg19	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	9.651	1.141524	0.21205	.	.	ENSG00000147274	ENST00000431446	T	0.07444	3.19	5.61	5.61	0.85477	.	.	.	.	.	T	0.07279	0.0184	.	.	.	0.80722	D	1	B	0.22276	0.067	B	0.17098	0.017	T	0.19549	-1.0302	8	0.87932	D	0	.	5.5363	0.17013	0.7132:0.1587:0.1281:0.0	.	159	B4E3U4	.	A	159	ENSP00000411989:V159A	ENSP00000411989:V159A	V	-	2	0	RBMX	135784975	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.576000	0.46033	1.989000	0.58080	0.486000	0.48141	GTC	.	.		0.388	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
MAMLD1	10046	hgsc.bcm.edu	37	X	149638231	149638231	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:149638231T>C	ENST00000370401.2	+	4	696	c.386T>C	c.(385-387)tTa>tCa	p.L129S	MAMLD1_ENST00000262858.5_Missense_Mutation_p.L129S|MAMLD1_ENST00000455522.2_5'Flank|MAMLD1_ENST00000432680.2_Missense_Mutation_p.L104S|MAMLD1_ENST00000426613.2_Missense_Mutation_p.L104S|MAMLD1_ENST00000468306.1_3'UTR			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	129					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					GGCCAGTCATTACTGCTGGAG	0.517																																					p.L129S		Atlas-SNP	.											.	MAMLD1	263	.	0			c.T386C						.						85.0	77.0	80.0					X																	149638231		2203	4300	6503	SO:0001583	missense	10046	exon3			AGTCATTACTGCT	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.386T>C	chrX.hg19:g.149638231T>C	ENSP00000359428:p.Leu129Ser	130.0	0.0		141.0	19.0	NM_005491	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	hg19	CCDS14693.2	.	.	.	.	.	.	.	.	.	.	T	9.822	1.185984	0.21870	.	.	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000358892;ENST00000262858;ENST00000426613	T;T;T;T	0.70164	-0.06;-0.46;-0.06;-0.06	5.36	4.17	0.49024	.	0.202399	0.30383	N	0.009744	T	0.67813	0.2933	L	0.54323	1.7	0.25087	N	0.990884	P;D;P;D	0.56746	0.763;0.959;0.904;0.977	B;P;P;P	0.53593	0.288;0.647;0.625;0.73	T	0.58418	-0.7640	10	0.16896	T	0.51	-3.1352	10.9972	0.47582	0.1415:0.0:0.0:0.8585	.	91;104;104;129	F6WVG1;Q13495-4;Q13495-3;Q13495	.;.;.;MAMD1_HUMAN	S	91;129;104;129;129;104	ENSP00000359428:L129S;ENSP00000414517:L104S;ENSP00000262858:L129S;ENSP00000397438:L104S	ENSP00000262858:L129S	L	+	2	0	MAMLD1	149388889	0.081000	0.21417	0.001000	0.08648	0.004000	0.04260	1.883000	0.39658	0.650000	0.30769	0.486000	0.48141	TTA	.	.		0.517	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491	
IRAK1	3654	hgsc.bcm.edu	37	X	153284220	153284220	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:153284220C>T	ENST00000369980.3	-	5	726	c.559G>A	c.(559-561)Gtg>Atg	p.V187M	IRAK1_ENST00000393687.2_Missense_Mutation_p.V187M|IRAK1_ENST00000429936.2_Missense_Mutation_p.V213M|IRAK1_ENST00000393682.1_Missense_Mutation_p.V213M|MIR718_ENST00000390190.2_RNA|IRAK1_ENST00000369974.2_Missense_Mutation_p.V187M|IRAK1_ENST00000477274.1_5'Flank	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	187	ProST region.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGGAGGGACACTGAGCTCTCT	0.637																																					p.V187M		Atlas-SNP	.											.	IRAK1	107	.	0			c.G559A						.						27.0	27.0	27.0					X																	153284220		2202	4294	6496	SO:0001583	missense	3654	exon5			GGGACACTGAGCT	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.559G>A	chrX.hg19:g.153284220C>T	ENSP00000358997:p.Val187Met	190.0	0.0		192.0	28.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Missense_Mutation	SNP	ENST00000369980.3	hg19	CCDS14740.1	.	.	.	.	.	.	.	.	.	.	.	9.937	1.216444	0.22373	.	.	ENSG00000184216	ENST00000369980;ENST00000369974;ENST00000393682;ENST00000393687;ENST00000429936	T;T;T;T;T	0.74315	-0.83;-0.83;-0.79;-0.8;-0.82	3.82	-0.987	0.10249	Protein kinase-like domain (1);	1.564670	0.04105	N	0.313659	T	0.58293	0.2112	N	0.22421	0.69	0.09310	N	1	B;B;B	0.26081	0.141;0.049;0.081	B;B;B	0.21151	0.03;0.015;0.033	T	0.43147	-0.9409	10	0.38643	T	0.18	-0.1308	5.2916	0.15729	0.0:0.4002:0.3677:0.2321	.	187;187;187	P51617-4;P51617;P51617-2	.;IRAK1_HUMAN;.	M	187;187;213;187;213	ENSP00000358997:V187M;ENSP00000358991:V187M;ENSP00000377287:V213M;ENSP00000377291:V187M;ENSP00000392662:V213M	ENSP00000358990:V213M	V	-	1	0	IRAK1	152937414	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.090000	0.11163	-0.126000	0.11682	0.529000	0.55759	GTG	.	.		0.637	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3		
FLNA	2316	hgsc.bcm.edu	37	X	153580981	153580981	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrX:153580981G>T	ENST00000369850.3	-	40	6678	c.6442C>A	c.(6442-6444)Cgt>Agt	p.R2148S	FLNA_ENST00000369856.3_Missense_Mutation_p.R281S|FLNA_ENST00000344736.4_Missense_Mutation_p.R2108S|FLNA_ENST00000498491.1_5'Flank|FLNA_ENST00000360319.4_Missense_Mutation_p.R2140S|FLNA_ENST00000422373.1_Missense_Mutation_p.R2140S	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	2148					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGAGCCCGACGCCTGCGGGTG	0.637																																					p.R2148S		Atlas-SNP	.											.	FLNA	373	.	0			c.C6442A						.						37.0	38.0	38.0					X																	153580981		1951	4131	6082	SO:0001583	missense	2316	exon40			CCCGACGCCTGCG	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.6442C>A	chrX.hg19:g.153580981G>T	ENSP00000358866:p.Arg2148Ser	228.0	0.0		162.0	28.0	NM_001110556	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	hg19	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.338146	0.24253	.	.	ENSG00000196924	ENST00000360319;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736	D;D;D;T;D	0.86366	-2.1;-2.1;-2.11;-0.81;-2.1	5.64	3.89	0.44902	.	0.075157	0.50627	D	0.000117	D	0.83142	0.5190	M	0.64997	1.995	0.45390	D	0.998375	B;B;B;B	0.26975	0.006;0.01;0.165;0.165	B;B;B;B	0.29716	0.012;0.018;0.106;0.106	T	0.75419	-0.3324	10	0.33940	T	0.23	.	6.6402	0.22904	0.1591:0.0:0.6565:0.1844	.	281;2140;2148;2148	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	S	2140;2140;2148;281;2108	ENSP00000353467:R2140S;ENSP00000416926:R2140S;ENSP00000358866:R2148S;ENSP00000358872:R281S;ENSP00000358863:R2108S	ENSP00000358863:R2108S	R	-	1	0	FLNA	153234175	0.008000	0.16893	1.000000	0.80357	0.785000	0.44390	0.602000	0.24134	0.564000	0.29238	-0.305000	0.09177	CGT	.	.		0.637	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
MT-ND5	4540	hgsc.bcm.edu	37	M	13267	13267	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chrM:13267G>A	ENST00000361567.2	+	1	931	c.931G>A	c.(931-933)Gga>Aga	p.G311R	MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TR_ENST00000387439.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	311					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CAAGTCAACTAGGACTCATAA	0.458																																					p.G311X		Atlas-SNP	.											.	.	.	.	0			c.G931A						.																																			SO:0001583	missense	0	exon1			CAACTAGGACTCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.931G>A	chrM.hg19:g.13267G>A	ENSP00000354813:p.Gly311Arg	48.0	0.0		14.0	11.0	ENST00000361567	Q34773|Q8WCY3	Nonsense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.458	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
CDHR1	92211	hgsc.bcm.edu	37	10	85972935	85972935	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr10:85972935delC	ENST00000372117.3	+	16	1974	c.1871delC	c.(1870-1872)tccfs	p.S624fs	CDHR1_ENST00000332904.3_Frame_Shift_Del_p.S624fs|CDHR1_ENST00000440770.2_Frame_Shift_Del_p.S328fs	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	624	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						GACATCAATTCCCACACGGGG	0.577																																					p.S624fs		Atlas-Indel,Pindel	.											.	CDHR1	122	.	0			c.1870delT						.						120.0	106.0	111.0					10																	85972935		2203	4300	6503	SO:0001589	frameshift_variant	92211	exon16			.	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1871delC	chr10.hg19:g.85972935delC	ENSP00000361189:p.Ser624fs	155.0	0.0		163.0	54.0	NM_001171971	Q69YZ8|Q8IXY5	Frame_Shift_Del	DEL	ENST00000372117.3	hg19	CCDS7372.1																																																																																			.	.		0.577	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
PRKCB	5579	hgsc.bcm.edu	37	16	24202416	24202416	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:24202416delG	ENST00000321728.7	+	16	1903	c.1728delG	c.(1726-1728)atgfs	p.M576fs	PRKCB_ENST00000303531.7_Frame_Shift_Del_p.M576fs	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	576	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	CGAAGCTGATGACCAAACACC	0.403																																					p.M576fs		Atlas-Indel,Pindel	.											.	PRKCB	383	.	0			c.1727delT						.						79.0	78.0	78.0					16																	24202416		2197	4300	6497	SO:0001589	frameshift_variant	5579	exon16			.	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1728delG	chr16.hg19:g.24202416delG	ENSP00000318315:p.Met576fs	118.0	0.0		97.0	29.0	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Frame_Shift_Del	DEL	ENST00000321728.7	hg19	CCDS10618.1																																																																																			.	.		0.403	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
CDH15	1013	hgsc.bcm.edu	37	16	89256907	89256907	+	Intron	DEL	G	G	-			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr16:89256907delG	ENST00000289746.2	+	8	1297					NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)						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)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		AGGCTCAGGTGGGGCTCCTGA	0.672																																					.		Atlas-Indel,Pindel	.											.	CDH15	54	.	0			c.1232+2G>-						.						10.0	11.0	11.0					16																	89256907		2184	4283	6467	SO:0001627	intron_variant	1013	exon8			.	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.1232+3G>-	chr16.hg19:g.89256907delG		38.0	0.0		35.0	14.0	NM_004933		Splice_Site	DEL	ENST00000289746.2	hg19	CCDS10976.1																																																																																			.	.		0.672	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
CACNA1B	774	hgsc.bcm.edu	37	9	140880973	140880973	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr9:140880973delG	ENST00000371372.1	+	14	2023	c.1878delG	c.(1876-1878)ctgfs	p.L626fs	CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371355.4_Frame_Shift_Del_p.L627fs|CACNA1B_ENST00000277551.2_Frame_Shift_Del_p.L626fs|CACNA1B_ENST00000371363.1_Frame_Shift_Del_p.L626fs|CACNA1B_ENST00000371357.1_Frame_Shift_Del_p.L627fs	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	626					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TCGCCCTGCTGGGGATGCAGC	0.612																																					p.L626fs		Atlas-Indel,Pindel	.											.	CACNA1B	266	.	0			c.1877delT						.						52.0	54.0	53.0					9																	140880973		2065	4229	6294	SO:0001589	frameshift_variant	774	exon14			.	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1878delG	chr9.hg19:g.140880973delG	ENSP00000360423:p.Leu626fs	165.0	0.0		183.0	62.0	NM_001243812	B1AQK5	Frame_Shift_Del	DEL	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.		0.612	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110401347	110401347	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr8:110401347delT	ENST00000378402.5	+	8	767	c.663delT	c.(661-663)ggtfs	p.G221fs		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	221	IPT/TIG 2.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAGATATGGGTTCTATGGTTT	0.313										HNSCC(38;0.096)																											p.G221fs		Atlas-Indel,Pindel	.											.	PKHD1L1	522	.	0			c.662delG						.						203.0	195.0	197.0					8																	110401347		1849	4087	5936	SO:0001589	frameshift_variant	93035	exon8			.	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.663delT	chr8.hg19:g.110401347delT	ENSP00000367655:p.Gly221fs	130.0	0.0		142.0	26.0	NM_177531	Q567P2|Q9UF27	Frame_Shift_Del	DEL	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.313	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
RPS9	6203	hgsc.bcm.edu	37	19	54705416	54705416	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr19:54705416delC	ENST00000302907.4	+	3	331	c.159delC	c.(157-159)atcfs	p.I53fs	RPS9_ENST00000402367.1_Frame_Shift_Del_p.I53fs|RPS9_ENST00000391752.1_Frame_Shift_Del_p.I53fs|RPS9_ENST00000391753.2_Frame_Shift_Del_p.I53fs|RPS9_ENST00000441429.1_Frame_Shift_Del_p.I53fs|AC012314.20_ENST00000426213.1_RNA|RPS9_ENST00000391751.3_Frame_Shift_Del_p.I53fs	NM_001013.3	NP_001004.2	P46781	RS9_HUMAN	ribosomal protein S9	53					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of cell proliferation (GO:0008284)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			NS(1)|breast(1)|kidney(11)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	20	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.18)		TGGCCAAGATCCGCAAGGCCG	0.607																																					p.I53fs		Atlas-Indel,Pindel	.											.	RPS9	27	.	0			c.158delT						.						38.0	35.0	36.0					19																	54705416		2203	4300	6503	SO:0001589	frameshift_variant	6203	exon3			.	U14971	CCDS12884.1	19q13.4	2011-04-05			ENSG00000170889	ENSG00000170889		"""S ribosomal proteins"""	10442	protein-coding gene	gene with protein product	"""40S ribosomal protein S9"""	603631				7772601, 9582194	Standard	XM_005259135		Approved	S9	uc002qdx.3	P46781	OTTHUMG00000066618	ENST00000302907.4:c.159delC	chr19.hg19:g.54705416delC	ENSP00000302896:p.Ile53fs	71.0	0.0		122.0	36.0	NM_001013	A9C4C1|Q4QRK7|Q9BVZ0	Frame_Shift_Del	DEL	ENST00000302907.4	hg19	CCDS12884.1																																																																																			.	.		0.607	RPS9-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142834.3	NM_001013	
SEMA6A	57556	hgsc.bcm.edu	37	5	115838016	115838016	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A9-01A-11D-A25V-10	TCGA-DD-A3A9-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	96517058-18d2-4847-8085-768ca8aa1565	790941e2-4315-4425-9eeb-9b3ae2377bcb	g.chr5:115838016delT	ENST00000343348.6	-	3	895	c.108delA	c.(106-108)aaafs	p.K36fs	SEMA6A_ENST00000257414.8_Frame_Shift_Del_p.K36fs|SEMA6A_ENST00000503962.1_5'UTR|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000510263.1_Frame_Shift_Del_p.K36fs	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	36	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		CCGGATACTGTTTTGTATCTG	0.493																																					p.Q37fs		Pindel	.											.	SEMA6A	93	.	0			c.109delC						.						168.0	163.0	165.0					5																	115838016		1986	4167	6153	SO:0001589	frameshift_variant	57556	exon3			.	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.108delA	chr5.hg19:g.115838016delT	ENSP00000345512:p.Lys36fs	296.0	0.0		323.0	53.0	NM_020796	Q9P2H9	Frame_Shift_Del	DEL	ENST00000343348.6	hg19	CCDS47256.1																																																																																			.	.		0.493	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
