#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
CDA	978	hgsc.bcm.edu	37	1	20940339	20940339	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:20940339A>G	ENST00000375071.3	+	3	453	c.271A>G	c.(271-273)Atg>Gtg	p.M91V	CDA_ENST00000461985.1_Intron	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	91	CMP/dCMP deaminase zinc-binding.				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)	CCCCAGTGACATGCAAGATGA	0.468																																					p.M91V	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.A271G						.						133.0	111.0	119.0					1																	20940339		2203	4300	6503	SO:0001583	missense	978	exon3			AGTGACATGCAAG	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.271A>G	chr1.hg19:g.20940339A>G	ENSP00000364212:p.Met91Val	80.0	0.0		68.0	6.0	NM_001785		Missense_Mutation	SNP	ENST00000375071.3	hg19	CCDS210.1	.	.	.	.	.	.	.	.	.	.	A	1.698	-0.502234	0.04261	.	.	ENSG00000158825	ENST00000375071	T	0.41065	1.01	5.38	-10.1	0.00402	APOBEC/CMP deaminase, zinc-binding (1);Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.426630	0.24182	N	0.040793	T	0.10637	0.0260	N	0.12422	0.21	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.42515	-0.9447	10	0.02654	T	1	.	1.7827	0.03035	0.3143:0.3583:0.1065:0.2208	.	91	P32320	CDD_HUMAN	V	91	ENSP00000364212:M91V	ENSP00000364212:M91V	M	+	1	0	CDA	20812926	0.000000	0.05858	0.894000	0.35097	0.770000	0.43624	-4.067000	0.00302	-1.137000	0.02888	-0.669000	0.03829	ATG	.	.		0.468	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785	
LRRC7	57554	hgsc.bcm.edu	37	1	70300494	70300494	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:70300494C>T	ENST00000035383.5	+	4	448	c.418C>T	c.(418-420)Ctg>Ttg	p.L140L	LRRC7_ENST00000370958.1_Silent_p.L178L|LRRC7_ENST00000310961.5_Silent_p.L145L|LRRC7_ENST00000415775.2_5'UTR	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	140						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						GCTCCTAAACCTGACCCAGCT	0.348																																					p.L140L		Atlas-SNP	.											.	LRRC7	400	.	0			c.C418T						.						156.0	146.0	149.0					1																	70300494		2203	4300	6503	SO:0001819	synonymous_variant	57554	exon4			CTAAACCTGACCC		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.418C>T	chr1.hg19:g.70300494C>T		96.0	0.0		106.0	18.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	hg19	CCDS645.1																																																																																			.	.		0.348	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794	
LRRC53	100144878	hgsc.bcm.edu	37	1	74957809	74957809	+	Intron	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:74957809G>A	ENST00000294635.4	-	2	89				TNNI3K_ENST00000370891.2_Missense_Mutation_p.S838N|TNNI3K_ENST00000326637.3_Missense_Mutation_p.S737N|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.S851N			A6NM62	LRC53_HUMAN	leucine rich repeat containing 53							integral component of membrane (GO:0016021)				NS(1)|breast(1)|lung(2)	4						AGTAACAGCAGTGGGTCTCTC	0.463																																					p.S838N		Atlas-SNP	.											.	.	.	.	0			c.G2513A						.						203.0	204.0	203.0					1																	74957809		2203	4300	6503	SO:0001627	intron_variant	100526835	exon25			ACAGCAGTGGGTC			1p31.3	2010-08-31			ENSG00000162621	ENSG00000162621			25255	protein-coding gene	gene with protein product							Standard			Approved			A6NM62	OTTHUMG00000009621	ENST00000294635.4:c.26-8750C>T	chr1.hg19:g.74957809G>A		151.0	0.0		117.0	29.0	NM_001112808		Missense_Mutation	SNP	ENST00000294635.4	hg19		.	.	.	.	.	.	.	.	.	.	G	30	5.052662	0.93793	.	.	ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000557284;ENST00000370891;ENST00000326637	T;T;T	0.75050	-0.9;-0.9;-0.88	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.72309	0.3444	N	0.19112	0.55	0.58432	D	0.999995	D;D	0.67145	0.993;0.996	D;D	0.75484	0.968;0.986	T	0.69525	-0.5122	10	0.25106	T	0.35	.	19.8247	0.96612	0.0:0.0:1.0:0.0	.	737;838	Q59H18;Q59H18-1	TNI3K_HUMAN;.	N	838;838;737	ENSP00000450895:S838N;ENSP00000359928:S838N;ENSP00000322251:S737N	ENSP00000322251:S737N	S	+	2	0	RP11-653A5.2;AC093158.1	74730397	1.000000	0.71417	0.991000	0.47740	0.954000	0.61252	5.987000	0.70571	2.696000	0.92011	0.655000	0.94253	AGT	.	.		0.463	LRRC53-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000026515.2		
IGSF3	3321	hgsc.bcm.edu	37	1	117156546	117156546	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:117156546C>T	ENST00000369486.3	-	4	1438	c.673G>A	c.(673-675)Ggg>Agg	p.G225R	IGSF3_ENST00000369483.1_Missense_Mutation_p.G225R|IGSF3_ENST00000318837.6_Missense_Mutation_p.G225R	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	225	Ig-like C2-type 2.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GTGGTCCTCCCCAGCTTGTCC	0.627																																					p.G225R		Atlas-SNP	.											.	IGSF3	294	.	0			c.G673A						.						34.0	34.0	34.0					1																	117156546		2202	4295	6497	SO:0001583	missense	3321	exon4			TCCTCCCCAGCTT	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.673G>A	chr1.hg19:g.117156546C>T	ENSP00000358498:p.Gly225Arg	138.0	0.0		124.0	27.0	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069490	0.76301	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.22539	1.95;1.95;1.95	4.77	4.77	0.60923	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054090	0.85682	D	0.000000	T	0.38374	0.1038	M	0.75085	2.285	0.46336	D	0.99899	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.17198	-1.0377	10	0.52906	T	0.07	-49.4997	15.3267	0.74168	0.0:1.0:0.0:0.0	.	225;225	O75054;A6NJZ6	IGSF3_HUMAN;.	R	225	ENSP00000358498:G225R;ENSP00000358495:G225R;ENSP00000321184:G225R	ENSP00000321184:G225R	G	-	1	0	IGSF3	116958069	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.743000	0.47442	2.470000	0.83445	0.557000	0.71058	GGG	.	.		0.627	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144868126	144868126	+	Silent	SNP	G	G	A	rs369950064		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:144868126G>A	ENST00000369354.3	-	33	5502	c.5313C>T	c.(5311-5313)aaC>aaT	p.N1771N	PDE4DIP_ENST00000313382.9_Silent_p.N1665N|PDE4DIP_ENST00000369359.4_Silent_p.N1907N|PDE4DIP_ENST00000369356.4_Silent_p.N1771N|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Silent_p.N1856N|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1771					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)		CTTCCAAGTCGTTGCTCAGCA	0.522			T	PDGFRB	MPD								.|||	1	0.000199681	0.0	0.0	5008	,	,		37801	0.0		0.0	False		,,,				2504	0.001				p.N1771N		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C5313T						.	G	,,	0,4406		0,0,2203	123.0	127.0	126.0		4995,5313,5313	1.1	0.1	1		126	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	,,	1665/2241,1771/2363,1771/2347	144868126	1,12997	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon33			CAAGTCGTTGCTC	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.5313C>T	chr1.hg19:g.144868126G>A		99.0	0.0		185.0	9.0	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.		0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
TCHH	7062	hgsc.bcm.edu	37	1	152080721	152080721	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152080721C>T	ENST00000368804.1	-	2	4971	c.4972G>A	c.(4972-4974)Gaa>Aaa	p.E1658K		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1658	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCTGTTGTTCGCGCTCCTGG	0.607																																					p.E1658K		Atlas-SNP	.											.	TCHH	275	.	0			c.G4972A						.						68.0	69.0	69.0					1																	152080721		1905	4126	6031	SO:0001583	missense	7062	exon3			GTTGTTCGCGCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4972G>A	chr1.hg19:g.152080721C>T	ENSP00000357794:p.Glu1658Lys	114.0	0.0		232.0	24.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.409197	0.25378	.	.	ENSG00000159450	ENST00000368804	T	0.08282	3.11	3.47	3.47	0.39725	.	.	.	.	.	T	0.08670	0.0215	M	0.73217	2.22	0.09310	N	1	D	0.71674	0.998	P	0.52856	0.711	T	0.18085	-1.0348	9	0.23302	T	0.38	-6.1047	12.459	0.55721	0.0:1.0:0.0:0.0	.	1658	Q07283	TRHY_HUMAN	K	1658	ENSP00000357794:E1658K	ENSP00000357794:E1658K	E	-	1	0	TCHH	150347345	0.001000	0.12720	0.010000	0.14722	0.029000	0.11900	0.018000	0.13422	1.790000	0.52503	0.411000	0.27672	GAA	.	.		0.607	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
IVL	3713	hgsc.bcm.edu	37	1	152882767	152882767	+	Missense_Mutation	SNP	A	A	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152882767A>C	ENST00000368764.3	+	2	558	c.494A>C	c.(493-495)cAc>cCc	p.H165P	IVL_ENST00000392667.2_Missense_Mutation_p.H19P			P07476	INVO_HUMAN	involucrin	165	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			cacctgaagcacctagagcag	0.602																																					p.H165P		Atlas-SNP	.											.	IVL	100	.	0			c.A494C						.						33.0	36.0	35.0					1																	152882767		2203	4300	6503	SO:0001583	missense	3713	exon2			TGAAGCACCTAGA	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.494A>C	chr1.hg19:g.152882767A>C	ENSP00000357753:p.His165Pro	244.0	1.0		402.0	177.0	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.272630	0.23221	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10668	3.08;2.85	3.42	-4.4	0.03600	.	.	.	.	.	T	0.01421	0.0046	N	0.24115	0.695	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.46925	-0.9156	9	0.28530	T	0.3	.	2.2701	0.04088	0.2656:0.4459:0.1055:0.183	.	165	P07476	INVO_HUMAN	P	165;19	ENSP00000357753:H165P;ENSP00000376435:H19P	ENSP00000357753:H165P	H	+	2	0	IVL	151149391	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.002000	0.03686	-0.886000	0.03966	-0.782000	0.03352	CAC	.	.		0.602	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
IVL	3713	hgsc.bcm.edu	37	1	152883444	152883444	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152883444G>A	ENST00000368764.3	+	2	1235	c.1171G>A	c.(1171-1173)Ggg>Agg	p.G391R	IVL_ENST00000392667.2_Missense_Mutation_p.G245R			P07476	INVO_HUMAN	involucrin	391	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggaggaggaggggcagctgaa	0.657																																					p.G391R		Atlas-SNP	.											.	IVL	100	.	0			c.G1171A						.																																			SO:0001583	missense	3713	exon2			GAGGAGGGGCAGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1171G>A	chr1.hg19:g.152883444G>A	ENSP00000357753:p.Gly391Arg	131.0	0.0		235.0	19.0	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	hg19	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.855193	0.32791	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.24538	2.13;1.85	4.22	-8.45	0.00946	.	.	.	.	.	T	0.03220	0.0094	N	0.24115	0.695	0.09310	N	1	B	0.21905	0.062	B	0.21360	0.034	T	0.33624	-0.9861	9	0.16896	T	0.51	.	5.757	0.18178	0.2041:0.5081:0.1987:0.0892	.	391	P07476	INVO_HUMAN	R	391;245	ENSP00000357753:G391R;ENSP00000376435:G245R	ENSP00000357753:G391R	G	+	1	0	IVL	151150068	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.922000	0.28734	-1.815000	0.01222	-0.309000	0.09137	GGG	.	.		0.657	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
CKS1B	1163	hgsc.bcm.edu	37	1	154950543	154950543	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:154950543G>A	ENST00000308987.5	+	2	187	c.140G>A	c.(139-141)gGc>gAc	p.G47D	CKS1B_ENST00000368436.1_Missense_Mutation_p.G47D|CKS1B_ENST00000368439.1_Missense_Mutation_p.G31D|CKS1B_ENST00000471245.1_3'UTR|MIR4258_ENST00000580920.1_RNA	NM_001826.2	NP_001817.1	P61024	CKS1_HUMAN	CDC28 protein kinase regulatory subunit 1B	47					cell division (GO:0051301)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|large_intestine(1)|lung(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AGGAATCTTGGCGTTCAGCAG	0.468																																					p.G47D		Atlas-SNP	.											.	CKS1B	5	.	0			c.G140A						.						66.0	60.0	63.0					1																	154950543		2203	4297	6500	SO:0001583	missense	1163	exon2			ATCTTGGCGTTCA	BC007751	CCDS1077.1	1q21.2	2011-04-28	2002-10-07		ENSG00000173207	ENSG00000173207			19083	protein-coding gene	gene with protein product		116900	"""CDC28 protein kinase 1B"""			2227411	Standard	NM_001826		Approved	ckshs1, CKS1	uc001fgb.3	P61024	OTTHUMG00000037413	ENST00000308987.5:c.140G>A	chr1.hg19:g.154950543G>A	ENSP00000311083:p.Gly47Asp	125.0	0.0		188.0	27.0	NM_001826	P33551	Missense_Mutation	SNP	ENST00000308987.5	hg19	CCDS1077.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448626	0.96205	.	.	ENSG00000173207	ENST00000368439;ENST00000368436;ENST00000308987	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.81814	0.4902	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82261	-0.0545	8	0.87932	D	0	.	19.6509	0.95805	0.0:0.0:1.0:0.0	.	47	P61024	CKS1_HUMAN	D	31;47;47	.	ENSP00000311083:G47D	G	+	2	0	CKS1B	153217167	1.000000	0.71417	0.970000	0.41538	0.971000	0.66376	9.256000	0.95535	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.468	CKS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091078.1	NM_001826	
SPTA1	6708	hgsc.bcm.edu	37	1	158646066	158646066	+	Missense_Mutation	SNP	T	T	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:158646066T>G	ENST00000368147.4	-	8	1157	c.977A>C	c.(976-978)aAa>aCa	p.K326T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	326					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTTCTCTGCTTTAGCACATAA	0.478																																					p.K326T		Atlas-SNP	.											.	SPTA1	720	.	0			c.A977C						.						192.0	180.0	184.0					1																	158646066		1919	4136	6055	SO:0001583	missense	6708	exon8			TCTGCTTTAGCAC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.977A>C	chr1.hg19:g.158646066T>G	ENSP00000357129:p.Lys326Thr	82.0	0.0		149.0	15.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205185	0.79127	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.46819	0.86;0.86	5.24	5.24	0.73138	.	0.000000	0.34067	N	0.004297	T	0.27098	0.0664	L	0.28556	0.865	0.44660	D	0.997644	P	0.36495	0.556	B	0.41917	0.37	T	0.08827	-1.0703	10	0.25751	T	0.34	.	14.1225	0.65198	0.0:0.0:0.0:1.0	.	326	P02549	SPTA1_HUMAN	T	326	ENSP00000357130:K326T;ENSP00000357129:K326T	ENSP00000357129:K326T	K	-	2	0	SPTA1	156912690	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.129000	0.64739	2.186000	0.69663	0.533000	0.62120	AAA	.	.		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
NR1I3	9970	hgsc.bcm.edu	37	1	161205749	161205749	+	Missense_Mutation	SNP	G	G	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:161205749G>C	ENST00000367982.4	-	3	281	c.126C>G	c.(124-126)agC>agG	p.S42R	NR1I3_ENST00000504010.1_Missense_Mutation_p.S13R|NR1I3_ENST00000367983.4_Missense_Mutation_p.S42R|NR1I3_ENST00000428574.2_Missense_Mutation_p.S42R|NR1I3_ENST00000367985.3_Missense_Mutation_p.S42R|NR1I3_ENST00000437437.2_Missense_Mutation_p.S13R|NR1I3_ENST00000412844.2_Missense_Mutation_p.S13R|NR1I3_ENST00000515452.1_Missense_Mutation_p.S42R|NR1I3_ENST00000506209.1_Missense_Mutation_p.S13R|NR1I3_ENST00000508387.1_Missense_Mutation_p.S13R|NR1I3_ENST00000515621.1_5'UTR|NR1I3_ENST00000502985.1_Missense_Mutation_p.S42R|NR1I3_ENST00000511748.1_Missense_Mutation_p.S13R|NR1I3_ENST00000511676.1_Missense_Mutation_p.S13R|NR1I3_ENST00000367984.4_Missense_Mutation_p.S42R|NR1I3_ENST00000442691.2_Missense_Mutation_p.S42R|NR1I3_ENST00000367979.2_Missense_Mutation_p.S42R|NR1I3_ENST00000505005.1_Missense_Mutation_p.S42R|NR1I3_ENST00000367980.2_Missense_Mutation_p.S42R|NR1I3_ENST00000511944.1_Missense_Mutation_p.S42R|NR1I3_ENST00000512372.1_Missense_Mutation_p.S13R|NR1I3_ENST00000508740.1_Missense_Mutation_p.S13R|NR1I3_ENST00000367981.3_Missense_Mutation_p.S13R			Q14994	NR1I3_HUMAN	nuclear receptor subfamily 1, group I, member 3	42					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor activity (GO:0004882)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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 transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	15	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TGGGACCAATGCTTTTGCTGA	0.532																																					p.S42R		Atlas-SNP	.											.	NR1I3	74	.	0			c.C126G						.						91.0	82.0	85.0					1																	161205749		2203	4300	6503	SO:0001583	missense	9970	exon3			ACCAATGCTTTTG	Z30425	CCDS1228.1, CCDS41427.1, CCDS41428.1, CCDS41429.1, CCDS41430.1, CCDS44260.1, CCDS44261.1, CCDS44262.1, CCDS53405.1, CCDS53406.1, CCDS53407.1, CCDS53408.1, CCDS53409.1, CCDS53410.1, CCDS53411.1	1q23.3	2013-01-16			ENSG00000143257	ENSG00000143257		"""Nuclear hormone receptors"""	7969	protein-coding gene	gene with protein product	"""constitutive androstane receptor"""	603881				8114692	Standard	NM_001077480		Approved	MB67, CAR1, CAR	uc001fzp.3	Q14994	OTTHUMG00000034347	ENST00000367982.4:c.126C>G	chr1.hg19:g.161205749G>C	ENSP00000356961:p.Ser42Arg	69.0	0.0		125.0	7.0	NM_005122	E9PB75|E9PC13|E9PDU3|E9PGH6|E9PH10|E9PHC8|E9PHN4|F1D8Q0|F1D8Q1|Q0VAC9|Q4U0F0|Q5VTW5|Q5VTW6|Q6GZ68|Q6GZ76|Q6GZ77|Q6GZ78|Q6GZ79|Q6GZ82|Q6GZ83|Q6GZ84|Q6GZ85|Q6GZ87|Q6GZ89	Missense_Mutation	SNP	ENST00000367982.4	hg19	CCDS41430.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.053648	0.36277	.	.	ENSG00000143257	ENST00000512372;ENST00000367983;ENST00000367980;ENST00000437437;ENST00000442691;ENST00000412844;ENST00000428574;ENST00000505005;ENST00000508740;ENST00000367982;ENST00000508387;ENST00000504010;ENST00000511676;ENST00000502985;ENST00000367981;ENST00000511944;ENST00000511748;ENST00000367984;ENST00000367985;ENST00000367979;ENST00000506209;ENST00000515452	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0	5.33	-2.65	0.06095	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	1.262690	0.04830	N	0.438628	D	0.90577	0.7046	L	0.43152	1.355	0.32520	N	0.536328	B;B;P;B;P;B;B;B;P;B;P;B;B;P;B;P;B;P;P	0.50443	0.071;0.27;0.584;0.036;0.714;0.172;0.172;0.172;0.584;0.259;0.935;0.172;0.43;0.714;0.172;0.585;0.298;0.584;0.584	B;B;B;B;B;B;B;B;B;B;P;B;B;B;B;P;B;B;B	0.49953	0.156;0.315;0.438;0.062;0.34;0.188;0.188;0.188;0.345;0.133;0.627;0.188;0.111;0.438;0.142;0.487;0.111;0.34;0.345	D	0.83977	0.0330	9	0.62326	D	0.03	.	1.96	0.03384	0.3158:0.1734:0.3963:0.1145	.	42;13;13;42;42;42;42;42;42;13;42;42;13;13;13;13;13;13;42	B7Z8R7;E9PCF2;E9PHN4;Q6GZ85;E9PHC8;Q0VAC9;F1D8Q1;Q14994;E9PC13;Q6GZ70;Q6GZ72;Q4U0F0;Q6GZ87;E9PDU3;Q6GZ68;E9PH10;Q6GZ84;E9PGH6;E9PB75	.;.;.;.;.;.;.;NR1I3_HUMAN;.;.;.;.;.;.;.;.;.;.;.	R	13;42;42;13;42;13;42;42;13;42;13;13;13;42;13;42;13;42;42;42;13;42	ENSP00000425417:S13R;ENSP00000356962:S42R;ENSP00000356959:S42R;ENSP00000407446:S13R;ENSP00000406493:S42R;ENSP00000399361:S13R;ENSP00000412672:S42R;ENSP00000424934:S42R;ENSP00000423666:S13R;ENSP00000356961:S42R;ENSP00000422982:S13R;ENSP00000424345:S13R;ENSP00000427175:S13R;ENSP00000421374:S42R;ENSP00000356960:S13R;ENSP00000426292:S42R;ENSP00000427600:S13R;ENSP00000356963:S42R;ENSP00000356965:S42R;ENSP00000356958:S42R;ENSP00000423089:S13R;ENSP00000427034:S42R	ENSP00000356958:S42R	S	-	3	2	NR1I3	159472373	0.000000	0.05858	0.000000	0.03702	0.329000	0.28539	-0.424000	0.07025	0.005000	0.14708	-0.373000	0.07131	AGC	.	.		0.532	NR1I3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083048.2		
MAEL	84944	hgsc.bcm.edu	37	1	166958660	166958660	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:166958660G>A	ENST00000367872.4	+	1	315	c.71G>A	c.(70-72)cGa>cAa	p.R24Q	MAEL_ENST00000367870.2_Missense_Mutation_p.R24Q	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	24					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						GAACTACGGCGACGAGGCCTG	0.612																																					p.R24Q		Atlas-SNP	.											.	MAEL	95	.	0			c.G71A						.						46.0	38.0	41.0					1																	166958660		2203	4298	6501	SO:0001583	missense	84944	exon1			TACGGCGACGAGG	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"""cancer/testis antigen 128"", ""spermatogenesis associated 35"""	611368	"""maelstrom homolog (Drosophila)"""			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.71G>A	chr1.hg19:g.166958660G>A	ENSP00000356846:p.Arg24Gln	84.0	0.0		160.0	18.0	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	hg19	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839097	0.32513	.	.	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.14640	2.49;2.49;2.49	5.49	4.58	0.56647	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);Domain of unknown function DUF1898 (1);	0.341713	0.25106	N	0.033093	T	0.03095	0.0091	N	0.14661	0.345	0.41059	D	0.985363	B;B	0.33103	0.341;0.397	B;B	0.26416	0.05;0.069	T	0.44174	-0.9345	10	0.31617	T	0.26	.	13.113	0.59285	0.0775:0.0:0.9225:0.0	.	24;24	E9JVC3;Q96JY0	.;MAEL_HUMAN	Q	24	ENSP00000356846:R24Q;ENSP00000356844:R24Q;ENSP00000402143:R24Q	ENSP00000356844:R24Q	R	+	2	0	MAEL	165225284	0.912000	0.30974	0.565000	0.28409	0.198000	0.23893	1.982000	0.40638	1.562000	0.49601	0.655000	0.94253	CGA	.	.		0.612	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858	
FAM129A	116496	hgsc.bcm.edu	37	1	184801016	184801016	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:184801016C>T	ENST00000367511.3	-	6	875	c.682G>A	c.(682-684)Ggt>Agt	p.G228S	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	228					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						TCCCAGGAACCATAGTGACCC	0.423																																					p.G228S		Atlas-SNP	.											.	FAM129A	98	.	0			c.G682A						.						111.0	108.0	109.0					1																	184801016		2203	4300	6503	SO:0001583	missense	116496	exon6			AGGAACCATAGTG	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.682G>A	chr1.hg19:g.184801016C>T	ENSP00000356481:p.Gly228Ser	190.0	0.0		275.0	29.0	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	hg19	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	C	33	5.287556	0.95517	.	.	ENSG00000135842	ENST00000367511	T	0.17691	2.26	5.61	5.61	0.85477	.	0.153223	0.64402	D	0.000015	T	0.45357	0.1338	M	0.77313	2.365	0.51233	D	0.999915	D	0.89917	1.0	D	0.97110	1.0	T	0.29181	-1.0020	10	0.52906	T	0.07	-27.5979	17.7743	0.88502	0.0:1.0:0.0:0.0	.	228	Q9BZQ8	NIBAN_HUMAN	S	228	ENSP00000356481:G228S	ENSP00000356481:G228S	G	-	1	0	FAM129A	183067639	1.000000	0.71417	0.990000	0.47175	0.989000	0.77384	5.999000	0.70665	2.793000	0.96121	0.655000	0.94253	GGT	.	.		0.423	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
TRIM67	440730	hgsc.bcm.edu	37	1	231299711	231299711	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:231299711C>T	ENST00000366653.5	+	1	996	c.996C>T	c.(994-996)caC>caT	p.H332H	TRIM67_ENST00000366652.2_Silent_p.H332H|TRIM67_ENST00000449018.3_Silent_p.H270H|TRIM67_ENST00000444294.3_Silent_p.H332H			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	332					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				AGGGCCGGCACGCCAAGCACG	0.632																																					p.H332H		Atlas-SNP	.											.	TRIM67	160	.	0			c.C996T						.						16.0	19.0	18.0					1																	231299711		2047	4196	6243	SO:0001819	synonymous_variant	440730	exon1			CCGGCACGCCAAG	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.996C>T	chr1.hg19:g.231299711C>T		108.0	0.0		174.0	35.0	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	hg19	CCDS44333.1																																																																																			.	.		0.632	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
WDR33	55339	hgsc.bcm.edu	37	2	128480544	128480544	+	Missense_Mutation	SNP	G	G	T	rs200713285		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:128480544G>T	ENST00000322313.4	-	13	1524	c.1366C>A	c.(1366-1368)Caa>Aaa	p.Q456K		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	456					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		ATCTGTTCTTGTTCCATAGCT	0.328																																					p.Q456K		Atlas-SNP	.											.	WDR33	136	.	0			c.C1366A						.						135.0	120.0	125.0					2																	128480544		2203	4300	6503	SO:0001583	missense	55339	exon13			GTTCTTGTTCCAT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.1366C>A	chr2.hg19:g.128480544G>T	ENSP00000325377:p.Gln456Lys	144.0	0.0		147.0	29.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.786664	0.70337	.	.	ENSG00000136709	ENST00000322313	D	0.88818	-2.43	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.90710	0.7085	L	0.36672	1.1	0.80722	D	1	P	0.49447	0.924	P	0.59424	0.857	D	0.89556	0.3803	10	0.34782	T	0.22	-10.532	18.7096	0.91651	0.0:0.0:1.0:0.0	.	456	Q9C0J8	WDR33_HUMAN	K	456	ENSP00000325377:Q456K	ENSP00000325377:Q456K	Q	-	1	0	WDR33	128197014	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.155000	0.94700	2.484000	0.83849	0.650000	0.86243	CAA	.	G|1.000;C|0.000		0.328	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
MAP2	4133	hgsc.bcm.edu	37	2	210560690	210560690	+	Silent	SNP	A	A	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:210560690A>C	ENST00000360351.4	+	7	4302	c.3796A>C	c.(3796-3798)Agg>Cgg	p.R1266R	MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Silent_p.R1262R|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1266					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CTCAGGTGCCAGGGAGGAATT	0.483																																					p.R1266R	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A3796C						.						119.0	122.0	121.0					2																	210560690		2203	4300	6503	SO:0001819	synonymous_variant	4133	exon7			GGTGCCAGGGAGG		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3796A>C	chr2.hg19:g.210560690A>C		111.0	0.0		130.0	22.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.		0.483	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
CPS1	1373	hgsc.bcm.edu	37	2	211525234	211525234	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:211525234C>T	ENST00000233072.5	+	32	3978	c.3782C>T	c.(3781-3783)tCt>tTt	p.S1261F	CPS1_ENST00000451903.2_Missense_Mutation_p.S810F|CPS1_ENST00000430249.2_Missense_Mutation_p.S1267F	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1261	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TTGAGAGCTTCTCGATCCTTC	0.398																																					p.S1267F		Atlas-SNP	.											.	CPS1	485	.	0			c.C3800T						.						271.0	249.0	257.0					2																	211525234		2203	4300	6503	SO:0001583	missense	1373	exon33			GAGCTTCTCGATC	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3782C>T	chr2.hg19:g.211525234C>T	ENSP00000233072:p.Ser1261Phe	143.0	0.0		121.0	26.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934509	0.92458	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.98313	-4.86;-4.86;-4.86	5.98	5.98	0.97165	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.99090	4.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97880	1.0291	10	0.72032	D	0.01	-10.4337	20.4434	0.99119	0.0:1.0:0.0:0.0	.	1271;1261	Q59HF8;P31327	.;CPSM_HUMAN	F	1267;1269;1261;810	ENSP00000402608:S1267F;ENSP00000233072:S1261F;ENSP00000406136:S810F	ENSP00000233072:S1261F	S	+	2	0	CPS1	211233479	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.398000	0.79919	2.838000	0.97847	0.655000	0.94253	TCT	.	.		0.398	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
AZI2	64343	hgsc.bcm.edu	37	3	28382058	28382058	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:28382058G>A	ENST00000479665.1	-	2	582	c.51C>T	c.(49-51)gcC>gcT	p.A17A	AZI2_ENST00000457172.1_Silent_p.A17A|AZI2_ENST00000334100.6_Silent_p.A17A|AZI2_ENST00000295748.3_5'UTR|AZI2_ENST00000420543.2_Silent_p.A17A	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	17	Homodimerization. {ECO:0000250}.				dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						CTCTCTTATGGGCTTTTTCAT	0.348																																					p.A17A		Atlas-SNP	.											.	AZI2	33	.	0			c.C51T						.						103.0	106.0	105.0					3																	28382058		2203	4300	6503	SO:0001819	synonymous_variant	64343	exon2			CTTATGGGCTTTT	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.51C>T	chr3.hg19:g.28382058G>A		208.0	0.0		194.0	43.0	NM_001134432	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Silent	SNP	ENST00000479665.1	hg19	CCDS2647.1																																																																																			.	.		0.348	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326	
RBMS3	27303	hgsc.bcm.edu	37	3	29938929	29938929	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:29938929C>T	ENST00000383767.2	+	9	1187	c.851C>T	c.(850-852)aCg>aTg	p.T284M	RBMS3_ENST00000273139.9_Missense_Mutation_p.T284M|RBMS3_ENST00000396583.3_Missense_Mutation_p.T297M|RBMS3_ENST00000452462.1_Missense_Mutation_p.T284M|RBMS3_ENST00000434693.2_Missense_Mutation_p.T283M|RBMS3_ENST00000383766.2_Missense_Mutation_p.T283M|RBMS3_ENST00000456853.1_Missense_Mutation_p.T297M			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	284					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				ACATCTATCACGCCATTCATT	0.418																																					p.T297M		Atlas-SNP	.											RBMS3_ENST00000383767,NS,carcinoma,0,1	RBMS3	62	.	0			c.C890T						.						277.0	251.0	260.0					3																	29938929		2203	4300	6503	SO:0001583	missense	27303	exon10			CTATCACGCCATT	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"""RNA binding motif (RRM) containing"""	13427	protein-coding gene	gene with protein product	"""RNA-binding protein"""	605786	"""RNA binding motif, single stranded interacting protein"""			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.851C>T	chr3.hg19:g.29938929C>T	ENSP00000373277:p.Thr284Met	110.0	0.0		103.0	20.0	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Missense_Mutation	SNP	ENST00000383767.2	hg19	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.914916	0.92178	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	T;T;T;T;T;T;T	0.27402	1.71;1.67;1.71;1.71;1.79;1.7;1.68	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.44456	0.1294	L	0.39633	1.23	0.80722	D	1	P;D;D;P	0.63046	0.614;0.992;0.992;0.679	B;P;P;B	0.60286	0.228;0.872;0.872;0.174	T	0.15809	-1.0424	9	.	.	.	.	18.754	0.91825	0.0:1.0:0.0:0.0	.	284;297;283;284	G5E9J9;Q6XE24-2;Q6XE24-3;Q6XE24	.;.;.;RBMS3_HUMAN	M	283;297;284;284;283;284;297	ENSP00000395592:T283M;ENSP00000379828:T297M;ENSP00000373277:T284M;ENSP00000273139:T284M;ENSP00000373276:T283M;ENSP00000397926:T284M;ENSP00000400519:T297M	.	T	+	2	0	RBMS3	29913933	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.433000	0.82419	0.655000	0.94253	ACG	.	.		0.418	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266113	41266113	+	Missense_Mutation	SNP	C	C	T	rs121913416|rs121913403		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:41266113C>T	ENST00000349496.5	+	3	390	c.110C>T	c.(109-111)tCt>tTt	p.S37F	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37F(172)|p.S37C(141)|p.A5_A80del(53)|p.S37Y(31)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGAATCCATTCTGGTGCCACT	0.498	S37C(JHUEM2_ENDOMETRIUM)|S37C(SNU398_LIVER)|S37F(HUTU80_SMALL_INTESTINE)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.S37F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	474	Substitution - Missense(344)|Deletion - In frame(102)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(145)|endometrium(64)|stomach(38)|skin(34)|ovary(33)|central_nervous_system(28)|pancreas(28)|large_intestine(22)|pituitary(22)|lung(21)|biliary_tract(15)|thyroid(4)|soft_tissue(4)|urinary_tract(4)|small_intestine(3)|oesophagus(3)|adrenal_gland(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|breast(1)	c.C110T						.						93.0	78.0	83.0					3																	41266113		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCCATTCTGGTGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.110C>T	chr3.hg19:g.41266113C>T	ENSP00000344456:p.Ser37Phe	165.0	0.0		141.0	31.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513375	0.85389	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	-15.9763	19.9596	0.97236	0.0:1.0:0.0:0.0	.	37	P35222	CTNB1_HUMAN	F	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30F;ENSP00000385604:S37F;ENSP00000412219:S37F;ENSP00000379486:S37F;ENSP00000344456:S37F;ENSP00000411226:S30F;ENSP00000379488:S37F;ENSP00000409302:S37F;ENSP00000401599:S37F	ENSP00000344456:S37F	S	+	2	0	CTNNB1	41241117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
ULK4	54986	hgsc.bcm.edu	37	3	41831172	41831172	+	Missense_Mutation	SNP	T	T	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:41831172T>A	ENST00000301831.4	-	21	2636	c.2174A>T	c.(2173-2175)cAa>cTa	p.Q725L		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	725					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GATTAGTCTTTGAAGATGAAT	0.388																																					p.Q725L		Atlas-SNP	.											.	ULK4	150	.	0			c.A2174T						.						94.0	89.0	90.0					3																	41831172		1886	4109	5995	SO:0001583	missense	54986	exon21			AGTCTTTGAAGAT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2174A>T	chr3.hg19:g.41831172T>A	ENSP00000301831:p.Gln725Leu	113.0	0.0		123.0	24.0	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	hg19	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.021352	0.75275	.	.	ENSG00000168038	ENST00000301831	T	0.61274	0.12	5.91	5.91	0.95273	Armadillo-like helical (1);Armadillo-type fold (2);	0.206736	0.42053	U	0.000777	T	0.61986	0.2391	L	0.52573	1.65	0.80722	D	1	P;D	0.55172	0.947;0.97	P;P	0.50934	0.576;0.654	T	0.59532	-0.7437	10	0.31617	T	0.26	.	16.3453	0.83126	0.0:0.0:0.0:1.0	.	725;725	B4E2M4;Q96C45	.;ULK4_HUMAN	L	725	ENSP00000301831:Q725L	ENSP00000301831:Q725L	Q	-	2	0	ULK4	41806176	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	6.369000	0.73109	2.261000	0.74972	0.533000	0.62120	CAA	.	.		0.388	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
TOPAZ1	375337	hgsc.bcm.edu	37	3	44332377	44332377	+	Splice_Site	SNP	A	A	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:44332377A>C	ENST00000309765.4	+	12	3964	c.3796A>C	c.(3796-3798)Agg>Cgg	p.R1266R		NM_001145030.1	NP_001138502.1	Q8N9V7	TOPZ1_HUMAN	testis and ovary specific PAZ domain containing 1	1266						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)										AATGAAATCGAGGTGAGAAAA	0.353																																					p.R1266R		Atlas-SNP	.											.	.	.	.	0			c.A3796C						.						49.0	42.0	44.0					3																	44332377		692	1591	2283	SO:0001630	splice_region_variant	375337	exon12			AAATCGAGGTGAG	AK093476	CCDS46809.1	3p21.33	2012-10-08	2012-10-08	2012-10-08	ENSG00000173769	ENSG00000173769			24746	protein-coding gene	gene with protein product		614412	"""chromosome 3 open reading frame 77"""	C3orf77		22069478	Standard	NM_001145030		Approved	FLJ36157	uc003cna.4	Q8N9V7	OTTHUMG00000156172	ENST00000309765.4:c.3797+1A>C	chr3.hg19:g.44332377A>C		180.0	0.0		173.0	36.0	NM_001145030		Silent	SNP	ENST00000309765.4	hg19	CCDS46809.1																																																																																			.	.		0.353	TOPAZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343247.1	NM_001145030	Silent
LZTFL1	54585	hgsc.bcm.edu	37	3	45875746	45875746	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:45875746G>A	ENST00000296135.6	-	4	542	c.368C>T	c.(367-369)aCa>aTa	p.T123I	LZTFL1_ENST00000536047.1_Missense_Mutation_p.T106I|LZTFL1_ENST00000539217.1_Missense_Mutation_p.T119I|LZTFL1_ENST00000490463.1_5'UTR	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	123					establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		GTTTGAAGATGTAATCTCTGC	0.269																																					p.T123I		Atlas-SNP	.											.	LZTFL1	37	.	0			c.C368T						.						47.0	49.0	48.0					3																	45875746		2195	4294	6489	SO:0001583	missense	54585	exon4			GAAGATGTAATCT	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.368C>T	chr3.hg19:g.45875746G>A	ENSP00000296135:p.Thr123Ile	92.0	0.0		86.0	6.0	NM_020347	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Missense_Mutation	SNP	ENST00000296135.6	hg19	CCDS2731.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.776451	0.31411	.	.	ENSG00000163818	ENST00000296135;ENST00000536047;ENST00000539217	T;T;T	0.25749	1.78;1.78;1.78	5.96	2.17	0.27698	.	0.403999	0.31347	N	0.007802	T	0.24812	0.0602	L	0.59436	1.845	0.27164	N	0.961093	B	0.06786	0.001	B	0.09377	0.004	T	0.18053	-1.0349	10	0.52906	T	0.07	-8.0E-4	10.8925	0.47004	0.2517:0.0:0.7483:0.0	.	123	Q9NQ48	LZTL1_HUMAN	I	123;106;119	ENSP00000296135:T123I;ENSP00000439522:T106I;ENSP00000441784:T119I	ENSP00000296135:T123I	T	-	2	0	LZTFL1	45850750	0.990000	0.36364	0.868000	0.34077	0.726000	0.41606	0.497000	0.22514	0.120000	0.18254	-0.140000	0.14226	ACA	.	.		0.269	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347	
CCR3	1232	hgsc.bcm.edu	37	3	46307580	46307580	+	Missense_Mutation	SNP	T	T	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:46307580T>A	ENST00000357422.2	+	4	1474	c.931T>A	c.(931-933)Tac>Aac	p.Y311N	CCR3_ENST00000395940.2_Missense_Mutation_p.Y311N|CCR3_ENST00000541018.1_Missense_Mutation_p.Y311N|CCR3_ENST00000545097.1_Missense_Mutation_p.Y332N|CCR3_ENST00000395942.2_Missense_Mutation_p.Y311N			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	311					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		GTTCCGGAAGTACCTGCGCCA	0.552																																					p.Y332N		Atlas-SNP	.											.	CCR3	52	.	0			c.T994A						.						109.0	91.0	97.0					3																	46307580		2203	4300	6503	SO:0001583	missense	1232	exon3			CGGAAGTACCTGC	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.931T>A	chr3.hg19:g.46307580T>A	ENSP00000350003:p.Tyr311Asn	73.0	0.0		64.0	13.0	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	hg19	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.375870	0.24857	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21	5.55	0.263	0.15602	.	0.486738	0.18614	N	0.136063	T	0.36026	0.0952	M	0.69823	2.125	0.31785	N	0.630359	B;B	0.22541	0.071;0.042	B;B	0.32624	0.149;0.071	T	0.40459	-0.9562	10	0.72032	D	0.01	.	5.3126	0.15839	0.1281:0.3515:0.0:0.5204	.	332;311	F5GWL6;P51677	.;CCR3_HUMAN	N	311;332;311;311;311	ENSP00000350003:Y311N;ENSP00000441600:Y332N;ENSP00000440097:Y311N;ENSP00000379271:Y311N;ENSP00000379273:Y311N	ENSP00000350003:Y311N	Y	+	1	0	CCR3	46282584	0.011000	0.17503	0.611000	0.29010	0.350000	0.29205	-0.103000	0.10940	-0.186000	0.10533	-0.250000	0.11733	TAC	.	.		0.552	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2		
GBE1	2632	hgsc.bcm.edu	37	3	81630426	81630426	+	Splice_Site	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:81630426G>A	ENST00000429644.2	-	11	1979	c.1336C>T	c.(1336-1338)Cta>Tta	p.L446L	GBE1_ENST00000489715.1_Splice_Site_p.L405L	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	446					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		TCTTTAAGTAGCTAGACACAA	0.343									Glycogen Storage Disease, type IV																												p.L446L		Atlas-SNP	.											.	GBE1	111	.	0			c.C1336T						.						106.0	95.0	98.0					3																	81630426		1832	4088	5920	SO:0001630	splice_region_variant	2632	exon11	Familial Cancer Database	Andersen Disease, Brancher deficiency	TAAGTAGCTAGAC		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"""glycogen branching enzyme"", ""Andersen disease"", ""glycogen storage disease type IV"""	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.1336-1C>T	chr3.hg19:g.81630426G>A		77.0	0.0		86.0	9.0	NM_000158	B3KWV3|Q96EN0	Silent	SNP	ENST00000429644.2	hg19	CCDS54612.1																																																																																			.	.		0.343	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		Silent
EPHA3	2042	hgsc.bcm.edu	37	3	89528604	89528604	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:89528604C>T	ENST00000336596.2	+	17	3129	c.2904C>T	c.(2902-2904)agC>agT	p.S968S	EPHA3_ENST00000494014.1_3'UTR	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	968	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TCATCAGTAGCATTAAAGCTC	0.463										TSP Lung(6;0.00050)																											p.S968S		Atlas-SNP	.											.	EPHA3	501	.	0			c.C2904T						.						100.0	88.0	92.0					3																	89528604		2203	4300	6503	SO:0001819	synonymous_variant	2042	exon17			CAGTAGCATTAAA	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2904C>T	chr3.hg19:g.89528604C>T		292.0	0.0		314.0	13.0	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.463	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
PLOD2	5352	hgsc.bcm.edu	37	3	145824364	145824364	+	Missense_Mutation	SNP	A	A	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:145824364A>T	ENST00000360060.3	-	5	747	c.570T>A	c.(568-570)gaT>gaA	p.D190E	PLOD2_ENST00000494950.1_Missense_Mutation_p.D135E|PLOD2_ENST00000282903.5_Missense_Mutation_p.D190E|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	190					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	AGAGCTGATCATCATCATTAT	0.343																																					p.D190E		Atlas-SNP	.											.	PLOD2	81	.	0			c.T570A						.						161.0	159.0	159.0					3																	145824364		2203	4300	6503	SO:0001583	missense	5352	exon5			CTGATCATCATCA	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.570T>A	chr3.hg19:g.145824364A>T	ENSP00000353170:p.Asp190Glu	147.0	0.0		141.0	11.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.414748	0.83449	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950;ENST00000469350	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.24	-1.66	0.08265	.	0.000000	0.85682	D	0.000000	T	0.60431	0.2268	M	0.90595	3.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.987	D;D;D	0.91635	0.994;0.999;0.928	T	0.62478	-0.6846	10	0.87932	D	0	-20.3189	10.1756	0.42937	0.6636:0.0:0.3364:0.0	.	135;190;190	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	E	190;190;135;162	ENSP00000282903:D190E;ENSP00000353170:D190E;ENSP00000420094:D135E;ENSP00000419963:D162E	ENSP00000282903:D190E	D	-	3	2	PLOD2	147307054	0.920000	0.31207	0.984000	0.44739	0.998000	0.95712	0.164000	0.16542	-0.562000	0.06086	0.533000	0.62120	GAT	.	.		0.343	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
FNDC3B	64778	hgsc.bcm.edu	37	3	171944729	171944729	+	Missense_Mutation	SNP	A	A	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:171944729A>C	ENST00000336824.4	+	4	355	c.256A>C	c.(256-258)Atc>Ctc	p.I86L	FNDC3B_ENST00000415807.2_Missense_Mutation_p.I86L|FNDC3B_ENST00000416957.1_Missense_Mutation_p.I86L	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	86					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)		TCCAGGTTATATCTCACAGGT	0.443																																					p.I86L		Atlas-SNP	.											.	FNDC3B	118	.	0			c.A256C						.						145.0	130.0	135.0					3																	171944729		2203	4300	6503	SO:0001583	missense	64778	exon4			GGTTATATCTCAC	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.256A>C	chr3.hg19:g.171944729A>C	ENSP00000338523:p.Ile86Leu	82.0	0.0		104.0	27.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.590756	0.66219	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957;ENST00000443501	T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69	5.95	5.95	0.96441	.	0.043534	0.85682	D	0.000000	T	0.80523	0.4639	L	0.54323	1.7	0.80722	D	1	P;B	0.51147	0.942;0.435	D;B	0.64595	0.927;0.155	T	0.79541	-0.1761	10	0.42905	T	0.14	-25.5664	16.4237	0.83790	1.0:0.0:0.0:0.0	.	86;86	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	L	86;86;86;59	ENSP00000411242:I86L;ENSP00000338523:I86L;ENSP00000389094:I86L;ENSP00000389064:I59L	ENSP00000338523:I86L	I	+	1	0	FNDC3B	173427423	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.224000	0.65288	2.279000	0.76181	0.533000	0.62120	ATC	.	.		0.443	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
N4BP2	55728	hgsc.bcm.edu	37	4	40122641	40122641	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:40122641G>A	ENST00000261435.6	+	9	3326	c.2910G>A	c.(2908-2910)ggG>ggA	p.G970G		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	970					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AGAGTCATGGGCAACACACAT	0.418																																					p.G970G		Atlas-SNP	.											.	N4BP2	166	.	0			c.G2910A						.						87.0	85.0	86.0					4																	40122641		2203	4300	6503	SO:0001819	synonymous_variant	55728	exon9			TCATGGGCAACAC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2910G>A	chr4.hg19:g.40122641G>A		142.0	0.0		147.0	33.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Silent	SNP	ENST00000261435.6	hg19	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.902404	0.00512	.	.	ENSG00000078177	ENST00000513269	.	.	.	4.99	-3.09	0.05331	.	.	.	.	.	T	0.17450	0.0419	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25572	-1.0128	4	.	.	.	0.0169	0.5399	0.00644	0.3149:0.2013:0.2877:0.1962	.	.	.	.	T	617	.	.	A	+	1	0	N4BP2	39799036	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.765000	0.04730	-0.437000	0.07243	0.655000	0.94253	GCA	.	.		0.418	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
AFM	173	hgsc.bcm.edu	37	4	74357714	74357714	+	Silent	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:74357714A>G	ENST00000226355.3	+	8	1062	c.969A>G	c.(967-969)ccA>ccG	p.P323P		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	323	Albumin 2. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATGATAGACCAAAGGATTTAT	0.378																																					p.P323P		Atlas-SNP	.											.	AFM	101	.	0			c.A969G						.						82.0	85.0	84.0					4																	74357714		2203	4300	6503	SO:0001819	synonymous_variant	173	exon8			TAGACCAAAGGAT	L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.969A>G	chr4.hg19:g.74357714A>G		472.0	0.0		400.0	92.0	NM_001133	A8K3E1|Q32MR3|Q4W5C5	Silent	SNP	ENST00000226355.3	hg19	CCDS3557.1																																																																																			.	.		0.378	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2		
PTPN13	5783	hgsc.bcm.edu	37	4	87556471	87556471	+	Missense_Mutation	SNP	T	T	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:87556471T>C	ENST00000411767.2	+	2	125	c.62T>C	c.(61-63)aTa>aCa	p.I21T	PTPN13_ENST00000427191.2_Missense_Mutation_p.I21T|PTPN13_ENST00000436978.1_Missense_Mutation_p.I21T|PTPN13_ENST00000316707.6_Missense_Mutation_p.I21T|PTPN13_ENST00000511467.1_Missense_Mutation_p.I21T|PTPN13_ENST00000502971.1_Missense_Mutation_p.I21T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	21	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GAGGAAGAAATATGGGCTGTA	0.453																																					p.I21T		Atlas-SNP	.											.	PTPN13	203	.	0			c.T62C						.						61.0	63.0	63.0					4																	87556471		1928	4128	6056	SO:0001583	missense	5783	exon2			AAGAAATATGGGC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.62T>C	chr4.hg19:g.87556471T>C	ENSP00000407249:p.Ile21Thr	129.0	0.0		95.0	16.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.335229	0.81801	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000502971;ENST00000316707;ENST00000411767;ENST00000507902;ENST00000511467	T;T;T;T;T;T;T	0.33438	2.02;2.02;1.41;2.02;2.02;2.02;2.02	5.54	5.54	0.83059	KIND (2);	0.103582	0.42294	D	0.000735	T	0.45597	0.1350	L	0.42245	1.32	0.43317	D	0.995332	D;B;B;B	0.60575	0.988;0.374;0.258;0.374	P;B;B;B	0.61201	0.885;0.354;0.193;0.354	T	0.42155	-0.9468	10	0.72032	D	0.01	.	15.3531	0.74405	0.0:0.0:0.0:1.0	.	21;21;21;21	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	T	21	ENSP00000408368:I21T;ENSP00000394794:I21T;ENSP00000423531:I21T;ENSP00000322675:I21T;ENSP00000407249:I21T;ENSP00000422835:I21T;ENSP00000426626:I21T	ENSP00000322675:I21T	I	+	2	0	PTPN13	87775495	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.354000	0.79424	2.086000	0.62901	0.528000	0.53228	ATA	.	.		0.453	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
PKD2	5311	hgsc.bcm.edu	37	4	88996722	88996722	+	Missense_Mutation	SNP	G	G	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:88996722G>T	ENST00000508588.1	+	10	1432	c.1037G>T	c.(1036-1038)gGt>gTt	p.G346V	PKD2_ENST00000237596.2_Missense_Mutation_p.G928V|PKD2_ENST00000502363.1_Missense_Mutation_p.G346V|PKD2_ENST00000511337.1_3'UTR			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|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 fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		ATCAGTCATGGTTTAGGCACG	0.532																																					p.G928V		Atlas-SNP	.											.	PKD2	82	.	0			c.G2783T						.						164.0	149.0	154.0					4																	88996722		2203	4300	6503	SO:0001583	missense	5311	exon15			GTCATGGTTTAGG	U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""EF-hand domain containing"""	9009	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 2"""	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.1037G>T	chr4.hg19:g.88996722G>T	ENSP00000427131:p.Gly346Val	140.0	0.0		101.0	20.0	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.81	1.749711	0.30955	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.91843	-0.14;-2.92;-2.92	5.2	5.2	0.72013	.	0.435283	0.27048	N	0.021190	D	0.85548	0.5722	N	0.22421	0.69	0.33176	D	0.548938	P	0.39391	0.671	B	0.32289	0.143	D	0.87601	0.2497	10	0.30078	T	0.28	-10.9556	18.7273	0.91718	0.0:0.0:1.0:0.0	.	928	Q13563	PKD2_HUMAN	V	928;346;346	ENSP00000237596:G928V;ENSP00000427131:G346V;ENSP00000425289:G346V	ENSP00000237596:G928V	G	+	2	0	PKD2	89215746	0.990000	0.36364	0.027000	0.17364	0.597000	0.36814	4.424000	0.59868	2.409000	0.81822	0.585000	0.79938	GGT	.	.		0.532	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297	
ANKRD50	57182	hgsc.bcm.edu	37	4	125631232	125631232	+	Missense_Mutation	SNP	G	G	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:125631232G>C	ENST00000504087.1	-	2	1472	c.435C>G	c.(433-435)gaC>gaG	p.D145E	ANKRD50_ENST00000515641.1_Intron	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	145										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CCCTTAGCTTGTCCTCATATC	0.483																																					p.D145E		Atlas-SNP	.											.	ANKRD50	136	.	0			c.C435G						.						74.0	75.0	74.0					4																	125631232		2203	4300	6503	SO:0001583	missense	57182	exon2			TAGCTTGTCCTCA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.435C>G	chr4.hg19:g.125631232G>C	ENSP00000425658:p.Asp145Glu	44.0	0.0		69.0	29.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	G	0.301	-0.973918	0.02215	.	.	ENSG00000151458	ENST00000504087	T	0.16897	2.31	5.16	3.37	0.38596	.	0.056907	0.64402	D	0.000002	T	0.06234	0.0161	N	0.03917	-0.325	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26950	-1.0088	10	0.05721	T	0.95	.	10.7728	0.46332	0.1604:0.0:0.8396:0.0	.	145	Q9ULJ7	ANR50_HUMAN	E	145	ENSP00000425658:D145E	ENSP00000425658:D145E	D	-	3	2	ANKRD50	125850682	1.000000	0.71417	1.000000	0.80357	0.326000	0.28443	3.157000	0.50716	0.519000	0.28406	0.462000	0.41574	GAC	.	.		0.483	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
CDH9	1007	hgsc.bcm.edu	37	5	26902786	26902786	+	Missense_Mutation	SNP	T	T	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:26902786T>G	ENST00000231021.4	-	7	1224	c.1052A>C	c.(1051-1053)aAc>aCc	p.N351T		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	351	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						AGGGTGAGTGTTACTTGCATC	0.353																																					p.N351T	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,NS,carcinoma,0,1	CDH9	305	.	0			c.A1052C						.						90.0	89.0	89.0					5																	26902786		2203	4300	6503	SO:0001583	missense	1007	exon7			TGAGTGTTACTTG	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1052A>C	chr5.hg19:g.26902786T>G	ENSP00000231021:p.Asn351Thr	109.0	0.0		93.0	17.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.457689	0.84317	.	.	ENSG00000113100	ENST00000231021	T	0.55052	0.54	5.62	5.62	0.85841	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.81616	0.4860	H	0.96576	3.845	0.54753	D	0.999986	D	0.89917	1.0	D	0.91635	0.999	D	0.87790	0.2618	9	.	.	.	.	14.6446	0.68751	0.0:0.0:0.0:1.0	.	351	Q9ULB4	CADH9_HUMAN	T	351	ENSP00000231021:N351T	.	N	-	2	0	CDH9	26938543	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.671000	0.83941	2.139000	0.66308	0.528000	0.53228	AAC	.	.		0.353	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
NUP155	9631	hgsc.bcm.edu	37	5	37352900	37352900	+	Silent	SNP	C	C	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:37352900C>A	ENST00000231498.3	-	5	698	c.495G>T	c.(493-495)ctG>ctT	p.L165L	NUP155_ENST00000381843.2_Silent_p.L106L|NUP155_ENST00000513532.1_Silent_p.L165L	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	165					atrial cardiac muscle cell action potential (GO:0086014)|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 export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|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 pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCGCCAAAACCAGGAGGTGTC	0.393																																					p.L165L		Atlas-SNP	.											.	NUP155	116	.	0			c.G495T						.						88.0	84.0	85.0					5																	37352900		2203	4300	6503	SO:0001819	synonymous_variant	9631	exon5			CAAAACCAGGAGG	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"""nucleoporin 155kD"""			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.495G>T	chr5.hg19:g.37352900C>A		161.0	0.0		163.0	27.0	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	hg19	CCDS3921.1																																																																																			.	.		0.393	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54649070	54649070	+	Silent	SNP	C	C	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:54649070C>G	ENST00000230640.5	+	14	1760	c.1506C>G	c.(1504-1506)cgC>cgG	p.R502R	SKIV2L2_ENST00000545714.1_Silent_p.R401R	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	502	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				CAAATGCCCGCAAATTTGATG	0.328																																					p.R502R	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.C1506G						.						85.0	91.0	89.0					5																	54649070		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon14			TGCCCGCAAATTT	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1506C>G	chr5.hg19:g.54649070C>G		92.0	0.0		99.0	7.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.328	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
CCNB1	891	hgsc.bcm.edu	37	5	68470853	68470853	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:68470853G>A	ENST00000256442.5	+	6	1108	c.855G>A	c.(853-855)atG>atA	p.M285I	snoU13_ENST00000459230.1_RNA	NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	285					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to iron(III) ion (GO:0071283)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle checkpoint (GO:0071174)|mitotic spindle stabilization (GO:0043148)|negative regulation of gene expression (GO:0010629)|negative regulation of protein phosphorylation (GO:0001933)|oocyte maturation (GO:0001556)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of chromosome condensation (GO:0060623)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to DDT (GO:0046680)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|spermatogenesis (GO:0007283)|tissue regeneration (GO:0042246)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase activity (GO:0016301)|patched binding (GO:0005113)|protein kinase binding (GO:0019901)			large_intestine(2)|lung(5)|skin(1)	8		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TCAGACAGATGGAAATGAAGA	0.403																																					p.M285I		Atlas-SNP	.											.	CCNB1	36	.	0			c.G855A						.						140.0	142.0	141.0					5																	68470853		2203	4300	6503	SO:0001583	missense	891	exon6			ACAGATGGAAATG	U22364	CCDS3997.1	5q12	2008-07-18			ENSG00000134057	ENSG00000134057			1579	protein-coding gene	gene with protein product	"""G2/mitotic-specific cyclin B1"""	123836		CCNB		1386342	Standard	NM_031966		Approved		uc003jvm.3	P14635	OTTHUMG00000097817	ENST00000256442.5:c.855G>A	chr5.hg19:g.68470853G>A	ENSP00000256442:p.Met285Ile	145.0	0.0		177.0	23.0	NM_031966	A8K066|Q5TZP9	Missense_Mutation	SNP	ENST00000256442.5	hg19	CCDS3997.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.452138	0.84209	.	.	ENSG00000134057	ENST00000256442;ENST00000506572;ENST00000508407;ENST00000505500;ENST00000507798	T;T;T;T;T	0.15487	2.42;2.42;2.42;2.42;2.42	6.16	6.16	0.99307	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.56775	0.2008	H	0.95470	3.675	0.80722	D	1	P;D;D	0.64830	0.857;0.96;0.994	P;P;D	0.67548	0.785;0.887;0.952	T	0.67902	-0.5550	10	0.87932	D	0	.	19.6313	0.95704	0.0:0.0:1.0:0.0	.	285;285;285	E9PC90;Q5TZP9;P14635	.;.;CCNB1_HUMAN	I	285;285;232;285;101	ENSP00000256442:M285I;ENSP00000423387:M285I;ENSP00000426092:M232I;ENSP00000424588:M285I;ENSP00000426230:M101I	ENSP00000256442:M285I	M	+	3	0	CCNB1	68506609	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.941000	0.87700	2.937000	0.99478	0.650000	0.86243	ATG	.	.		0.403	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966	
EDIL3	10085	hgsc.bcm.edu	37	5	83239361	83239361	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:83239361G>A	ENST00000296591.5	-	11	1738	c.1320C>T	c.(1318-1320)gaC>gaT	p.D440D	EDIL3_ENST00000380138.3_Silent_p.D430D	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	440	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		TTCTGTGAGTGTCATTGTCAA	0.418																																					p.D440D		Atlas-SNP	.											.	EDIL3	94	.	0			c.C1320T						.						126.0	120.0	122.0					5																	83239361		2203	4300	6503	SO:0001819	synonymous_variant	10085	exon11			GTGAGTGTCATTG	U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.1320C>T	chr5.hg19:g.83239361G>A		118.0	0.0		117.0	21.0	NM_005711	B2R763|O43855|Q5D094|Q8N610	Silent	SNP	ENST00000296591.5	hg19	CCDS4062.1																																																																																			.	.		0.418	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711	
LARP1	23367	hgsc.bcm.edu	37	5	154172335	154172335	+	Nonsense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:154172335C>T	ENST00000336314.4	+	4	511	c.487C>T	c.(487-489)Cga>Tga	p.R163*		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	240					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GGATTGCCAGCGAGGCGGGCA	0.512																																					p.R163X		Atlas-SNP	.											.,2	LARP1	187	.	0			c.C487T						.						109.0	109.0	109.0					5																	154172335		2203	4300	6503	SO:0001587	stop_gained	23367	exon4			TGCCAGCGAGGCG	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"""La ribonucleoprotein domain containing"""	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.487C>T	chr5.hg19:g.154172335C>T	ENSP00000336721:p.Arg163*	105.0	0.0		110.0	11.0	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Nonsense_Mutation	SNP	ENST00000336314.4	hg19	CCDS4328.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.169644|8.169644	0.98688|0.98688	.|.	.|.	ENSG00000155506|ENSG00000155506	ENST00000517616;ENST00000518194|ENST00000336314;ENST00000518297;ENST00000519931;ENST00000524248;ENST00000523163	.|.	.|.	.|.	5.63|5.63	3.52|3.52	0.40303|0.40303	.|.	.|0.120525	.|0.53938	.|D	.|0.000045	T|.	0.27900|.	0.0687|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.28996|.	-1.0026|.	3|.	.|0.05525	.|T	.|0.97	-6.0673|-6.0673	12.1582|12.1582	0.54089|0.54089	0.5659:0.4341:0.0:0.0|0.5659:0.4341:0.0:0.0	.|.	.|.	.|.	.|.	V|X	142;1|163;240;35;35;15	.|.	.|ENSP00000336721:R163X	A|R	+|+	2|1	0|2	LARP1|LARP1	154152528|154152528	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.616000|4.616000	0.61197|0.61197	1.438000|1.438000	0.47492|0.47492	0.655000|0.655000	0.94253|0.94253	GCG|CGA	.	.		0.512	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551	
HLA-B	3106	hgsc.bcm.edu	37	6	31323270	31323270	+	Missense_Mutation	SNP	G	G	A	rs151341351		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:31323270G>A	ENST00000412585.2	-	4	747	c.719C>T	c.(718-720)aCc>aTc	p.T240I		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	240	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCGCTGCCAGGTCAGTGTGAT	0.607									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.T240I		Atlas-SNP	.											.	HLA-B	54	.	0			c.C719T						.						92.0	86.0	88.0					6																	31323270		2203	4300	6503	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	TGCCAGGTCAGTG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.719C>T	chr6.hg19:g.31323270G>A	ENSP00000399168:p.Thr240Ile	129.0	0.0		152.0	31.0	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	hg19	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	12.54	1.969553	0.34754	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596	T	0.03358	3.96	3.06	3.06	0.35304	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.452724	0.16632	U	0.206027	T	0.06508	0.0167	M	0.64630	1.985	0.28228	N	0.926237	D	0.89917	1.0	D	0.91635	0.999	T	0.09640	-1.0665	10	0.87932	D	0	.	7.6422	0.28300	0.0:0.0:0.7472:0.2528	.	240	P01889	1B07_HUMAN	I	240;119;119	ENSP00000399168:T240I	ENSP00000399168:T240I	T	-	2	0	HLA-B	31431249	0.609000	0.26975	0.999000	0.59377	0.838000	0.47535	-0.280000	0.08468	1.742000	0.51746	0.442000	0.29010	ACC	.	.		0.607	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
VARS	7407	hgsc.bcm.edu	37	6	31747209	31747209	+	Silent	SNP	C	C	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:31747209C>A	ENST00000375663.3	-	28	3833	c.3393G>T	c.(3391-3393)cgG>cgT	p.R1131R	VWA7_ENST00000375688.4_5'Flank|VWA7_ENST00000447450.1_5'Flank|VWA7_ENST00000375686.3_5'Flank|VWA7_ENST00000467576.1_5'Flank|Y_RNA_ENST00000364685.1_RNA|VARS_ENST00000482996.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1131					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CACAGTCAGGCCGGATCCGGG	0.667																																					p.R1131R		Atlas-SNP	.											.	VARS	76	.	0			c.G3393T						.						41.0	34.0	36.0					6																	31747209		1509	2706	4215	SO:0001819	synonymous_variant	7407	exon28			GTCAGGCCGGATC	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.3393G>T	chr6.hg19:g.31747209C>A		89.0	0.0		77.0	25.0	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Silent	SNP	ENST00000375663.3	hg19	CCDS34412.1																																																																																			.	.		0.667	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	
ITPR3	3710	hgsc.bcm.edu	37	6	33631619	33631619	+	Missense_Mutation	SNP	C	C	G	rs2229630	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:33631619C>G	ENST00000374316.5	+	12	2170	c.1110C>G	c.(1108-1110)gaC>gaG	p.D370E	ITPR3_ENST00000605930.1_Missense_Mutation_p.D370E			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	370	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TTGAGCTGGACCCCACCACCT	0.612																																					p.D370E		Atlas-SNP	.											.	ITPR3	409	.	0			c.C1110G						.						79.0	76.0	77.0					6																	33631619		2203	4300	6503	SO:0001583	missense	3710	exon11			GCTGGACCCCACC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.1110C>G	chr6.hg19:g.33631619C>G	ENSP00000363435:p.Asp370Glu	65.0	0.0		94.0	29.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.553799	0.65425	.	.	ENSG00000096433	ENST00000374316	D	0.87256	-2.23	4.74	0.62	0.17637	MIR motif (2);MIR (2);	0.111192	0.64402	D	0.000010	D	0.88779	0.6529	M	0.78456	2.415	0.50632	D	0.999889	D	0.67145	0.996	D	0.69479	0.964	D	0.87333	0.2326	10	0.48119	T	0.1	-39.8685	10.1744	0.42931	0.0:0.6136:0.0:0.3864	.	370	Q14573	ITPR3_HUMAN	E	370	ENSP00000363435:D370E	ENSP00000363435:D370E	D	+	3	2	ITPR3	33739597	1.000000	0.71417	0.999000	0.59377	0.868000	0.49771	2.001000	0.40825	0.221000	0.20879	0.484000	0.47621	GAC	.	C|0.995;T|0.005		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
MOCS1	4337	hgsc.bcm.edu	37	6	39881105	39881105	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:39881105C>T	ENST00000340692.5	-	6	716	c.713G>A	c.(712-714)gGc>gAc	p.G238D	MOCS1_ENST00000373195.3_Missense_Mutation_p.G151D|MOCS1_ENST00000308559.7_Missense_Mutation_p.G238D|MOCS1_ENST00000432280.2_Missense_Mutation_p.G209D|MOCS1_ENST00000373175.4_Missense_Mutation_p.G209D|MOCS1_ENST00000425303.2_Missense_Mutation_p.G238D|MOCS1_ENST00000373186.4_Missense_Mutation_p.G238D|MOCS1_ENST00000373188.2_Missense_Mutation_p.G238D			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	238	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					CAGGGGGAGGCCCTCAGTCAA	0.587																																					p.G238D	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.G713A						.						109.0	95.0	100.0					6																	39881105		2203	4300	6503	SO:0001583	missense	4337	exon5			GGGAGGCCCTCAG	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.713G>A	chr6.hg19:g.39881105C>T	ENSP00000344794:p.Gly238Asp	114.0	0.0		122.0	25.0	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	hg19		.	.	.	.	.	.	.	.	.	.	C	0.011	-1.722757	0.00700	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	4.68	3.81	0.43845	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);	0.354601	0.30193	N	0.010183	T	0.02342	0.0072	N	0.00102	-2.13	0.34074	D	0.658831	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.002;0.001;0.002;0.002	T	0.36383	-0.9750	9	.	.	.	-15.5051	6.1159	0.20126	0.0:0.6601:0.0:0.3399	.	238;238;238;238;238	Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;.;MOCS1_HUMAN;.;.	D	238;238;209;238;151;238;238;209	ENSP00000362282:G238D;ENSP00000309843:G238D;ENSP00000362270:G209D;ENSP00000362284:G238D;ENSP00000362291:G151D;ENSP00000344794:G238D;ENSP00000416478:G238D;ENSP00000410809:G209D	.	G	-	2	0	MOCS1	39989083	0.910000	0.30920	0.875000	0.34327	0.062000	0.15995	1.586000	0.36611	0.980000	0.38523	0.655000	0.94253	GGC	.	.		0.587	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943	
KCNQ5	56479	hgsc.bcm.edu	37	6	73787165	73787165	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:73787165A>G	ENST00000370398.1	+	4	846	c.737A>G	c.(736-738)gAc>gGc	p.D246G	KCNQ5_ENST00000403813.2_Missense_Mutation_p.D246G|KCNQ5_ENST00000402622.2_Missense_Mutation_p.D246G|KCNQ5_ENST00000355194.4_Missense_Mutation_p.D246G|KCNQ5_ENST00000414165.2_Missense_Mutation_p.D246G|KCNQ5_ENST00000370392.1_Missense_Mutation_p.D246G|KCNQ5_ENST00000355635.3_Missense_Mutation_p.D246G|KCNQ5_ENST00000342056.2_Missense_Mutation_p.D246G	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	246					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GTGCGCATGGACCGAAGGGGA	0.428																																					p.D246G	GBM(142;1375 1859 14391 23261 44706)	Atlas-SNP	.											.	KCNQ5	153	.	0			c.A737G						.						77.0	74.0	75.0					6																	73787165		2203	4300	6503	SO:0001583	missense	56479	exon4			GCATGGACCGAAG	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.737A>G	chr6.hg19:g.73787165A>G	ENSP00000359425:p.Asp246Gly	84.0	0.0		105.0	8.0	NM_001160132	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	hg19	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.714811	0.89112	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000370392;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D;D	0.98455	-4.94;-4.94;-4.94;-4.94;-4.94;-4.94;-4.94;-4.94	5.84	5.84	0.93424	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98333	0.9447	L	0.52905	1.665	0.80722	D	1	P;D;D;D;D;D	0.89917	0.712;1.0;0.989;0.986;1.0;0.985	P;D;D;D;D;D	0.81914	0.493;0.986;0.929;0.962;0.995;0.972	D	0.99904	1.1174	10	0.72032	D	0.01	.	16.2194	0.82247	1.0:0.0:0.0:0.0	.	246;246;246;246;246;246	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82;Q9NR82-4	.;.;.;.;KCNQ5_HUMAN;.	G	246	ENSP00000345055:D246G;ENSP00000347326:D246G;ENSP00000359425:D246G;ENSP00000359419:D246G;ENSP00000385501:D246G;ENSP00000347853:D246G;ENSP00000384453:D246G;ENSP00000409861:D246G	ENSP00000345055:D246G	D	+	2	0	KCNQ5	73843886	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.234000	0.73211	0.528000	0.53228	GAC	.	.		0.428	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
SENP6	26054	hgsc.bcm.edu	37	6	76423528	76423528	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:76423528A>G	ENST00000447266.2	+	23	3594	c.3116A>G	c.(3115-3117)gAg>gGg	p.E1039G	SENP6_ENST00000370010.2_Missense_Mutation_p.E1032G|SENP6_ENST00000370014.3_Missense_Mutation_p.E1039G|SENP6_ENST00000541192.1_3'UTR	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	1039	Protease.				protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				CAGTATGTAGAGAGCTTTTTT	0.318																																					p.E1039G		Atlas-SNP	.											.	SENP6	189	.	0			c.A3116G						.						99.0	91.0	93.0					6																	76423528		1820	4077	5897	SO:0001583	missense	26054	exon23			ATGTAGAGAGCTT		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.3116A>G	chr6.hg19:g.76423528A>G	ENSP00000402527:p.Glu1039Gly	182.0	0.0		222.0	71.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.359393	0.82353	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000447266	T;T;T	0.40756	1.02;1.02;1.02	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.67183	0.2866	M	0.93854	3.465	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.72338	0.935;0.977	T	0.77981	-0.2383	10	0.87932	D	0	-7.1117	14.9661	0.71196	1.0:0.0:0.0:0.0	.	1032;1039	Q9GZR1-2;Q9GZR1	.;SENP6_HUMAN	G	1032;1039;1039	ENSP00000359027:E1032G;ENSP00000359031:E1039G;ENSP00000402527:E1039G	ENSP00000359027:E1032G	E	+	2	0	SENP6	76480248	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	8.910000	0.92685	2.005000	0.58758	0.460000	0.39030	GAG	.	.		0.318	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
RSPO3	84870	hgsc.bcm.edu	37	6	127440418	127440418	+	Silent	SNP	A	A	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:127440418A>T	ENST00000356698.4	+	1	670	c.81A>T	c.(79-81)ggA>ggT	p.G27G	RSPO3_ENST00000368317.3_Silent_p.G27G	NM_032784.3	NP_116173.2	Q9BXY4	RSPO3_HUMAN	R-spondin 3	27					branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)	extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		PTPRK/RSPO3(10)	breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17				GBM - Glioblastoma multiforme(226;0.0555)		CCTCCCGGGGAAGGCGCCAGC	0.537																																					p.G27G		Atlas-SNP	.											.	RSPO3	32	.	0			c.A81T						.						150.0	164.0	160.0					6																	127440418		2203	4300	6503	SO:0001819	synonymous_variant	84870	exon1			CCGGGGAAGGCGC	BC022367	CCDS5135.1	6q22.33	2013-02-28	2011-06-29	2005-08-08	ENSG00000146374	ENSG00000146374		"""Endogenous ligands"""	20866	protein-coding gene	gene with protein product		610574	"""thrombospondin, type I, domain containing 2"", ""R-spondin 3 homolog (Xenopus laevis)"""	THSD2		10842357, 15469841	Standard	NM_032784		Approved	FLJ14440	uc003qar.3	Q9BXY4	OTTHUMG00000015521	ENST00000356698.4:c.81A>T	chr6.hg19:g.127440418A>T		137.0	0.0		163.0	16.0	NM_032784	B2RC27|Q5VTV4|Q96K87	Silent	SNP	ENST00000356698.4	hg19	CCDS5135.1																																																																																			.	.		0.537	RSPO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042111.1	NM_032784	
TXLNB	167838	hgsc.bcm.edu	37	6	139609802	139609802	+	Nonsense_Mutation	SNP	T	T	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr6:139609802T>A	ENST00000358430.3	-	2	467	c.235A>T	c.(235-237)Aaa>Taa	p.K79*	RP11-445F6.2_ENST00000441249.1_RNA|RP11-445F6.2_ENST00000440518.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	79						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		GAGCCCTCTTTCCCTGCTGTG	0.527																																					p.K79X		Atlas-SNP	.											.	TXLNB	96	.	0			c.A235T						.						113.0	111.0	111.0					6																	139609802		2203	4300	6503	SO:0001587	stop_gained	167838	exon2			CCTCTTTCCCTGC		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"""chromosome 6 open reading frame 198"""	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.235A>T	chr6.hg19:g.139609802T>A	ENSP00000351206:p.Lys79*	129.0	0.0		128.0	47.0	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Nonsense_Mutation	SNP	ENST00000358430.3	hg19	CCDS34545.1	.	.	.	.	.	.	.	.	.	.	T	34	5.314079	0.95655	.	.	ENSG00000164440	ENST00000358430	.	.	.	5.98	-0.911	0.10507	.	1.115670	0.06832	N	0.794182	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.3354	6.5519	0.22438	0.0:0.1984:0.4327:0.3689	.	.	.	.	X	79	.	.	K	-	1	0	TXLNB	139651495	0.687000	0.27671	0.001000	0.08648	0.002000	0.02628	-0.488000	0.06497	-0.130000	0.11599	-1.123000	0.02005	AAA	.	.		0.527	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
MICALL2	79778	hgsc.bcm.edu	37	7	1484651	1484651	+	Missense_Mutation	SNP	G	G	A	rs375853882		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:1484651G>A	ENST00000297508.7	-	6	1230	c.1055C>T	c.(1054-1056)gCc>gTc	p.A352V	MICALL2_ENST00000405088.4_Missense_Mutation_p.A140V	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	352	Mediates targeting to the cell plasma membrane. {ECO:0000250}.|Necessary and sufficient for interaction with actinins. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		TGTGCACGGGGCAGCTGACGA	0.736																																					p.A352V		Atlas-SNP	.											.	MICALL2	63	.	0			c.C1055T						.		VAL/ALA	1,4099		0,1,2049	8.0	7.0	8.0		1055	2.1	0.0	7		8	0,8082		0,0,4041	no	missense	MICALL2	NM_182924.3	64	0,1,6090	AA,AG,GG		0.0,0.0244,0.0082	possibly-damaging	352/905	1484651	1,12181	2050	4041	6091	SO:0001583	missense	79778	exon6			CACGGGGCAGCTG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.1055C>T	chr7.hg19:g.1484651G>A	ENSP00000297508:p.Ala352Val	66.0	0.0		70.0	6.0	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	hg19	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.115906	0.56505	2.44E-4	0.0	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.69040	2.38;-0.37	3.99	2.12	0.27331	.	0.759254	0.10766	N	0.636615	T	0.66327	0.2778	L	0.32530	0.975	0.09310	N	1	D	0.67145	0.996	D	0.63381	0.914	T	0.52290	-0.8595	10	0.29301	T	0.29	.	5.5566	0.17119	0.118:0.2202:0.6618:0.0	.	352	Q8IY33	MILK2_HUMAN	V	140;352	ENSP00000385928:A140V;ENSP00000297508:A352V	ENSP00000297508:A352V	A	-	2	0	MICALL2	1451177	0.012000	0.17670	0.002000	0.10522	0.003000	0.03518	1.192000	0.32150	0.271000	0.22005	0.561000	0.74099	GCC	.	.		0.736	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
SEMA3E	9723	hgsc.bcm.edu	37	7	83014671	83014671	+	Missense_Mutation	SNP	C	C	A	rs145707650		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:83014671C>A	ENST00000307792.3	-	16	2281	c.1814G>T	c.(1813-1815)cGa>cTa	p.R605L	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R545L	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	605	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TTGTAAAGATCGTGGGGTACA	0.398																																					p.R605L		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G1814T						.	C	LEU/ARG,LEU/ARG	0,4406		0,0,2203	203.0	182.0	189.0		1634,1814	5.5	1.0	7	dbSNP_134	189	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SEMA3E	NM_001178129.1,NM_012431.2	102,102	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	545/716,605/776	83014671	1,13005	2203	4300	6503	SO:0001583	missense	9723	exon16			AAAGATCGTGGGG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1814G>T	chr7.hg19:g.83014671C>A	ENSP00000303212:p.Arg605Leu	162.0	0.0		203.0	40.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573826	0.86542	0.0	1.16E-4	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.21734	1.99;1.99	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.45776	0.1359	M	0.78456	2.415	0.58432	D	0.999999	P	0.51449	0.945	D	0.62955	0.909	T	0.21484	-1.0244	10	0.30854	T	0.27	.	16.4843	0.84180	0.0:0.8692:0.1308:0.0	.	605	O15041	SEM3E_HUMAN	L	605;545;605	ENSP00000303212:R605L;ENSP00000405052:R545L	ENSP00000303212:R605L	R	-	2	0	SEMA3E	82852607	0.997000	0.39634	0.977000	0.42913	0.990000	0.78478	4.558000	0.60789	2.597000	0.87782	0.650000	0.86243	CGA	.	C|1.000;A|0.000		0.398	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
ACHE	43	hgsc.bcm.edu	37	7	100490028	100490028	+	Nonsense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:100490028G>A	ENST00000412389.1	-	2	1635	c.1480C>T	c.(1480-1482)Cga>Tga	p.R494*	ACHE_ENST00000241069.5_Nonsense_Mutation_p.R494*|ACHE_ENST00000419336.2_Nonsense_Mutation_p.R406*|ACHE_ENST00000411582.1_Nonsense_Mutation_p.R494*|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000302913.4_Nonsense_Mutation_p.R494*|ACHE_ENST00000428317.1_Nonsense_Mutation_p.R494*			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	494					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	GTGTAGTTTCGAGAGGGGTCC	0.597																																					p.R494X		Atlas-SNP	.											.	ACHE	80	.	0			c.C1480T						.						48.0	47.0	48.0					7																	100490028		2203	4300	6503	SO:0001587	stop_gained	43	exon3			AGTTTCGAGAGGG		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"""Blood group antigens"""	108	protein-coding gene	gene with protein product	"""Yt blood group"""	100740	"""acetylcholinesterase (YT blood group)"", ""acetylcholinesterase (Yt blood group)"", ""acetylcholinesterase"""	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1480C>T	chr7.hg19:g.100490028G>A	ENSP00000394976:p.Arg494*	131.0	0.0		162.0	22.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Nonsense_Mutation	SNP	ENST00000412389.1	hg19	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122826	0.77436	.	.	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000411582;ENST00000422451	.	.	.	3.92	3.0	0.34707	.	0.269718	0.29493	N	0.011991	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	5.8005	0.18412	0.2592:0.0:0.7408:0.0	.	.	.	.	X	406;494;494;494;494;494;494	.	ENSP00000241069:R494X	R	-	1	2	ACHE	100327964	0.964000	0.33143	0.869000	0.34112	0.560000	0.35617	2.190000	0.42630	0.942000	0.37525	0.491000	0.48974	CGA	.	.		0.597	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
KMT2E	55904	hgsc.bcm.edu	37	7	104730539	104730539	+	Missense_Mutation	SNP	T	T	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:104730539T>C	ENST00000311117.3	+	14	1987	c.1442T>C	c.(1441-1443)aTc>aCc	p.I481T	KMT2E_ENST00000257745.4_Missense_Mutation_p.I481T|KMT2E_ENST00000476671.1_Missense_Mutation_p.I481T|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000334877.4_Missense_Mutation_p.I481T	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	481					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										ATGGAAAATATCAATAGTGGT	0.353																																					p.I481T		Atlas-SNP	.											.	MLL5	173	.	0			c.T1442C						.						106.0	120.0	115.0					7																	104730539		2202	4298	6500	SO:0001583	missense	55904	exon13			AAAATATCAATAG	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.1442T>C	chr7.hg19:g.104730539T>C	ENSP00000312379:p.Ile481Thr	427.0	0.0		539.0	189.0	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312204	0.60414	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95724	-2.91;-2.53;-2.91;-3.79;-3.26	5.83	5.83	0.93111	.	0.063289	0.64402	D	0.000005	D	0.93239	0.7846	L	0.34521	1.04	0.80722	D	1	D;P	0.59357	0.985;0.867	P;B	0.50537	0.643;0.288	D	0.91244	0.5024	10	0.11182	T	0.66	.	14.7838	0.69787	0.0:0.0:0.0:1.0	.	481;481	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	T	481;481;481;481;481;339;481;415	ENSP00000312379:I481T;ENSP00000335599:I481T;ENSP00000257745:I481T;ENSP00000419883:I339T;ENSP00000417888:I481T	ENSP00000257745:I481T	I	+	2	0	MLL5	104517775	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.319000	0.79040	2.236000	0.73375	0.533000	0.62120	ATC	.	.		0.353	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
IFRD1	3475	hgsc.bcm.edu	37	7	112102091	112102091	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:112102091C>T	ENST00000403825.3	+	7	915	c.654C>T	c.(652-654)atC>atT	p.I218I	IFRD1_ENST00000005558.4_Silent_p.I218I|IFRD1_ENST00000486688.1_3'UTR|IFRD1_ENST00000535603.1_Silent_p.I168I	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	218					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						TGGAAAATATCTTCACTAAAT	0.343																																					p.I218I		Atlas-SNP	.											.	IFRD1	46	.	0			c.C654T						.						105.0	102.0	103.0					7																	112102091		2203	4300	6503	SO:0001819	synonymous_variant	3475	exon8			AAATATCTTCACT	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.654C>T	chr7.hg19:g.112102091C>T		106.0	0.0		153.0	35.0	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Silent	SNP	ENST00000403825.3	hg19	CCDS34736.1																																																																																			.	.		0.343	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	
KIAA1549	57670	hgsc.bcm.edu	37	7	138601674	138601674	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr7:138601674G>A	ENST00000422774.1	-	2	2746	c.2698C>T	c.(2698-2700)Ctg>Ttg	p.L900L	KIAA1549_ENST00000440172.1_Silent_p.L900L|KIAA1549_ENST00000242365.4_Silent_p.L850L			Q9HCM3	K1549_HUMAN	KIAA1549	900						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TCACCCATCAGGGTGGAGTCG	0.632			O	BRAF	pilocytic astrocytoma																																p.L900L	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C2698T						.						31.0	38.0	36.0					7																	138601674		2124	4223	6347	SO:0001819	synonymous_variant	57670	exon2			CCATCAGGGTGGA		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.2698C>T	chr7.hg19:g.138601674G>A		82.0	0.0		102.0	14.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.632	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905384	1905384	+	Silent	SNP	G	G	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:1905384G>T	ENST00000398564.1	+	29	4065	c.4065G>T	c.(4063-4065)ctG>ctT	p.L1355L	ARHGEF10_ENST00000262112.6_Silent_p.L1326L|ARHGEF10_ENST00000349830.3_Silent_p.L1330L|ARHGEF10_ENST00000520359.1_Silent_p.L1292L|ARHGEF10_ENST00000518288.1_Silent_p.L1354L			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1355					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		AGGAAGAGCTGGCGCCGACCG	0.627																																					p.L1330L		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.G3990T						.																																			SO:0001819	synonymous_variant	9639	exon29			AGAGCTGGCGCCG	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.4065G>T	chr8.hg19:g.1905384G>T		78.0	0.0		65.0	12.0	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	hg19																																																																																				.	.		0.627	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
PXDNL	137902	hgsc.bcm.edu	37	8	52321956	52321956	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:52321956C>T	ENST00000356297.4	-	17	2328	c.2228G>A	c.(2227-2229)gGc>gAc	p.G743D	PXDNL_ENST00000543296.1_Missense_Mutation_p.G743D	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	743					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAGCGCCGCGCCCCACGTGGG	0.721																																					p.G743D		Atlas-SNP	.											.	PXDNL	414	.	0			c.G2228A						.						14.0	16.0	15.0					8																	52321956		1958	4127	6085	SO:0001583	missense	137902	exon17			GCCGCGCCCCACG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2228G>A	chr8.hg19:g.52321956C>T	ENSP00000348645:p.Gly743Asp	51.0	0.0		60.0	26.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442651	0.63067	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.96300	-3.97;-3.97	3.71	3.71	0.42584	.	.	.	.	.	D	0.98912	0.9631	H	0.99104	4.43	0.45239	D	0.998242	D	0.89917	1.0	D	0.97110	1.0	D	0.98713	1.0705	9	0.87932	D	0	.	13.2908	0.60270	0.0:1.0:0.0:0.0	.	743	A1KZ92	PXDNL_HUMAN	D	743	ENSP00000348645:G743D;ENSP00000444865:G743D	ENSP00000348645:G743D	G	-	2	0	PXDNL	52484509	1.000000	0.71417	0.126000	0.21872	0.260000	0.26232	4.946000	0.63576	1.779000	0.52309	0.555000	0.69702	GGC	.	.		0.721	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
ZFHX4	79776	hgsc.bcm.edu	37	8	77618110	77618110	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:77618110G>A	ENST00000521891.2	+	2	2235	c.1787G>A	c.(1786-1788)aGt>aAt	p.S596N	ZFHX4_ENST00000050961.6_Missense_Mutation_p.S596N|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S596N|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S596N|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	596					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTTACCCCGAGTACTCCTGGC	0.582										HNSCC(33;0.089)																											p.S596N		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G1787A						.						70.0	76.0	74.0					8																	77618110		2107	4222	6329	SO:0001583	missense	79776	exon2			CCCCGAGTACTCC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.1787G>A	chr8.hg19:g.77618110G>A	ENSP00000430497:p.Ser596Asn	122.0	0.0		164.0	48.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	11.47	1.648758	0.29336	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.51071	0.72;0.77;0.73;0.72	5.65	5.65	0.86999	.	0.000000	0.52532	U	0.000066	T	0.44244	0.1284	L	0.44542	1.39	0.38445	D	0.946816	B;P;P;B	0.35272	0.361;0.493;0.493;0.185	B;B;B;B	0.33620	0.075;0.167;0.157;0.117	T	0.37244	-0.9714	10	0.34782	T	0.22	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	596;596;596;596	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	N	596	ENSP00000430497:S596N;ENSP00000399605:S596N;ENSP00000050961:S596N;ENSP00000430848:S596N	ENSP00000050961:S596N	S	+	2	0	ZFHX4	77780665	0.986000	0.35501	0.010000	0.14722	0.104000	0.19210	4.713000	0.61895	2.941000	0.99782	0.655000	0.94253	AGT	.	.		0.582	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
AGO2	27161	hgsc.bcm.edu	37	8	141595331	141595331	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:141595331G>A	ENST00000220592.5	-	2	214	c.102C>T	c.(100-102)tcC>tcT	p.S34S	AGO2_ENST00000519980.1_Silent_p.S34S|AGO2_ENST00000517293.1_5'UTR	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	34					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										TTGTTCTCCCGGAGGTCCCAA	0.507																																					p.S34S		Atlas-SNP	.											.	.	.	.	0			c.C102T						.						77.0	79.0	78.0					8																	141595331		2203	4300	6503	SO:0001819	synonymous_variant	27161	exon2			TCTCCCGGAGGTC	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.102C>T	chr8.hg19:g.141595331G>A		141.0	0.0		211.0	53.0	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Silent	SNP	ENST00000220592.5	hg19	CCDS6380.1																																																																																			.	.		0.507	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
TSNARE1	203062	hgsc.bcm.edu	37	8	143395792	143395792	+	Missense_Mutation	SNP	C	C	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:143395792C>G	ENST00000307180.3	-	9	1201	c.1084G>C	c.(1084-1086)Gaa>Caa	p.E362Q	TSNARE1_ENST00000519651.1_Missense_Mutation_p.E142Q|TSNARE1_ENST00000518928.1_5'UTR|TSNARE1_ENST00000524325.1_Missense_Mutation_p.E361Q|TSNARE1_ENST00000520166.1_Missense_Mutation_p.E361Q	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	362					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CTGGACTTTTCTGCAATTTTC	0.522																																					p.E362Q		Atlas-SNP	.											.	TSNARE1	59	.	0			c.G1084C						.						58.0	55.0	56.0					8																	143395792		2203	4300	6503	SO:0001583	missense	203062	exon9			ACTTTTCTGCAAT			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.1084G>C	chr8.hg19:g.143395792C>G	ENSP00000303437:p.Glu362Gln	84.0	0.0		101.0	46.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490894	0.64074	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	4.27	4.27	0.50696	t-SNARE (1);	0.000000	0.32608	U	0.005866	T	0.49355	0.1552	M	0.77820	2.39	0.24415	N	0.994649	D;D;D;D	0.89917	0.998;1.0;0.998;0.998	D;D;D;D	0.80764	0.991;0.994;0.991;0.991	T	0.39921	-0.9590	10	0.46703	T	0.11	.	12.201	0.54326	0.0:1.0:0.0:0.0	.	361;142;362;362	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	Q	361;362;361;142	ENSP00000428763:E361Q;ENSP00000303437:E362Q;ENSP00000427770:E361Q;ENSP00000429679:E142Q	ENSP00000303437:E362Q	E	-	1	0	TSNARE1	143393699	0.946000	0.32159	0.979000	0.43373	0.993000	0.82548	3.506000	0.53364	1.915000	0.55452	0.655000	0.94253	GAA	.	.		0.522	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
PTPRD	5789	hgsc.bcm.edu	37	9	8733790	8733790	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr9:8733790C>T	ENST00000381196.4	-	9	597	c.54G>A	c.(52-54)acG>acA	p.T18T	PTPRD_ENST00000397606.3_Silent_p.T18T|PTPRD_ENST00000356435.5_Silent_p.T18T|PTPRD_ENST00000358503.5_Silent_p.T18T|PTPRD_ENST00000360074.4_Silent_p.T18T|PTPRD_ENST00000537002.1_Silent_p.T18T|PTPRD_ENST00000397611.3_Silent_p.T18T|PTPRD_ENST00000486161.1_Silent_p.T18T|PTPRD_ENST00000540109.1_Silent_p.T18T|PTPRD_ENST00000355233.5_Silent_p.T18T|PTPRD_ENST00000463477.1_Silent_p.T18T|PTPRD_ENST00000397617.3_Silent_p.T18T	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	18					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TCTCAGCATCCGTGCGGAGGA	0.567										TSP Lung(15;0.13)																											p.T18T		Atlas-SNP	.											.	PTPRD	1348	.	0			c.G54A						.						67.0	54.0	59.0					9																	8733790		2167	4230	6397	SO:0001819	synonymous_variant	5789	exon1			AGCATCCGTGCGG	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.54G>A	chr9.hg19:g.8733790C>T		82.0	0.0		92.0	24.0	NM_001040712	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.567	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
RALGPS1	9649	hgsc.bcm.edu	37	9	129973041	129973041	+	Intron	SNP	C	C	A	rs555036312		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr9:129973041C>A	ENST00000259351.5	+	15	1514				RALGPS1_ENST00000373434.1_Silent_p.R369R|RALGPS1_ENST00000424082.2_Silent_p.R369R	NM_014636.2	NP_055451.1	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1						intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ral GTPase activity (GO:0032852)|regulation of Ral protein signal transduction (GO:0032485)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ral guanyl-nucleotide exchange factor activity (GO:0008321)			kidney(2)|large_intestine(6)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						TCCCAGAACCCGGAGCTGTGT	0.493																																					p.R369R		Atlas-SNP	.											.	RALGPS1	86	.	0			c.C1105A						.																																			SO:0001627	intron_variant	9649	exon13			AGAACCCGGAGCT	AB002349	CCDS35143.1, CCDS55344.1, CCDS55345.1, CCDS55346.1	9q33.3	2013-01-10			ENSG00000136828	ENSG00000136828		"""Pleckstrin homology (PH) domain containing"""	16851	protein-coding gene	gene with protein product		614444				9205841, 10747847	Standard	NM_001190728		Approved	RALGPS1A, RALGEF2, KIAA0351	uc004bqo.2	Q5JS13	OTTHUMG00000020696	ENST00000259351.5:c.1248-1369C>A	chr9.hg19:g.129973041C>A		104.0	0.0		106.0	27.0	NM_001190729	B4DR86|E9PBQ5|O15059|Q5JT60|Q5JT65|Q5JUG5|Q8N4S6|Q8N5H4|Q8WUV7|Q9NZ16	Silent	SNP	ENST00000259351.5	hg19	CCDS35143.1																																																																																			.	.		0.493	RALGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054133.1	NM_014636	
PRRC2B	84726	hgsc.bcm.edu	37	9	134357810	134357810	+	Missense_Mutation	SNP	C	C	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr9:134357810C>A	ENST00000357304.4	+	20	5091	c.5036C>A	c.(5035-5037)tCt>tAt	p.S1679Y	PRRC2B_ENST00000458550.1_Missense_Mutation_p.S985Y|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000405995.1_Missense_Mutation_p.S985Y	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1679							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AGTGCCGAGTCTCGGGAGTCG	0.592																																					p.S1679Y		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C5036A						.						148.0	155.0	153.0					9																	134357810		1992	4172	6164	SO:0001583	missense	84726	exon20			CCGAGTCTCGGGA	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.5036C>A	chr9.hg19:g.134357810C>A	ENSP00000349856:p.Ser1679Tyr	187.0	0.0		184.0	41.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768602	0.69878	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.04809	3.55;3.93;3.55	4.92	4.92	0.64577	.	0.000000	0.41605	U	0.000852	T	0.20414	0.0491	M	0.68593	2.085	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.967;0.991	T	0.00350	-1.1797	10	0.72032	D	0.01	-23.5277	17.105	0.86660	0.0:1.0:0.0:0.0	.	411;1679	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	Y	985;1679;985	ENSP00000384606:S985Y;ENSP00000349856:S1679Y;ENSP00000398853:S985Y	ENSP00000349856:S1679Y	S	+	2	0	PRRC2B	133347631	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	4.343000	0.59348	2.275000	0.75901	0.561000	0.74099	TCT	.	.		0.592	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ANK3	288	hgsc.bcm.edu	37	10	62149211	62149211	+	Missense_Mutation	SNP	C	C	T	rs373407780		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:62149211C>T	ENST00000280772.2	-	1	277	c.86G>A	c.(85-87)cGc>cAc	p.R29H	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	29					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GGACCGTTTGCGGTGTTTCCT	0.398																																					p.R29H		Atlas-SNP	.											.	ANK3	703	.	0			c.G86A						.	C	,,HIS/ARG	0,4406		0,0,2203	172.0	165.0	168.0		,,86	6.0	1.0	10		168	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,missense	ANK3	NM_001204403.1,NM_001204404.1,NM_020987.3	,,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,possibly-damaging	,,29/4378	62149211	1,13005	2203	4300	6503	SO:0001583	missense	288	exon1			CGTTTGCGGTGTT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.86G>A	chr10.hg19:g.62149211C>T	ENSP00000280772:p.Arg29His	81.0	0.0		100.0	6.0	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.039705	0.55003	0.0	1.16E-4	ENSG00000151150	ENST00000280772	T	0.64618	-0.11	5.96	5.96	0.96718	.	0.000000	0.33959	U	0.004385	T	0.65302	0.2678	N	0.08118	0	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.72472	-0.4283	10	0.66056	D	0.02	.	19.4101	0.94667	0.0:1.0:0.0:0.0	.	29	Q12955	ANK3_HUMAN	H	29	ENSP00000280772:R29H	ENSP00000280772:R29H	R	-	2	0	ANK3	61819217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.931000	0.70113	2.832000	0.97577	0.655000	0.94253	CGC	.	.		0.398	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
SEC24C	9632	hgsc.bcm.edu	37	10	75528787	75528787	+	Silent	SNP	T	T	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:75528787T>C	ENST00000339365.2	+	18	2463	c.2301T>C	c.(2299-2301)ttT>ttC	p.F767F	SEC24C_ENST00000345254.4_Silent_p.F767F|SEC24C_ENST00000496827.1_3'UTR|SEC24C_ENST00000540668.1_Silent_p.F15F|SEC24C_ENST00000535742.1_Silent_p.F15F|SEC24C_ENST00000411652.2_Silent_p.F648F	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	767					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)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	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)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TAGATTTCTTTGGAGCTTTCT	0.512																																					p.F767F		Atlas-SNP	.											SEC24C,colon,carcinoma,0,1	SEC24C	86	.	0			c.T2301C						.						101.0	90.0	93.0					10																	75528787		2203	4300	6503	SO:0001819	synonymous_variant	9632	exon17			TTTCTTTGGAGCT	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.2301T>C	chr10.hg19:g.75528787T>C		106.0	0.0		136.0	31.0	NM_198597	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	hg19	CCDS7332.1																																																																																			.	.		0.512	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
LIPJ	142910	hgsc.bcm.edu	37	10	90356037	90356037	+	Splice_Site	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:90356037G>A	ENST00000371939.3	+	7	754	c.440G>A	c.(439-441)gGt>gAt	p.G147D		NM_001010939.2	NP_001010939.2	Q5W064	LIPJ_HUMAN	lipase, family member J	147					lipid catabolic process (GO:0016042)		hydrolase activity, acting on ester bonds (GO:0016788)			large_intestine(4)|lung(4)|ovary(1)	9		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)		TTTATTTTAGGTTTCATAACA	0.264																																					p.G147D		Atlas-SNP	.											.	LIPJ	32	.	0			c.G440A						.						12.0	12.0	12.0					10																	90356037		2099	4175	6274	SO:0001630	splice_region_variant	142910	exon7			TTTTAGGTTTCAT	BC031219	CCDS31240.1	10q23.31	2008-02-04	2008-02-04	2007-02-27	ENSG00000204022	ENSG00000204022			21773	protein-coding gene	gene with protein product		613921	"""lipase-like, ab-hydrolase domain containing 1"", ""lipase, family member J"""	LIPL1			Standard	NM_001010939		Approved	bA425M17.2	uc001kff.3	Q5W064	OTTHUMG00000018691	ENST00000371939.3:c.440-1G>A	chr10.hg19:g.90356037G>A		359.0	0.0		508.0	52.0	NM_001010939	A8MT98|Q0P671	Missense_Mutation	SNP	ENST00000371939.3	hg19	CCDS31240.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.242293	0.39598	.	.	ENSG00000204022	ENST00000371939;ENST00000531458	T;T	0.71817	-0.6;-0.6	4.46	-5.17	0.02849	Alpha/beta hydrolase fold-1 (1);	0.686580	0.12597	N	0.455039	T	0.77089	0.4079	M	0.65320	2	0.26196	N	0.979516	D	0.64830	0.994	P	0.61592	0.891	T	0.73924	-0.3829	9	.	.	.	.	16.5221	0.84320	0.0977:0.2467:0.6555:0.0	.	147	Q5W064	LIPJ_HUMAN	D	147;11	ENSP00000361007:G147D;ENSP00000434211:G11D	.	G	+	2	0	LIPJ	90346017	0.045000	0.20229	0.213000	0.23690	0.432000	0.31715	-0.294000	0.08309	-0.777000	0.04572	-0.142000	0.14014	GGT	.	.		0.264	LIPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049248.2	XM_084377	Missense_Mutation
MYOF	26509	hgsc.bcm.edu	37	10	95134586	95134586	+	Silent	SNP	T	T	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:95134586T>A	ENST00000359263.4	-	23	2234	c.2235A>T	c.(2233-2235)acA>acT	p.T745T	MYOF_ENST00000371501.4_Silent_p.T745T|MYOF_ENST00000371502.4_Silent_p.T745T|MYOF_ENST00000358334.5_Silent_p.T732T	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	745					blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ACTTCACATCTGTGGCTTCCG	0.483																																					p.T745T		Atlas-SNP	.											.	MYOF	177	.	0			c.A2235T						.						76.0	79.0	78.0					10																	95134586		1922	4134	6056	SO:0001819	synonymous_variant	26509	exon23			CACATCTGTGGCT	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.2235A>T	chr10.hg19:g.95134586T>A		128.0	0.0		148.0	47.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	hg19	CCDS41551.1																																																																																			.	.		0.483	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
CWF19L1	55280	hgsc.bcm.edu	37	10	102013179	102013179	+	Splice_Site	SNP	G	G	A	rs150239404		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:102013179G>A	ENST00000354105.4	-	6	708	c.622C>T	c.(622-624)Cga>Tga	p.R208*	CWF19L1_ENST00000478047.1_5'UTR	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	208							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		GCTACTCACCGATATGGAAGC	0.383																																					p.R208X		Atlas-SNP	.											.	CWF19L1	39	.	0			c.C622T						.	G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	113.0	115.0	114.0		622	5.4	1.0	10	dbSNP_134	114	2,8598	2.2+/-6.3	0,2,4298	yes	stop-gained-near-splice	CWF19L1	NM_018294.4		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		208/539	102013179	3,13003	2203	4300	6503	SO:0001630	splice_region_variant	55280	exon6			CTCACCGATATGG	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.623+1C>T	chr10.hg19:g.102013179G>A		104.0	0.0		104.0	18.0	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Nonsense_Mutation	SNP	ENST00000354105.4	hg19	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	G	36	5.749544	0.96890	2.27E-4	2.33E-4	ENSG00000095485	ENST00000354105	.	.	.	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.254	11.7084	0.51610	0.0:0.0:0.8235:0.1765	.	.	.	.	X	208	.	ENSP00000326411:R208X	R	-	1	2	CWF19L1	102003169	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.735000	0.62051	2.516000	0.84829	0.561000	0.74099	CGA	.	G|1.000;A|0.000		0.383	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	Nonsense_Mutation
INA	9118	hgsc.bcm.edu	37	10	105037736	105037736	+	Silent	SNP	G	G	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:105037736G>T	ENST00000369849.4	+	1	817	c.768G>T	c.(766-768)gtG>gtT	p.V256V		NM_032727.3	NP_116116.1	Q16352	AINX_HUMAN	internexin neuronal intermediate filament protein, alpha	256	Linker 2.|Rod.				cell differentiation (GO:0030154)|neurofilament cytoskeleton organization (GO:0060052)|substantia nigra development (GO:0021762)	cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular space (GO:0005615)|neurofilament (GO:0005883)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)	13				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		ACGTGACTGTGGCTAAACCAG	0.647																																					p.V256V		Atlas-SNP	.											.	INA	34	.	0			c.G768T						.						38.0	32.0	34.0					10																	105037736		2201	4299	6500	SO:0001819	synonymous_variant	9118	exon1			GACTGTGGCTAAA	S78296	CCDS7545.1	10q24	2013-01-16			ENSG00000148798	ENSG00000148798		"""Intermediate filaments type IV"""	6057	protein-coding gene	gene with protein product		605338		NEF5		7769995	Standard	NM_032727		Approved	NF-66	uc001kws.3	Q16352	OTTHUMG00000018986	ENST00000369849.4:c.768G>T	chr10.hg19:g.105037736G>T		165.0	0.0		170.0	27.0	NM_032727	B1AQK0|Q9BRC5	Silent	SNP	ENST00000369849.4	hg19	CCDS7545.1																																																																																			.	.		0.647	INA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050145.1	NM_032727	
LHPP	64077	hgsc.bcm.edu	37	10	126205791	126205791	+	Missense_Mutation	SNP	G	G	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr10:126205791G>T	ENST00000368842.5	+	6	695	c.667G>T	c.(667-669)Gcc>Tcc	p.A223S	LHPP_ENST00000368839.1_Intron	NM_022126.3	NP_071409.3	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	223					phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|phosphohistidine phosphatase activity (GO:0008969)|protein homodimerization activity (GO:0042803)			large_intestine(2)|lung(2)	4		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)		CGTCGGCGGTGCCCAGCGGTG	0.577																																					p.A223S	GBM(165;1980 2715 15999 18454)	Atlas-SNP	.											LHPP,NS,carcinoma,0,1	LHPP	18	.	0			c.G667T						.						80.0	72.0	75.0					10																	126205791		2203	4299	6502	SO:0001583	missense	64077	exon6			GGCGGTGCCCAGC	AB049629	CCDS7640.1, CCDS53587.1	10q26.2	2010-02-17			ENSG00000107902	ENSG00000107902	3.6.1.1		30042	protein-coding gene	gene with protein product						12801912, 16430861	Standard	NM_022126		Approved	HDHD2B	uc001lhs.2	Q9H008	OTTHUMG00000019214	ENST00000368842.5:c.667G>T	chr10.hg19:g.126205791G>T	ENSP00000357835:p.Ala223Ser	68.0	0.0		77.0	17.0	NM_022126	B3KP20|Q2TBE9|Q5VUV9|Q5VUW0	Missense_Mutation	SNP	ENST00000368842.5	hg19	CCDS7640.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.874671	0.91664	.	.	ENSG00000107902	ENST00000368842	T	0.52526	0.66	4.83	4.83	0.62350	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.73410	0.3583	M	0.90425	3.115	0.80722	D	1	D	0.62365	0.991	D	0.67900	0.954	T	0.80165	-0.1496	10	0.72032	D	0.01	-16.3445	16.4736	0.84125	0.0:0.0:1.0:0.0	.	223	Q9H008	LHPP_HUMAN	S	223	ENSP00000357835:A223S	ENSP00000357835:A223S	A	+	1	0	LHPP	126195781	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.106000	0.77039	2.404000	0.81709	0.484000	0.47621	GCC	.	.		0.577	LHPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050870.1	NM_022126	
OR51G2	81282	hgsc.bcm.edu	37	11	4936102	4936102	+	Silent	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:4936102A>G	ENST00000322013.3	-	1	820	c.792T>C	c.(790-792)tcT>tcC	p.S264S	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGGATGACAGAGAGGCCAA	0.517																																					p.S264S		Atlas-SNP	.											.	OR51G2	70	.	0			c.T792C						.						139.0	122.0	128.0					11																	4936102		2201	4298	6499	SO:0001819	synonymous_variant	81282	exon1			GATGACAGAGAGG	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"""GPCR / Class A : Olfactory receptors"""	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.792T>C	chr11.hg19:g.4936102A>G		163.0	0.0		164.0	37.0	NM_001005238	Q6IFH7	Silent	SNP	ENST00000322013.3	hg19	CCDS31365.1																																																																																			.	.		0.517	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238	
ABTB2	25841	hgsc.bcm.edu	37	11	34192494	34192494	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:34192494C>T	ENST00000435224.2	-	5	1946	c.1522G>A	c.(1522-1524)Gag>Aag	p.E508K	ABTB2_ENST00000530814.1_5'Flank|ABTB2_ENST00000298992.2_Missense_Mutation_p.E322K	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	508					cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CCCAAGGCCTCGATGGCTTGG	0.567																																					p.E508K		Atlas-SNP	.											.	ABTB2	101	.	0			c.G1522A						.						109.0	93.0	98.0					11																	34192494		2202	4298	6500	SO:0001583	missense	25841	exon5			AGGCCTCGATGGC	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.1522G>A	chr11.hg19:g.34192494C>T	ENSP00000410157:p.Glu508Lys	85.0	0.0		81.0	11.0	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	hg19	CCDS7890.2	.	.	.	.	.	.	.	.	.	.	C	12.83	2.054543	0.36277	.	.	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.66638	-0.22;-0.22	5.03	5.03	0.67393	Ankyrin repeat-containing domain (1);	0.663526	0.15490	N	0.259639	T	0.52709	0.1751	N	0.25031	0.7	0.30151	N	0.803068	B	0.24533	0.105	B	0.20955	0.032	T	0.50499	-0.8821	10	0.28530	T	0.3	-1.0545	14.0228	0.64568	0.0:0.8486:0.1514:0.0	.	322	Q8N961	ABTB2_HUMAN	K	508;322	ENSP00000410157:E508K;ENSP00000298992:E322K	ENSP00000298992:E322K	E	-	1	0	ABTB2	34149070	0.200000	0.23398	0.996000	0.52242	0.359000	0.29487	2.092000	0.41700	2.329000	0.79093	0.491000	0.48974	GAG	.	.		0.567	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
OR5M10	390167	hgsc.bcm.edu	37	11	56344374	56344374	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:56344374G>A	ENST00000526812.2	-	1	889	c.824C>T	c.(823-825)gCa>gTa	p.A275V		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	275						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)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						ATAAAAGACTGCAATTATTTT	0.413																																					p.A275V		Atlas-SNP	.											.	OR5M10	56	.	0			c.C824T						.						202.0	197.0	198.0					11																	56344374		1832	4087	5919	SO:0001583	missense	390167	exon1			AAGACTGCAATTA	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"""GPCR / Class A : Olfactory receptors"""	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.824C>T	chr11.hg19:g.56344374G>A	ENSP00000436004:p.Ala275Val	308.0	0.0		276.0	55.0	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	hg19	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629812	0.46944	.	.	ENSG00000254834	ENST00000526812	T	0.00202	8.56	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00580	0.0019	M	0.79011	2.435	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.54132	-0.8339	9	0.72032	D	0.01	.	15.6851	0.77402	0.0:0.0:1.0:0.0	.	275	Q6IEU7	OR5MA_HUMAN	V	275	ENSP00000436004:A275V	ENSP00000436004:A275V	A	-	2	0	OR5M10	56100950	0.696000	0.27757	0.101000	0.21167	0.437000	0.31866	4.921000	0.63397	2.316000	0.78162	0.632000	0.83419	GCA	.	.		0.413	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741	
C11orf24	53838	hgsc.bcm.edu	37	11	68029219	68029219	+	Missense_Mutation	SNP	G	G	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:68029219G>C	ENST00000304271.6	-	4	1646	c.1244C>G	c.(1243-1245)aCa>aGa	p.T415R	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'Flank	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	415						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						AACCAAGACTGTGATGAAAAG	0.527																																					p.T415R	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.C1244G						.						111.0	105.0	107.0					11																	68029219		2200	4294	6494	SO:0001583	missense	53838	exon4			AAGACTGTGATGA	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.1244C>G	chr11.hg19:g.68029219G>C	ENSP00000307264:p.Thr415Arg	127.0	0.0		142.0	19.0	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	hg19	CCDS8180.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040772	0.75732	.	.	ENSG00000171067	ENST00000304271	T	0.34472	1.36	4.89	1.87	0.25490	.	0.719989	0.11457	N	0.562140	T	0.46425	0.1392	L	0.43152	1.355	0.09310	N	0.999998	D	0.76494	0.999	D	0.65010	0.931	T	0.25293	-1.0136	10	0.72032	D	0.01	-0.4645	8.0294	0.30457	0.1461:0.1304:0.7235:0.0	.	415	Q96F05	CK024_HUMAN	R	415	ENSP00000307264:T415R	ENSP00000307264:T415R	T	-	2	0	C11orf24	67785795	0.739000	0.28196	0.001000	0.08648	0.987000	0.75469	2.777000	0.47717	0.488000	0.27723	0.484000	0.47621	ACA	.	.		0.527	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
PAK1	5058	hgsc.bcm.edu	37	11	77060308	77060308	+	Silent	SNP	T	T	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:77060308T>A	ENST00000356341.3	-	9	1392	c.861A>T	c.(859-861)gcA>gcT	p.A287A	PAK1_ENST00000278568.4_Silent_p.A287A|PAK1_ENST00000528203.1_Silent_p.A189A|PAK1_ENST00000530617.1_Silent_p.A287A|PAK1_ENST00000525542.1_5'UTR	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	287	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					CCACATCCATTGCTGTGTACA	0.428																																					p.A287A		Atlas-SNP	.											.	PAK1	89	.	0			c.A861T						.						79.0	62.0	68.0					11																	77060308		2200	4292	6492	SO:0001819	synonymous_variant	5058	exon9			ATCCATTGCTGTG	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"""STE20 homolog, yeast"""	602590	"""p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)"", ""p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"""			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.861A>T	chr11.hg19:g.77060308T>A		122.0	0.0		86.0	18.0	NM_001128620	O75561|Q13567|Q32M53|Q32M54|Q86W79	Silent	SNP	ENST00000356341.3	hg19	CCDS8250.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.785341	0.31593	.	.	ENSG00000149269	ENST00000533285	.	.	.	5.91	-0.562	0.11781	.	.	.	.	.	T	0.38878	0.1057	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25779	-1.0122	4	.	.	.	.	0.1874	0.00130	0.2304:0.2046:0.237:0.3281	.	.	.	.	Y	9	.	.	N	-	1	0	PAK1	76737956	0.841000	0.29509	0.997000	0.53966	0.987000	0.75469	-0.164000	0.09983	-0.109000	0.12044	0.533000	0.62120	AAT	.	.		0.428	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576	
TENM4	26011	hgsc.bcm.edu	37	11	78387340	78387340	+	Missense_Mutation	SNP	G	G	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:78387340G>C	ENST00000278550.7	-	30	5815	c.5353C>G	c.(5353-5355)Cac>Gac	p.H1785D		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1785					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GCCAGCAAGTGGGGCTCAGTC	0.642																																					p.H1785D		Atlas-SNP	.											.	.	.	.	0			c.C5353G						.						31.0	38.0	35.0					11																	78387340		2157	4249	6406	SO:0001583	missense	26011	exon30			GCAAGTGGGGCTC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5353C>G	chr11.hg19:g.78387340G>C	ENSP00000278550:p.His1785Asp	60.0	0.0		62.0	10.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.855005	0.91355	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.90197	-2.63;0.81	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.94686	0.8286	M	0.72118	2.19	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	D	0.94188	0.7438	9	.	.	.	.	18.2069	0.89858	0.0:0.0:1.0:0.0	.	1785	Q6N022	TEN4_HUMAN	D	1785;249	ENSP00000278550:H1785D;ENSP00000431711:H249D	.	H	-	1	0	ODZ4	78064988	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.580000	0.98207	2.584000	0.87258	0.650000	0.86243	CAC	.	.		0.642	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
FAT3	120114	hgsc.bcm.edu	37	11	92533209	92533209	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:92533209G>A	ENST00000298047.6	+	9	7047	c.7030G>A	c.(7030-7032)Ggc>Agc	p.G2344S	FAT3_ENST00000409404.2_Missense_Mutation_p.G2344S|FAT3_ENST00000525166.1_Missense_Mutation_p.G2194S			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2344	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TAGCTCAAGTGGCTTAATCCT	0.398										TCGA Ovarian(4;0.039)																											p.G2344S		Atlas-SNP	.											.	FAT3	1822	.	0			c.G7030A						.						98.0	92.0	94.0					11																	92533209		1955	4145	6100	SO:0001583	missense	120114	exon9			TCAAGTGGCTTAA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7030G>A	chr11.hg19:g.92533209G>A	ENSP00000298047:p.Gly2344Ser	103.0	0.0		113.0	5.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	22.6	4.309725	0.81247	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.69561	-0.41;-0.41;-0.41	5.95	5.95	0.96441	.	.	.	.	.	D	0.90277	0.6959	H	0.98818	4.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93438	0.6791	9	0.87932	D	0	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	2344	Q8TDW7-3	.	S	2344;2344;2194	ENSP00000298047:G2344S;ENSP00000387040:G2344S;ENSP00000432586:G2194S	ENSP00000298047:G2344S	G	+	1	0	FAT3	92172857	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.787000	0.99055	2.824000	0.97209	0.655000	0.94253	GGC	.	.		0.398	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
HTR3B	9177	hgsc.bcm.edu	37	11	113803709	113803709	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:113803709A>G	ENST00000260191.2	+	6	847	c.590A>G	c.(589-591)gAc>gGc	p.D197G	HTR3B_ENST00000537778.1_Missense_Mutation_p.D186G	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	197					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	ATTCAGCATGACAAAAAGGCG	0.473																																					p.D197G		Atlas-SNP	.											.	HTR3B	50	.	0			c.A590G						.						141.0	129.0	133.0					11																	113803709		2201	4296	6497	SO:0001583	missense	9177	exon6			AGCATGACAAAAA	AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5298	protein-coding gene	gene with protein product		604654	"""5-hydroxytryptamine (serotonin) receptor 3B"""			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.590A>G	chr11.hg19:g.113803709A>G	ENSP00000260191:p.Asp197Gly	102.0	0.0		123.0	42.0	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	hg19	CCDS8364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.02|19.02	3.746905|3.746905	0.69418|0.69418	.|.	.|.	ENSG00000149305|ENSG00000149305	ENST00000260191;ENST00000537778|ENST00000543092	T;T|.	0.80909|.	-1.43;-1.43|.	6.17|6.17	6.17|6.17	0.99709|0.99709	Neurotransmitter-gated ion-channel ligand-binding (3);|.	0.049670|.	0.85682|.	D|.	0.000000|.	D|D	0.86928|0.86928	0.6051|0.6051	H|H	0.94698|0.94698	3.57|3.57	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.996;0.987|.	D;P|.	0.65233|.	0.933;0.831|.	D|D	0.90300|0.90300	0.4329|0.4329	10|5	0.87932|.	D|.	0|.	-9.1491|-9.1491	15.8048|15.8048	0.78491|0.78491	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	186;197|.	O95264-2;O95264|.	.;5HT3B_HUMAN|.	G|A	197;186|126	ENSP00000260191:D197G;ENSP00000443118:D186G|.	ENSP00000260191:D197G|.	D|T	+|+	2|1	0|0	HTR3B|HTR3B	113308919|113308919	1.000000|1.000000	0.71417|0.71417	0.848000|0.848000	0.33437|0.33437	0.327000|0.327000	0.28475|0.28475	8.181000|8.181000	0.89696|0.89696	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.473	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028	
ROBO4	54538	hgsc.bcm.edu	37	11	124756912	124756912	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr11:124756912G>A	ENST00000306534.3	-	15	2881	c.2396C>T	c.(2395-2397)gCc>gTc	p.A799V	RP11-664I21.5_ENST00000524453.1_RNA|ROBO4_ENST00000533054.1_Missense_Mutation_p.A654V	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	799					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CAAGCACAGGGCTACCTCCTC	0.592																																					p.A799V		Atlas-SNP	.											.	ROBO4	130	.	0			c.C2396T						.						79.0	80.0	80.0					11																	124756912		2201	4299	6500	SO:0001583	missense	54538	exon15			CACAGGGCTACCT	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.2396C>T	chr11.hg19:g.124756912G>A	ENSP00000304945:p.Ala799Val	157.0	0.0		132.0	33.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	g	19.79	3.893829	0.72639	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.71934	-0.61;-0.31	4.83	4.83	0.62350	.	0.000000	0.36034	N	0.002826	D	0.82802	0.5116	M	0.71581	2.175	0.33596	D	0.601664	P;D;D	0.76494	0.954;0.999;0.999	D;D;D	0.72075	0.943;0.976;0.946	D	0.88109	0.2824	10	0.56958	D	0.05	.	16.5107	0.84284	0.0:0.0:1.0:0.0	.	799;689;799	Q8WZ75-2;Q8WZ75-3;Q8WZ75	.;.;ROBO4_HUMAN	V	799;689;654	ENSP00000304945:A799V;ENSP00000437129:A654V	ENSP00000304945:A799V	A	-	2	0	ROBO4	124262122	1.000000	0.71417	0.999000	0.59377	0.742000	0.42306	3.239000	0.51360	2.231000	0.72958	0.651000	0.88453	GCC	.	.		0.592	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
GPR162	27239	hgsc.bcm.edu	37	12	6933599	6933599	+	Missense_Mutation	SNP	T	T	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:6933599T>G	ENST00000311268.3	+	2	1322	c.535T>G	c.(535-537)Ttt>Gtt	p.F179V	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						CGGCCTCGGCTTTGGCGTTTG	0.597																																					p.F179V		Atlas-SNP	.											.	GPR162	55	.	0			c.T535G						.						86.0	82.0	83.0					12																	6933599		2203	4300	6503	SO:0001583	missense	27239	exon2			CTCGGCTTTGGCG	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.535T>G	chr12.hg19:g.6933599T>G	ENSP00000311528:p.Phe179Val	82.0	0.0		93.0	17.0	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.688914	0.88735	.	.	ENSG00000250510	ENST00000311268	T	0.69561	-0.41	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.71143	0.3305	L	0.34521	1.04	0.80722	D	1	D;P	0.59767	0.986;0.856	D;P	0.64144	0.922;0.635	T	0.75139	-0.3423	9	0.87932	D	0	.	13.6533	0.62323	0.0:0.0:0.0:1.0	.	179;179	B7Z3U3;Q16538	.;GP162_HUMAN	V	179	ENSP00000311528:F179V	ENSP00000311528:F179V	F	+	1	0	GPR162	6803860	1.000000	0.71417	0.738000	0.30950	0.883000	0.51084	7.858000	0.86971	1.826000	0.53198	0.402000	0.26972	TTT	.	.		0.597	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
GPR162	27239	hgsc.bcm.edu	37	12	6933713	6933713	+	Missense_Mutation	SNP	C	C	T	rs375616091		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:6933713C>T	ENST00000311268.3	+	2	1436	c.649C>T	c.(649-651)Cgg>Tgg	p.R217W	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						TCGGCAGGCCCGGAGAGTGGG	0.662																																					p.R217W		Atlas-SNP	.											GPR162,trunk,malignant_melanoma,-1,1	GPR162	55	.	0			c.C649T						.	C	,TRP/ARG	1,4405		0,1,2202	31.0	37.0	35.0		,649	3.6	1.0	12		35	0,8598		0,0,4299	no	intron,missense	GPR162	NM_014449.1,NM_019858.1	,101	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	,benign	,217/589	6933713	1,13003	2203	4299	6502	SO:0001583	missense	27239	exon2			CAGGCCCGGAGAG	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.649C>T	chr12.hg19:g.6933713C>T	ENSP00000311528:p.Arg217Trp	65.0	1.0		68.0	21.0	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804265	0.70682	2.27E-4	0.0	ENSG00000250510	ENST00000311268	T	0.73469	-0.75	4.48	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.57373	0.2049	N	0.14661	0.345	0.80722	D	1	B;B	0.15141	0.001;0.012	B;B	0.08055	0.002;0.003	T	0.56044	-0.8044	9	0.72032	D	0.01	.	10.6787	0.45802	0.0:0.9108:0.0:0.0892	.	217;217	B7Z3U3;Q16538	.;GP162_HUMAN	W	217	ENSP00000311528:R217W	ENSP00000311528:R217W	R	+	1	2	GPR162	6803974	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	1.176000	0.31957	1.117000	0.41842	0.491000	0.48974	CGG	.	.		0.662	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
ITGB7	3695	hgsc.bcm.edu	37	12	53585410	53585410	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:53585410G>A	ENST00000267082.5	-	16	2558	c.2327C>T	c.(2326-2328)cCt>cTt	p.P776L	ITGB7_ENST00000550743.2_Missense_Mutation_p.P628L|ITGB7_ENST00000422257.3_Missense_Mutation_p.P776L|ITGB7_ENST00000338737.4_Missense_Mutation_p.P628L	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	776					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTTGTAGAGAGGATTACTGTC	0.498																																					p.P776L		Atlas-SNP	.											.	ITGB7	60	.	0			c.C2327T						.						174.0	161.0	165.0					12																	53585410		2203	4300	6503	SO:0001583	missense	3695	exon16			TAGAGAGGATTAC		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.2327C>T	chr12.hg19:g.53585410G>A	ENSP00000267082:p.Pro776Leu	114.0	0.0		111.0	20.0	NM_000889	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	hg19	CCDS8849.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.169747	0.78452	.	.	ENSG00000139626	ENST00000422257;ENST00000267082;ENST00000338737	D;D;D	0.99737	-6.59;-6.59;-6.59	4.05	4.05	0.47172	Integrin beta subunit, cytoplasmic (2);	0.000000	0.37348	N	0.002128	D	0.99739	0.9897	M	0.92268	3.29	0.45995	D	0.998801	D	0.89917	1.0	D	0.91635	0.999	D	0.97017	0.9740	10	0.87932	D	0	.	14.5236	0.67870	0.0:0.0:1.0:0.0	.	776	P26010	ITB7_HUMAN	L	776;776;628	ENSP00000408741:P776L;ENSP00000267082:P776L;ENSP00000345501:P628L	ENSP00000267082:P776L	P	-	2	0	ITGB7	51871677	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	7.352000	0.79404	2.571000	0.86741	0.563000	0.77884	CCT	.	.		0.498	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2		
MON2	23041	hgsc.bcm.edu	37	12	62902146	62902146	+	Silent	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:62902146A>G	ENST00000393632.2	+	8	1261	c.870A>G	c.(868-870)agA>agG	p.R290R	MON2_ENST00000549378.1_3'UTR|MON2_ENST00000393630.3_Silent_p.R290R|MON2_ENST00000546600.1_Silent_p.R290R|MON2_ENST00000393629.2_Silent_p.R290R|MON2_ENST00000280379.6_Silent_p.R290R|MON2_ENST00000552115.1_Silent_p.R290R|MON2_ENST00000552738.1_Silent_p.R290R	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	290					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TAAAGTTCAGACAAGGTTCCA	0.388																																					p.R290R		Atlas-SNP	.											.	MON2	160	.	0			c.A870G						.						125.0	118.0	120.0					12																	62902146		2202	4300	6502	SO:0001819	synonymous_variant	23041	exon8			GTTCAGACAAGGT		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.870A>G	chr12.hg19:g.62902146A>G		167.0	0.0		225.0	9.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	hg19	CCDS31849.1																																																																																			.	.		0.388	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
MYF6	4618	hgsc.bcm.edu	37	12	81101722	81101722	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:81101722G>A	ENST00000228641.3	+	1	446	c.224G>A	c.(223-225)gGc>gAc	p.G75D		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	75					muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						CACTGCCCCGGCCAGTGTCTG	0.647																																					p.G75D		Atlas-SNP	.											.	MYF6	74	.	0			c.G224A						.						29.0	36.0	33.0					12																	81101722		2202	4300	6502	SO:0001583	missense	4618	exon1			GCCCCGGCCAGTG		CCDS9019.1	12q21	2013-05-21				ENSG00000111046		"""Basic helix-loop-helix proteins"""	7566	protein-coding gene	gene with protein product	"""muscle-specific regulatory factor 4"""	159991				8978788	Standard	NM_002469		Approved	MRF4, bHLHc4	uc001szf.2	P23409		ENST00000228641.3:c.224G>A	chr12.hg19:g.81101722G>A	ENSP00000228641:p.Gly75Asp	64.0	0.0		104.0	25.0	NM_002469	B2R898|Q53X80|Q6FHI9	Missense_Mutation	SNP	ENST00000228641.3	hg19	CCDS9019.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.755048	0.89843	.	.	ENSG00000111046	ENST00000228641	D	0.91351	-2.83	5.62	5.62	0.85841	Myogenic basic muscle-specific protein (2);	0.000000	0.85682	D	0.000000	D	0.96018	0.8703	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96185	0.9133	10	0.87932	D	0	-14.9884	19.6517	0.95819	0.0:0.0:1.0:0.0	.	75	P23409	MYF6_HUMAN	D	75	ENSP00000228641:G75D	ENSP00000228641:G75D	G	+	2	0	MYF6	79625853	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	9.476000	0.97823	2.662000	0.90505	0.655000	0.94253	GGC	.	.		0.647	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469	
BTBD11	121551	hgsc.bcm.edu	37	12	108013779	108013779	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:108013779G>A	ENST00000280758.5	+	11	2997	c.2469G>A	c.(2467-2469)ctG>ctA	p.L823L	BTBD11_ENST00000420571.2_Silent_p.L704L|BTBD11_ENST00000490090.2_Silent_p.L823L|RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000357167.4_Silent_p.L360L	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	823						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CGTGGACTCTGCACACGTGGC	0.602																																					p.L823L		Atlas-SNP	.											.	BTBD11	122	.	0			c.G2469A						.						32.0	30.0	31.0					12																	108013779		2203	4300	6503	SO:0001819	synonymous_variant	121551	exon11			GACTCTGCACACG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2469G>A	chr12.hg19:g.108013779G>A		50.0	0.0		68.0	6.0	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	hg19	CCDS31893.1																																																																																			.	.		0.602	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
ARPC3	10094	hgsc.bcm.edu	37	12	110874389	110874389	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:110874389C>T	ENST00000228825.7	-	5	498	c.352G>A	c.(352-354)Gcc>Acc	p.A118T	RP11-478C19.2_ENST00000550231.1_RNA	NM_001278556.1|NM_005719.2	NP_001265485.1|NP_005710.1	O15145	ARPC3_HUMAN	actin related protein 2/3 complex, subunit 3, 21kDa	118					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			lung(1)|ovary(1)	2						GCAGGTTTGGCATAAATTGCG	0.428																																					p.A118T		Atlas-SNP	.											.	ARPC3	7	.	0			c.G352A						.						189.0	173.0	179.0					12																	110874389		2203	4300	6503	SO:0001583	missense	10094	exon5			GTTTGGCATAAAT	AF006086	CCDS9146.1	12q24	2011-07-06	2002-08-29		ENSG00000111229	ENSG00000111229		"""Actin related protein 2/3 complex subunits"""	706	protein-coding gene	gene with protein product		604225	"""actin related protein 2/3 complex, subunit 3 (21 kD)"""			9230079, 9359840	Standard	NM_001278556		Approved	p21-Arc, ARC21	uc001tqq.3	O15145	OTTHUMG00000134333	ENST00000228825.7:c.352G>A	chr12.hg19:g.110874389C>T	ENSP00000228825:p.Ala118Thr	46.0	0.0		65.0	8.0	NM_005719	O00554	Missense_Mutation	SNP	ENST00000228825.7	hg19	CCDS9146.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372719	0.61624	.	.	ENSG00000111229	ENST00000228825;ENST00000392683	.	.	.	5.95	5.95	0.96441	.	0.140386	0.64402	D	0.000004	T	0.55909	0.1950	L	0.28694	0.88	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.50849	-0.8779	9	0.87932	D	0	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	118	O15145	ARPC3_HUMAN	T	118	.	ENSP00000228825:A118T	A	-	1	0	ARPC3	109358772	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.444000	0.80532	2.824000	0.97209	0.655000	0.94253	GCC	.	.		0.428	ARPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259487.2		
CCDC60	160777	hgsc.bcm.edu	37	12	119957988	119957988	+	Missense_Mutation	SNP	T	T	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr12:119957988T>C	ENST00000327554.2	+	9	1496	c.1031T>C	c.(1030-1032)cTc>cCc	p.L344P	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	344										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CAGACCACTCTCAAATCAAGG	0.507																																					p.L344P		Atlas-SNP	.											.	CCDC60	84	.	0			c.T1031C						.						125.0	124.0	124.0					12																	119957988		2203	4300	6503	SO:0001583	missense	160777	exon9			CCACTCTCAAATC	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1031T>C	chr12.hg19:g.119957988T>C	ENSP00000333374:p.Leu344Pro	68.0	0.0		72.0	13.0	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	hg19	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	T	0.128	-1.116803	0.01799	.	.	ENSG00000183273	ENST00000327554	T	0.24151	1.87	3.94	-7.87	0.01183	.	2.297300	0.01611	N	0.022527	T	0.13586	0.0329	N	0.22421	0.69	0.09310	N	1	P	0.34757	0.467	B	0.31686	0.134	T	0.08973	-1.0696	9	.	.	.	6.0E-4	6.1289	0.20194	0.1612:0.0:0.3382:0.5006	.	344	Q8IWA6	CCD60_HUMAN	P	344	ENSP00000333374:L344P	.	L	+	2	0	CCDC60	118442371	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.430000	0.02434	-2.578000	0.00464	-2.093000	0.00369	CTC	.	.		0.507	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
PABPC3	5042	hgsc.bcm.edu	37	13	25671865	25671865	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr13:25671865C>T	ENST00000281589.3	+	1	1566	c.1529C>T	c.(1528-1530)gCg>gTg	p.A510V		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	510					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAATATGCTGCGGGAGTTCGC	0.527																																					p.A510V		Atlas-SNP	.											.	PABPC3	129	.	0			c.C1529T						.						64.0	60.0	62.0					13																	25671865		2203	4300	6503	SO:0001583	missense	5042	exon1			ATGCTGCGGGAGT	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1529C>T	chr13.hg19:g.25671865C>T	ENSP00000281589:p.Ala510Val	70.0	0.0		71.0	13.0	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	hg19	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254611	0.22965	.	.	ENSG00000151846	ENST00000281589	T	0.43688	0.94	1.0	0.0783	0.14411	Polyadenylate-binding protein/Hyperplastic disc protein (1);	0.134298	0.31381	N	0.007744	T	0.24928	0.0605	L	0.31752	0.955	0.34986	D	0.754589	B	0.06786	0.001	B	0.01281	0.0	T	0.08554	-1.0716	10	0.36615	T	0.2	.	6.1155	0.20124	0.3017:0.6983:0.0:0.0	.	510	Q9H361	PABP3_HUMAN	V	510	ENSP00000281589:A510V	ENSP00000281589:A510V	A	+	2	0	PABPC3	24569865	0.988000	0.35896	0.503000	0.27626	0.034000	0.12701	3.257000	0.51500	0.003000	0.14656	-0.361000	0.07541	GCG	.	.		0.527	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
OLFM4	10562	hgsc.bcm.edu	37	13	53603061	53603061	+	Silent	SNP	C	C	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr13:53603061C>A	ENST00000219022.2	+	1	168	c.90C>A	c.(88-90)ccC>ccA	p.P30P		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	30					cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		CTCCAATTCCCAGCCCCGGCT	0.607																																					p.P30P		Atlas-SNP	.											.	OLFM4	94	.	0			c.C90A						.						104.0	110.0	108.0					13																	53603061		2203	4300	6503	SO:0001819	synonymous_variant	10562	exon1			AATTCCCAGCCCC	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.90C>A	chr13.hg19:g.53603061C>A		91.0	0.0		65.0	12.0	NM_006418	O95362|Q5VWG0|Q86T22	Silent	SNP	ENST00000219022.2	hg19	CCDS9440.1																																																																																			.	.		0.607	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418	
SCEL	8796	hgsc.bcm.edu	37	13	78211328	78211328	+	Splice_Site	SNP	A	A	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr13:78211328A>T	ENST00000349847.3	+	30	1921	c.1837A>T	c.(1837-1839)Agg>Tgg	p.R613W	SCEL_ENST00000377246.3_Splice_Site_p.R593W|SCEL_ENST00000535157.1_Splice_Site_p.R571W	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	613					embryo development (GO:0009790)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(18)|ovary(5)|prostate(1)|stomach(1)|urinary_tract(1)	40		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AACTTCTGATAGGTGAGTATG	0.328																																					p.R613W		Atlas-SNP	.											.	SCEL	85	.	0			c.A1837T						.						87.0	81.0	83.0					13																	78211328		2203	4298	6501	SO:0001630	splice_region_variant	8796	exon30			TCTGATAGGTGAG	AF045941	CCDS9458.1, CCDS9459.1, CCDS53877.1	13q22	2008-07-18			ENSG00000136155	ENSG00000136155			10573	protein-coding gene	gene with protein product		604112				9813070	Standard	NM_003843		Approved	FLJ21667, MGC22531	uc001vki.3	O95171	OTTHUMG00000017107	ENST00000349847.3:c.1838+1A>T	chr13.hg19:g.78211328A>T		55.0	0.0		58.0	9.0	NM_144777	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	hg19	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.289698	0.80914	.	.	ENSG00000136155	ENST00000535157;ENST00000377246;ENST00000349847	D;D;D	0.81659	-1.52;-1.52;-1.52	5.93	4.69	0.59074	.	0.000000	0.64402	D	0.000004	T	0.81163	0.4765	L	0.38953	1.18	0.42116	D	0.991407	P;P;D	0.56521	0.949;0.949;0.976	P;P;D	0.63877	0.889;0.879;0.919	T	0.81885	-0.0727	10	0.72032	D	0.01	-12.9835	6.396	0.21613	0.682:0.1624:0.0:0.1556	.	571;593;613	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	W	571;593;613	ENSP00000437895:R571W;ENSP00000366454:R593W;ENSP00000302579:R613W	ENSP00000302579:R613W	R	+	1	2	SCEL	77109329	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.402000	0.34600	2.263000	0.75096	0.533000	0.62120	AGG	.	.		0.328	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	Missense_Mutation
RNASE12	493901	hgsc.bcm.edu	37	14	21058715	21058715	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:21058715C>T	ENST00000556526.1	-	1	267	c.168G>A	c.(166-168)agG>agA	p.R56R	RNASE11_ENST00000555283.1_Intron|RP11-14J7.6_ENST00000554993.1_RNA|RP11-14J7.6_ENST00000554006.1_RNA|RNASE11_ENST00000555841.1_5'Flank|RNASE11_ENST00000610205.1_5'Flank|RNASE11_ENST00000398009.2_5'Flank|RNASE11_ENST00000553849.1_5'Flank|RNASE11_ENST00000432835.2_5'Flank|RNASE11_ENST00000398008.2_5'Flank|RP11-14J7.6_ENST00000556487.1_RNA|RP11-14J7.6_ENST00000554529.1_RNA|RP11-14J7.6_ENST00000553604.1_RNA	NM_001024822.2	NP_001019993.1	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	56						extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			kidney(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		GGTCAGGTTCCCTGATAACTC	0.438																																					p.R56R		Atlas-SNP	.											.	RNASE12	19	.	0			c.G168A						.						149.0	123.0	132.0					14																	21058715		2203	4300	6503	SO:0001819	synonymous_variant	493901	exon1			AGGTTCCCTGATA		CCDS32037.1	14q11.1	2012-10-05			ENSG00000258436	ENSG00000258436		"""Ribonucleases, RNase A"""	24211	protein-coding gene	gene with protein product							Standard	NM_001024822		Approved		uc001vxt.3	Q5GAN4	OTTHUMG00000170991	ENST00000556526.1:c.168G>A	chr14.hg19:g.21058715C>T		165.0	0.0		119.0	22.0	NM_001024822		Silent	SNP	ENST00000556526.1	hg19	CCDS32037.1																																																																																			.	.		0.438	RNASE12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411107.1		
C14orf93	60686	hgsc.bcm.edu	37	14	23467696	23467696	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:23467696C>T	ENST00000299088.6	-	2	966	c.537G>A	c.(535-537)agG>agA	p.R179R	C14orf93_ENST00000397382.4_Silent_p.R179R|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000397379.3_Silent_p.R179R|RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000557513.1_5'Flank|C14orf93_ENST00000397377.1_5'UTR|C14orf93_ENST00000341470.4_Silent_p.R179R|C14orf93_ENST00000406429.2_Silent_p.R179R	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	179						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		GCCGCATGTCCCTCTGAGTTG	0.657																																					p.R179R		Atlas-SNP	.											.	C14orf93	33	.	0			c.G537A						.						16.0	17.0	17.0					14																	23467696		2203	4296	6499	SO:0001819	synonymous_variant	60686	exon2			CATGTCCCTCTGA	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.537G>A	chr14.hg19:g.23467696C>T		155.0	0.0		152.0	26.0	NM_021944	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Silent	SNP	ENST00000299088.6	hg19	CCDS9583.1																																																																																			.	.		0.657	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944	
LRFN5	145581	hgsc.bcm.edu	37	14	42356164	42356164	+	Silent	SNP	T	T	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:42356164T>G	ENST00000298119.4	+	3	1525	c.336T>G	c.(334-336)acT>acG	p.T112T	LRFN5_ENST00000554120.1_Silent_p.T112T|LRFN5_ENST00000554171.1_Silent_p.T112T	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	112						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		ACAGATTGACTAAAATTACAA	0.358										HNSCC(30;0.082)																											p.T112T		Atlas-SNP	.											.	LRFN5	269	.	0			c.T336G						.						65.0	65.0	65.0					14																	42356164		2203	4300	6503	SO:0001819	synonymous_variant	145581	exon3			ATTGACTAAAATT	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	20360	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 8"""	612811	"""chromosome 14 open reading frame 146"""	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.336T>G	chr14.hg19:g.42356164T>G		150.0	0.0		144.0	24.0	NM_152447	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	hg19	CCDS9678.1																																																																																			.	.		0.358	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447	
ESRRB	2103	hgsc.bcm.edu	37	14	76957890	76957890	+	Silent	SNP	C	C	T	rs139812473		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr14:76957890C>T	ENST00000509242.1	+	7	986	c.888C>T	c.(886-888)gaC>gaT	p.D296D	ESRRB_ENST00000380887.2_Silent_p.D296D|ESRRB_ENST00000261532.7_Silent_p.D296D|ESRRB_ENST00000556177.1_Silent_p.D296D	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	296					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		TGCCCTATGACGACAAGCTGG	0.617																																					p.D296D		Atlas-SNP	.											.	ESRRB	114	.	0			c.C888T						.	C		1,4403		0,1,2201	61.0	46.0	51.0		888	-8.9	0.2	14	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	ESRRB	NM_004452.3		0,1,6501	TT,TC,CC		0.0,0.0227,0.0077		296/509	76957890	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	2103	exon8			CTATGACGACAAG	X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"""Nuclear hormone receptors"""	3473	protein-coding gene	gene with protein product		602167	"""deafness, autosomal recessive 35"""	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.888C>T	chr14.hg19:g.76957890C>T		136.0	0.0		110.0	19.0	NM_004452	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Silent	SNP	ENST00000509242.1	hg19	CCDS9850.2																																																																																			.	C|1.000;T|0.000		0.617	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1		
RYR3	6263	hgsc.bcm.edu	37	15	33954906	33954906	+	Silent	SNP	G	G	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:33954906G>T	ENST00000389232.4	+	35	5245	c.5175G>T	c.(5173-5175)gtG>gtT	p.V1725V	RYR3_ENST00000415757.3_Silent_p.V1725V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1725	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTGTGCCTGTGCTGAAACTCA	0.557																																					p.V1725V		Atlas-SNP	.											.	RYR3	760	.	0			c.G5175T						.						96.0	103.0	101.0					15																	33954906		2141	4267	6408	SO:0001819	synonymous_variant	6263	exon35			GCCTGTGCTGAAA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.5175G>T	chr15.hg19:g.33954906G>T		109.0	0.0		115.0	19.0	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.557	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
MEIS2	4212	hgsc.bcm.edu	37	15	37242602	37242602	+	Splice_Site	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:37242602C>T	ENST00000561208.1	-	9	1319		c.e9-1		MEIS2_ENST00000557796.2_Splice_Site|MEIS2_ENST00000397620.2_Splice_Site|MEIS2_ENST00000340545.5_Splice_Site|MEIS2_ENST00000444725.1_Splice_Site|MEIS2_ENST00000559561.1_Splice_Site|MEIS2_ENST00000219869.9_Splice_Site|MEIS2_ENST00000559085.1_Splice_Site|MEIS2_ENST00000397624.3_Splice_Site|MEIS2_ENST00000424352.2_Splice_Site|MEIS2_ENST00000382766.2_Splice_Site|MEIS2_ENST00000338564.5_Splice_Site			O14770	MEIS2_HUMAN	Meis homeobox 2						eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		GGTACGGATGCTAATGGAAAA	0.378																																					.		Atlas-SNP	.											.	MEIS2	99	.	0			c.901-1G>A						.						160.0	152.0	155.0					15																	37242602		2201	4297	6498	SO:0001630	splice_region_variant	4212	exon10			CGGATGCTAATGG	AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"""Homeoboxes / TALE class"""	7001	protein-coding gene	gene with protein product		601740	"""Meis (mouse) homolog 2"", ""Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"""			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.901-1G>A	chr15.hg19:g.37242602C>T		99.0	0.0		140.0	14.0	NM_170677	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Splice_Site	SNP	ENST00000561208.1	hg19	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719292	0.68844	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5721	0.95425	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MEIS2	35029894	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.651000	0.83577	2.857000	0.98124	0.650000	0.86243	.	.	.		0.378	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677	Intron
MGA	23269	hgsc.bcm.edu	37	15	41988636	41988636	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:41988636C>T	ENST00000570161.1	+	2	1428	c.1428C>T	c.(1426-1428)gtC>gtT	p.V476V	MGA_ENST00000219905.7_Silent_p.V476V|MGA_ENST00000545763.1_Silent_p.V476V|MGA_ENST00000566586.1_Silent_p.V476V|MGA_ENST00000389936.4_Silent_p.V476V|MGA_ENST00000568630.1_3'UTR			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CCTGTGCTGTCACCAGAAGCA	0.423																																					p.V476V		Atlas-SNP	.											.	MGA	264	.	0			c.C1428T						.						72.0	69.0	70.0					15																	41988636		1847	4096	5943	SO:0001819	synonymous_variant	23269	exon3			TGCTGTCACCAGA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1428C>T	chr15.hg19:g.41988636C>T		103.0	0.0		148.0	27.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.423	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
ARID3B	10620	hgsc.bcm.edu	37	15	74836644	74836644	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:74836644C>T	ENST00000346246.5	+	2	598	c.367C>T	c.(367-369)Cat>Tat	p.H123Y		NM_006465.2	NP_006456.1	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B (BRIGHT-like)	123						nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2)	14						AAAATATTTTCATGTGCAGAA	0.502																																					p.H123Y		Atlas-SNP	.											.	ARID3B	35	.	0			c.C367T						.						31.0	30.0	30.0					15																	74836644		2197	4292	6489	SO:0001583	missense	10620	exon2			TATTTTCATGTGC		CCDS10264.1	15q24	2013-02-07	2006-11-08		ENSG00000179361	ENSG00000179361		"""-"""	14350	protein-coding gene	gene with protein product		612457	"""AT rich interactive domain 3B (BRIGHT- like)"""				Standard	NM_006465		Approved	BDP, DRIL2	uc002ayd.3	Q8IVW6	OTTHUMG00000141321	ENST00000346246.5:c.367C>T	chr15.hg19:g.74836644C>T	ENSP00000343126:p.His123Tyr	216.0	0.0		288.0	24.0	NM_006465	O95443|Q59HC9|Q6P9C9	Missense_Mutation	SNP	ENST00000346246.5	hg19	CCDS10264.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823804	0.71143	.	.	ENSG00000179361	ENST00000382537;ENST00000346246;ENST00000395077	T	0.52295	0.67	5.5	4.58	0.56647	.	0.327366	0.32093	N	0.006584	T	0.55386	0.1917	L	0.32530	0.975	0.35248	D	0.778469	D;D;D	0.63880	0.993;0.991;0.993	D;P;D	0.70227	0.968;0.851;0.968	T	0.61505	-0.7049	10	0.25106	T	0.35	-2.8674	14.7359	0.69414	0.0:0.8557:0.1443:0.0	.	123;123;123	Q8IVW6;Q8IVW6-4;B4DQB0	ARI3B_HUMAN;.;.	Y	123	ENSP00000343126:H123Y	ENSP00000343126:H123Y	H	+	1	0	ARID3B	72623697	0.757000	0.28394	0.854000	0.33618	0.915000	0.54546	2.363000	0.44178	1.310000	0.45006	0.650000	0.86243	CAT	.	.		0.502	ARID3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280688.2	NM_006465	
ABHD17C	58489	hgsc.bcm.edu	37	15	81046707	81046707	+	Missense_Mutation	SNP	C	C	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:81046707C>G	ENST00000258884.4	+	3	1113	c.986C>G	c.(985-987)tCc>tGc	p.S329C	ABHD17C_ENST00000559506.1_3'UTR|ABHD17C_ENST00000560609.1_Missense_Mutation_p.S94C|ABHD17C_ENST00000558464.1_Missense_Mutation_p.S295C	NM_021214.1	NP_067037.1	Q6PCB6	AB17C_HUMAN	abhydrolase domain containing 17C	329							hydrolase activity (GO:0016787)										CTTCCTAATTCCTGAAGACAA	0.413																																					p.S329C		Atlas-SNP	.											.	FAM108C1	12	.	0			c.C986G						.						53.0	51.0	51.0					15																	81046707		1903	4128	6031	SO:0001583	missense	58489	exon3			CTAATTCCTGAAG		CCDS45323.1	15q25.1	2013-03-15	2013-03-15	2013-03-15	ENSG00000136379	ENSG00000136379		"""Abhydrolase domain containing"""	26925	protein-coding gene	gene with protein product			"""family with sequence similarity 108, member C1"""	FAM108C1			Standard	NM_021214		Approved		uc002bfu.3	Q6PCB6		ENST00000258884.4:c.986C>G	chr15.hg19:g.81046707C>G	ENSP00000258884:p.Ser329Cys	76.0	0.0		83.0	30.0	NM_021214	Q1RMD6|Q9NPM1	Missense_Mutation	SNP	ENST00000258884.4	hg19	CCDS45323.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211228	0.58343	.	.	ENSG00000136379	ENST00000258884	T	0.34667	1.35	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.39784	0.1091	N	0.08118	0	0.58432	D	0.999996	D;D	0.71674	0.992;0.998	P;D	0.63113	0.751;0.911	T	0.54296	-0.8315	10	0.87932	D	0	.	18.21	0.89867	0.0:1.0:0.0:0.0	.	329;295	Q6PCB6;Q6PCB6-2	F108C_HUMAN;.	C	329	ENSP00000258884:S329C	ENSP00000258884:S329C	S	+	2	0	FAM108C1	78833762	1.000000	0.71417	0.994000	0.49952	0.514000	0.34195	4.230000	0.58632	2.297000	0.77311	0.555000	0.69702	TCC	.	.		0.413	ABHD17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417652.1	NM_021214	
PRR35	146325	hgsc.bcm.edu	37	16	613614	613614	+	Missense_Mutation	SNP	C	C	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:613614C>A	ENST00000409413.3	+	2	599	c.320C>A	c.(319-321)cCc>cAc	p.P107H		NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		107	Pro-rich.									central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						GGAGCACGGCCCACAGGTGCT	0.746																																					p.P107H		Atlas-SNP	.											.	C16orf11	27	.	0			c.C320A						.						14.0	14.0	14.0					16																	613614		1895	4082	5977	SO:0001583	missense	146325	exon2			CACGGCCCACAGG																												ENST00000409413.3:c.320C>A	chr16.hg19:g.613614C>A	ENSP00000386499:p.Pro107His	48.0	0.0		47.0	5.0	NM_145270	B8ZZ27|Q8N233|Q96AX3|Q96S23	Missense_Mutation	SNP	ENST00000409413.3	hg19	CCDS45365.1	.	.	.	.	.	.	.	.	.	.	C	7.201	0.593465	0.13875	.	.	ENSG00000161992	ENST00000409413	.	.	.	1.83	-0.627	0.11541	.	1.619920	0.04669	U	0.410413	T	0.17619	0.0423	L	0.36672	1.1	0.09310	N	1	P	0.43352	0.804	B	0.28784	0.094	T	0.24621	-1.0155	9	0.38643	T	0.18	.	4.2979	0.10910	0.0:0.5055:0.0:0.4945	.	107	P0CG20	CP011_HUMAN	H	107	.	ENSP00000386499:P107H	P	+	2	0	C16orf11	553615	0.003000	0.15002	0.001000	0.08648	0.000000	0.00434	-0.154000	0.10130	0.016000	0.14998	-0.384000	0.06662	CCC	.	.		0.746	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1		
PRSS27	83886	hgsc.bcm.edu	37	16	2764244	2764244	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:2764244C>T	ENST00000302641.3	-	4	384	c.330G>A	c.(328-330)gtG>gtA	p.V110V	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	110	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						GGTTGCTCTCCACCTGCCTCA	0.657																																					p.V110V		Atlas-SNP	.											.	PRSS27	20	.	0			c.G330A						.						39.0	35.0	36.0					16																	2764244		2198	4300	6498	SO:0001819	synonymous_variant	83886	exon4			GCTCTCCACCTGC	AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"""Serine peptidases / Serine peptidases"""	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.330G>A	chr16.hg19:g.2764244C>T		41.0	0.0		41.0	10.0	NM_031948		Silent	SNP	ENST00000302641.3	hg19	CCDS10476.1																																																																																			.	.		0.657	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948	
MEFV	4210	hgsc.bcm.edu	37	16	3296531	3296531	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:3296531A>G	ENST00000219596.1	-	6	1643	c.1604T>C	c.(1603-1605)tTg>tCg	p.L535S	MEFV_ENST00000536379.1_Missense_Mutation_p.L324S|MEFV_ENST00000339854.4_Missense_Mutation_p.L355S|MEFV_ENST00000541159.1_Missense_Mutation_p.L324S	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	535	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GTACCTGTGCAAGATGTCTCC	0.557																																					p.L535S		Atlas-SNP	.											.	MEFV	170	.	0			c.T1604C						.						86.0	81.0	83.0					16																	3296531		2197	4300	6497	SO:0001583	missense	4210	exon6			CTGTGCAAGATGT	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1604T>C	chr16.hg19:g.3296531A>G	ENSP00000219596:p.Leu535Ser	44.0	0.0		60.0	8.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.937014	0.52972	.	.	ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000541159;ENST00000536379;ENST00000534868	T;T;T;T	0.70399	-0.48;-0.05;-0.31;-0.02	5.41	5.41	0.78517	.	0.000000	0.41938	D	0.000785	D	0.83644	0.5299	M	0.80616	2.505	0.38573	D	0.949999	D	0.89917	1.0	D	0.71870	0.975	D	0.87288	0.2297	10	0.87932	D	0	-25.6511	13.6884	0.62531	1.0:0.0:0.0:0.0	.	535	O15553	MEFV_HUMAN	S	535;535;355;324;324;324	ENSP00000219596:L535S;ENSP00000339639:L355S;ENSP00000438711:L324S;ENSP00000445079:L324S	ENSP00000219596:L535S	L	-	2	0	MEFV	3236532	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	5.608000	0.67654	2.188000	0.69820	0.533000	0.62120	TTG	.	.		0.557	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
TMC7	79905	hgsc.bcm.edu	37	16	19056299	19056299	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:19056299C>T	ENST00000304381.5	+	10	1561	c.1431C>T	c.(1429-1431)tgC>tgT	p.C477C	TMC7_ENST00000421369.3_Silent_p.C367C|TMC7_ENST00000569532.1_Silent_p.C477C	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	477					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						GTGACCTTTGCGGCTACAACC	0.562																																					p.C477C		Atlas-SNP	.											.	TMC7	75	.	0			c.C1431T						.						117.0	113.0	115.0					16																	19056299		2197	4300	6497	SO:0001819	synonymous_variant	79905	exon10			CCTTTGCGGCTAC	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1431C>T	chr16.hg19:g.19056299C>T		86.0	0.0		113.0	32.0	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	hg19	CCDS10573.1																																																																																			.	.		0.562	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	
RBBP6	5930	hgsc.bcm.edu	37	16	24583041	24583041	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:24583041A>G	ENST00000319715.4	+	18	5086	c.4654A>G	c.(4654-4656)Aaa>Gaa	p.K1552E	RBBP6_ENST00000381039.3_Missense_Mutation_p.K712E|RBBP6_ENST00000348022.2_Missense_Mutation_p.K1518E	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1552					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TTATGATACTAAACGGCCAAA	0.368																																					p.K1552E		Atlas-SNP	.											RBBP6,bladder,carcinoma,0,1	RBBP6	158	.	0			c.A4654G						.						60.0	56.0	57.0					16																	24583041		2197	4300	6497	SO:0001583	missense	5930	exon18			GATACTAAACGGC		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.4654A>G	chr16.hg19:g.24583041A>G	ENSP00000317872:p.Lys1552Glu	428.0	0.0		495.0	85.0	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.149581	0.57151	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.21543	2.0;2.39;2.35	6.03	6.03	0.97812	.	0.138745	0.51477	D	0.000090	T	0.16981	0.0408	L	0.32530	0.975	0.29183	N	0.876348	P;P;P	0.52316	0.952;0.952;0.919	B;B;B	0.43413	0.419;0.419;0.152	T	0.08229	-1.0732	10	0.11485	T	0.65	-26.416	13.011	0.58731	0.8657:0.1343:0.0:0.0	.	712;1518;1552	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	E	712;1552;1518	ENSP00000370427:K712E;ENSP00000317872:K1552E;ENSP00000316291:K1518E	ENSP00000317872:K1552E	K	+	1	0	RBBP6	24490542	1.000000	0.71417	0.990000	0.47175	0.890000	0.51754	7.541000	0.82084	2.313000	0.78055	0.455000	0.32223	AAA	.	.		0.368	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
MVP	9961	hgsc.bcm.edu	37	16	29858633	29858633	+	Missense_Mutation	SNP	A	A	C	rs555637285		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:29858633A>C	ENST00000357402.5	+	14	2519	c.2381A>C	c.(2380-2382)aAg>aCg	p.K794T	MVP_ENST00000395353.1_Missense_Mutation_p.K794T	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	794					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						GAGGTGAAGAAGTTCAAGCAG	0.602													A|||	1	0.000199681	0.0	0.0	5008	,	,		19421	0.001		0.0	False		,,,				2504	0.0				p.K794T		Atlas-SNP	.											.	MVP	80	.	0			c.A2381C						.						62.0	53.0	56.0					16																	29858633		2197	4300	6497	SO:0001583	missense	9961	exon14			TGAAGAAGTTCAA	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.2381A>C	chr16.hg19:g.29858633A>C	ENSP00000349977:p.Lys794Thr	56.0	0.0		66.0	8.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	hg19	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.396759	0.83120	.	.	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.49432	0.78;0.78	6.17	6.17	0.99709	.	0.046352	0.85682	D	0.000000	T	0.60573	0.2279	M	0.71581	2.175	0.80722	D	1	D	0.59357	0.985	P	0.52856	0.711	T	0.65261	-0.6211	10	0.87932	D	0	-41.6928	14.7743	0.69713	1.0:0.0:0.0:0.0	.	794	Q14764	MVP_HUMAN	T	794	ENSP00000349977:K794T;ENSP00000378760:K794T	ENSP00000349977:K794T	K	+	2	0	MVP	29766134	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.041000	0.64196	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.602	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
NRN1L	123904	hgsc.bcm.edu	37	16	67920015	67920015	+	Silent	SNP	C	C	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:67920015C>A	ENST00000339176.3	+	3	450	c.351C>A	c.(349-351)gcC>gcA	p.A117A	NRN1L_ENST00000576147.1_Missense_Mutation_p.P44H|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_198443.1	NP_940845.1	Q496H8	NRN1L_HUMAN	neuritin 1-like	117					nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)		TGTGCGGTGCCCCGGTGCATG	0.662																																					p.A117A		Atlas-SNP	.											.	NRN1L	13	.	0			c.C351A						.						38.0	35.0	36.0					16																	67920015		2197	4300	6497	SO:0001819	synonymous_variant	123904	exon3			CGGTGCCCCGGTG	AY358782	CCDS10850.1	16q22.1	2008-02-05			ENSG00000188038	ENSG00000188038			29811	protein-coding gene	gene with protein product						12975309	Standard	NM_198443		Approved	UNQ2446, MRCC2446	uc002euu.3	Q496H8	OTTHUMG00000137541	ENST00000339176.3:c.351C>A	chr16.hg19:g.67920015C>A		28.0	0.0		42.0	7.0	NM_198443	Q6UWH7	Silent	SNP	ENST00000339176.3	hg19	CCDS10850.1																																																																																			.	.		0.662	NRN1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268872.2	NM_198443	
DNAAF1	123872	hgsc.bcm.edu	37	16	84188219	84188219	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:84188219G>A	ENST00000378553.5	+	4	514	c.390G>A	c.(388-390)ggG>ggA	p.G130G	DNAAF1_ENST00000334315.5_Silent_p.G130G	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	130					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						AGTACACAGGGCTGCGCTGTC	0.507																																					p.G130G		Atlas-SNP	.											.	DNAAF1	81	.	0			c.G390A						.						98.0	93.0	95.0					16																	84188219		2200	4300	6500	SO:0001819	synonymous_variant	123872	exon4			CACAGGGCTGCGC	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.390G>A	chr16.hg19:g.84188219G>A		102.0	0.0		122.0	43.0	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	hg19	CCDS10943.2																																																																																			.	.		0.507	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
ANKRD11	29123	hgsc.bcm.edu	37	16	89347979	89347979	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr16:89347979C>T	ENST00000301030.4	-	9	5431	c.4971G>A	c.(4969-4971)tcG>tcA	p.S1657S	ANKRD11_ENST00000378330.2_Silent_p.S1657S	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1657					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GAATAGGAGTCGACTCTTTGA	0.562																																					p.S1657S		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G4971A						.						131.0	143.0	139.0					16																	89347979		2198	4300	6498	SO:0001819	synonymous_variant	29123	exon9			AGGAGTCGACTCT	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4971G>A	chr16.hg19:g.89347979C>T		76.0	0.0		123.0	13.0	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.		0.562	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
CHRNB1	1140	hgsc.bcm.edu	37	17	7359261	7359261	+	Splice_Site	SNP	G	G	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:7359261G>C	ENST00000306071.2	+	10	1432		c.e10+1		CHRNB1_ENST00000575379.1_Splice_Site|CHRNB1_ENST00000536404.2_Splice_Site|CHRNB1_ENST00000576360.1_Splice_Site	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)						behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	CCACGATGCGGTATGTCCAAC	0.582																																					.		Atlas-SNP	.											.	CHRNB1	46	.	0			c.1365+1G>C						.						57.0	50.0	52.0					17																	7359261		2203	4300	6503	SO:0001630	splice_region_variant	1140	exon10			GATGCGGTATGTC	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1961	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 1 (muscle)"""	100710	"""cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"""	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.1365+1G>C	chr17.hg19:g.7359261G>C		82.0	0.0		125.0	10.0	NM_000747	B7Z5H1|Q8IZ46|Q96FB8	Splice_Site	SNP	ENST00000306071.2	hg19	CCDS11106.1	.	.	.	.	.	.	.	.	.	.	G	9.570	1.120824	0.20877	.	.	ENSG00000170175	ENST00000306071;ENST00000536404	.	.	.	5.37	4.38	0.52667	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0982	0.59206	0.0:0.0:0.8381:0.1619	.	.	.	.	.	-1	.	.	.	+	.	.	CHRNB1	7299985	1.000000	0.71417	0.845000	0.33349	0.004000	0.04260	6.696000	0.74598	1.231000	0.43661	-0.719000	0.03609	.	.	.		0.582	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3		Intron
VPS25	84313	hgsc.bcm.edu	37	17	40925774	40925774	+	Missense_Mutation	SNP	G	G	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:40925774G>T	ENST00000253794.2	+	2	117	c.77G>T	c.(76-78)cGg>cTg	p.R26L		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	26					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		GTGGACACTCGGCAGAAGCAG	0.617																																					p.R26L		Atlas-SNP	.											.	VPS25	11	.	0			c.G77T						.						78.0	82.0	81.0					17																	40925774		2203	4300	6503	SO:0001583	missense	84313	exon2			ACACTCGGCAGAA	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"""vacuolar protein sorting 25 (yeast)"""			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.77G>T	chr17.hg19:g.40925774G>T	ENSP00000253794:p.Arg26Leu	66.0	0.0		81.0	13.0	NM_032353	B2R581	Missense_Mutation	SNP	ENST00000253794.2	hg19	CCDS11438.1	.	.	.	.	.	.	.	.	.	.	G	36	5.647018	0.96714	.	.	ENSG00000131475	ENST00000253794	T	0.51574	0.7	5.5	5.5	0.81552	ESCRT-II complex, Vps25 subunit, N-terminal winged helix (1);	0.000000	0.85682	D	0.000000	T	0.49898	0.1584	M	0.67517	2.055	0.80722	D	1	D	0.52996	0.957	B	0.41988	0.372	T	0.51403	-0.8710	10	0.30854	T	0.27	-32.2901	18.975	0.92731	0.0:0.0:1.0:0.0	.	26	Q9BRG1	VPS25_HUMAN	L	26	ENSP00000253794:R26L	ENSP00000253794:R26L	R	+	2	0	VPS25	38179300	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.241000	0.78201	2.584000	0.87258	0.655000	0.94253	CGG	.	.		0.617	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353	
APOH	350	hgsc.bcm.edu	37	17	64219853	64219853	+	Silent	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:64219853C>T	ENST00000205948.6	-	4	415	c.378G>A	c.(376-378)gaG>gaA	p.E126E		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	126	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			ATTTTCCTTCCTCAGTGCACT	0.443																																					p.E126E	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.G378A						.						110.0	107.0	108.0					17																	64219853		2203	4300	6503	SO:0001819	synonymous_variant	350	exon4			TCCTTCCTCAGTG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.378G>A	chr17.hg19:g.64219853C>T		115.0	0.0		114.0	22.0	NM_000042	B2R9M3|Q9UCN7	Silent	SNP	ENST00000205948.6	hg19	CCDS11663.1																																																																																			.	.		0.443	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
DNAH17	8632	hgsc.bcm.edu	37	17	76567433	76567433	+	Missense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:76567433C>T	ENST00000585328.1	-	5	884	c.760G>A	c.(760-762)Gtt>Att	p.V254I	DNAH17_ENST00000389840.5_Missense_Mutation_p.V254I	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	254	Stem. {ECO:0000250}.				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(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			AGGATCTCAACAATCTTGTTC	0.502																																					p.V254I		Atlas-SNP	.											.	DNAH17	347	.	0			c.G760A						.						96.0	93.0	94.0					17																	76567433		2019	4189	6208	SO:0001583	missense	8632	exon5			TCTCAACAATCTT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.760G>A	chr17.hg19:g.76567433C>T	ENSP00000465516:p.Val254Ile	159.0	0.0		181.0	20.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.04	1.241185	0.22711	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.55588	0.51	4.58	4.58	0.56647	.	.	.	.	.	T	0.48150	0.1484	L	0.40543	1.245	0.09310	N	1	.	.	.	.	.	.	T	0.34675	-0.9819	7	0.21014	T	0.42	.	11.6264	0.51147	0.1776:0.8224:0.0:0.0	.	.	.	.	I	254	ENSP00000374490:V254I	ENSP00000300671:V254I	V	-	1	0	DNAH17	74079028	0.591000	0.26824	0.232000	0.24009	0.936000	0.57629	2.064000	0.41432	2.267000	0.75376	0.561000	0.74099	GTT	.	.		0.502	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
L3MBTL4	91133	hgsc.bcm.edu	37	18	6263997	6263997	+	Missense_Mutation	SNP	C	C	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr18:6263997C>G	ENST00000284898.6	-	5	368	c.168G>C	c.(166-168)tgG>tgC	p.W56C	L3MBTL4_ENST00000400104.3_Missense_Mutation_p.W56C|L3MBTL4_ENST00000317931.7_Missense_Mutation_p.W56C|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.W56C	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	56					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				CTTTCAAGTACCACTCCCAAG	0.438																																					p.W56C	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.G168C						.						87.0	89.0	89.0					18																	6263997		2203	4300	6503	SO:0001583	missense	91133	exon5			CAAGTACCACTCC	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"""Sterile alpha motif (SAM) domain containing"""	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.168G>C	chr18.hg19:g.6263997C>G	ENSP00000284898:p.Trp56Cys	111.0	0.0		108.0	10.0	NM_173464	A8MTL8|Q8IXS3	Missense_Mutation	SNP	ENST00000284898.6	hg19	CCDS11839.2	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406748	0.25378	.	.	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000400104	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	5.04	5.04	0.67666	.	0.187021	0.34676	N	0.003775	T	0.69975	0.3171	N	0.14661	0.345	0.80722	D	1	B	0.28324	0.207	B	0.16722	0.016	T	0.71341	-0.4622	10	0.66056	D	0.02	.	14.2378	0.65938	0.0:1.0:0.0:0.0	.	56	Q8NA19	LMBL4_HUMAN	C	56	ENSP00000382976:W56C;ENSP00000318543:W56C;ENSP00000284898:W56C;ENSP00000382975:W56C	ENSP00000284898:W56C	W	-	3	0	L3MBTL4	6253997	0.310000	0.24527	1.000000	0.80357	0.978000	0.69477	0.617000	0.24359	2.519000	0.84933	0.650000	0.86243	TGG	.	.		0.438	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464	
GREB1L	80000	hgsc.bcm.edu	37	18	19024334	19024334	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr18:19024334A>G	ENST00000580732.2	+	11	1738	c.1357A>G	c.(1357-1359)Atg>Gtg	p.M453V	GREB1L_ENST00000400483.4_Missense_Mutation_p.M453V|GREB1L_ENST00000431264.1_Missense_Mutation_p.M453V|GREB1L_ENST00000424526.1_Missense_Mutation_p.M453V|RP11-296E23.1_ENST00000584611.1_RNA|GREB1L_ENST00000269218.6_Missense_Mutation_p.M453V|GREB1L_ENST00000578368.1_3'UTR			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like	453						integral component of membrane (GO:0016021)				breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						CGTGGAAAACATGATTCTTCT	0.403																																					p.M453V		Atlas-SNP	.											.	GREB1L	69	.	0			c.A1357G						.						223.0	186.0	197.0					18																	19024334		692	1591	2283	SO:0001583	missense	80000	exon11			GAAAACATGATTC	AK023749	CCDS45836.1	18q11.2	2009-09-08	2009-09-08	2009-09-08					31042	protein-coding gene	gene with protein product			"""KIAA1772"""	KIAA1772		11214970	Standard	NM_001142966		Approved	FLJ13687, C18orf6	uc010xam.2	Q9C091		ENST00000580732.2:c.1357A>G	chr18.hg19:g.19024334A>G	ENSP00000464162:p.Met453Val	126.0	0.0		96.0	21.0	NM_001142966	A4QN17|Q9H8F1	Missense_Mutation	SNP	ENST00000580732.2	hg19	CCDS45836.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.475827	0.44044	.	.	ENSG00000141449	ENST00000424526;ENST00000269218;ENST00000400483;ENST00000431264	T;T;T;T	0.14144	3.27;3.23;2.53;2.53	5.98	4.81	0.61882	.	.	.	.	.	T	0.15696	0.0378	M	0.64997	1.995	0.41065	D	0.985406	B;B	0.19706	0.038;0.038	B;B	0.21151	0.033;0.033	T	0.04140	-1.0974	9	0.17832	T	0.49	-4.9569	12.6631	0.56826	0.8761:0.0:0.0:0.1238	.	453;453	Q9C091;Q9C091-2	GRB1L_HUMAN;.	V	453	ENSP00000412060:M453V;ENSP00000269218:M453V;ENSP00000383331:M453V;ENSP00000393125:M453V	ENSP00000269218:M453V	M	+	1	0	GREB1L	17278332	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	4.795000	0.62489	1.061000	0.40601	0.533000	0.62120	ATG	.	.		0.403	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2	NM_024935	
CACTIN	58509	hgsc.bcm.edu	37	19	3626733	3626733	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:3626733G>A	ENST00000429344.2	-	1	80	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	CACTIN_ENST00000248420.5_Missense_Mutation_p.R10W|CACTIN_ENST00000221899.3_5'UTR	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	10					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CCCGCGGACCGCGAGCGCGAG	0.741																																					p.R10W		Atlas-SNP	.											.	.	.	.	0			c.C28T						.						3.0	4.0	3.0					19																	3626733		1709	3746	5455	SO:0001583	missense	58509	exon1			CGGACCGCGAGCG	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"""NY REN 24 antigen"", ""functional spliceosome-associated protein c"", ""cactin homolog (Drosophila)"""		"""chromosome 19 open reading frame 29"""	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.28C>T	chr19.hg19:g.3626733G>A	ENSP00000415078:p.Arg10Trp	66.0	0.0		53.0	19.0	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	hg19	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607780	0.46527	.	.	ENSG00000105298	ENST00000429344;ENST00000248420;ENST00000446452	.	.	.	4.21	4.21	0.49690	.	.	.	.	.	T	0.51278	0.1665	N	0.08118	0	0.35815	D	0.824164	D	0.89917	1.0	D	0.75020	0.985	T	0.64867	-0.6306	8	0.72032	D	0.01	.	12.249	0.54587	0.0:0.0:1.0:0.0	.	10	Q8WUQ7	CS029_HUMAN	W	10	.	ENSP00000248420:R10W	R	-	1	2	C19orf29	3577733	0.973000	0.33851	0.993000	0.49108	0.220000	0.24768	2.369000	0.44231	2.352000	0.79861	0.555000	0.69702	CGG	.	.		0.741	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
FEM1A	55527	hgsc.bcm.edu	37	19	4793065	4793065	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:4793065A>G	ENST00000269856.3	+	1	1338	c.1199A>G	c.(1198-1200)tAc>tGc	p.Y400C	AC005523.2_ENST00000596170.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000601192.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	400					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)		GGTGCCGTGTACGCCGACTCG	0.622																																					p.Y400C		Atlas-SNP	.											.	FEM1A	41	.	0			c.A1199G						.						55.0	52.0	53.0					19																	4793065		2203	4300	6503	SO:0001583	missense	55527	exon1			CCGTGTACGCCGA	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.1199A>G	chr19.hg19:g.4793065A>G	ENSP00000269856:p.Tyr400Cys	49.0	0.0		53.0	6.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Missense_Mutation	SNP	ENST00000269856.3	hg19	CCDS12135.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.391030	0.62066	.	.	ENSG00000141965	ENST00000269856	T	0.68181	-0.31	4.88	4.88	0.63580	Tetratricopeptide-like helical (1);	0.000000	0.64402	U	0.000002	T	0.82263	0.4999	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84180	0.0439	10	0.49607	T	0.09	-22.1428	14.4967	0.67694	1.0:0.0:0.0:0.0	.	400	Q9BSK4	FEM1A_HUMAN	C	400	ENSP00000269856:Y400C	ENSP00000269856:Y400C	Y	+	2	0	FEM1A	4744065	1.000000	0.71417	0.989000	0.46669	0.681000	0.39784	9.119000	0.94362	1.824000	0.53156	0.402000	0.26972	TAC	.	.		0.622	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1		
SAFB2	9667	hgsc.bcm.edu	37	19	5592867	5592867	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:5592867G>A	ENST00000252542.4	-	16	2503	c.2239C>T	c.(2239-2241)Cgt>Tgt	p.R747C		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	747	Arg-rich.|Interacts with SAFB1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		ATTGCCACACGCTTTCCTTCT	0.498																																					p.R747C	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											SAFB2,NS,carcinoma,0,1	SAFB2	90	.	0			c.C2239T						.						140.0	108.0	119.0					19																	5592867		2203	4300	6503	SO:0001583	missense	9667	exon16			CCACACGCTTTCC	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.2239C>T	chr19.hg19:g.5592867G>A	ENSP00000252542:p.Arg747Cys	101.0	0.0		113.0	16.0	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	hg19	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.979611	0.34942	.	.	ENSG00000130254	ENST00000252542	T	0.16073	2.37	4.7	2.35	0.29111	.	0.000000	0.51477	D	0.000087	T	0.37100	0.0991	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.23261	-1.0193	10	0.87932	D	0	-13.958	11.8841	0.52592	0.0:0.0:0.5478:0.4522	.	747	Q14151	SAFB2_HUMAN	C	747	ENSP00000252542:R747C	ENSP00000252542:R747C	R	-	1	0	SAFB2	5543867	1.000000	0.71417	0.134000	0.22075	0.153000	0.21895	2.719000	0.47244	0.928000	0.37168	0.561000	0.74099	CGT	.	.		0.498	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649	
RAVER1	125950	hgsc.bcm.edu	37	19	10431330	10431330	+	Splice_Site	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:10431330C>T	ENST00000293677.6	-	9	1903		c.e9+1		CTD-2369P2.12_ENST00000586529.1_Splice_Site	NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1							cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			CAGGCACTCACCGAGGGGTAG	0.597																																					.		Atlas-SNP	.											.	RAVER1	67	.	0			c.1821+1G>A						.						6.0	6.0	6.0					19																	10431330		1986	4163	6149	SO:0001630	splice_region_variant	125950	exon10			CACTCACCGAGGG		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"""RNA binding motif (RRM) containing"""	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.1821+1G>A	chr19.hg19:g.10431330C>T		114.0	0.0		116.0	12.0	NM_133452	A6NMU4|Q8IY60|Q8TF24	Splice_Site	SNP	ENST00000293677.6	hg19	CCDS45960.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484246	0.44147	.	.	ENSG00000161847	ENST00000293677	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2398	0.54536	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAVER1	10292330	1.000000	0.71417	0.998000	0.56505	0.491000	0.33493	4.226000	0.58606	1.951000	0.56629	0.561000	0.74099	.	.	.		0.597	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	Intron
CACNA1A	773	hgsc.bcm.edu	37	19	13476260	13476260	+	Missense_Mutation	SNP	T	T	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:13476260T>C	ENST00000360228.5	-	5	654	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	CACNA1A_ENST00000573710.2_Missense_Mutation_p.I219V	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	219					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCTTCATGATCGACTTCAGG	0.488																																					p.I219V		Atlas-SNP	.											.	CACNA1A	715	.	0			c.A655G						.						56.0	56.0	56.0					19																	13476260		1921	4135	6056	SO:0001583	missense	773	exon5			TCATGATCGACTT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.655A>G	chr19.hg19:g.13476260T>C	ENSP00000353362:p.Ile219Val	187.0	0.0		255.0	51.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756994	0.49362	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98400	-4.91	5.55	5.55	0.83447	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98175	0.9397	L	0.46157	1.445	0.48696	D	0.999694	D;D	0.63880	0.958;0.993	D;D	0.76071	0.97;0.987	D	0.98068	1.0397	10	0.30854	T	0.27	.	14.6926	0.69096	0.0:0.0:0.0:1.0	.	219;219	O00555;Q9NS88	CAC1A_HUMAN;.	V	219	ENSP00000353362:I219V	ENSP00000317661:I219V	I	-	1	0	CACNA1A	13337260	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	7.800000	0.85949	2.105000	0.64084	0.533000	0.62120	ATC	.	.		0.488	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
SIN3B	23309	hgsc.bcm.edu	37	19	16952599	16952599	+	Silent	SNP	G	G	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:16952599G>C	ENST00000248054.5	+	4	423	c.402G>C	c.(400-402)ggG>ggC	p.G134G	SIN3B_ENST00000379803.1_Silent_p.G134G|CTD-2538G9.5_ENST00000600987.1_RNA|SIN3B_ENST00000596802.1_Silent_p.G134G					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACAACCACGGGGACGGTGCAG	0.552																																					p.G134G		Atlas-SNP	.											.	SIN3B	90	.	0			c.G402C						.						91.0	86.0	87.0					19																	16952599		2203	4300	6503	SO:0001819	synonymous_variant	23309	exon4			CCACGGGGACGGT	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"""SIN3 homolog B, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog B (yeast)"""			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.402G>C	chr19.hg19:g.16952599G>C		147.0	0.0		172.0	23.0	NM_015260		Silent	SNP	ENST00000248054.5	hg19																																																																																				.	.		0.552	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260	
MPV17L2	84769	hgsc.bcm.edu	37	19	18306856	18306856	+	Silent	SNP	A	A	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:18306856A>C	ENST00000599612.2	+	5	712	c.612A>C	c.(610-612)cgA>cgC	p.R204R		NM_032683.2	NP_116072.2	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2	204						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(1)|lung(2)|urinary_tract(1)	4						TGGACACCCGAGCAGACTGAA	0.612																																					p.R204R		Atlas-SNP	.											.	MPV17L2	12	.	0			c.A612C						.						96.0	106.0	102.0					19																	18306856		2069	4192	6261	SO:0001819	synonymous_variant	84769	exon5			CACCCGAGCAGAC	AK094091	CCDS42522.1	19p13.11	2011-05-26			ENSG00000254858	ENSG00000254858			28177	protein-coding gene	gene with protein product						12477932	Standard	NM_032683		Approved	FKSG24, MGC12972	uc002nid.3	Q567V2	OTTHUMG00000165628	ENST00000599612.2:c.612A>C	chr19.hg19:g.18306856A>C		51.0	0.0		70.0	30.0	NM_032683	Q96P34|Q96QA0|Q9BSG4	Silent	SNP	ENST00000599612.2	hg19	CCDS42522.1																																																																																			.	.		0.612	MPV17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466294.2	NM_032683	
FCGBP	8857	hgsc.bcm.edu	37	19	40368475	40368475	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:40368475G>A	ENST00000221347.6	-	28	12880	c.12873C>T	c.(12871-12873)ttC>ttT	p.F4291F		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4291	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCAGGTGGTGAAGGGGCCCC	0.617																																					p.F4291F		Atlas-SNP	.											.	FCGBP	416	.	0			c.C12873T						.						104.0	99.0	101.0					19																	40368475		2203	4298	6501	SO:0001819	synonymous_variant	8857	exon28			GGTGGTGAAGGGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12873C>T	chr19.hg19:g.40368475G>A		104.0	0.0		146.0	16.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.617	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CYP2B6	1555	hgsc.bcm.edu	37	19	41512811	41512811	+	Splice_Site	SNP	G	G	T	rs150862336	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:41512811G>T	ENST00000324071.4	+	4	493	c.486G>T	c.(484-486)ggG>ggT	p.G162G	CYP2B6_ENST00000330446.5_Intron|CYP2B6_ENST00000598834.1_3'UTR|CYP2B6_ENST00000593831.1_Intron	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	162					cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	TCTTCCTAGGGGCCCTCATGG	0.512																																					p.G162G		Atlas-SNP	.											.	CYP2B6	79	.	0			c.G486T						.						58.0	54.0	56.0					19																	41512811		2203	4300	6503	SO:0001630	splice_region_variant	1555	exon4			CCTAGGGGCCCTC	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"""Cytochrome P450s"""	2615	protein-coding gene	gene with protein product		123930	"""cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6"", ""cytochrome P450, family 2, subfamily B"", ""cytochrome P450, subfamily IIB (phenobarbital-inducible)"""	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.485-1G>T	chr19.hg19:g.41512811G>T		54.0	0.0		74.0	10.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Silent	SNP	ENST00000324071.4	hg19	CCDS12570.1																																																																																			.	G|0.999;A|0.001		0.512	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	Silent
ZNF845	91664	hgsc.bcm.edu	37	19	53854546	53854546	+	Silent	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:53854546G>A	ENST00000595091.1	+	5	837	c.618G>A	c.(616-618)caG>caA	p.Q206Q	ZNF845_ENST00000458035.1_Silent_p.Q206Q			Q96IR2	ZN845_HUMAN	zinc finger protein 845	206					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(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						CACAAAAGCAGGAAGTACACA	0.353																																					p.Q206Q		Atlas-SNP	.											.	ZNF845	101	.	0			c.G618A						.						60.0	45.0	50.0					19																	53854546		692	1591	2283	SO:0001819	synonymous_variant	91664	exon4			AAAGCAGGAAGTA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.618G>A	chr19.hg19:g.53854546G>A		159.0	0.0		160.0	28.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.353	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
RBL1	5933	hgsc.bcm.edu	37	20	35695127	35695127	+	Splice_Site	SNP	C	C	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:35695127C>G	ENST00000373664.3	-	6	912	c.846G>C	c.(844-846)aaG>aaC	p.K282N	RBL1_ENST00000344359.3_Splice_Site_p.K282N	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	282					chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				AGTACAGTACCTTCCTGTCAA	0.343																																					p.K282N		Atlas-SNP	.											.	RBL1	114	.	0			c.G846C						.						91.0	93.0	92.0					20																	35695127		2203	4300	6503	SO:0001630	splice_region_variant	5933	exon6			CAGTACCTTCCTG	L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839			9893	protein-coding gene	gene with protein product		116957				1833063	Standard	NM_183404		Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.846+1G>C	chr20.hg19:g.35695127C>G		91.0	0.0		121.0	45.0	NM_183404	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	Missense_Mutation	SNP	ENST00000373664.3	hg19	CCDS13289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.22|18.22	3.576476|3.576476	0.65878|0.65878	.|.	.|.	ENSG00000080839|ENSG00000080839	ENST00000373664;ENST00000344359|ENST00000525052	D;D|.	0.93076|.	-2.94;-3.16|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.206543|.	0.49916|.	D|.	0.000126|.	T|T	0.67268|0.67268	0.2875|0.2875	L|L	0.43152|0.43152	1.355|1.355	0.53688|0.53688	D|D	0.999975|0.999975	P;B|.	0.35684|.	0.515;0.031|.	B;B|.	0.41299|.	0.353;0.037|.	T|T	0.63585|0.63585	-0.6604|-0.6604	9|5	.|.	.|.	.|.	-7.0251|-7.0251	18.3499|18.3499	0.90335|0.90335	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	282;282|.	P28749-2;P28749|.	.;RBL1_HUMAN|.	N|T	282|87	ENSP00000362768:K282N;ENSP00000343646:K282N|.	.|.	K|R	-|-	3|2	2|0	RBL1|RBL1	35128541|35128541	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.823000|0.823000	0.46562|0.46562	5.660000|5.660000	0.68018|0.68018	2.575000|2.575000	0.86900|0.86900	0.313000|0.313000	0.20887|0.20887	AAG|AGA	.	.		0.343	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079067.2	NM_002895	Missense_Mutation
PCIF1	63935	hgsc.bcm.edu	37	20	44574977	44574977	+	Missense_Mutation	SNP	T	T	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:44574977T>C	ENST00000372409.3	+	14	1931	c.1567T>C	c.(1567-1569)Tac>Cac	p.Y523H	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	523					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						CTTCCGCCAGTACTGTTCTGC	0.632																																					p.Y523H		Atlas-SNP	.											PCIF1,colon,carcinoma,0,1	PCIF1	51	.	0			c.T1567C						.						122.0	116.0	118.0					20																	44574977		2203	4300	6503	SO:0001583	missense	63935	exon14			CGCCAGTACTGTT	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 121"""		"""chromosome 20 open reading frame 67"""	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.1567T>C	chr20.hg19:g.44574977T>C	ENSP00000361486:p.Tyr523His	55.0	0.0		49.0	17.0	NM_022104	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	hg19	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.212107	0.79240	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.06	3.97	0.46021	Phosphorylated CTD interacting factor 1, WW domain (1);	0.134024	0.52532	D	0.000074	T	0.80417	0.4619	M	0.89601	3.045	0.53688	D	0.999976	D	0.89917	1.0	D	0.79108	0.992	T	0.82214	-0.0568	9	0.87932	D	0	-23.2464	9.6689	0.40000	0.0:0.0809:0.0:0.9191	.	523	Q9H4Z3	PCIF1_HUMAN	H	523	.	ENSP00000361486:Y523H	Y	+	1	0	PCIF1	44008384	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.640000	0.83355	0.972000	0.38314	0.379000	0.24179	TAC	.	.		0.632	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104	
ARFGEF2	10564	hgsc.bcm.edu	37	20	47601303	47601303	+	Nonsense_Mutation	SNP	C	C	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:47601303C>T	ENST00000371917.4	+	15	1996	c.1996C>T	c.(1996-1998)Cag>Tag	p.Q666*		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	666	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			CCAGTTTCTCCAGGAGCAGGG	0.512																																					p.Q666X	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.C1996T						.						133.0	133.0	133.0					20																	47601303		2203	4300	6503	SO:0001587	stop_gained	10564	exon15			TTTCTCCAGGAGC	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1996C>T	chr20.hg19:g.47601303C>T	ENSP00000360985:p.Gln666*	156.0	0.0		199.0	31.0	NM_006420	Q5TFT9|Q9NTS1	Nonsense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	C	39	7.589342	0.98374	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	.	.	.	5.85	5.85	0.93711	.	0.162448	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.1588	0.98128	0.0:1.0:0.0:0.0	.	.	.	.	X	666	.	ENSP00000360985:Q666X	Q	+	1	0	ARFGEF2	47034710	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.818000	0.86416	2.770000	0.95276	0.563000	0.77884	CAG	.	.		0.512	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
SALL4	57167	hgsc.bcm.edu	37	20	50408507	50408507	+	Missense_Mutation	SNP	G	G	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:50408507G>C	ENST00000217086.4	-	2	626	c.515C>G	c.(514-516)gCc>gGc	p.A172G	SALL4_ENST00000395997.3_Missense_Mutation_p.A172G|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	172					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTGCCTTTGGCTAAATAGCT	0.587																																					p.A172G		Atlas-SNP	.											.	SALL4	168	.	0			c.C515G						.						130.0	129.0	130.0					20																	50408507		2203	4300	6503	SO:0001583	missense	57167	exon2			CCTTTGGCTAAAT	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.515C>G	chr20.hg19:g.50408507G>C	ENSP00000217086:p.Ala172Gly	72.0	0.0		75.0	13.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	hg19	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	G	4.897	0.166660	0.09339	.	.	ENSG00000101115	ENST00000217086;ENST00000395997	T;T	0.08370	3.1;3.34	5.29	5.29	0.74685	.	0.155634	0.30714	N	0.009023	T	0.04048	0.0113	N	0.02539	-0.55	0.80722	D	1	B;B	0.14438	0.01;0.01	B;B	0.13407	0.005;0.009	T	0.42292	-0.9460	10	0.08179	T	0.78	-34.4665	18.9212	0.92526	0.0:0.0:1.0:0.0	.	172;172	A2A2D8;Q9UJQ4	.;SALL4_HUMAN	G	172	ENSP00000217086:A172G;ENSP00000379319:A172G	ENSP00000217086:A172G	A	-	2	0	SALL4	49841914	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	3.104000	0.50306	2.466000	0.83321	0.655000	0.94253	GCC	.	.		0.587	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
GNAS	2778	hgsc.bcm.edu	37	20	57484420	57484420	+	Missense_Mutation	SNP	C	C	T	rs11554273		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:57484420C>T	ENST00000371085.3	+	8	1025	c.601C>T	c.(601-603)Cgt>Tgt	p.R201C	GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186C|GNAS_ENST00000371102.4_Missense_Mutation_p.R830C|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000354359.7_Missense_Mutation_p.R202C|GNAS_ENST00000371100.4_Missense_Mutation_p.R844C|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000306090.10_Missense_Mutation_p.R187C|GNAS_ENST00000371095.3_Missense_Mutation_p.R187C	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.R844C	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	GNAS_ENST00000371100,NS,adenocarcinoma,0,338	GNAS	867	.	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	c.C2530T						.						80.0	78.0	79.0					20																	57484420		2203	4300	6503	SO:0001583	missense	2778	exon8			CGCTGCCGTGTCC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>T	chr20.hg19:g.57484420C>T	ENSP00000360126:p.Arg201Cys	135.0	0.0		119.0	34.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	hg19	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215896	0.79352	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99466	-5.95;-5.95;-5.95;-5.95;-5.95;-2.99;-5.95	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99775	0.9907	H	0.99732	4.735	0.80722	D	1	D;D;D;D	0.89917	0.999;0.983;0.979;1.0	D;P;P;D	0.97110	0.939;0.845;0.643;1.0	D	0.96814	0.9599	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	rs11554273	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	C	844;830;187;201;202;186;187	ENSP00000360141:R844C;ENSP00000360143:R830C;ENSP00000360136:R187C;ENSP00000360126:R201C;ENSP00000346328:R202C;ENSP00000265620:R186C;ENSP00000304472:R187C	ENSP00000265620:R186C	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT	.	C|1.000		0.428	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516	
LIPI	149998	hgsc.bcm.edu	37	21	15535777	15535777	+	Silent	SNP	A	A	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr21:15535777A>T	ENST00000536861.1	-	7	968	c.969T>A	c.(967-969)acT>acA	p.T323T	LIPI_ENST00000344577.2_Silent_p.T344T			Q6XZB0	LIPI_HUMAN	lipase, member I	323					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)		CCAAAAACACAGTGGTCCTAA	0.299																																					p.T344T		Atlas-SNP	.											.	LIPI	95	.	0			c.T1032A						.						112.0	118.0	116.0					21																	15535777		2203	4297	6500	SO:0001819	synonymous_variant	149998	exon7			AAACACAGTGGTC	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.969T>A	chr21.hg19:g.15535777A>T		168.0	0.0		195.0	20.0	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	hg19																																																																																				.	.		0.299	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
ETS2	2114	hgsc.bcm.edu	37	21	40186286	40186286	+	Missense_Mutation	SNP	A	A	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr21:40186286A>C	ENST00000360214.3	+	5	734	c.274A>C	c.(274-276)Aag>Cag	p.K92Q	ETS2_ENST00000360938.3_Missense_Mutation_p.K92Q	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	92	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TGGCTTCAAAAAGGAACAGCG	0.493																																					p.K232Q		Atlas-SNP	.											.	ETS2	87	.	0			c.A694C						.						73.0	75.0	74.0					21																	40186286		2203	4300	6503	SO:0001583	missense	2114	exon5			TTCAAAAAGGAAC		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.274A>C	chr21.hg19:g.40186286A>C	ENSP00000353344:p.Lys92Gln	97.0	0.0		109.0	19.0	NM_001256295	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	hg19	CCDS13659.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.340215	0.41398	.	.	ENSG00000157557	ENST00000360214;ENST00000360938;ENST00000432278;ENST00000456966	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.77	5.77	0.91146	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.095829	0.64402	D	0.000001	T	0.58177	0.2104	M	0.86651	2.83	0.58432	D	0.999994	D;P	0.69078	0.997;0.536	P;B	0.59889	0.865;0.329	T	0.66217	-0.5979	10	0.72032	D	0.01	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	92;92	P15036;C9JAG2	ETS2_HUMAN;.	Q	92	ENSP00000353344:K92Q;ENSP00000354194:K92Q;ENSP00000401273:K92Q;ENSP00000411086:K92Q	ENSP00000353344:K92Q	K	+	1	0	ETS2	39108156	1.000000	0.71417	0.946000	0.38457	0.013000	0.08279	8.537000	0.90631	2.326000	0.78906	0.533000	0.62120	AAG	.	.		0.493	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
EP300	2033	hgsc.bcm.edu	37	22	41523630	41523630	+	Missense_Mutation	SNP	A	A	G			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr22:41523630A>G	ENST00000263253.7	+	4	2265	c.1046A>G	c.(1045-1047)cAc>cGc	p.H349R		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	349					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TTGCATGCTCACAAGTGCCAG	0.547			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.H349R		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A1046G						.						109.0	104.0	106.0					22																	41523630		2203	4300	6503	SO:0001583	missense	2033	exon4	Familial Cancer Database	Broad Thumb-Hallux syndrome	ATGCTCACAAGTG	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.1046A>G	chr22.hg19:g.41523630A>G	ENSP00000263253:p.His349Arg	146.0	0.0		146.0	22.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.004834	0.93287	.	.	ENSG00000100393	ENST00000263253	D	0.81659	-1.52	6.02	6.02	0.97574	Zinc finger, TAZ-type (5);	0.000000	0.51477	D	0.000095	D	0.86497	0.5947	L	0.48935	1.535	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.85146	0.0983	10	0.35671	T	0.21	-12.8324	16.542	0.84395	1.0:0.0:0.0:0.0	.	349	Q09472	EP300_HUMAN	R	349	ENSP00000263253:H349R	ENSP00000263253:H349R	H	+	2	0	EP300	39853576	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.304000	0.77564	0.528000	0.53228	CAC	.	.		0.547	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
CYP2D6	1565	hgsc.bcm.edu	37	22	42522650	42522650	+	Missense_Mutation	SNP	G	G	A	rs185772085		TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr22:42522650G>A	ENST00000360608.5	-	9	1534	c.1420C>T	c.(1420-1422)Cgg>Tgg	p.R474W	NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.R423W|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.R474W|NDUFA6-AS1_ENST00000416037.2_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	474					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TGGCTGGGCCGGGGCTGTCCA	0.637																																					p.R474W		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C1420T						.						28.0	24.0	26.0					22																	42522650		2192	4298	6490	SO:0001583	missense	1565	exon9			TGGGCCGGGGCTG	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1420C>T	chr22.hg19:g.42522650G>A	ENSP00000353820:p.Arg474Trp	195.0	0.0		167.0	22.0	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	hg19	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.047842	0.55110	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.69040	-0.37;-0.37;-0.37	4.85	1.21	0.21127	.	0.980175	0.08291	N	0.968458	T	0.79112	0.4391	M	0.70595	2.14	0.24748	N	0.992996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.979;0.987;0.979	T	0.63550	-0.6612	10	0.87932	D	0	.	9.0849	0.36574	0.0:0.1323:0.4633:0.4044	.	474;423;474	C1ID54;Q6NXU8;Q6NWU0	.;.;.	W	474;474;420;423;423	ENSP00000353820:R474W;ENSP00000374620:R474W;ENSP00000351927:R423W	ENSP00000351927:R423W	R	-	1	2	CYP2D6	40852594	0.000000	0.05858	0.656000	0.29637	0.011000	0.07611	-0.224000	0.09164	0.384000	0.24942	0.555000	0.69702	CGG	.	G|1.000;T|0.000		0.637	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
ZIC3	7547	hgsc.bcm.edu	37	X	136649430	136649430	+	Missense_Mutation	SNP	G	G	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chrX:136649430G>T	ENST00000287538.5	+	1	1130	c.580G>T	c.(580-582)Ggc>Tgc	p.G194C	RP1-137H15.2_ENST00000442841.1_RNA|ZIC3_ENST00000370606.3_Missense_Mutation_p.G194C	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	194					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					GGAGCTGTTCGGCCGTGCTGA	0.677																																					p.G194C		Atlas-SNP	.											.	ZIC3	93	.	0			c.G580T						.						24.0	27.0	26.0					X																	136649430		2184	4239	6423	SO:0001583	missense	7547	exon1			CTGTTCGGCCGTG	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"""Zinc fingers, C2H2-type"""	12874	protein-coding gene	gene with protein product		300265	"""heterotaxy 1"", ""Zic family member 3 (odd-paired homolog, Drosophila)"""	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.580G>T	chrX.hg19:g.136649430G>T	ENSP00000287538:p.Gly194Cys	109.0	0.0		120.0	34.0	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	hg19	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	g	21.3	4.129498	0.77549	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	T;T	0.61510	0.1;0.1	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.73860	0.3641	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77593	-0.2530	10	0.87932	D	0	.	15.2367	0.73436	0.0:0.0:1.0:0.0	.	194	O60481	ZIC3_HUMAN	C	194	ENSP00000287538:G194C;ENSP00000359638:G194C	ENSP00000287538:G194C	G	+	1	0	ZIC3	136477096	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	9.189000	0.94928	2.155000	0.67459	0.597000	0.82753	GGC	.	.		0.677	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1		
MT-ND5	4540	hgsc.bcm.edu	37	M	13915	13915	+	Missense_Mutation	SNP	G	G	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chrM:13915G>A	ENST00000361567.2	+	1	1579	c.1579G>A	c.(1579-1581)Gga>Aga	p.G527R	MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	527					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						CCAACATACTCGGATTCTACC	0.443																																					p.G527X		Atlas-SNP	.											.	.	.	.	0			c.G1579A						.																																			SO:0001583	missense	0	exon1			ATACTCGGATTCT			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.1579G>A	chrM.hg19:g.13915G>A	ENSP00000354813:p.Gly527Arg	22.0	0.0		84.0	17.0	ENST00000361567	Q34773|Q8WCY3	Nonsense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	A|0.036;C|0.964		0.443	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MT-CYB	4519	hgsc.bcm.edu	37	M	15489	15489	+	Missense_Mutation	SNP	A	A	C			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chrM:15489A>C	ENST00000361789.2	+	1	743	c.743A>C	c.(742-744)gAc>gCc	p.D248A	MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	248					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						ATTCTCACCAGACCTCCTAGG	0.458											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.D248A		Atlas-SNP	.											.	.	.	.	0			c.A743C						.																																			SO:0001583	missense	0	exon1			CACCAGACCTCCT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.743A>C	chrM.hg19:g.15489A>C	ENSP00000354554:p.Asp248Ala	23.0	0.0	585	84.0	77.0	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	hg19																																																																																				.	.		0.458	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
ATP8B4	79895	hgsc.bcm.edu	37	15	50223353	50223354	+	Frame_Shift_Ins	INS	-	-	A	rs146835330	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr15:50223353_50223354insA	ENST00000284509.6	-	16	1745_1746	c.1604_1605insT	c.(1603-1605)ttgfs	p.L535fs	ATP8B4_ENST00000559829.1_Frame_Shift_Ins_p.L535fs	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	535						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		TGTTGAAATCCAAAAAGGCAAG	0.371																																					p.L535fs		Atlas-Indel,Pindel	.											.	ATP8B4	173	.	0			c.1605_1606insT						.																																			SO:0001589	frameshift_variant	79895	exon16			.	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"""ATPases / P-type"""	13536	protein-coding gene	gene with protein product		609123	"""ATPase, Class I, type 8B, member 4"""			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1605dupT	chr15.hg19:g.50223358_50223358dupA	ENSP00000284509:p.Leu535fs	160.0	0.0		212.0	36.0	NM_024837	Q9H727	Frame_Shift_Ins	INS	ENST00000284509.6	hg19	CCDS32238.1																																																																																			.	.		0.371	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837	
LCE1F	353137	hgsc.bcm.edu	37	1	152749024	152749025	+	In_Frame_Ins	INS	-	-	TGCAGCTCTGGGGGCTGC			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr1:152749024_152749025insTGCAGCTCTGGGGGCTGC	ENST00000334371.2	+	1	177_178	c.177_178insTGCAGCTCTGGGGGCTGC	c.(178-180)tgc>TGCAGCTCTGGGGGCTGCtgc	p.60_60C>CSSGGCC		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	60					keratinization (GO:0031424)			p.C59C(1)		kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGGGGCTGCTGCAGCTCTGG	0.678																																					p.C59delinsCCSSGGC		Atlas-INDEL	.											LCE1F,colon,carcinoma,0,1	LCE1F	42	.	1	Substitution - coding silent(1)	large_intestine(1)	c.177_178insTGCAGCTCTGGGGGCTGC						.																																			SO:0001652	inframe_insertion	353137	exon1			.		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"""Late cornified envelopes"""	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	Exception_encountered	chr1.hg19:g.152749024_152749025insTGCAGCTCTGGGGGCTGC	ENSP00000334187:p.SerSerGlyGlyCysCys60dup	202.0	0.0		366.0	81.0	NM_178354		In_Frame_Ins	INS	ENST00000334371.2	hg19	CCDS1023.1																																																																																			.	.		0.678	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354	
NKIRAS2	28511	hgsc.bcm.edu	37	17	40174526	40174543	+	In_Frame_Del	DEL	GGCCGAACTGCCCCGACA	GGCCGAACTGCCCCGACA	-			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	GGCCGAACTGCCCCGACA	GGCCGAACTGCCCCGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:40174526_40174543delGGCCGAACTGCCCCGACA	ENST00000307641.5	+	3	825_842	c.204_221delGGCCGAACTGCCCCGACA	c.(202-222)ggggccgaactgccccgacac>ggc	p.AELPRH69del	NKIRAS2_ENST00000462043.2_Intron|NKIRAS2_ENST00000316082.4_In_Frame_Del_p.AELPRH69del|NKIRAS2_ENST00000393884.2_In_Frame_Del_p.AELPRH67del|NKIRAS2_ENST00000393880.1_In_Frame_Del_p.AELPRH69del|NKIRAS2_ENST00000393881.3_In_Frame_Del_p.AELPRH69del|NKIRAS2_ENST00000479407.1_Intron|NKIRAS2_ENST00000449471.4_Intron|NKIRAS2_ENST00000393885.4_In_Frame_Del_p.AELPRH69del	NM_001001349.2	NP_001001349.1	Q9NYR9	KBRS2_HUMAN	NFKB inhibitor interacting Ras-like 2	69	Small GTPase-like.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R73Q(1)		large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	9		all_cancers(22;1.1e-05)|Breast(137;0.000143)|all_epithelial(22;0.000319)				TCCGAGATGGGGCCGAACTGCCCCGACACTGCTTCTCT	0.569																																					p.68_74del		Atlas-INDEL	.											.	NKIRAS2	15	.	1	Substitution - Missense(1)	large_intestine(1)	c.203_220del						.																																			SO:0001651	inframe_deletion	28511	exon3			.	AF229840	CCDS11415.1, CCDS45679.1, CCDS45680.1	17q21.31	2014-05-09	2004-05-20		ENSG00000168256	ENSG00000168256			17898	protein-coding gene	gene with protein product		604497	"""NFKB inhibitor interacting Ras-like protein 2"""			10657303	Standard	NM_001001349		Approved	KBRAS2, DKFZP434N1526, kappaB-Ras2	uc002hys.3	Q9NYR9	OTTHUMG00000133503	ENST00000307641.5:c.204_221delGGCCGAACTGCCCCGACA	chr17.hg19:g.40174526_40174543delGGCCGAACTGCCCCGACA	ENSP00000303580:p.Ala69_His74del	60.0	0.0		73.0	12.0	NM_017595	A6NCZ5|B3KNN0|B4DNM3|Q6PK52|Q96KC7|Q9NSX1	In_Frame_Del	DEL	ENST00000307641.5	hg19	CCDS11415.1																																																																																			.	.		0.569	NKIRAS2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257457.1	NM_017595	
SALL4	57167	hgsc.bcm.edu	37	20	50408510	50408510	+	Frame_Shift_Del	DEL	A	A	-			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr20:50408510delA	ENST00000217086.4	-	2	623	c.512delT	c.(511-513)ttafs	p.L171fs	SALL4_ENST00000395997.3_Frame_Shift_Del_p.L171fs|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	171					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GCCTTTGGCTAAATAGCTTAT	0.592																																					p.L171fs		Atlas-INDEL	.											.	SALL4	168	.	0			c.513delA						.						130.0	130.0	130.0					20																	50408510		2203	4300	6503	SO:0001589	frameshift_variant	57167	exon2			.	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.512delT	chr20.hg19:g.50408510delA	ENSP00000217086:p.Leu171fs	73.0	0.0		76.0	13.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Del	DEL	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.592	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
TRPA1	8989	hgsc.bcm.edu	37	8	72936129	72936130	+	Frame_Shift_Ins	INS	-	-	A			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:72936129_72936130insA	ENST00000262209.4	-	26	3275_3276	c.3068_3069insT	c.(3067-3069)ttafs	p.L1023fs	RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	1023					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CAGTGCAAAATAAAAAACAGAA	0.302																																					p.L1023fs		Atlas-Indel,Pindel	.											.,1	TRPA1	256	.	0			c.3069_3070insT						.																																			SO:0001589	frameshift_variant	8989	exon26			.	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.3069dupT	chr8.hg19:g.72936135_72936135dupA	ENSP00000262209:p.Leu1023fs	238.0	0.0		374.0	86.0	NM_007332	A6NIN6	Frame_Shift_Ins	INS	ENST00000262209.4	hg19	CCDS34908.1																																																																																			.	.		0.302	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
NPLOC4	55666	hgsc.bcm.edu	37	17	79556001	79556011	+	Frame_Shift_Del	DEL	CTGCTAGACTC	CTGCTAGACTC	-			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	CTGCTAGACTC	CTGCTAGACTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr17:79556001_79556011delCTGCTAGACTC	ENST00000331134.6	-	12	1455_1465	c.1240_1250delGAGTCTAGCAG	c.(1240-1251)gagtctagcagtfs	p.ESSS414fs	NPLOC4_ENST00000374747.5_Frame_Shift_Del_p.ESSS414fs|NPLOC4_ENST00000539314.1_Frame_Shift_Del_p.ESSS253fs	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	414					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GTACTGCTCACTGCTAGACTCCTTGGCGTAG	0.483																																					p.414_417del		Atlas-Indel,Pindel	.											.	NPLOC4	27	.	0			c.1241_1251del						.																																			SO:0001589	frameshift_variant	55666	exon12			.	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.1240_1250delGAGTCTAGCAG	chr17.hg19:g.79556001_79556011delCTGCTAGACTC	ENSP00000331487:p.Glu414fs	128.0	0.0		131.0	12.0	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Frame_Shift_Del	DEL	ENST00000331134.6	hg19	CCDS45812.1																																																																																			.	.		0.483	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
EPHB1	2047	hgsc.bcm.edu	37	3	134898792	134898793	+	Frame_Shift_Ins	INS	-	-	T			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr3:134898792_134898793insT	ENST00000398015.3	+	10	2220_2221	c.1850_1851insT	c.(1849-1854)tcttttfs	p.SF617fs	EPHB1_ENST00000493838.1_Frame_Shift_Ins_p.SF178fs	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	617					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						ATTGATGTATCTTTTGTGAAAA	0.485																																					p.S617fs		Atlas-Indel,Pindel	.											.	EPHB1	519	.	0			c.1850_1851insT						.																																			SO:0001589	frameshift_variant	2047	exon10			.	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1854dupT	chr3.hg19:g.134898796_134898796dupT	ENSP00000381097:p.Ser617fs	131.0	0.0		131.0	47.0	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Frame_Shift_Ins	INS	ENST00000398015.3	hg19	CCDS46921.1																																																																																			.	.		0.485	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
LRRC24	441381	hgsc.bcm.edu	37	8	145748697	145748698	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr8:145748697_145748698delAT	ENST00000529415.2	-	5	820_821	c.703_704delAT	c.(703-705)atgfs	p.M235fs	LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Frame_Shift_Del_p.M232fs|LRRC14_ENST00000292524.1_3'UTR			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	235	LRRCT.					integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTCTGCACACATGATCTTCCTG	0.658																																					p.235_235del		Atlas-Indel,Pindel	.											.	LRRC24	11	.	0			c.704_705del						.																																			SO:0001589	frameshift_variant	441381	exon5			.	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"""Immunoglobulin superfamily / I-set domain containing"""	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.703_704delAT	chr8.hg19:g.145748697_145748698delAT	ENSP00000434849:p.Met235fs	85.0	0.0		111.0	25.0	NM_001024678		Frame_Shift_Del	DEL	ENST00000529415.2	hg19	CCDS34969.1																																																																																			.	.		0.658	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678	
PELO	53918	hgsc.bcm.edu	37	5	52097577	52097577	+	Frame_Shift_Del	DEL	A	A	-			TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr5:52097577delA	ENST00000274311.2	+	3	2046	c.1061delA	c.(1060-1062)gaafs	p.E354fs	ITGA1_ENST00000282588.6_Intron|ITGA1_ENST00000504086.1_Intron|PELO_ENST00000506949.1_3'UTR	NM_015946.4	NP_057030.3	Q9BRX2	PELO_HUMAN	pelota homolog (Drosophila)	354					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA catabolic process, non-stop decay (GO:0070481)|RNA surveillance (GO:0071025)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	11		Lung NSC(810;4.94e-05)|Breast(144;0.0848)				GTTTCTGGGGAACAGCTCAGC	0.517																																					p.E354fs		Atlas-Indel,Pindel	.											.	PELO	25	.	0			c.1060delG						.						65.0	61.0	62.0					5																	52097577		2203	4300	6503	SO:0001589	frameshift_variant	53918	exon3			.		CCDS3956.1	5q11.2	2008-07-18	2001-11-28		ENSG00000152684	ENSG00000152684			8829	protein-coding gene	gene with protein product		605757	"""pelota (Drosophila) homolog"""			11060452	Standard	NM_015946		Approved		uc003jos.3	Q9BRX2	OTTHUMG00000096973	ENST00000274311.2:c.1061delA	chr5.hg19:g.52097577delA	ENSP00000274311:p.Glu354fs	106.0	0.0		127.0	16.0	NM_015946	Q9GZS6|Q9Y306	Frame_Shift_Del	DEL	ENST00000274311.2	hg19	CCDS3956.1																																																																																			.	.		0.517	PELO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214040.1	NM_015946	
CPS1	1373	hgsc.bcm.edu	37	2	211473265	211473444	+	Splice_Site	DEL	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	-	rs553030521|rs542398928|rs141106588|rs59741271|rs376315320	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr2:211473265_211473444delTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	ENST00000233072.5	+	19	2569_2587	c.2373_2391delTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA	c.(2371-2391)tctatgaaaagtgtaggagag>tc	p.SMKSVGE791del	CPS1_ENST00000451903.2_Splice_Site_p.SMKSVGE340del|CPS1_ENST00000430249.2_Splice_Site_p.SMKSVGE797del	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	791					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TTGGTAGCTCTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAATATGCTAACA	0.392																																					p.797_803del		Pindel	.											.	CPS1	485	.	0			c.2390_2409del						.																																			SO:0001630	splice_region_variant	1373	exon20			.	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2391+1TATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA>-	chr2.hg19:g.211473265_211473444delTATGAAAAGTGTAGGAGAGGTGAGTCCTTGGTTTATTACGCTTTTCTTCTTGTTCTCAGTTATTTTGTTAAATTTGTGACACCATTGACAGTGTTAAAGTTGCCTGGATACCATCAACACATGGACAGTGTTAAAGGTGCAATTGACAGTGTTAAAGTTGCCTGAATATTAGCATACTAA		81.0	0.0		60.0	18.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Frame_Shift_Del	DEL	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.392	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		In_Frame_Del
KLKB1	3818	hgsc.bcm.edu	37	4	187158050	187158051	+	Frame_Shift_Ins	INS	-	-	T	rs560588447	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr4:187158050_187158051insT	ENST00000264690.6	+	5	631_632	c.444_445insT	c.(445-447)tttfs	p.F149fs	KLKB1_ENST00000513864.1_Frame_Shift_Ins_p.F149fs	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	149	Apple 2. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		TTCGCTGCCAGTTTTTTTCATA	0.401													|||unknown(NO_COVERAGE)	18	0.00359425	0.0136	0.0	5008	,	,		14583	0.0		0.0	False		,,,				2504	0.0				p.Q148fs		Pindel	.											.	KLKB1	155	.	0			c.444_445insT						.			65,4201		1,63,2069						-9.8	0.3			116	2,8252		0,2,4125	no	frameshift	KLKB1	NM_000892.3		1,65,6194	A1A1,A1R,RR		0.0242,1.5237,0.5351				67,12453				SO:0001589	frameshift_variant	3818	exon5			.	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.451dupT	chr4.hg19:g.187158057_187158057dupT	ENSP00000264690:p.Phe149fs	125.0	0.0		133.0	17.0	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Frame_Shift_Ins	INS	ENST00000264690.6	hg19	CCDS34120.1																																																																																			.	.		0.401	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	
ZNF626	199777	hgsc.bcm.edu	37	19	20807134	20807300	+	Frame_Shift_Del	DEL	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	-	rs200411264|rs4808252|rs4808251|rs190319020|rs4809071|rs4809072|rs547337333|rs76605719|rs10408597|rs71332197|rs549423118|rs78715171|rs4808250|rs376295094|rs78217174|rs375690494|rs35575803|rs71174721	byFrequency	TCGA-5C-A9VG-01A-11D-A36X-10	TCGA-5C-A9VG-10A-01D-A370-10	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13e306ac-a7ee-42ba-ad29-886a69f4a281	c2b2e35f-2bd4-46f6-8aaa-7c6c21fdf3d2	g.chr19:20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENST00000601440.1	-	4	1529_1695	c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	c.(1381-1551)gcttttaagtgctcctctaaccttactacacataagaaaattcatactggagagagaccctacaaatgtgaagaatgtggcaaagccttcaaccagtcctcaatccttactacacatgagagaatcatactggagagaaattctacaaatgtgaagaatgtggcaaagcctfs	p.FKCSSNLTTHKKIHTGERPYKCEECGKAFNQSSILTTHERIILERNSTNVKNVAKP462fs	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	462					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K473R(2)|p.E484K(1)|p.I502F(1)		breast(1)|endometrium(1)|lung(3)|skin(1)	6						CCGCTTGAAGGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAAGCTTTGCCAC	0.384																																					p.462_517del		Pindel	.											.	ZNF626	121	.	4	Substitution - Missense(4)	lung(3)|central_nervous_system(1)	c.1384_1550del						.																																			SO:0001589	frameshift_variant	199777	exon4			.	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	chr19.hg19:g.20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENSP00000469958:p.Phe462fs	35.0	0.0		32.0	19.0	NM_001076675	Q8N8T4|Q96QM1	Frame_Shift_Del	DEL	ENST00000601440.1	hg19	CCDS42535.1																																																																																			.	.		0.384	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
