#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
AGRN	375790	hgsc.bcm.edu	37	1	981185	981185	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:981185C>T	ENST00000379370.2	+	15	2659	c.2609C>T	c.(2608-2610)cCc>cTc	p.P870L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	870	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TCGTGTAAGCCCGGGGTGGCT	0.672																																					p.P870L		Atlas-SNP	.											.	AGRN	110	.	0			c.C2609T						.						73.0	75.0	74.0					1																	981185		2203	4300	6503	SO:0001583	missense	375790	exon15			GTAAGCCCGGGGT	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.2609C>T	chr1.hg19:g.981185C>T	ENSP00000368678:p.Pro870Leu	149.0	0.0		79.0	4.0	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	hg19	CCDS30551.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.258046	0.59321	.	.	ENSG00000188157	ENST00000379370	T	0.62639	0.01	5.46	4.46	0.54185	EGF-like, laminin (3);EGF-like region, conserved site (1);	0.078972	0.48286	D	0.000187	T	0.76407	0.3983	M	0.79011	2.435	0.49389	D	0.999783	P	0.46621	0.881	P	0.56343	0.796	T	0.80183	-0.1488	10	0.72032	D	0.01	-15.6578	16.9092	0.86136	0.1369:0.8631:0.0:0.0	.	870	O00468	AGRIN_HUMAN	L	870	ENSP00000368678:P870L	ENSP00000368678:P870L	P	+	2	0	AGRN	971048	0.938000	0.31826	0.981000	0.43875	0.040000	0.13550	2.413000	0.44618	2.548000	0.85928	0.655000	0.94253	CCC	.	.		0.672	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
PIK3CD	5293	hgsc.bcm.edu	37	1	9781914	9781914	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:9781914A>G	ENST00000377346.4	+	16	2246	c.2051A>G	c.(2050-2052)aAg>aGg	p.K684R	PIK3CD_ENST00000543390.1_3'UTR|PIK3CD_ENST00000361110.2_Missense_Mutation_p.K708R|PIK3CD_ENST00000536656.1_Missense_Mutation_p.K708R	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	684					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	GTGCTGATGAAGCAGGTGAGG	0.711											OREG0013082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K684R		Atlas-SNP	.											.	PIK3CD	86	.	0			c.A2051G						.						33.0	38.0	36.0					1																	9781914		2195	4292	6487	SO:0001583	missense	5293	exon16			TGATGAAGCAGGT		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2051A>G	chr1.hg19:g.9781914A>G	ENSP00000366563:p.Lys684Arg	33.0	0.0	659	28.0	4.0	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.699697	0.30142	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	D;D;D	0.82255	-1.59;-1.59;-1.59	5.9	4.78	0.61160	Phosphoinositide 3-kinase, accessory (PIK) domain (1);Protein kinase-like domain (1);	0.046560	0.85682	N	0.000000	T	0.69931	0.3166	N	0.16066	0.365	0.80722	D	1	P;P;B	0.36990	0.476;0.577;0.432	B;B;B	0.41619	0.361;0.191;0.344	T	0.63607	-0.6599	10	0.17832	T	0.49	-36.5769	8.3882	0.32512	0.8498:0.0:0.1502:0.0	.	683;708;684	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	R	708;684;708;708	ENSP00000446444:K708R;ENSP00000366563:K684R;ENSP00000354410:K708R	ENSP00000353766:K708R	K	+	2	0	PIK3CD	9704501	1.000000	0.71417	0.997000	0.53966	0.082000	0.17680	3.749000	0.55150	1.050000	0.40346	0.533000	0.62120	AAG	.	.		0.711	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026	
PIK3CD	5293	hgsc.bcm.edu	37	1	9782115	9782115	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:9782115A>G	ENST00000377346.4	+	17	2333	c.2138A>G	c.(2137-2139)gAg>gGg	p.E713G	PIK3CD_ENST00000543390.1_3'UTR|PIK3CD_ENST00000361110.2_Missense_Mutation_p.E737G|PIK3CD_ENST00000536656.1_Missense_Mutation_p.E737G	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	713					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	CAGACCAAGGAGCTGATGCAC	0.612											OREG0013082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E713G		Atlas-SNP	.											.	PIK3CD	86	.	0			c.A2138G						.						66.0	74.0	71.0					1																	9782115		2203	4300	6503	SO:0001583	missense	5293	exon17			CCAAGGAGCTGAT		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2138A>G	chr1.hg19:g.9782115A>G	ENSP00000366563:p.Glu713Gly	147.0	0.0	659	82.0	4.0	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.795517	0.90453	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	D;D;D	0.82433	-1.61;-1.61;-1.61	5.4	5.4	0.78164	Protein kinase-like domain (1);	0.107748	0.64402	D	0.000006	D	0.88016	0.6324	L	0.61218	1.895	0.80722	D	1	P;D;D	0.57571	0.57;0.98;0.975	B;P;P	0.59056	0.334;0.851;0.821	D	0.89223	0.3572	10	0.72032	D	0.01	-40.3082	14.6236	0.68605	1.0:0.0:0.0:0.0	.	712;737;713	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	G	737;713;737;737	ENSP00000446444:E737G;ENSP00000366563:E713G;ENSP00000354410:E737G	ENSP00000353766:E737G	E	+	2	0	PIK3CD	9704702	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	9.194000	0.94962	2.045000	0.60652	0.459000	0.35465	GAG	.	.		0.612	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026	
UBE4B	10277	hgsc.bcm.edu	37	1	10190866	10190866	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:10190866G>T	ENST00000253251.8	+	13	2358	c.1519G>T	c.(1519-1521)Gga>Tga	p.G507*	UBE4B_ENST00000475795.1_3'UTR|UBE4B_ENST00000343090.6_Nonsense_Mutation_p.G636*|UBE4B_ENST00000377157.3_Nonsense_Mutation_p.G391*					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CTTAGAGCTCGGAAGGGTAAG	0.423																																					p.G636X		Atlas-SNP	.											.	UBE4B	233	.	0			c.G1906T						.						100.0	101.0	100.0					1																	10190866		2203	4300	6503	SO:0001587	stop_gained	10277	exon14			GAGCTCGGAAGGG	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.1519G>T	chr1.hg19:g.10190866G>T	ENSP00000253251:p.Gly507*	116.0	0.0		77.0	4.0	NM_001105562		Nonsense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	48	14.290143	0.99788	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	.	.	.	5.74	5.74	0.90152	.	0.049441	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-21.1601	19.9265	0.97104	0.0:0.0:1.0:0.0	.	.	.	.	X	507;391;636	.	ENSP00000253251:G507X	G	+	1	0	UBE4B	10113453	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.823000	0.99369	2.723000	0.93209	0.591000	0.81541	GGA	.	.		0.423	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
VPS13D	55187	hgsc.bcm.edu	37	1	12389898	12389898	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:12389898T>C	ENST00000358136.3	+	37	8340	c.8210T>C	c.(8209-8211)cTt>cCt	p.L2737P	VPS13D_ENST00000356315.4_Missense_Mutation_p.L2737P	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CTGAATTTTCTTCAGCGTGTA	0.433																																					p.L2737P		Atlas-SNP	.											.	VPS13D	316	.	0			c.T8210C						.						96.0	88.0	91.0					1																	12389898		2203	4300	6503	SO:0001583	missense	55187	exon37			ATTTTCTTCAGCG	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.8210T>C	chr1.hg19:g.12389898T>C	ENSP00000350854:p.Leu2737Pro	116.0	0.0		68.0	4.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.47|18.47	3.630866|3.630866	0.67015|0.67015	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136	.|T;T	.|0.48836	.|0.8;0.8	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.062472	.|0.64402	.|D	.|0.000003	T|T	0.64091|0.64091	0.2567|0.2567	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	.|D;P;P	.|0.71674	.|0.998;0.49;0.488	.|D;B;B	.|0.63488	.|0.915;0.296;0.155	T|T	0.61192|0.61192	-0.7112|-0.7112	5|10	.|0.29301	.|T	.|0.29	.|.	15.8735|15.8735	0.79141|0.79141	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|644;2737;2737	.|B1AJZ2;Q5THJ4-2;Q5THJ4	.|.;.;VP13D_HUMAN	L|P	1560|2737	.|ENSP00000348666:L2737P;ENSP00000350854:L2737P	.|ENSP00000348666:L2737P	F|L	+|+	1|2	0|0	VPS13D|VPS13D	12312485|12312485	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.964000|0.964000	0.63967|0.63967	7.265000|7.265000	0.78442|0.78442	2.285000|2.285000	0.76669|0.76669	0.528000|0.528000	0.53228|0.53228	TTC|CTT	.	.		0.433	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
AGMAT	79814	hgsc.bcm.edu	37	1	15901266	15901266	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:15901266G>T	ENST00000375826.3	-	6	1113	c.971C>A	c.(970-972)cCg>cAg	p.P324Q	DNAJC16_ENST00000375849.1_Missense_Mutation_p.R654L|DNAJC16_ENST00000483270.1_3'UTR	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	324					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		AAGATCATACGGTGGTGAAAC	0.468																																					p.P324Q	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.C971A						.						110.0	96.0	100.0					1																	15901266		2203	4300	6503	SO:0001583	missense	79814	exon6			TCATACGGTGGTG	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.971C>A	chr1.hg19:g.15901266G>T	ENSP00000364986:p.Pro324Gln	83.0	0.0		64.0	4.0	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	hg19	CCDS160.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.566|9.566	1.119660|1.119660	0.20877|0.20877	.|.	.|.	ENSG00000116771|ENSG00000116138	ENST00000375826|ENST00000375849	D|T	0.84223|0.70631	-1.82|-0.5	5.93|5.93	-4.84|-4.84	0.03151|0.03151	Ureohydrolase domain (1);|.	1.007650|.	0.07957|.	N|.	0.981860|.	T|T	0.67268|0.67268	0.2875|0.2875	L|L	0.61218|0.61218	1.895|1.895	0.09310|0.09310	N|N	1|1	B|.	0.23854|.	0.092|.	B|.	0.36808|.	0.233|.	T|T	0.62690|0.62690	-0.6801|-0.6801	10|6	0.72032|.	D|.	0.01|.	0.0126|0.0126	8.29|8.29	0.31952|0.31952	0.3792:0.0:0.5066:0.1143|0.3792:0.0:0.5066:0.1143	.|.	324|.	Q9BSE5|.	SPEB_HUMAN|.	Q|L	324|654	ENSP00000364986:P324Q|ENSP00000365009:R654L	ENSP00000364986:P324Q|.	P|R	-|+	2|2	0|0	AGMAT|DNAJC16	15773853|15773853	0.005000|0.005000	0.15991|0.15991	0.000000|0.000000	0.03702|0.03702	0.055000|0.055000	0.15305|0.15305	1.808000|1.808000	0.38912|0.38912	-0.729000|-0.729000	0.04875|0.04875	-0.332000|-0.332000	0.08345|0.08345	CCG|CGG	.	.		0.468	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
VWA5B1	127731	hgsc.bcm.edu	37	1	20656794	20656794	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:20656794T>C	ENST00000375079.2	+	10	1572	c.1376T>C	c.(1375-1377)cTc>cCc	p.L459P	VWA5B1_ENST00000289815.8_Missense_Mutation_p.L459P|VWA5B1_ENST00000289825.4_Missense_Mutation_p.L176P|VWA5B1_ENST00000375083.4_Missense_Mutation_p.L459P	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	459	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						CACCCGCGGCTCCTCTTCGTG	0.597																																					p.L459P		Atlas-SNP	.											.	VWA5B1	44	.	0			c.T1376C						.						54.0	59.0	58.0					1																	20656794		692	1591	2283	SO:0001583	missense	127731	exon10			CGCGGCTCCTCTT	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.1376T>C	chr1.hg19:g.20656794T>C	ENSP00000364220:p.Leu459Pro	149.0	0.0		81.0	4.0	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	hg19		.	.	.	.	.	.	.	.	.	.	T	14.30	2.493599	0.44352	.	.	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000289825;ENST00000375079	T;T;T;T	0.08282	3.11;3.11;3.11;3.11	4.94	4.94	0.65067	von Willebrand factor, type A (3);	0.080102	0.52532	D	0.000068	T	0.27765	0.0683	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	0.961;1.0;1.0	D;D;D	0.76575	0.936;0.983;0.988	T	0.02257	-1.1187	10	0.31617	T	0.26	-8.7899	13.4543	0.61189	0.0:0.0:0.0:1.0	.	459;459;176	Q5TIE3;Q5TIE3-2;Q5TIE3-3	VW5B1_HUMAN;.;.	P	459;459;459;176;459	ENSP00000289815:L459P;ENSP00000364224:L459P;ENSP00000289825:L176P;ENSP00000364220:L459P	ENSP00000289815:L459P	L	+	2	0	VWA5B1	20529381	1.000000	0.71417	0.210000	0.23637	0.014000	0.08584	3.798000	0.55522	1.849000	0.53698	0.523000	0.50628	CTC	.	.		0.597	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
KIF17	57576	hgsc.bcm.edu	37	1	21014288	21014288	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:21014288C>A	ENST00000247986.2	-	8	1841	c.1531G>T	c.(1531-1533)Gat>Tat	p.D511Y	KIF17_ENST00000375044.1_Missense_Mutation_p.D411Y|KIF17_ENST00000400463.3_Missense_Mutation_p.D511Y|KIF17_ENST00000490034.1_Intron			Q9P2E2	KIF17_HUMAN	kinesin family member 17	511					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TTGGAGACATCGTCACTGGGC	0.552																																					p.D511Y		Atlas-SNP	.											.	KIF17	130	.	0			c.G1531T						.						88.0	83.0	84.0					1																	21014288		2203	4300	6503	SO:0001583	missense	57576	exon8			AGACATCGTCACT	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1531G>T	chr1.hg19:g.21014288C>A	ENSP00000247986:p.Asp511Tyr	124.0	0.0		73.0	4.0	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	hg19	CCDS213.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.608443	0.28623	.	.	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.72394	-0.65;-0.53;-0.53	5.04	-0.415	0.12355	.	1.268100	0.06187	U	0.680688	T	0.58395	0.2119	L	0.39898	1.24	0.09310	N	1	P;P	0.51240	0.943;0.935	B;B	0.42851	0.4;0.3	T	0.51220	-0.8733	10	0.62326	D	0.03	.	1.369	0.02207	0.2948:0.3934:0.1435:0.1684	.	511;511	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	Y	411;511;511	ENSP00000364184:D411Y;ENSP00000383311:D511Y;ENSP00000247986:D511Y	ENSP00000247986:D511Y	D	-	1	0	KIF17	20886875	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.066000	0.14489	-0.227000	0.09884	-0.229000	0.12294	GAT	.	.		0.552	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
ALPL	249	hgsc.bcm.edu	37	1	21894730	21894730	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:21894730C>A	ENST00000374840.3	+	7	1032	c.782C>A	c.(781-783)cCg>cAg	p.P261Q	ALPL_ENST00000425315.2_Missense_Mutation_p.P261Q|ALPL_ENST00000374830.1_5'Flank|ALPL_ENST00000374832.1_Missense_Mutation_p.P261Q|ALPL_ENST00000539907.1_Missense_Mutation_p.P184Q|ALPL_ENST00000540617.1_Missense_Mutation_p.P206Q	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	261					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	AGCTTCAAACCGAGATACAAG	0.567																																					p.P261Q		Atlas-SNP	.											.	ALPL	50	.	0			c.C782A						.						76.0	68.0	71.0					1																	21894730		2203	4300	6503	SO:0001583	missense	249	exon7			TCAAACCGAGATA	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.782C>A	chr1.hg19:g.21894730C>A	ENSP00000363973:p.Pro261Gln	159.0	0.0		101.0	5.0	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Missense_Mutation	SNP	ENST00000374840.3	hg19	CCDS217.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.464296	0.26335	.	.	ENSG00000162551	ENST00000539907;ENST00000540617;ENST00000374840;ENST00000374832;ENST00000425315	D;D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81;-3.81	3.97	3.97	0.46021	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.223479	0.47093	D	0.000260	D	0.95620	0.8576	L	0.33189	0.99	0.30549	N	0.765602	D;P;D	0.89917	1.0;0.932;1.0	D;P;D	0.85130	0.997;0.825;0.997	D	0.92700	0.6174	10	0.33141	T	0.24	-1.3343	15.1393	0.72599	0.0:1.0:0.0:0.0	.	184;209;261	B7Z387;B7Z1D1;P05186	.;.;PPBT_HUMAN	Q	184;206;261;261;261	ENSP00000437674:P184Q;ENSP00000442672:P206Q;ENSP00000363973:P261Q;ENSP00000363965:P261Q;ENSP00000394765:P261Q	ENSP00000363965:P261Q	P	+	2	0	ALPL	21767317	0.131000	0.22433	0.979000	0.43373	0.703000	0.40648	1.460000	0.35244	2.210000	0.71456	0.561000	0.74099	CCG	.	.		0.567	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478	
USP48	84196	hgsc.bcm.edu	37	1	22084236	22084236	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:22084236C>A	ENST00000308271.9	-	2	823	c.175G>T	c.(175-177)Ggt>Tgt	p.G59C	USP48_ENST00000421625.2_Missense_Mutation_p.G59C|USP48_ENST00000400301.1_Missense_Mutation_p.G59C|USP48_ENST00000529637.1_Missense_Mutation_p.G59C	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	59					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		ATATGCTCACCAATACCAACC	0.333																																					p.G59C		Atlas-SNP	.											USP48,colon,carcinoma,+2,1	USP48	91	.	0			c.G175T						.						108.0	100.0	103.0					1																	22084236		2203	4300	6503	SO:0001583	missense	84196	exon2			GCTCACCAATACC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.175G>T	chr1.hg19:g.22084236C>A	ENSP00000309262:p.Gly59Cys	104.0	0.0		78.0	5.0	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906411	0.92107	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000529637;ENST00000421625	T;T;T;T	0.09538	3.0;2.97;2.97;3.24	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.36413	0.0966	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;1.0;1.0	T	0.04427	-1.0952	10	0.87932	D	0	.	18.8507	0.92227	0.0:1.0:0.0:0.0	.	59;59;59;59;59;59	B7ZKS7;B7ZKS3;Q86UV5-7;Q86UV5-3;Q86UV5-2;Q86UV5	.;.;.;.;.;UBP48_HUMAN	C	59	ENSP00000383157:G59C;ENSP00000309262:G59C;ENSP00000431949:G59C;ENSP00000406256:G59C	ENSP00000309262:G59C	G	-	1	0	USP48	21956823	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.343000	0.79319	2.689000	0.91719	0.655000	0.94253	GGT	.	.		0.333	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
HSPG2	3339	hgsc.bcm.edu	37	1	22180694	22180694	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:22180694T>C	ENST00000374695.3	-	50	6510	c.6431A>G	c.(6430-6432)tAc>tGc	p.Y2144C	HSPG2_ENST00000430507.1_Intron	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2144	Ig-like C2-type 6.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ACCTGGGGTGTAGCTGGGGCC	0.622																																					p.Y2144C		Atlas-SNP	.											.	HSPG2	311	.	0			c.A6431G						.						12.0	14.0	14.0					1																	22180694		2196	4293	6489	SO:0001583	missense	3339	exon50			GGGGTGTAGCTGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6431A>G	chr1.hg19:g.22180694T>C	ENSP00000363827:p.Tyr2144Cys	109.0	0.0		58.0	4.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.005774	0.35415	.	.	ENSG00000142798	ENST00000374695	T	0.76186	-1.0	5.34	1.34	0.21922	Immunoglobulin-like (1);	1.023810	0.07853	N	0.964982	T	0.74222	0.3688	M	0.68952	2.095	0.09310	N	1	P;P	0.47106	0.86;0.89	P;B	0.44359	0.447;0.41	T	0.60954	-0.7160	10	0.40728	T	0.16	.	10.314	0.43725	0.0:0.0:0.5136:0.4864	.	84;2144	Q59EG0;P98160	.;PGBM_HUMAN	C	2144	ENSP00000363827:Y2144C	ENSP00000363827:Y2144C	Y	-	2	0	HSPG2	22053281	0.000000	0.05858	0.028000	0.17463	0.294000	0.27393	-0.282000	0.08445	0.302000	0.22762	-0.313000	0.08912	TAC	.	.		0.622	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
CDC42	998	hgsc.bcm.edu	37	1	22417973	22417973	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:22417973C>T	ENST00000344548.3	+	7	790	c.539C>T	c.(538-540)cCa>cTa	p.P180L	CDC42_ENST00000400259.1_Missense_Mutation_p.P180L|CDC42_ENST00000421089.2_Missense_Mutation_p.P222L	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	180					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		CTGGAGCCTCCAGAACCGAAG	0.453																																					p.P180L		Atlas-SNP	.											.	CDC42	26	.	0			c.C539T						.						55.0	60.0	59.0					1																	22417973		2203	4300	6503	SO:0001583	missense	998	exon7			AGCCTCCAGAACC	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"""GTP binding protein, 25kDa"""	116952	"""cell division cycle 42 (GTP-binding protein, 25kD)"", ""cell division cycle 42 (GTP binding protein, 25kDa)"""			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.539C>T	chr1.hg19:g.22417973C>T	ENSP00000341072:p.Pro180Leu	167.0	0.0		77.0	4.0	NM_001039802	P21181|P25763|Q7L8R5|Q9UDI2	Missense_Mutation	SNP	ENST00000344548.3	hg19	CCDS221.1	.	.	.	.	.	.	.	.	.	.	c	15.69	2.908707	0.52439	.	.	ENSG00000070831	ENST00000400259;ENST00000344548;ENST00000421089	T;T;T	0.67171	-0.25;-0.25;0.11	5.22	5.22	0.72569	.	0.102632	0.64402	D	0.000002	T	0.67702	0.2921	M	0.74647	2.275	0.80722	D	1	B;B;B;B	0.28178	0.202;0.009;0.202;0.003	B;B;B;B	0.21151	0.025;0.033;0.025;0.005	T	0.69774	-0.5054	10	0.66056	D	0.02	.	17.3462	0.87310	0.0:1.0:0.0:0.0	.	222;225;222;180	E7ETU3;B4E1U9;B4DMH5;P60953	.;.;.;CDC42_HUMAN	L	180;180;222	ENSP00000383118:P180L;ENSP00000341072:P180L;ENSP00000398592:P222L	ENSP00000341072:P180L	P	+	2	0	CDC42	22290560	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.426000	0.80270	2.443000	0.82685	0.455000	0.32223	CCA	.	.		0.453	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791	
SYTL1	84958	hgsc.bcm.edu	37	1	27677307	27677307	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:27677307T>C	ENST00000543823.1	+	10	1490	c.1028T>C	c.(1027-1029)cTt>cCt	p.L343P	SYTL1_ENST00000318074.5_Missense_Mutation_p.L331P|SYTL1_ENST00000490170.1_3'UTR			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	343	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CAGGCCGAGCTTCAGGGCCGC	0.637																																					p.L343P		Atlas-SNP	.											.	SYTL1	57	.	0			c.T1028C						.						57.0	53.0	54.0					1																	27677307		2203	4300	6503	SO:0001583	missense	84958	exon11			CCGAGCTTCAGGG	AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.1028T>C	chr1.hg19:g.27677307T>C	ENSP00000440704:p.Leu343Pro	137.0	0.0		100.0	4.0	NM_001193308	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Missense_Mutation	SNP	ENST00000543823.1	hg19	CCDS53286.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.48|16.48	3.136012|3.136012	0.56936|0.56936	.|.	.|.	ENSG00000142765|ENSG00000142765	ENST00000496001|ENST00000318074;ENST00000543823;ENST00000485269	.|T;T	.|0.11930	.|2.73;2.73	4.49|4.49	4.49|4.49	0.54785|0.54785	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.46776|0.46776	0.1410|0.1410	M|M	0.93241|0.93241	3.395|3.395	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;1.0	T|T	0.60611|0.60611	-0.7229|-0.7229	5|10	.|0.87932	.|D	.|0	-22.0434|-22.0434	12.9621|12.9621	0.58464|0.58464	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|343;331	.|Q8IYJ3;Q8IYJ3-2	.|SYTL1_HUMAN;.	L|P	191|331;343;96	.|ENSP00000316464:L331P;ENSP00000440704:L343P	.|ENSP00000316464:L331P	F|L	+|+	1|2	0|0	SYTL1|SYTL1	27549894|27549894	1.000000|1.000000	0.71417|0.71417	0.901000|0.901000	0.35422|0.35422	0.216000|0.216000	0.24613|0.24613	4.702000|4.702000	0.61817|0.61817	1.894000|1.894000	0.54839|0.54839	0.374000|0.374000	0.22700|0.22700	TTC|CTT	.	.		0.637	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872	
MAP3K6	9064	hgsc.bcm.edu	37	1	27691344	27691344	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:27691344C>T	ENST00000493901.1	-	3	639	c.400G>A	c.(400-402)Ggt>Agt	p.G134S	MAP3K6_ENST00000374040.3_Missense_Mutation_p.G134S|MAP3K6_ENST00000357582.2_Missense_Mutation_p.G134S	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	134					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TCACGCACACCAAGGTGGTAG	0.642																																					p.G134S		Atlas-SNP	.											.	MAP3K6	134	.	0			c.G400A						.						79.0	70.0	73.0					1																	27691344		2203	4300	6503	SO:0001583	missense	9064	exon2			GCACACCAAGGTG	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.400G>A	chr1.hg19:g.27691344C>T	ENSP00000419591:p.Gly134Ser	165.0	0.0		123.0	5.0	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	hg19	CCDS299.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349369	0.82132	.	.	ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000357582	T;T;T	0.22539	1.95;1.95;1.95	5.4	4.48	0.54585	.	.	.	.	.	T	0.30634	0.0771	M	0.75085	2.285	0.58432	D	0.99999	B;P	0.34934	0.421;0.476	B;B	0.40101	0.213;0.319	T	0.14839	-1.0458	9	0.87932	D	0	.	12.1337	0.53957	0.0:0.9203:0.0:0.0797	.	134;134	O95382-3;O95382	.;M3K6_HUMAN	S	134	ENSP00000363152:G134S;ENSP00000419591:G134S;ENSP00000350195:G134S	ENSP00000350195:G134S	G	-	1	0	MAP3K6	27563931	0.996000	0.38824	0.064000	0.19789	0.923000	0.55619	5.057000	0.64294	1.515000	0.48885	0.655000	0.94253	GGT	.	.		0.642	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
STX12	23673	hgsc.bcm.edu	37	1	28128323	28128323	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:28128323T>C	ENST00000373943.4	+	4	548	c.423T>C	c.(421-423)ctT>ctC	p.L141L	STX12_ENST00000468761.1_3'UTR	NM_177424.2	NP_803173.1	Q86Y82	STX12_HUMAN	syntaxin 12	141					cholesterol efflux (GO:0033344)|intracellular protein transport (GO:0006886)|protein stabilization (GO:0050821)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|central_nervous_system(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|all_lung(284;9.43e-05)|Lung NSC(340;0.000185)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;3.96e-24)|Colorectal(126;3.46e-08)|COAD - Colon adenocarcinoma(152;1.83e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00258)|KIRC - Kidney renal clear cell carcinoma(1967;0.00302)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0649)		GATCTCGTCTTTCTGTAAGTT	0.388																																					p.L141L	Ovarian(5;5 342 2097 9488 34083)	Atlas-SNP	.											.	STX12	26	.	0			c.T423C						.						86.0	82.0	83.0					1																	28128323		2203	4300	6503	SO:0001819	synonymous_variant	23673	exon4			TCGTCTTTCTGTA	BC046999	CCDS310.1	1p35.3	2008-05-14			ENSG00000117758	ENSG00000117758			11430	protein-coding gene	gene with protein product		606892				9507000	Standard	NM_177424		Approved	STX13, STX14	uc001bou.4	Q86Y82	OTTHUMG00000003730	ENST00000373943.4:c.423T>C	chr1.hg19:g.28128323T>C		135.0	0.0		99.0	4.0	NM_177424	B1AJQ7|O95564	Silent	SNP	ENST00000373943.4	hg19	CCDS310.1																																																																																			.	.		0.388	STX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010519.1	NM_177424	
DNAJC8	22826	hgsc.bcm.edu	37	1	28536549	28536549	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:28536549C>T	ENST00000263697.4	-	5	359	c.333G>A	c.(331-333)ctG>ctA	p.L111L	DNAJC8_ENST00000489277.1_5'UTR	NM_014280.2	NP_055095.2	O75937	DNJC8_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 8	111	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)				kidney(1)|large_intestine(3)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;4.08e-05)|all_lung(284;4.29e-05)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.0105)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		OV - Ovarian serous cystadenocarcinoma(117;2.81e-22)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00275)|BRCA - Breast invasive adenocarcinoma(304;0.0059)|STAD - Stomach adenocarcinoma(196;0.00671)|READ - Rectum adenocarcinoma(331;0.0649)		GCTCCTGATCCAGTAGCAACT	0.413																																					p.L111L		Atlas-SNP	.											.	DNAJC8	13	.	0			c.G333A						.						108.0	93.0	98.0					1																	28536549		1854	4099	5953	SO:0001819	synonymous_variant	22826	exon5			CTGATCCAGTAGC	AF083190	CCDS41292.1	1p35	2011-09-02			ENSG00000126698	ENSG00000126698		"""Heat shock proteins / DNAJ (HSP40)"""	15470	protein-coding gene	gene with protein product						11147971	Standard	NM_014280		Approved	SPF31	uc001bpn.3	O75937	OTTHUMG00000003538	ENST00000263697.4:c.333G>A	chr1.hg19:g.28536549C>T		132.0	0.0		74.0	4.0	NM_014280	B4DUU4|D3DPM0|Q6IBA4|Q8N4Z5|Q9P051|Q9P067	Silent	SNP	ENST00000263697.4	hg19	CCDS41292.1																																																																																			.	.		0.413	DNAJC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009860.1	NM_014280	
HCRTR1	3061	hgsc.bcm.edu	37	1	32087137	32087137	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:32087137C>T	ENST00000373706.5	+	4	835	c.682C>T	c.(682-684)Ctg>Ttg	p.L228L	HCRTR1_ENST00000403528.2_Silent_p.L228L|HCRTR1_ENST00000468521.1_3'UTR|HCRTR1_ENST00000373705.1_Silent_p.L228L			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	228					feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		CCTGGCCCCACTGGGCCTCAT	0.582																																					p.L228L		Atlas-SNP	.											.	HCRTR1	20	.	0			c.C682T						.						166.0	164.0	165.0					1																	32087137		2203	4300	6503	SO:0001819	synonymous_variant	3061	exon6			GCCCCACTGGGCC	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"""GPCR / Class A : Hypocretin (orexin) receptors"""	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.682C>T	chr1.hg19:g.32087137C>T		115.0	0.0		75.0	4.0	NM_001525	A8K3A6|Q9HBV6	Silent	SNP	ENST00000373706.5	hg19	CCDS344.1																																																																																			.	.		0.582	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525	
HMGB4	127540	hgsc.bcm.edu	37	1	34330051	34330051	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:34330051A>G	ENST00000522796.1	+	4	2164	c.259A>G	c.(259-261)Aag>Gag	p.K87E	HMGB4_ENST00000519684.1_Missense_Mutation_p.K87E|HMGB4_ENST00000425537.1_3'UTR|CSMD2_ENST00000373381.4_Intron			Q8WW32	HMGB4_HUMAN	high mobility group box 4	87						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GAAACGGAGAAAGCGGGATCC	0.507																																					p.K87E		Atlas-SNP	.											.	HMGB4	27	.	0			c.A259G						.						131.0	148.0	142.0					1																	34330051		2203	4300	6503	SO:0001583	missense	127540	exon2			CGGAGAAAGCGGG		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"""High-mobility group / Canonical"""	24954	protein-coding gene	gene with protein product			"""high-mobility group box 4"""				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.259A>G	chr1.hg19:g.34330051A>G	ENSP00000430919:p.Lys87Glu	178.0	0.0		94.0	4.0	NM_145205	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	hg19	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.791465	0.70452	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	D;D	0.94280	-3.39;-3.39	5.58	5.58	0.84498	.	0.059922	0.64402	D	0.000004	D	0.90998	0.7169	M	0.63208	1.945	0.42581	D	0.993215	P	0.49090	0.919	B	0.39465	0.3	D	0.91774	0.5430	10	0.66056	D	0.02	.	12.0666	0.53592	1.0:0.0:0.0:0.0	.	87	B2R4X7	.	E	87	ENSP00000429214:K87E;ENSP00000430919:K87E	ENSP00000429214:K87E	K	+	1	0	HMGB4	34102638	1.000000	0.71417	0.969000	0.41365	0.925000	0.55904	3.935000	0.56560	2.343000	0.79666	0.496000	0.49642	AAG	.	.		0.507	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35928256	35928256	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:35928256A>G	ENST00000325722.3	-	8	1494	c.1260T>C	c.(1258-1260)tcT>tcC	p.S420S	KIAA0319L_ENST00000485551.1_5'UTR	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	420	PKD 2. {ECO:0000255|PROSITE- ProRule:PRU00151}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGGTTGGCAAAGAGATCTCCT	0.443																																					p.S420S		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T1260C						.						89.0	82.0	85.0					1																	35928256		2203	4300	6503	SO:0001819	synonymous_variant	79932	exon8			TGGCAAAGAGATC	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.1260T>C	chr1.hg19:g.35928256A>G		96.0	0.0		56.0	4.0	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Silent	SNP	ENST00000325722.3	hg19	CCDS390.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.348828	0.24426	.	.	ENSG00000142687	ENST00000431916	.	.	.	5.54	4.4	0.53042	.	.	.	.	.	T	0.44350	0.1289	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42172	-0.9467	4	.	.	.	-6.7581	1.2872	0.02053	0.5356:0.1665:0.1489:0.149	.	.	.	.	L	250	.	.	F	-	1	0	KIAA0319L	35700843	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.630000	0.24553	0.923000	0.37045	0.533000	0.62120	TTT	.	.		0.443	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
AGO4	192670	hgsc.bcm.edu	37	1	36298149	36298149	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:36298149C>T	ENST00000373210.3	+	11	1602	c.1357C>T	c.(1357-1359)Caa>Taa	p.Q453*		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	453					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)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										ACCTCAGAAACAATGTAGGGA	0.398																																					p.Q453X		Atlas-SNP	.											EIF2C4,bladder,carcinoma,0,1	.	.	.	0			c.C1357T						.						122.0	126.0	124.0					1																	36298149		2203	4300	6503	SO:0001587	stop_gained	192670	exon11			CAGAAACAATGTA	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"""Argonaute/PIWI family"""	18424	protein-coding gene	gene with protein product	"""argonaute 4"""	607356	"""eukaryotic translation initiation factor 2C, 4"""	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.1357C>T	chr1.hg19:g.36298149C>T	ENSP00000362306:p.Gln453*	119.0	0.0		82.0	4.0	NM_017629	A7MD27	Nonsense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	C	39	7.414465	0.98269	.	.	ENSG00000134698	ENST00000373210	.	.	.	5.36	5.36	0.76844	.	0.164660	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-2.5418	19.0955	0.93249	0.0:1.0:0.0:0.0	.	.	.	.	X	453	.	ENSP00000362306:Q453X	Q	+	1	0	EIF2C4	36070736	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.511000	0.84671	0.655000	0.94253	CAA	.	.		0.398	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629	
AGO3	192669	hgsc.bcm.edu	37	1	36439085	36439085	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:36439085A>G	ENST00000373191.4	+	5	980	c.631A>G	c.(631-633)Atg>Gtg	p.M211V	AGO3_ENST00000246314.6_Intron|AGO3_ENST00000324350.5_Missense_Mutation_p.M211V|AGO3_ENST00000397828.2_Missense_Mutation_p.M211V	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	211					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)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										TCGGCCTGCCATGTGGAAAAT	0.448																																					p.M211V		Atlas-SNP	.											.	.	.	.	0			c.A631G						.						202.0	200.0	201.0					1																	36439085		2203	4300	6503	SO:0001583	missense	192669	exon5			CCTGCCATGTGGA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.631A>G	chr1.hg19:g.36439085A>G	ENSP00000362287:p.Met211Val	236.0	0.0		139.0	6.0	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	hg19	CCDS399.1	.	.	.	.	.	.	.	.	.	.	A	16.69	3.192029	0.58017	.	.	ENSG00000126070	ENST00000324350;ENST00000373191;ENST00000397828	T;T;T	0.09073	3.02;3.02;3.02	5.62	5.62	0.85841	Domain of unknown function DUF1785 (1);	0.000000	0.85682	D	0.000000	T	0.07954	0.0199	N	0.12502	0.225	0.80722	D	1	B;B	0.23249	0.082;0.005	B;B	0.33121	0.158;0.008	T	0.36089	-0.9762	10	0.54805	T	0.06	-32.6353	15.8286	0.78733	1.0:0.0:0.0:0.0	.	211;211	Q9H9G7;Q5TA56	AGO3_HUMAN;.	V	211	ENSP00000317425:M211V;ENSP00000362287:M211V;ENSP00000380928:M211V	ENSP00000317425:M211V	M	+	1	0	EIF2C3	36211672	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.024000	0.70857	2.141000	0.66446	0.460000	0.39030	ATG	.	.		0.448	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
MFSD2A	84879	hgsc.bcm.edu	37	1	40430920	40430920	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:40430920T>C	ENST00000372809.5	+	4	573	c.430T>C	c.(430-432)Ttc>Ctc	p.F144L	MFSD2A_ENST00000480630.1_3'UTR|MFSD2A_ENST00000420632.2_5'UTR|MFSD2A_ENST00000372811.5_Missense_Mutation_p.F131L	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	144					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						CATTGCCTACTTCCTCATCTG	0.582																																					p.F144L		Atlas-SNP	.											.	MFSD2A	53	.	0			c.T430C						.						165.0	139.0	148.0					1																	40430920		2203	4300	6503	SO:0001583	missense	84879	exon4			GCCTACTTCCTCA	AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"""major facilitator superfamily domain containing 2"""	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.430T>C	chr1.hg19:g.40430920T>C	ENSP00000361895:p.Phe144Leu	116.0	0.0		95.0	4.0	NM_001136493	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	hg19	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.799871	0.50208	.	.	ENSG00000168389	ENST00000372811;ENST00000434861;ENST00000372809	T;D;T	0.86562	-1.17;-2.14;-1.17	5.51	5.51	0.81932	Major facilitator superfamily domain, general substrate transporter (1);	0.089074	0.85682	D	0.000000	D	0.85669	0.5750	M	0.75615	2.305	0.80722	D	1	B;B;B	0.16396	0.017;0.013;0.002	B;B;B	0.24974	0.057;0.05;0.017	T	0.81068	-0.1100	10	0.31617	T	0.26	-18.0473	9.3296	0.38014	0.0:0.0799:0.0:0.9201	.	94;144;131	B4DNN7;Q8NA29;Q8NA29-2	.;MFS2A_HUMAN;.	L	131;129;144	ENSP00000361898:F131L;ENSP00000407606:F129L;ENSP00000361895:F144L	ENSP00000361895:F144L	F	+	1	0	MFSD2A	40203507	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	2.578000	0.46051	2.085000	0.62840	0.459000	0.35465	TTC	.	.		0.582	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793	
ZNF691	51058	hgsc.bcm.edu	37	1	43317025	43317025	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:43317025G>T	ENST00000372506.1	+	4	736	c.396G>T	c.(394-396)cgG>cgT	p.R132R	ZNF691_ENST00000397044.3_Silent_p.R163R|ZNF691_ENST00000372502.1_Silent_p.R154R|ZNF691_ENST00000372508.3_Silent_p.R132R|ZNF691_ENST00000372504.1_Silent_p.R154R|ZNF691_ENST00000372507.1_Silent_p.R132R	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	163						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|ovary(2)|prostate(1)	7	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCACGAGCGGATCCACCTGG	0.562																																					p.R163R		Atlas-SNP	.											.	ZNF691	30	.	0			c.G489T						.						48.0	47.0	47.0					1																	43317025		2203	4300	6503	SO:0001819	synonymous_variant	51058	exon4			CGAGCGGATCCAC		CCDS476.1, CCDS55595.1	1p34.2	2013-01-08			ENSG00000164011	ENSG00000164011		"""Zinc fingers, C2H2-type"""	28028	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001242739		Approved	Zfp691	uc021omh.1	Q5VV52	OTTHUMG00000007623	ENST00000372506.1:c.396G>T	chr1.hg19:g.43317025G>T		74.0	0.0		48.0	4.0	NM_001242739	A8MXP6|B4DJR7|O95878|Q9NWE8	Silent	SNP	ENST00000372506.1	hg19	CCDS476.1																																																																																			.	.		0.562	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911	
SZT2	23334	hgsc.bcm.edu	37	1	43913358	43913358	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:43913358G>T	ENST00000562955.1	+	66	9258	c.9258G>T	c.(9256-9258)tcG>tcT	p.S3086S	SZT2_ENST00000372442.1_Silent_p.S2244S|SZT2-AS1_ENST00000396885.2_RNA	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	3143					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CCCTGGTGTCGGCATGGCACA	0.572																																					p.S3086S		Atlas-SNP	.											SZT2_ENST00000562955,colon,carcinoma,0,3	SZT2	383	.	0			c.G9258T						.						45.0	41.0	42.0					1																	43913358		2203	4300	6503	SO:0001819	synonymous_variant	23334	exon66			GGTGTCGGCATGG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.9258G>T	chr1.hg19:g.43913358G>T		42.0	0.0		53.0	3.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.572	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
KLF17	128209	hgsc.bcm.edu	37	1	44595054	44595054	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:44595054C>T	ENST00000372299.3	+	2	169	c.111C>T	c.(109-111)aaC>aaT	p.N37N	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	37					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					CCATCTTGAACATGTCTTCAT	0.502																																					p.N37N		Atlas-SNP	.											.	KLF17	92	.	0			c.C111T						.						124.0	115.0	118.0					1																	44595054		2203	4300	6503	SO:0001819	synonymous_variant	128209	exon2			CTTGAACATGTCT	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.111C>T	chr1.hg19:g.44595054C>T		144.0	0.0		84.0	4.0	NM_173484	Q86VQ7|Q8N805	Silent	SNP	ENST00000372299.3	hg19	CCDS508.1																																																																																			.	.		0.502	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
RNF220	55182	hgsc.bcm.edu	37	1	45092001	45092001	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:45092001A>G	ENST00000355387.2	+	5	1287	c.837A>G	c.(835-837)gaA>gaG	p.E279E	RNF220_ENST00000443020.2_Silent_p.E40E|RNF220_ENST00000372247.2_Silent_p.E279E|RNF220_ENST00000361799.2_Silent_p.E279E			Q5VTB9	RN220_HUMAN	ring finger protein 220	279					protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						TCAAGAGGGAAGGAGAGTCTC	0.537																																					p.E279E		Atlas-SNP	.											.	RNF220	56	.	0			c.A837G						.						115.0	96.0	102.0					1																	45092001		2203	4300	6503	SO:0001819	synonymous_variant	55182	exon5			GAGGGAAGGAGAG	AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"""RING-type (C3HC4) zinc fingers"""	25552	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 164"""	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.837A>G	chr1.hg19:g.45092001A>G		109.0	0.0		64.0	4.0	NM_018150	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	Silent	SNP	ENST00000355387.2	hg19	CCDS510.1	.	.	.	.	.	.	.	.	.	.	A	10.25	1.298112	0.23650	.	.	ENSG00000187147	ENST00000453863	.	.	.	5.32	4.2	0.49525	.	.	.	.	.	T	0.62208	0.2409	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60042	-0.7340	4	.	.	.	.	11.2096	0.48790	0.9287:0.0:0.0713:0.0	.	.	.	.	G	2	.	.	R	+	1	2	RNF220	44864588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.349000	0.59385	1.157000	0.42530	0.519000	0.50382	AGG	.	.		0.537	RNF220-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020683.4	NM_018150	
ZSWIM5	57643	hgsc.bcm.edu	37	1	45525908	45525908	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:45525908G>T	ENST00000359600.5	-	3	1169	c.964C>A	c.(964-966)Ccc>Acc	p.P322T		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	322						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					CCAGCTGTGGGGTCAGGGGCA	0.478																																					p.P322T		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.C964A						.						49.0	45.0	46.0					1																	45525908		1884	4114	5998	SO:0001583	missense	57643	exon3			CTGTGGGGTCAGG	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"""Zinc fingers, SWIM-type"""	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.964C>A	chr1.hg19:g.45525908G>T	ENSP00000352614:p.Pro322Thr	123.0	0.0		85.0	4.0	NM_020883	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	hg19	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.673196	0.88445	.	.	ENSG00000162415	ENST00000359600	T	0.21932	1.98	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.54951	0.1890	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.64635	-0.6361	10	0.87932	D	0	-15.0487	18.8801	0.92352	0.0:0.0:1.0:0.0	.	322	Q9P217	ZSWM5_HUMAN	T	322	ENSP00000352614:P322T	ENSP00000352614:P322T	P	-	1	0	ZSWIM5	45298495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.615000	0.88500	0.557000	0.71058	CCC	.	.		0.478	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581	
MUTYH	4595	hgsc.bcm.edu	37	1	45800108	45800108	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:45800108T>C	ENST00000372098.3	-	2	245	c.112A>G	c.(112-114)Aag>Gag	p.K38E	MUTYH_ENST00000488731.2_Missense_Mutation_p.K24E|MUTYH_ENST00000529984.1_Missense_Mutation_p.K24E|MUTYH_ENST00000372100.5_Missense_Mutation_p.K24E|MUTYH_ENST00000372115.3_Missense_Mutation_p.K38E|MUTYH_ENST00000528013.2_Missense_Mutation_p.K24E|MUTYH_ENST00000456914.2_Missense_Mutation_p.K24E|MUTYH_ENST00000372104.1_Missense_Mutation_p.K24E|MUTYH_ENST00000372110.3_Missense_Mutation_p.K38E|MUTYH_ENST00000354383.6_Missense_Mutation_p.K24E|MUTYH_ENST00000528332.2_Missense_Mutation_p.K38E|MUTYH_ENST00000355498.2_Missense_Mutation_p.K24E|MUTYH_ENST00000450313.1_Missense_Mutation_p.K38E|MUTYH_ENST00000448481.1_Missense_Mutation_p.K24E|MUTYH_ENST00000531105.1_Missense_Mutation_p.K24E			Q9UIF7	MUTYH_HUMAN	mutY homolog	38					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TTAGCATGCTTCTGCCTCCCT	0.552			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.K38E		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.A112G						.						185.0	137.0	153.0					1																	45800108		2203	4300	6503	SO:0001583	missense	4595	exon2	Familial Cancer Database	MAP, MYH-associated polyposis	CATGCTTCTGCCT	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.112A>G	chr1.hg19:g.45800108T>C	ENSP00000361170:p.Lys38Glu	133.0	0.0		79.0	4.0	NM_012222	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	hg19	CCDS520.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.595861	0.28445	.	.	ENSG00000132781	ENST00000529984;ENST00000528332;ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000488731;ENST00000450313;ENST00000372100;ENST00000531105;ENST00000435155;ENST00000528013;ENST00000483127	T;D;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.91843	2.32;-2.92;3.2;3.24;3.2;3.21;3.2;3.22;3.19;3.18;2.32;3.2;3.24;0.52;1.93;0.89;0.81	4.28	1.88	0.25563	.	0.669254	0.14006	N	0.347799	D	0.88055	0.6334	L	0.48642	1.525	0.09310	N	1	B;B;B;B;B;B	0.28291	0.206;0.085;0.137;0.085;0.172;0.085	B;B;B;B;B;B	0.31101	0.124;0.026;0.085;0.039;0.039;0.039	T	0.79543	-0.1760	10	0.54805	T	0.06	-0.3653	8.5549	0.33476	0.0:0.0:0.4386:0.5614	.	38;38;38;38;38;24	B4DEX2;E5KP25;Q9UIF7-2;Q9UIF7;E5KP27;E5KP28	.;.;.;MUTYH_HUMAN;.;.	E	24;38;24;24;24;24;24;38;38;38;24;38;24;24;24;24;30	ENSP00000437093:K24E;ENSP00000433076:K38E;ENSP00000361176:K24E;ENSP00000409718:K24E;ENSP00000407590:K24E;ENSP00000346354:K24E;ENSP00000347685:K24E;ENSP00000361170:K38E;ENSP00000361182:K38E;ENSP00000361187:K38E;ENSP00000432330:K24E;ENSP00000408176:K38E;ENSP00000361172:K24E;ENSP00000431292:K24E;ENSP00000403655:K24E;ENSP00000433130:K24E;ENSP00000436469:K30E	ENSP00000346354:K24E	K	-	1	0	MUTYH	45572695	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.561000	0.23515	0.405000	0.25532	0.528000	0.53228	AAG	.	.		0.552	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
EFCAB14	9813	hgsc.bcm.edu	37	1	47149060	47149060	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:47149060C>T	ENST00000371933.3	-	10	2200	c.1224G>A	c.(1222-1224)ttG>ttA	p.L408L	EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14_ENST00000484461.1_5'Flank|EFCAB14_ENST00000544071.1_Silent_p.L344L	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	408							calcium ion binding (GO:0005509)										AAAATTTTGGCAATGCTGATG	0.353																																					p.L408L		Atlas-SNP	.											.	.	.	.	0			c.G1224A						.						112.0	114.0	113.0					1																	47149060		2203	4300	6503	SO:0001819	synonymous_variant	9813	exon10			TTTTGGCAATGCT	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"""EF-hand domain containing"""	29051	protein-coding gene	gene with protein product			"""KIAA0494"""	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1224G>A	chr1.hg19:g.47149060C>T		106.0	0.0		59.0	4.0	NM_014774	D3DQ23|Q5SXB8	Silent	SNP	ENST00000371933.3	hg19	CCDS30706.1																																																																																			.	.		0.353	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774	
CYP4A11	1579	hgsc.bcm.edu	37	1	47406949	47406949	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:47406949A>G	ENST00000310638.4	-	1	188	c.157T>C	c.(157-159)Tgc>Cgc	p.C53R	CYP4A11_ENST00000371904.4_Missense_Mutation_p.C53R|CYP4A11_ENST00000457840.2_5'UTR|CYP4A11_ENST00000462347.1_Missense_Mutation_p.C53R|CYP4A11_ENST00000371905.1_Missense_Mutation_p.C53R	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	53					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	GAGGGAGGGCACGGGAACTGC	0.617																																					p.C53R		Atlas-SNP	.											.	CYP4A11	77	.	0			c.T157C						.						67.0	60.0	63.0					1																	47406949		2203	4300	6503	SO:0001583	missense	1579	exon1			GAGGGCACGGGAA	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"""Cytochrome P450s"""	2642	protein-coding gene	gene with protein product		601310	"""cytochrome P450, subfamily IVA, polypeptide 11"""	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.157T>C	chr1.hg19:g.47406949A>G	ENSP00000311095:p.Cys53Arg	160.0	0.0		71.0	4.0	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	hg19	CCDS543.1	.	.	.	.	.	.	.	.	.	.	-	7.618	0.676158	0.14841	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905	T;T;T	0.67865	-0.29;-0.29;-0.29	4.92	-0.772	0.10998	.	0.378318	0.25200	N	0.032389	T	0.56992	0.2023	L	0.43923	1.385	0.09310	N	0.999993	B	0.34255	0.445	B	0.41412	0.356	T	0.53514	-0.8428	10	0.62326	D	0.03	.	6.1817	0.20476	0.3094:0.4541:0.0:0.2365	.	53	Q02928	CP4AB_HUMAN	R	53	ENSP00000311095:C53R;ENSP00000360971:C53R;ENSP00000360972:C53R	ENSP00000311095:C53R	C	-	1	0	CYP4A11	47179536	0.002000	0.14202	0.009000	0.14445	0.031000	0.12232	1.745000	0.38278	0.068000	0.16574	-0.331000	0.08364	TGC	.	.		0.617	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778	
TTC39A	22996	hgsc.bcm.edu	37	1	51767296	51767296	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:51767296T>C	ENST00000447632.2	-	12	1157	c.1109A>G	c.(1108-1110)aAg>aGg	p.K370R	TTC39A_ENST00000262675.7_Missense_Mutation_p.K307R|TTC39A_ENST00000413473.2_Missense_Mutation_p.K338R|TTC39A_ENST00000371750.5_Missense_Mutation_p.K335R|TTC39A_ENST00000371747.3_Missense_Mutation_p.K369R|TTC39A_ENST00000262676.5_3'UTR|TTC39A_ENST00000451380.1_Missense_Mutation_p.K334R			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	370								p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						GTAGGACATCTTCCACTGGCC	0.582																																					p.K338R		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A1013G						.						73.0	75.0	74.0					1																	51767296		2123	4237	6360	SO:0001583	missense	22996	exon12			GACATCTTCCACT	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"""Tetratricopeptide (TTC) repeat domain containing"""	18657	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 34"""	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1109A>G	chr1.hg19:g.51767296T>C	ENSP00000393952:p.Lys370Arg	100.0	0.0		44.0	4.0	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.02	3.005308	0.54254	.	.	ENSG00000085831	ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750;ENST00000371747	T;T;T;T;T;T	0.64260	0.88;0.88;0.88;0.88;0.88;-0.09	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.55465	0.1922	L	0.49571	1.57	0.49687	D	0.999812	B;B;B;B;B;B	0.17667	0.002;0.002;0.005;0.023;0.006;0.019	B;B;B;B;B;B	0.21546	0.012;0.021;0.013;0.035;0.034;0.021	T	0.51371	-0.8714	10	0.19147	T	0.46	-13.2017	13.8104	0.63260	0.0:0.0:0.0:1.0	.	338;334;307;334;370;335	Q5SRH9-4;E7EQY9;D3DQ30;B7Z782;Q5SRH9;G3XAF8	.;.;.;.;TT39A_HUMAN;.	R	370;338;307;334;335;369	ENSP00000393952:K370R;ENSP00000406144:K338R;ENSP00000262675:K307R;ENSP00000397207:K334R;ENSP00000360815:K335R;ENSP00000360812:K369R	ENSP00000262675:K307R	K	-	2	0	TTC39A	51539884	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.964000	0.70379	1.925000	0.55765	0.379000	0.24179	AAG	.	.		0.582	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
KTI12	112970	hgsc.bcm.edu	37	1	52499377	52499377	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:52499377T>C	ENST00000371614.1	-	1	111	c.57A>G	c.(55-57)gaA>gaG	p.E19E	TXNDC12_ENST00000371626.4_Intron|RP11-91A18.4_ENST00000425802.1_RNA|TXNDC12_ENST00000610127.1_3'UTR	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	19							ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CGCGCAACTCTTCAGCACGCC	0.682																																					p.E19E		Atlas-SNP	.											.	KTI12	30	.	0			c.A57G						.						16.0	17.0	17.0					1																	52499377		2196	4289	6485	SO:0001819	synonymous_variant	112970	exon1			CAACTCTTCAGCA		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.57A>G	chr1.hg19:g.52499377T>C		100.0	0.0		78.0	5.0	NM_138417		Silent	SNP	ENST00000371614.1	hg19	CCDS562.1																																																																																			.	.		0.682	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417	
ZYG11B	79699	hgsc.bcm.edu	37	1	53237069	53237069	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:53237069G>C	ENST00000294353.6	+	3	719	c.574G>C	c.(574-576)Gat>Cat	p.D192H	ZYG11B_ENST00000443756.2_Missense_Mutation_p.D192H|ZYG11B_ENST00000545132.1_Missense_Mutation_p.D192H	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	192										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						AGAGAGCTTGGATATTTCTAA	0.443																																					p.D192H		Atlas-SNP	.											.	ZYG11B	61	.	0			c.G574C						.						75.0	78.0	77.0					1																	53237069		2203	4300	6503	SO:0001583	missense	79699	exon3			AGCTTGGATATTT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"""ZYG11 cell cycle regulator family"""	25820	protein-coding gene	gene with protein product			"""zyg-11 homolog (C. elegans)"", ""zyg-11 homolog B (C. elegans)"""	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.574G>C	chr1.hg19:g.53237069G>C	ENSP00000294353:p.Asp192His	66.0	0.0		60.0	4.0	NM_024646	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	hg19	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354560	0.82243	.	.	ENSG00000162378	ENST00000443756;ENST00000545132;ENST00000294353	T;T;T	0.20463	2.07;2.07;2.07	5.16	5.16	0.70880	.	0.094477	0.64402	D	0.000001	T	0.49932	0.1586	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	T	0.50841	-0.8780	10	0.59425	D	0.04	.	18.9116	0.92487	0.0:0.0:1.0:0.0	.	192;192	B4DK95;Q9C0D3	.;ZY11B_HUMAN	H	192	ENSP00000400522:D192H;ENSP00000441315:D192H;ENSP00000294353:D192H	ENSP00000294353:D192H	D	+	1	0	ZYG11B	53009657	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.711000	0.84669	2.712000	0.92718	0.650000	0.86243	GAT	.	.		0.443	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	
SSBP3	23648	hgsc.bcm.edu	37	1	54717508	54717508	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:54717508T>C	ENST00000371320.3	-	8	943	c.533A>G	c.(532-534)cAg>cGg	p.Q178R	SSBP3_ENST00000371319.3_Missense_Mutation_p.Q151R|SSBP3_ENST00000417664.2_Missense_Mutation_p.Q68R|SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000357475.4_Missense_Mutation_p.Q158R	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	178	Gly-rich.|Pro-rich.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						CAGCAATGGCTGTGTCCCAGG	0.617																																					p.Q178R		Atlas-SNP	.											.	SSBP3	65	.	0			c.A533G						.						53.0	45.0	48.0					1																	54717508		2203	4300	6503	SO:0001583	missense	23648	exon8			AATGGCTGTGTCC		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"""single-stranded DNA-binding protein 3"""			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.533A>G	chr1.hg19:g.54717508T>C	ENSP00000360371:p.Gln178Arg	233.0	0.0		111.0	5.0	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	hg19	CCDS591.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.445087	0.83993	.	.	ENSG00000157216	ENST00000417664;ENST00000371320;ENST00000371319;ENST00000357475;ENST00000444533;ENST00000525990	.	.	.	4.68	4.68	0.58851	.	0.266749	0.34088	U	0.004271	T	0.70727	0.3257	M	0.69523	2.12	0.58432	D	0.999997	B;P;P	0.45283	0.417;0.855;0.776	B;P;P	0.51516	0.085;0.598;0.672	T	0.72434	-0.4295	9	0.42905	T	0.14	0.0018	14.585	0.68317	0.0:0.0:0.0:1.0	.	151;158;178	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	R	68;178;151;158;9;41	.	ENSP00000350067:Q158R	Q	-	2	0	SSBP3	54490096	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.573000	0.67417	2.086000	0.62901	0.533000	0.62120	CAG	.	.		0.617	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070	
ACOT11	26027	hgsc.bcm.edu	37	1	55050328	55050328	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:55050328G>T	ENST00000371316.3	+	2	116	c.34G>T	c.(34-36)Ggc>Tgc	p.G12C	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Splice_Site_p.G12C	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	12					fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						tgtaccccaGGGCTTGGCCTC	0.632																																					p.G12C	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											.	ACOT11	105	.	0			c.G34T						.						43.0	44.0	44.0					1																	55050328		2203	4300	6503	SO:0001630	splice_region_variant	26027	exon2			CCCCAGGGCTTGG	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	18156	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 14"""	606803	"""thioesterase, adipose associated"""	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.34-1G>T	chr1.hg19:g.55050328G>T		148.0	0.0		87.0	4.0	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Missense_Mutation	SNP	ENST00000371316.3	hg19	CCDS592.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.706460	0.48412	.	.	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.14022	2.7;2.54	4.82	2.94	0.34122	.	0.459241	0.20325	N	0.094551	T	0.22399	0.0540	L	0.56769	1.78	0.38776	D	0.95466	D;P	0.64830	0.994;0.895	P;P	0.54401	0.751;0.658	T	0.02477	-1.1153	9	.	.	.	-15.2949	9.1741	0.37100	0.1677:0.0:0.8323:0.0	.	12;12	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	C	12	ENSP00000340260:G12C;ENSP00000360366:G12C	.	G	+	1	0	ACOT11	54822916	1.000000	0.71417	0.964000	0.40570	0.274000	0.26718	0.580000	0.23803	0.579000	0.29504	0.655000	0.94253	GGC	.	.		0.632	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	Missense_Mutation
C8B	732	hgsc.bcm.edu	37	1	57406626	57406626	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:57406626T>C	ENST00000371237.4	-	9	1360	c.1294A>G	c.(1294-1296)Agt>Ggt	p.S432G	C8B_ENST00000535057.1_Missense_Mutation_p.S370G|C8B_ENST00000543257.1_Missense_Mutation_p.S380G	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	432	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ATGTGCTCACTTGCCCCTCCT	0.572																																					p.S432G		Atlas-SNP	.											.	C8B	107	.	0			c.A1294G						.						172.0	123.0	140.0					1																	57406626		2203	4300	6503	SO:0001583	missense	732	exon9			GCTCACTTGCCCC	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1294A>G	chr1.hg19:g.57406626T>C	ENSP00000360281:p.Ser432Gly	134.0	0.0		99.0	4.0	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	hg19	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.048161	0.93740	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.84370	-1.84;-1.84;-1.84	5.36	5.36	0.76844	Membrane attack complex component/perforin (MACPF) domain (3);	0.042609	0.85682	D	0.000000	D	0.92424	0.7595	M	0.84846	2.72	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74348	0.971;0.971;0.983	D	0.91938	0.5560	10	0.33940	T	0.23	-24.8754	15.643	0.77020	0.0:0.0:0.0:1.0	.	380;370;432	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	G	432;380;370	ENSP00000360281:S432G;ENSP00000442548:S380G;ENSP00000440113:S370G	ENSP00000360281:S432G	S	-	1	0	C8B	57179214	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.282000	0.78630	2.143000	0.66587	0.533000	0.62120	AGT	.	.		0.572	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
C1orf87	127795	hgsc.bcm.edu	37	1	60503758	60503758	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:60503758A>G	ENST00000371201.3	-	6	876	c.769T>C	c.(769-771)Tgg>Cgg	p.W257R	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	257							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TTTAAAAACCAGAGTAGCTTT	0.348																																					p.W257R	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.T769C						.						77.0	71.0	73.0					1																	60503758		2203	4300	6503	SO:0001583	missense	127795	exon6			AAAACCAGAGTAG	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"""carcinoma-related EF-hand protein"""					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.769T>C	chr1.hg19:g.60503758A>G	ENSP00000360244:p.Trp257Arg	154.0	0.0		86.0	4.0	NM_152377	Q6ZU07|Q8IVS0	Missense_Mutation	SNP	ENST00000371201.3	hg19	CCDS614.1	.	.	.	.	.	.	.	.	.	.	A	1.630	-0.519349	0.04171	.	.	ENSG00000162598	ENST00000371201	T	0.39406	1.08	5.65	-0.647	0.11468	.	0.996520	0.08136	N	0.992435	T	0.24392	0.0591	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.16289	0.015	T	0.28713	-1.0035	10	0.06625	T	0.88	8.1781	6.0477	0.19770	0.4679:0.1464:0.3858:0.0	.	257	Q8N0U7	CA087_HUMAN	R	257	ENSP00000360244:W257R	ENSP00000360244:W257R	W	-	1	0	C1orf87	60276346	0.078000	0.21339	0.251000	0.24312	0.464000	0.32679	0.515000	0.22801	-0.254000	0.09500	-0.256000	0.11100	TGG	.	.		0.348	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	
INADL	10207	hgsc.bcm.edu	37	1	62626601	62626601	+	Silent	SNP	C	C	A	rs528030209	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:62626601C>A	ENST00000371158.2	+	43	5514	c.5400C>A	c.(5398-5400)gcC>gcA	p.A1800A		NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1800					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AGATGACGGCCGATTAAAACG	0.413																																					p.A1800A		Atlas-SNP	.											.	INADL	179	.	0			c.C5400A						.						101.0	99.0	100.0					1																	62626601		1918	4122	6040	SO:0001819	synonymous_variant	10207	exon43			GACGGCCGATTAA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.5400C>A	chr1.hg19:g.62626601C>A		85.0	0.0		51.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.413	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
LEPR	3953	hgsc.bcm.edu	37	1	66067256	66067256	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:66067256T>C	ENST00000349533.6	+	9	1361	c.1176T>C	c.(1174-1176)acT>acC	p.T392T	LEPR_ENST00000371060.3_Silent_p.T392T|LEPR_ENST00000371059.3_Silent_p.T392T|LEPR_ENST00000344610.8_Silent_p.T392T|LEPR_ENST00000371058.1_Silent_p.T392T|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000406510.3_Intron	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GCAAAGTTACTTTTTTCAATC	0.373																																					p.T392T		Atlas-SNP	.											.	LEPR	284	.	0			c.T1176C						.						112.0	109.0	110.0					1																	66067256		2203	4300	6503	SO:0001819	synonymous_variant	3953	exon9			AGTTACTTTTTTC	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1176T>C	chr1.hg19:g.66067256T>C		166.0	0.0		90.0	4.0	NM_001003680	Q6FHL5	Silent	SNP	ENST00000349533.6	hg19	CCDS631.1																																																																																			.	.		0.373	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
WLS	79971	hgsc.bcm.edu	37	1	68610266	68610266	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:68610266A>G	ENST00000262348.4	-	10	1601	c.1348T>C	c.(1348-1350)Ttc>Ctc	p.F450L	WLS_ENST00000540432.1_Missense_Mutation_p.F450L|WLS_ENST00000491811.1_5'UTR|WLS_ENST00000370976.3_Missense_Mutation_p.F359L|WLS_ENST00000354777.2_Missense_Mutation_p.F448L|GNG12-AS1_ENST00000420587.1_RNA|GNG12-AS1_ENST00000434072.1_RNA|GNG12-AS1_ENST00000413628.1_RNA	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	450					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						CTAACGATGAAGAAGATGACA	0.443																																					p.F450L		Atlas-SNP	.											.	WLS	97	.	0			c.T1348C						.						125.0	129.0	128.0					1																	68610266		2203	4300	6503	SO:0001583	missense	79971	exon10			CGATGAAGAAGAT	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.1348T>C	chr1.hg19:g.68610266A>G	ENSP00000262348:p.Phe450Leu	111.0	0.0		62.0	4.0	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Missense_Mutation	SNP	ENST00000262348.4	hg19	CCDS642.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.884942	0.91814	.	.	ENSG00000116729	ENST00000540432;ENST00000354777;ENST00000262348;ENST00000370976	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.49779	0.1577	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.993;0.996;0.998;0.993	T	0.46428	-0.9192	10	0.32370	T	0.25	-24.4284	15.7591	0.78063	1.0:0.0:0.0:0.0	.	450;359;450;448	F5H4K0;Q5JRS7;Q5T9L3;Q5T9L3-2	.;.;WLS_HUMAN;.	L	450;448;450;359	ENSP00000446112:F450L;ENSP00000346829:F448L;ENSP00000262348:F450L;ENSP00000360015:F359L	ENSP00000262348:F450L	F	-	1	0	WLS	68382854	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.915000	0.92740	2.123000	0.65237	0.528000	0.53228	TTC	.	.		0.443	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911	
ELTD1	64123	hgsc.bcm.edu	37	1	79404924	79404924	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:79404924G>T	ENST00000370742.3	-	4	408	c.345C>A	c.(343-345)tgC>tgA	p.C115*		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	115					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		TATCTAAATGGCAGTTTGCAT	0.249																																					p.C115X		Atlas-SNP	.											.	ELTD1	143	.	0			c.C345A						.						41.0	41.0	41.0					1																	79404924		1780	4030	5810	SO:0001587	stop_gained	64123	exon4			TAAATGGCAGTTT	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.345C>A	chr1.hg19:g.79404924G>T	ENSP00000359778:p.Cys115*	450.0	1.0		278.0	219.0	NM_022159	B1AR71|Q5KU34	Nonsense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.904360	0.92035	.	.	ENSG00000162618	ENST00000370742	.	.	.	6.07	1.66	0.24008	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3662	0.44026	0.3935:0.0:0.6065:0.0	.	.	.	.	X	115	.	.	C	-	3	2	ELTD1	79177512	0.995000	0.38212	0.933000	0.37362	0.892000	0.51952	0.478000	0.22212	0.466000	0.27193	-0.237000	0.12165	TGC	.	.		0.249	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
CLCA2	9635	hgsc.bcm.edu	37	1	86900325	86900325	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:86900325C>T	ENST00000370565.4	+	6	1031	c.869C>T	c.(868-870)cCc>cTc	p.P290L		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	290					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CACAGCTTTCCCATGAATGGG	0.507																																					p.P290L	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C869T						.						215.0	181.0	192.0					1																	86900325		2203	4300	6503	SO:0001583	missense	9635	exon6			GCTTTCCCATGAA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.869C>T	chr1.hg19:g.86900325C>T	ENSP00000359596:p.Pro290Leu	131.0	0.0		89.0	4.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553198	0.96501	.	.	ENSG00000137975	ENST00000370565	T	0.03689	3.84	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.19327	0.0464	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00795	-1.1563	10	0.54805	T	0.06	-15.4545	19.4432	0.94831	0.0:1.0:0.0:0.0	.	290	Q9UQC9	CLCA2_HUMAN	L	290	ENSP00000359596:P290L	ENSP00000359596:P290L	P	+	2	0	CLCA2	86672913	0.954000	0.32549	0.272000	0.24630	0.640000	0.38277	3.925000	0.56484	2.941000	0.99782	0.655000	0.94253	CCC	.	.		0.507	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
GBP5	115362	hgsc.bcm.edu	37	1	89729496	89729496	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:89729496C>A	ENST00000370459.3	-	8	1412	c.1285G>T	c.(1285-1287)Gga>Tga	p.G429*	GBP5_ENST00000471171.1_5'Flank|RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Nonsense_Mutation_p.G429*			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	429						cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		TTATGGCCTCCTGGCTTAGAA	0.433																																					p.G429X		Atlas-SNP	.											.	GBP5	65	.	0			c.G1285T						.						173.0	173.0	173.0					1																	89729496		2203	4300	6503	SO:0001587	stop_gained	115362	exon9			GGCCTCCTGGCTT	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1285G>T	chr1.hg19:g.89729496C>A	ENSP00000359488:p.Gly429*	209.0	0.0		137.0	6.0	NM_052942	B2RCE1|Q86TM5	Nonsense_Mutation	SNP	ENST00000370459.3	hg19	CCDS722.1	.	.	.	.	.	.	.	.	.	.	C	57	29.251134	0.99975	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-21.8051	16.2143	0.82195	0.0:1.0:0.0:0.0	.	.	.	.	X	429	.	ENSP00000340396:G429X	G	-	1	0	GBP5	89502084	0.983000	0.35010	0.981000	0.43875	0.823000	0.46562	4.378000	0.59568	2.762000	0.94881	0.551000	0.68910	GGA	.	.		0.433	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	
GBP6	163351	hgsc.bcm.edu	37	1	89843997	89843997	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:89843997A>G	ENST00000370456.4	+	5	543	c.450A>G	c.(448-450)gaA>gaG	p.E150E	GBP6_ENST00000535065.1_Silent_p.E20E	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	150	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		AGCTCACAGAACTAATTAAGG	0.403																																					p.E150E		Atlas-SNP	.											.	GBP6	87	.	0			c.A450G						.						111.0	119.0	117.0					1																	89843997		2203	4300	6503	SO:0001819	synonymous_variant	163351	exon5			CACAGAACTAATT	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.450A>G	chr1.hg19:g.89843997A>G		95.0	0.0		64.0	4.0	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Silent	SNP	ENST00000370456.4	hg19	CCDS723.1																																																																																			.	.		0.403	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
LRRC8D	55144	hgsc.bcm.edu	37	1	90399028	90399028	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:90399028C>A	ENST00000337338.5	+	3	808	c.401C>A	c.(400-402)cCa>cAa	p.P134Q	LRRC8D_ENST00000394593.3_Missense_Mutation_p.P134Q	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	134					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		AAGAAAGATCCAACAGGTCGA	0.418																																					p.P134Q		Atlas-SNP	.											.	LRRC8D	78	.	0			c.C401A						.						64.0	63.0	63.0					1																	90399028		2203	4300	6503	SO:0001583	missense	55144	exon3			AAGATCCAACAGG	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"""leucine rich repeat containing 5"""	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.401C>A	chr1.hg19:g.90399028C>A	ENSP00000338887:p.Pro134Gln	136.0	0.0		95.0	4.0	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	hg19	CCDS726.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.117811	0.77323	.	.	ENSG00000171492	ENST00000337338;ENST00000394593;ENST00000527156;ENST00000441269	T;T;T	0.46063	1.49;1.49;0.88	6.07	6.07	0.98685	.	0.118552	0.56097	D	0.000022	T	0.24236	0.0587	N	0.08118	0	0.49798	D	0.999824	B	0.28378	0.209	B	0.43386	0.418	T	0.30387	-0.9980	9	.	.	.	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	134	Q7L1W4	LRC8D_HUMAN	Q	134	ENSP00000338887:P134Q;ENSP00000378093:P134Q;ENSP00000405784:P134Q	.	P	+	2	0	LRRC8D	90171616	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.074000	0.71253	2.885000	0.99019	0.655000	0.94253	CCA	.	.		0.418	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103	
ABCA4	24	hgsc.bcm.edu	37	1	94517230	94517230	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:94517230C>A	ENST00000370225.3	-	17	2698	c.2612G>T	c.(2611-2613)tGg>tTg	p.W871L	ABCA4_ENST00000535735.1_Missense_Mutation_p.W797L	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	871					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AAGAAAGTACCAAGGAAGTGG	0.413																																					p.W871L		Atlas-SNP	.											.	ABCA4	275	.	0			c.G2612T						.						74.0	69.0	71.0					1																	94517230		2203	4300	6503	SO:0001583	missense	24	exon17			AAGTACCAAGGAA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2612G>T	chr1.hg19:g.94517230C>A	ENSP00000359245:p.Trp871Leu	154.0	0.0		102.0	5.0	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.376159	0.61735	.	.	ENSG00000198691	ENST00000370225;ENST00000535735	T;T	0.76186	-1.0;-1.0	5.82	5.82	0.92795	.	0.174267	0.53938	D	0.000050	T	0.82222	0.4990	M	0.72576	2.205	0.37227	D	0.905509	D;B	0.61697	0.99;0.058	P;B	0.59546	0.859;0.049	D	0.83885	0.0281	10	0.87932	D	0	.	20.0852	0.97797	0.0:1.0:0.0:0.0	.	797;871	F5H6E5;P78363	.;ABCA4_HUMAN	L	871;797	ENSP00000359245:W871L;ENSP00000437682:W797L	ENSP00000359245:W871L	W	-	2	0	ABCA4	94289818	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	5.039000	0.64185	2.752000	0.94435	0.655000	0.94253	TGG	.	.		0.413	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
AGL	178	hgsc.bcm.edu	37	1	100366213	100366213	+	Silent	SNP	G	G	T	rs149393587	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:100366213G>T	ENST00000294724.4	+	26	3862	c.3384G>T	c.(3382-3384)gcG>gcT	p.A1128A	AGL_ENST00000361915.3_Silent_p.A1128A|AGL_ENST00000361302.3_Silent_p.A1112A|AGL_ENST00000370165.3_Silent_p.A1128A|AGL_ENST00000370163.3_Silent_p.A1128A|AGL_ENST00000370161.2_Silent_p.A1112A|AGL_ENST00000361522.4_Silent_p.A1111A	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1128					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)	p.A1128A(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TAGCATTTGCGGGTACCCTGA	0.398																																					p.A1128A		Atlas-SNP	.											.	AGL	137	.	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G3384T						.						213.0	208.0	210.0					1																	100366213		2203	4300	6503	SO:0001819	synonymous_variant	178	exon26			ATTTGCGGGTACC	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3384G>T	chr1.hg19:g.100366213G>T		163.0	0.0		106.0	6.0	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	hg19	CCDS759.1																																																																																			.	G|0.997;A|0.003		0.398	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
CELSR2	1952	hgsc.bcm.edu	37	1	109794818	109794818	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:109794818A>G	ENST00000271332.3	+	1	2178	c.2117A>G	c.(2116-2118)aAc>aGc	p.N706S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	706	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		ACCGACGCCAACACCCATCGT	0.572																																					p.N706S	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A2117G						.						73.0	67.0	69.0					1																	109794818		2203	4300	6503	SO:0001583	missense	1952	exon1			ACGCCAACACCCA	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.2117A>G	chr1.hg19:g.109794818A>G	ENSP00000271332:p.Asn706Ser	99.0	0.0		61.0	4.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	N	18.65	3.669841	0.67814	.	.	ENSG00000143126	ENST00000271332	T	0.70749	-0.51	4.95	4.95	0.65309	Cadherin (3);Cadherin-like (1);	.	.	.	.	D	0.87212	0.6121	H	0.96142	3.775	0.58432	D	0.999993	D	0.76494	0.999	D	0.85130	0.997	D	0.91307	0.5071	9	0.87932	D	0	.	14.8253	0.70107	1.0:0.0:0.0:0.0	.	706	Q9HCU4	CELR2_HUMAN	S	706	ENSP00000271332:N706S	ENSP00000271332:N706S	N	+	2	0	CELSR2	109596341	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.709000	0.91379	2.102000	0.63906	0.529000	0.55759	AAC	.	.		0.572	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
SLC16A4	9122	hgsc.bcm.edu	37	1	110918150	110918150	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:110918150T>C	ENST00000369779.4	-	8	1515	c.1266A>G	c.(1264-1266)acA>acG	p.T422T	SLC16A4_ENST00000437429.2_Silent_p.T312T|SLC16A4_ENST00000369781.4_Silent_p.T254T|RP5-1074L1.4_ENST00000609909.1_RNA|SLC16A4_ENST00000541986.1_Silent_p.T360T|SLC16A4_ENST00000472422.2_Silent_p.T374T	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	422					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	ACCTGTTTACTGTAGAATTCC	0.403																																					p.T422T		Atlas-SNP	.											.	SLC16A4	47	.	0			c.A1266G						.						81.0	83.0	82.0					1																	110918150		2203	4300	6503	SO:0001819	synonymous_variant	9122	exon8			GTTTACTGTAGAA	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.1266A>G	chr1.hg19:g.110918150T>C		169.0	0.0		85.0	5.0	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	hg19	CCDS823.1																																																																																			.	.		0.403	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
CHIA	27159	hgsc.bcm.edu	37	1	111857937	111857937	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:111857937C>A	ENST00000369740.1	+	6	463	c.360C>A	c.(358-360)atC>atA	p.I120I	CHIA_ENST00000343320.6_Silent_p.I120I|CHIA_ENST00000451398.2_5'UTR|CHIA_ENST00000430615.1_Silent_p.I12I|CHIA_ENST00000353665.6_Intron|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	120					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		AGACTTTCATCACCTCAGTCA	0.547																																					p.I120I		Atlas-SNP	.											.	CHIA	115	.	0			c.C360A						.						128.0	124.0	125.0					1																	111857937		2203	4300	6503	SO:0001819	synonymous_variant	27159	exon6			TTTCATCACCTCA	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.360C>A	chr1.hg19:g.111857937C>A		138.0	0.0		96.0	4.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	hg19	CCDS41368.1																																																																																			.	.		0.547	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
SYT6	148281	hgsc.bcm.edu	37	1	114682411	114682411	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:114682411C>T	ENST00000610222.1	-	2	484	c.338G>A	c.(337-339)gGc>gAc	p.G113D	SYT6_ENST00000393296.1_Missense_Mutation_p.G113D|SYT6_ENST00000607941.1_Missense_Mutation_p.G28D|SYT6_ENST00000609117.1_Missense_Mutation_p.G28D|SYT6_ENST00000369547.1_Missense_Mutation_p.G28D			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	113					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGCCATGTTGCCTCTGAAGCT	0.612																																					p.G28D		Atlas-SNP	.											.	SYT6	66	.	0			c.G83A						.						98.0	104.0	102.0					1																	114682411		2203	4300	6503	SO:0001583	missense	148281	exon2			ATGTTGCCTCTGA		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"""Synaptotagmins"""	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.338G>A	chr1.hg19:g.114682411C>T	ENSP00000476396:p.Gly113Asp	91.0	0.0		63.0	4.0	NM_205848	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.66	1.414048	0.25465	.	.	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545;ENST00000425037;ENST00000447981	T;T;T;T;T;T	0.56941	0.5;0.43;0.5;0.43;1.64;1.05	5.67	3.57	0.40892	.	0.617205	0.18348	N	0.143943	T	0.13457	0.0326	N	0.22421	0.69	0.32850	D	0.506496	B	0.02656	0.0	B	0.01281	0.0	T	0.10590	-1.0623	10	0.13470	T	0.59	.	4.1412	0.10194	0.0:0.5299:0.0:0.4701	.	113	Q5T7P8	SYT6_HUMAN	D	28;113;28;113;28;28	ENSP00000358560:G28D;ENSP00000376974:G113D;ENSP00000358559:G28D;ENSP00000358558:G113D;ENSP00000412443:G28D;ENSP00000389266:G28D	ENSP00000358558:G113D	G	-	2	0	SYT6	114483934	0.311000	0.24536	0.940000	0.37924	0.988000	0.76386	0.763000	0.26517	1.411000	0.46957	0.655000	0.94253	GGC	.	.		0.612	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848	
CSDE1	7812	hgsc.bcm.edu	37	1	115282361	115282361	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:115282361A>G	ENST00000358528.4	-	3	577	c.151T>C	c.(151-153)Ttc>Ctc	p.F51L	CSDE1_ENST00000369530.1_Missense_Mutation_p.F97L|CSDE1_ENST00000534699.1_Missense_Mutation_p.F51L|CSDE1_ENST00000261443.5_Missense_Mutation_p.F51L|CSDE1_ENST00000339438.6_Missense_Mutation_p.F51L|CSDE1_ENST00000438362.2_Missense_Mutation_p.F97L|CSDE1_ENST00000530886.1_Intron	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	51	CSD 1.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.F51L(1)		NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAACAGTGGAAGAAAAGTCTA	0.378																																					p.F97L		Atlas-SNP	.											CSDE1_ENST00000369530,NS,carcinoma,0,2	CSDE1	145	.	1	Substitution - Missense(1)	kidney(1)	c.T289C						.						209.0	220.0	216.0					1																	115282361		2203	4300	6503	SO:0001583	missense	7812	exon4			AGTGGAAGAAAAG		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.151T>C	chr1.hg19:g.115282361A>G	ENSP00000351329:p.Phe51Leu	139.0	0.0		41.0	3.0	NM_001130523	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	A	35	5.594471	0.96602	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000369530;ENST00000534699;ENST00000534389	.	.	.	5.81	5.81	0.92471	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);Cold-shock conserved site (1);	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	L	0.50993	1.605	0.80722	D	1	D;D;P	0.64830	0.994;0.979;0.954	D;D;D	0.78314	0.991;0.973;0.916	T	0.73861	-0.3849	9	0.87932	D	0	-11.4534	16.1616	0.81721	1.0:0.0:0.0:0.0	.	97;51;97	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	L	51;97;51;51;97;51;51	.	ENSP00000261443:F51L	F	-	1	0	CSDE1	115083884	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.218000	0.71995	0.377000	0.23210	TTC	.	.		0.378	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
TRIM45	80263	hgsc.bcm.edu	37	1	117661332	117661332	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:117661332G>T	ENST00000256649.4	-	2	1072	c.546C>A	c.(544-546)taC>taA	p.Y182*	TRIM45_ENST00000369461.3_Nonsense_Mutation_p.Y125*|TRIM45_ENST00000369464.3_Nonsense_Mutation_p.Y182*	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	182					bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		CAATCCGGCTGTAGCCTTTCA	0.517																																					p.Y182X		Atlas-SNP	.											.	TRIM45	55	.	0			c.C546A						.						88.0	94.0	92.0					1																	117661332		2186	4265	6451	SO:0001587	stop_gained	80263	exon2			CCGGCTGTAGCCT		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19018	protein-coding gene	gene with protein product		609318	"""tripartite motif-containing 45"""			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.546C>A	chr1.hg19:g.117661332G>T	ENSP00000256649:p.Tyr182*	137.0	0.0		87.0	4.0	NM_001145635	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Nonsense_Mutation	SNP	ENST00000256649.4	hg19	CCDS893.1	.	.	.	.	.	.	.	.	.	.	G	38	6.693022	0.97768	.	.	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	.	.	.	5.32	5.32	0.75619	.	0.527257	0.21274	N	0.077263	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-16.2132	18.1728	0.89752	0.0:0.0:1.0:0.0	.	.	.	.	X	182;182;125	.	ENSP00000256649:Y182X	Y	-	3	2	TRIM45	117462855	1.000000	0.71417	1.000000	0.80357	0.306000	0.27790	3.056000	0.49923	2.771000	0.95319	0.655000	0.94253	TAC	.	.		0.517	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
SPAG17	200162	hgsc.bcm.edu	37	1	118550817	118550817	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:118550817C>A	ENST00000336338.5	-	31	4502	c.4437G>T	c.(4435-4437)gaG>gaT	p.E1479D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1479						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TCCGAGGACCCTCGGCTACAA	0.507																																					p.E1479D		Atlas-SNP	.											.	SPAG17	263	.	0			c.G4437T						.						82.0	71.0	75.0					1																	118550817		2203	4300	6503	SO:0001583	missense	200162	exon31			AGGACCCTCGGCT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4437G>T	chr1.hg19:g.118550817C>A	ENSP00000337804:p.Glu1479Asp	78.0	0.0		77.0	4.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.810801	0.50421	.	.	ENSG00000155761	ENST00000336338	T	0.19806	2.12	5.53	0.226	0.15353	.	0.547480	0.20513	N	0.090843	T	0.06690	0.0171	L	0.54323	1.7	0.09310	N	1	B	0.17268	0.021	B	0.18263	0.021	T	0.29941	-0.9995	10	0.54805	T	0.06	.	5.3301	0.15928	0.0:0.1566:0.2802:0.5631	.	1479	Q6Q759	SPG17_HUMAN	D	1479	ENSP00000337804:E1479D	ENSP00000337804:E1479D	E	-	3	2	SPAG17	118352340	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.045000	0.14013	0.137000	0.18759	-0.339000	0.08088	GAG	.	.		0.507	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
CHD1L	9557	hgsc.bcm.edu	37	1	146724367	146724367	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:146724367A>G	ENST00000369258.4	+	2	237	c.217A>G	c.(217-219)Atg>Gtg	p.M73V	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_Intron|CHD1L_ENST00000431239.1_Missense_Mutation_p.M73V|RP11-337C18.10_ENST00000606856.1_RNA|CHD1L_ENST00000369259.3_Intron	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	73	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					GGGAGATGAGATGGGCCTGGG	0.527																																					p.M73V		Atlas-SNP	.											.	CHD1L	72	.	0			c.A217G						.						119.0	102.0	108.0					1																	146724367		2203	4300	6503	SO:0001583	missense	9557	exon2			GATGAGATGGGCC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.217A>G	chr1.hg19:g.146724367A>G	ENSP00000358262:p.Met73Val	99.0	0.0		120.0	5.0	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	hg19	CCDS927.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194011	0.78902	.	.	ENSG00000131778	ENST00000431239;ENST00000369258;ENST00000254086	D;D	0.93659	-3.26;-3.26	5.23	5.23	0.72850	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97427	0.9158	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	0.982;1.0	D;D	0.87578	0.961;0.998	D	0.98358	1.0547	10	0.87932	D	0	.	11.528	0.50591	1.0:0.0:0.0:0.0	.	73;73	Q86WJ1-2;Q86WJ1	.;CHD1L_HUMAN	V	73;73;35	ENSP00000389031:M73V;ENSP00000358262:M73V	ENSP00000254086:M35V	M	+	1	0	CHD1L	145190991	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.998000	0.88491	1.975000	0.57531	0.533000	0.62120	ATG	.	.		0.527	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
DENND4B	9909	hgsc.bcm.edu	37	1	153906108	153906108	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:153906108G>A	ENST00000361217.4	-	20	3599	c.3181C>T	c.(3181-3183)Ctc>Ttc	p.L1061F	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1061					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGCTGTTGGAGGCGGGCACCC	0.711																																					p.L1061F		Atlas-SNP	.											.	DENND4B	210	.	0			c.C3181T						.						5.0	8.0	7.0					1																	153906108		1897	4013	5910	SO:0001583	missense	9909	exon20			GTTGGAGGCGGGC	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.3181C>T	chr1.hg19:g.153906108G>A	ENSP00000354597:p.Leu1061Phe	220.0	0.0		379.0	219.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490643	0.44249	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.13538	2.84;2.58	5.09	4.12	0.48240	.	0.628844	0.16048	N	0.232095	T	0.04182	0.0116	L	0.27053	0.805	0.42662	D	0.993486	B	0.32968	0.392	B	0.27076	0.076	T	0.26780	-1.0093	10	0.56958	D	0.05	-18.3115	11.4825	0.50333	0.0:0.0:0.6125:0.3875	.	1061	O75064	DEN4B_HUMAN	F	1061;1072	ENSP00000354597:L1061F;ENSP00000357635:L1072F	ENSP00000354597:L1061F	L	-	1	0	DENND4B	152172732	0.997000	0.39634	1.000000	0.80357	0.940000	0.58332	1.030000	0.30153	1.191000	0.43056	0.462000	0.41574	CTC	.	.		0.711	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156908262	156908262	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:156908262A>G	ENST00000361409.2	-	37	4762	c.4020T>C	c.(4018-4020)agT>agC	p.S1340S	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Silent_p.S756S|MIR765_ENST00000390226.1_RNA|ARHGEF11_ENST00000368194.3_Silent_p.S1380S	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1340					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTGACTGGCCACTCTCTGGTA	0.557																																					p.S1380S		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.T4140C						.						92.0	82.0	86.0					1																	156908262		2203	4300	6503	SO:0001819	synonymous_variant	9826	exon38			CTGGCCACTCTCT	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.4020T>C	chr1.hg19:g.156908262A>G		106.0	0.0		117.0	6.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	hg19	CCDS1162.1																																																																																			.	.		0.557	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
CFAP45	25790	hgsc.bcm.edu	37	1	159846466	159846466	+	Missense_Mutation	SNP	C	C	T	rs377248471		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:159846466C>T	ENST00000368099.4	-	10	1296	c.1232G>A	c.(1231-1233)cGg>cAg	p.R411Q	CCDC19_ENST00000426543.2_Missense_Mutation_p.R326Q|CCDC19_ENST00000476696.1_5'UTR	NM_012337.2	NP_036469.2														endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			CATCTTCTTCCGCGCATTTTC	0.572																																					p.R411Q		Atlas-SNP	.											.	CCDC19	79	.	0			c.G1232A						.	T	GLN/ARG	0,4406		0,0,2203	134.0	105.0	115.0		1232	2.7	1.0	1		115	1,8599		0,1,4299	no	missense	CCDC19	NM_012337.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	411/552	159846466	1,13005	2203	4300	6503	SO:0001583	missense	25790	exon10			TTCTTCCGCGCAT																												ENST00000368099.4:c.1232G>A	chr1.hg19:g.159846466C>T	ENSP00000357079:p.Arg411Gln	851.0	1.0		1191.0	239.0	NM_012337		Missense_Mutation	SNP	ENST00000368099.4	hg19	CCDS30914.1	.	.	.	.	.	.	.	.	.	.	N	0.937	-0.710762	0.03230	0.0	1.16E-4	ENSG00000213085	ENST00000368099;ENST00000426543	T;T	0.09445	2.98;2.98	5.16	2.68	0.31781	.	0.524332	0.21595	N	0.072030	T	0.00845	0.0028	N	0.01297	-0.9	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48281	-0.9049	9	.	.	.	-30.5358	6.4566	0.21934	0.1391:0.0828:0.0:0.778	.	411	Q9UL16	CCD19_HUMAN	Q	411;326	ENSP00000357079:R411Q;ENSP00000403044:R326Q	.	R	-	2	0	CCDC19	158113090	0.454000	0.25728	0.985000	0.45067	0.362000	0.29581	0.222000	0.17699	0.900000	0.36469	-0.599000	0.04106	CGG	.	.		0.572	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1		
PIGM	93183	hgsc.bcm.edu	37	1	160000609	160000609	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:160000609G>T	ENST00000368090.2	-	1	1174	c.921C>A	c.(919-921)ttC>ttA	p.F307L		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	307					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGTAATAGGCGAAAGACACAG	0.428																																					p.F307L		Atlas-SNP	.											.	PIGM	27	.	0			c.C921A						.						118.0	129.0	125.0					1																	160000609		2203	4300	6503	SO:0001583	missense	93183	exon1			ATAGGCGAAAGAC	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	18858	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 1"", ""DPM:GlcN-(acyl-)PI mannosyltransferase"", ""dol-P-Man dependent GPI mannosyltransferase"""	610273	"""phosphatidylinositol glycan, class M"""			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.921C>A	chr1.hg19:g.160000609G>T	ENSP00000357069:p.Phe307Leu	75.0	0.0		94.0	4.0	NM_145167		Missense_Mutation	SNP	ENST00000368090.2	hg19	CCDS1192.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.649840	0.29336	.	.	ENSG00000143315	ENST00000368090	T	0.38401	1.14	5.35	-3.78	0.04333	.	0.515563	0.20386	N	0.093346	T	0.03608	0.0103	N	0.05351	-0.065	0.22378	N	0.999154	B	0.11235	0.004	B	0.17722	0.019	T	0.36114	-0.9761	9	.	.	.	-16.7466	1.8926	0.03251	0.3216:0.3505:0.2087:0.1192	.	307	Q9H3S5	PIGM_HUMAN	L	307	ENSP00000357069:F307L	.	F	-	3	2	PIGM	158267233	0.177000	0.23109	0.298000	0.25002	0.989000	0.77384	-0.159000	0.10056	-0.272000	0.09259	0.462000	0.41574	TTC	.	.		0.428	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167	
SUCO	51430	hgsc.bcm.edu	37	1	172525148	172525148	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:172525148C>A	ENST00000263688.3	+	4	647	c.428C>A	c.(427-429)cCa>cAa	p.P143Q	SUCO_ENST00000608151.1_Missense_Mutation_p.P302Q|SUCO_ENST00000367723.4_Missense_Mutation_p.P301Q|SUCO_ENST00000610051.1_Missense_Mutation_p.P106Q	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	143					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											GAAATCACTCCAATCTCAAAG	0.348																																					p.P143Q		Atlas-SNP	.											.	.	.	.	0			c.C428A						.						60.0	56.0	58.0					1																	172525148		2203	4299	6502	SO:0001583	missense	51430	exon4			TCACTCCAATCTC	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.428C>A	chr1.hg19:g.172525148C>A	ENSP00000263688:p.Pro143Gln	71.0	0.0		98.0	4.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.807431	0.70797	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.76	4.83	0.62350	.	0.145724	0.48767	D	0.000164	T	0.39172	0.1068	L	0.32530	0.975	0.36983	D	0.894405	B;P;D;P	0.54397	0.014;0.916;0.966;0.916	B;P;P;P	0.50754	0.005;0.649;0.641;0.506	T	0.38222	-0.9671	9	0.45353	T	0.12	-5.8702	14.095	0.65016	0.1517:0.8482:0.0:0.0	.	106;143;302;143	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	Q	302;143	.	ENSP00000263688:P143Q	P	+	2	0	C1orf9	170791771	1.000000	0.71417	0.951000	0.38953	0.991000	0.79684	3.746000	0.55127	1.527000	0.49086	0.655000	0.94253	CCA	.	.		0.348	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
CEP350	9857	hgsc.bcm.edu	37	1	180013222	180013222	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:180013222A>G	ENST00000367607.3	+	21	4954	c.4536A>G	c.(4534-4536)gaA>gaG	p.E1512E		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1512	Ser-rich.				microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						AGAGTAAAGAAGGGACCCTTG	0.323																																					p.E1512E		Atlas-SNP	.											.	CEP350	418	.	0			c.A4536G						.						49.0	44.0	46.0					1																	180013222		2197	4283	6480	SO:0001819	synonymous_variant	9857	exon21			TAAAGAAGGGACC	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.4536A>G	chr1.hg19:g.180013222A>G		70.0	0.0		96.0	5.0	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	4.179	0.031740	0.08101	.	.	ENSG00000135837	ENST00000418229	.	.	.	5.69	0.932	0.19466	.	.	.	.	.	T	0.55049	0.1896	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45352	-0.9267	4	.	.	.	.	7.9455	0.29985	0.5415:0.0:0.4585:0.0	.	.	.	.	G	121	.	.	R	+	1	2	CEP350	178279845	1.000000	0.71417	0.897000	0.35233	0.414000	0.31173	1.396000	0.34531	0.124000	0.18369	0.454000	0.30748	AGG	.	.		0.323	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
CRB1	23418	hgsc.bcm.edu	37	1	197391072	197391072	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:197391072C>A	ENST00000367400.3	+	6	2249	c.2114C>A	c.(2113-2115)cCc>cAc	p.P705H	CRB1_ENST00000543483.1_3'UTR|CRB1_ENST00000538660.1_Missense_Mutation_p.P705H|CRB1_ENST00000367399.2_Missense_Mutation_p.P593H|CRB1_ENST00000367397.1_Missense_Mutation_p.P86H|CRB1_ENST00000544212.1_Missense_Mutation_p.P186H|CRB1_ENST00000535699.1_Missense_Mutation_p.P636H	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	705	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TATGAAGGCCCCAACTGTCTG	0.522																																					p.P705H		Atlas-SNP	.											.	CRB1	284	.	0			c.C2114A						.						47.0	49.0	49.0					1																	197391072		2195	4300	6495	SO:0001583	missense	23418	exon6			AAGGCCCCAACTG		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2114C>A	chr1.hg19:g.197391072C>A	ENSP00000356370:p.Pro705His	67.0	0.0		92.0	4.0	NM_001257966	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	hg19	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	3.507	-0.100556	0.06967	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	D;D;D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05;-3.05;-3.05	5.65	-4.08	0.03963	Concanavalin A-like lectin/glucanase, subgroup (1);EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.88149	0.6359	L	0.37750	1.13	0.09310	N	0.999997	B;P;P;B;P	0.44281	0.001;0.776;0.776;0.012;0.831	B;P;P;B;P	0.50109	0.005;0.621;0.471;0.032;0.631	T	0.80030	-0.1553	9	0.33940	T	0.23	.	6.2783	0.20993	0.105:0.4879:0.3135:0.0935	.	705;636;593;354;705	B7Z5T2;F5H0L2;P82279-3;P82279-4;P82279	.;.;.;.;CRUM1_HUMAN	H	636;705;705;593;186;86;354	ENSP00000438786:P636H;ENSP00000438091:P705H;ENSP00000356370:P705H;ENSP00000356369:P593H;ENSP00000444556:P186H;ENSP00000356367:P86H	ENSP00000356367:P86H	P	+	2	0	CRB1	195657695	0.209000	0.23505	0.001000	0.08648	0.011000	0.07611	0.739000	0.26173	-0.731000	0.04862	0.650000	0.86243	CCC	.	.		0.522	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	
CR1L	1379	hgsc.bcm.edu	37	1	207890960	207890960	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:207890960C>T	ENST00000508064.2	+	11	1626	c.1566C>T	c.(1564-1566)atC>atT	p.I522I		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	522	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						AGAGCACCATCCGCCGCACAA	0.542																																					p.I522I		Atlas-SNP	.											.	CR1L	97	.	0			c.C1566T						.						152.0	150.0	151.0					1																	207890960		1960	4142	6102	SO:0001819	synonymous_variant	1379	exon11			CACCATCCGCCGC	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1566C>T	chr1.hg19:g.207890960C>T		361.0	0.0		546.0	77.0	NM_175710	Q32MC9|Q8NEU7	Silent	SNP	ENST00000508064.2	hg19	CCDS44310.1																																																																																			.	.		0.542	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
PLXNA2	5362	hgsc.bcm.edu	37	1	208202173	208202173	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:208202173A>G	ENST00000367033.3	-	30	6196		c.e30+1		PLXNA2_ENST00000483048.1_Splice_Site	NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2						axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGTGCTACTGACCTCTCCACC	0.577																																					.		Atlas-SNP	.											.	PLXNA2	178	.	0			c.5438+2T>C						.						85.0	80.0	82.0					1																	208202173		2203	4300	6503	SO:0001630	splice_region_variant	5362	exon31			CTACTGACCTCTC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.5438+1T>C	chr1.hg19:g.208202173A>G		81.0	0.0		84.0	4.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Splice_Site	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.295700	0.81025	.	.	ENSG00000076356	ENST00000367033	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3914	0.74747	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLXNA2	206268796	1.000000	0.71417	0.993000	0.49108	0.976000	0.68499	8.999000	0.93557	2.042000	0.60477	0.533000	0.62120	.	.	.		0.577	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	Intron
PROX1	5629	hgsc.bcm.edu	37	1	214170676	214170676	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:214170676G>T	ENST00000366958.4	+	2	1406	c.798G>T	c.(796-798)tcG>tcT	p.S266S	PROX1_ENST00000498508.2_Silent_p.S266S|PROX1_ENST00000261454.4_Silent_p.S266S|PROX1_ENST00000435016.1_Silent_p.S266S	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	266					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		GCACTGATTCGGAAAATGATG	0.522																																					p.S266S		Atlas-SNP	.											.	PROX1	124	.	0			c.G798T						.						58.0	57.0	57.0					1																	214170676		2203	4300	6503	SO:0001819	synonymous_variant	5629	exon2			TGATTCGGAAAAT	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"""Homeoboxes / PROS class"""	9459	protein-coding gene	gene with protein product		601546	"""prospero-related homeobox 1"""			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.798G>T	chr1.hg19:g.214170676G>T		69.0	0.0		88.0	4.0	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Silent	SNP	ENST00000366958.4	hg19	CCDS31021.1																																																																																			.	.		0.522	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763	
TGFB2	7042	hgsc.bcm.edu	37	1	218520057	218520057	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:218520057T>C	ENST00000366930.4	+	1	481	c.14T>C	c.(13-15)gTg>gCg	p.V5A	RP11-224O19.2_ENST00000414452.1_RNA|TGFB2_ENST00000366929.4_Missense_Mutation_p.V5A	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	5					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		CACTACTGTGTGCTGAGCGCT	0.408																																					p.V5A		Atlas-SNP	.											.	TGFB2	102	.	0			c.T14C						.						60.0	60.0	60.0					1																	218520057		2203	4300	6503	SO:0001583	missense	7042	exon1			ACTGTGTGCTGAG	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"""Endogenous ligands"""	11768	protein-coding gene	gene with protein product	"""prepro-transforming growth factor beta-2"""	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.14T>C	chr1.hg19:g.218520057T>C	ENSP00000355897:p.Val5Ala	47.0	0.0		78.0	4.0	NM_003238	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	hg19	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420489	0.62622	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.75589	-0.82;-0.95	5.8	5.8	0.92144	.	0.325329	0.32852	N	0.005570	T	0.59865	0.2225	N	0.17474	0.49	0.41815	D	0.98999	B;B;P	0.41080	0.0;0.0;0.737	B;B;B	0.39503	0.004;0.001;0.301	T	0.59931	-0.7361	10	0.13853	T	0.58	.	16.1269	0.81402	0.0:0.0:0.0:1.0	.	5;5;6	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	A	5	ENSP00000355897:V5A;ENSP00000355896:V5A	ENSP00000355896:V5A	V	+	2	0	TGFB2	216586680	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.485000	0.81204	2.203000	0.70933	0.482000	0.46254	GTG	.	.		0.408	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238	
EPRS	2058	hgsc.bcm.edu	37	1	220170686	220170686	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:220170686T>C	ENST00000366923.3	-	18	2451		c.e18-2			NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase						cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	AGCAGAGGTCTACCAAGAGAG	0.303																																					.		Atlas-SNP	.											.	EPRS	140	.	0			c.2182-2A>G						.						46.0	47.0	46.0					1																	220170686		2174	4287	6461	SO:0001630	splice_region_variant	2058	exon19			GAGGTCTACCAAG	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.2182-2A>G	chr1.hg19:g.220170686T>C		42.0	0.0		49.0	4.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Splice_Site	SNP	ENST00000366923.3	hg19	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.259670	0.39995	.	.	ENSG00000136628	ENST00000366923;ENST00000536921;ENST00000435048	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.41	0.67109	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EPRS	218237309	0.960000	0.32886	0.342000	0.25602	0.123000	0.20343	2.287000	0.43505	2.150000	0.67090	0.533000	0.62120	.	.	.		0.303	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	Intron
TMEM63A	9725	hgsc.bcm.edu	37	1	226059703	226059703	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:226059703T>C	ENST00000366835.3	-	5	587	c.317A>G	c.(316-318)gAc>gGc	p.D106G		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	106					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					ATTTTCAAAGTCTTGTTGACC	0.458																																					p.D106G		Atlas-SNP	.											.	TMEM63A	75	.	0			c.A317G						.						117.0	95.0	102.0					1																	226059703		2203	4300	6503	SO:0001583	missense	9725	exon5			TCAAAGTCTTGTT		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.317A>G	chr1.hg19:g.226059703T>C	ENSP00000355800:p.Asp106Gly	64.0	0.0		92.0	4.0	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	hg19	CCDS31042.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.011520	0.54468	.	.	ENSG00000196187	ENST00000366835;ENST00000436966	T	0.46063	0.88	4.97	4.97	0.65823	.	0.171002	0.47455	D	0.000237	T	0.35653	0.0939	L	0.59436	1.845	0.80722	D	1	B;P	0.34699	0.173;0.464	B;B	0.32928	0.102;0.155	T	0.12243	-1.0555	10	0.14252	T	0.57	-28.7201	11.3011	0.49306	0.0:0.0:0.0:1.0	.	106;106	B3KMR6;O94886	.;TM63A_HUMAN	G	106	ENSP00000355800:D106G	ENSP00000355800:D106G	D	-	2	0	TMEM63A	224126326	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	3.317000	0.51968	2.002000	0.58637	0.448000	0.29417	GAC	.	.		0.458	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
SNAP47	116841	hgsc.bcm.edu	37	1	227947130	227947130	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:227947130T>C	ENST00000366759.4	+	3	1481	c.1067T>C	c.(1066-1068)cTc>cCc	p.L356P	SNAP47_ENST00000315781.5_Missense_Mutation_p.L356P|SNAP47_ENST00000366760.1_Missense_Mutation_p.L114P	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	356					long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GCATTGGTGCTCAGAAGCGCA	0.502																																					p.L356P		Atlas-SNP	.											.	SNAP47	42	.	0			c.T1067C						.						137.0	133.0	134.0					1																	227947130		2203	4300	6503	SO:0001583	missense	116841	exon3			TGGTGCTCAGAAG	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 142"""	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.1067T>C	chr1.hg19:g.227947130T>C	ENSP00000355721:p.Leu356Pro	22.0	0.0		64.0	4.0	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	hg19	CCDS1562.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.506066	0.26949	.	.	ENSG00000143740	ENST00000366760;ENST00000366759;ENST00000315781	T;T;T	0.49432	0.78;2.09;1.97	5.04	3.92	0.45320	.	0.277555	0.40469	N	0.001087	T	0.36524	0.0970	L	0.42245	1.32	0.22918	N	0.998568	B;B;B;B;B	0.22003	0.002;0.023;0.063;0.028;0.023	B;B;B;B;B	0.22601	0.005;0.023;0.04;0.018;0.023	T	0.19844	-1.0293	10	0.23302	T	0.38	-7.6889	8.8361	0.35113	0.0:0.0886:0.0:0.9114	.	114;356;168;356;114	Q5SQN1-3;Q5SQN1;Q5TBZ4;Q5SQN1-2;Q5SQN1-4	.;SNP47_HUMAN;.;.;.	P	114;356;356	ENSP00000355722:L114P;ENSP00000355721:L356P;ENSP00000314157:L356P	ENSP00000314157:L356P	L	+	2	0	SNAP47	226013753	0.113000	0.22115	0.010000	0.14722	0.074000	0.17049	1.631000	0.37092	0.957000	0.37930	0.459000	0.35465	CTC	.	.		0.502	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052	
PCNXL2	80003	hgsc.bcm.edu	37	1	233136202	233136202	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:233136202A>G	ENST00000258229.9	-	30	5411	c.5177T>C	c.(5176-5178)gTc>gCc	p.V1726A	PCNXL2_ENST00000344698.2_Missense_Mutation_p.V378A	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1726						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GTGGCAGATGACCACCTTCTT	0.627																																					p.V1726A		Atlas-SNP	.											.	PCNXL2	204	.	0			c.T5177C						.						64.0	66.0	66.0					1																	233136202		2030	4179	6209	SO:0001583	missense	80003	exon30			CAGATGACCACCT	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5177T>C	chr1.hg19:g.233136202A>G	ENSP00000258229:p.Val1726Ala	77.0	0.0		97.0	4.0	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	A	34	5.307530	0.95629	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.49720	0.77;0.77	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.73916	0.3648	M	0.89095	3.005	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.99;0.995	T	0.79701	-0.1693	10	0.87932	D	0	.	16.1884	0.81971	1.0:0.0:0.0:0.0	.	1726;378	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	A	378;1726	ENSP00000340759:V378A;ENSP00000258229:V1726A	ENSP00000258229:V1726A	V	-	2	0	PCNXL2	231202825	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.948000	0.93006	2.285000	0.76669	0.528000	0.53228	GTC	.	.		0.627	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
FMN2	56776	hgsc.bcm.edu	37	1	240371184	240371184	+	Silent	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:240371184T>A	ENST00000319653.9	+	5	3302	c.3072T>A	c.(3070-3072)ccT>ccA	p.P1024P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1024	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTCCACCCCCTCTACCCGGAG	0.736																																					p.P1024P		Atlas-SNP	.											.	FMN2	451	.	0			c.T3072A						.						4.0	4.0	4.0					1																	240371184		1678	3388	5066	SO:0001819	synonymous_variant	56776	exon5			ACCCCCTCTACCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3072T>A	chr1.hg19:g.240371184T>A		173.0	0.0		226.0	16.0	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	hg19	CCDS31069.2																																																																																			.	.		0.736	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
OR2T3	343173	hgsc.bcm.edu	37	1	248637025	248637025	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:248637025A>G	ENST00000359594.2	+	1	399	c.374A>G	c.(373-375)tAt>tGt	p.Y125C		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCCATGGCCTATGACCGATAT	0.552																																					p.Y125C		Atlas-SNP	.											.	OR2T3	79	.	0			c.A374G						.						53.0	52.0	53.0					1																	248637025		2195	4295	6490	SO:0001583	missense	343173	exon1			TGGCCTATGACCG		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.374A>G	chr1.hg19:g.248637025A>G	ENSP00000352604:p.Tyr125Cys	545.0	0.0		787.0	209.0	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	hg19	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	a	9.872	1.199201	0.22121	.	.	ENSG00000196539	ENST00000359594	T	0.01347	4.99	2.65	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.05364	0.0142	M	0.90425	3.115	0.24293	N	0.995155	P	0.51653	0.947	P	0.47786	0.557	T	0.15578	-1.0432	9	0.62326	D	0.03	.	9.7894	0.40697	1.0:0.0:0.0:0.0	.	125	Q8NH03	OR2T3_HUMAN	C	125	ENSP00000352604:Y125C	ENSP00000352604:Y125C	Y	+	2	0	OR2T3	246703648	0.247000	0.23920	0.864000	0.33941	0.357000	0.29423	0.550000	0.23345	0.967000	0.38186	0.156000	0.16432	TAT	.	.		0.552	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
TPO	7173	hgsc.bcm.edu	37	2	1440156	1440156	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:1440156G>T	ENST00000345913.4	+	5	573	c.482G>T	c.(481-483)aGa>aTa	p.R161I	TPO_ENST00000382198.1_Splice_Site_p.R161I|TPO_ENST00000349624.3_Splice_Site_p.R161I|TPO_ENST00000337415.3_Splice_Site_p.R161I|TPO_ENST00000382201.3_Splice_Site_p.R161I|TPO_ENST00000497517.2_Intron|TPO_ENST00000539820.1_Splice_Site_p.R161I|TPO_ENST00000329066.4_Splice_Site_p.R161I|TPO_ENST00000382269.3_Splice_Site_p.R161I|TPO_ENST00000346956.3_Splice_Site_p.R161I	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	161					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGCAACAACAGGTATTGTTTG	0.458																																					p.R161I		Atlas-SNP	.											.	TPO	224	.	0			c.G482T						.						115.0	113.0	114.0					2																	1440156		2203	4300	6503	SO:0001630	splice_region_variant	7173	exon5			ACAACAGGTATTG		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.482+1G>T	chr2.hg19:g.1440156G>T		119.0	0.0		105.0	58.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464356	0.63513	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T;T;T;T	0.58797	0.45;0.31;0.31;0.31;0.31;0.45;0.31;0.31;0.31;0.31;0.31	5.07	5.07	0.68467	.	0.050880	0.85682	D	0.000000	T	0.71745	0.3376	L	0.53729	1.69	0.52099	D	0.999946	D;D;D;D;D	0.89917	0.995;0.999;1.0;0.997;0.996	D;D;D;D;D	0.91635	0.953;0.994;0.999;0.953;0.972	T	0.74444	-0.3663	10	0.72032	D	0.01	-16.0578	15.3642	0.74507	0.0:0.0:1.0:0.0	.	161;161;161;161;161	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	I	161;161;161;161;161;161;161;161;161;161;90	ENSP00000371704:R161I;ENSP00000337263:R161I;ENSP00000318820:R161I;ENSP00000263886:R161I;ENSP00000332044:R161I;ENSP00000444840:R161I;ENSP00000329869:R161I;ENSP00000371636:R161I;ENSP00000390994:R161I;ENSP00000371633:R161I;ENSP00000405788:R90I	ENSP00000329869:R161I	R	+	2	0	TPO	1419163	1.000000	0.71417	1.000000	0.80357	0.378000	0.30076	3.983000	0.56916	2.353000	0.79882	0.313000	0.20887	AGA	.	.		0.458	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	Missense_Mutation
OTOF	9381	hgsc.bcm.edu	37	2	26690270	26690270	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:26690270G>A	ENST00000272371.2	-	34	4316	c.4190C>T	c.(4189-4191)gCc>gTc	p.A1397V	OTOF_ENST00000402415.3_Missense_Mutation_p.A707V|OTOF_ENST00000339598.3_Missense_Mutation_p.A630V|OTOF_ENST00000338581.6_Missense_Mutation_p.A630V|OTOF_ENST00000403946.3_Missense_Mutation_p.A1397V	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1397					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCTCGGGGGCCTCGGACCC	0.582																																					p.A1397V	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C4190T						.						53.0	57.0	56.0					2																	26690270		2203	4300	6503	SO:0001583	missense	9381	exon34			TCGGGGGCCTCGG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4190C>T	chr2.hg19:g.26690270G>A	ENSP00000272371:p.Ala1397Val	129.0	0.0		117.0	5.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	G	1.494	-0.553961	0.03996	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.80214	-1.11;-1.11;-1.1;-1.35;-1.35	5.44	-1.62	0.08372	.	0.974058	0.08455	N	0.943283	T	0.50650	0.1628	N	0.00926	-1.1	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.0;0.001;0.003;0.002	T	0.38564	-0.9655	10	0.25106	T	0.35	-5.881	8.6969	0.34301	0.3889:0.1012:0.5099:0.0	.	1397;630;707;630	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	V	630;630;707;1397;1397	ENSP00000345137:A630V;ENSP00000344521:A630V;ENSP00000383906:A707V;ENSP00000272371:A1397V;ENSP00000385255:A1397V	ENSP00000272371:A1397V	A	-	2	0	OTOF	26543774	0.980000	0.34600	0.008000	0.14137	0.016000	0.09150	0.909000	0.28558	-0.212000	0.10109	-0.742000	0.03525	GCC	.	.		0.582	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
AGBL5	60509	hgsc.bcm.edu	37	2	27279548	27279548	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:27279548C>T	ENST00000360131.4	+	8	1582	c.1423C>T	c.(1423-1425)Cag>Tag	p.Q475*	AGBL5_ENST00000323064.8_Nonsense_Mutation_p.Q475*|RP11-503P10.1_ENST00000607407.1_RNA	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	475					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCGACTTCCAGGGCTGCAA	0.483																																					p.Q475X		Atlas-SNP	.											.	AGBL5	126	.	0			c.C1423T						.						109.0	115.0	113.0					2																	27279548		2203	4300	6503	SO:0001587	stop_gained	60509	exon8			GACTTCCAGGGCT	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 5"""	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.1423C>T	chr2.hg19:g.27279548C>T	ENSP00000353249:p.Gln475*	63.0	0.0		76.0	4.0	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Nonsense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	C	37	6.610929	0.97705	.	.	ENSG00000084693	ENST00000323064;ENST00000360131	.	.	.	6.17	6.17	0.99709	.	0.288263	0.39759	N	0.001266	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-16.3107	5.8667	0.18779	0.1418:0.6494:0.1365:0.0724	.	.	.	.	X	475	.	ENSP00000323681:Q475X	Q	+	1	0	AGBL5	27133052	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.666000	0.37460	2.941000	0.99782	0.655000	0.94253	CAG	.	.		0.483	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831	
GTF3C2	2976	hgsc.bcm.edu	37	2	27550059	27550059	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:27550059C>A	ENST00000359541.2	-	18	2931	c.2502G>T	c.(2500-2502)ctG>ctT	p.L834L	GTF3C2_ENST00000264720.3_Silent_p.L834L|MPV17_ENST00000357186.6_5'Flank			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	834					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAATAGCCTCCAGCTGCAGCC	0.537																																					p.N834N		Atlas-SNP	.											.	GTF3C2	73	.	0			c.C2502T						.						73.0	61.0	65.0					2																	27550059		2203	4300	6503	SO:0001819	synonymous_variant	2976	exon19			AGCCTCCAGCTGC	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.2502G>T	chr2.hg19:g.27550059C>A		64.0	0.0		44.0	4.0	NM_001521	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	hg19	CCDS1749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	8.056|8.056	0.767092|0.767092	0.15983|0.15983	.|.	.|.	ENSG00000115207|ENSG00000115207	ENST00000457098|ENST00000431028;ENST00000454704;ENST00000415683	.|.	.|.	.|.	4.95|4.95	-5.06|-5.06	0.02946|0.02946	.|.	.|.	.|.	.|.	.|.	.|T	.|0.35941	.|0.0949	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.36040	.|-0.9764	.|4	.|.	.|.	.|.	-11.0966|-11.0966	1.2024|1.2024	0.01887|0.01887	0.3202:0.2795:0.2405:0.1597|0.3202:0.2795:0.2405:0.1597	.|.	.|.	.|.	.|.	X|L	128|49;343;257	.|.	.|.	G|W	-|-	1|2	0|0	GTF3C2|GTF3C2	27403563|27403563	0.946000|0.946000	0.32159|0.32159	0.897000|0.897000	0.35233|0.35233	0.975000|0.975000	0.68041|0.68041	-0.216000|-0.216000	0.09266|0.09266	-1.068000|-1.068000	0.03156|0.03156	-0.881000|-0.881000	0.02953|0.02953	GGA|TGG	.	.		0.537	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		
C2orf16	84226	hgsc.bcm.edu	37	2	27803792	27803792	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:27803792T>C	ENST00000408964.2	+	1	4404	c.4353T>C	c.(4351-4353)ccT>ccC	p.P1451P	RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1451						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AACCCAGACCTCTTCGACTGC	0.512																																					p.P1451P		Atlas-SNP	.											.	C2orf16	357	.	0			c.T4353C						.						93.0	97.0	96.0					2																	27803792		1966	4152	6118	SO:0001819	synonymous_variant	84226	exon1			CAGACCTCTTCGA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4353T>C	chr2.hg19:g.27803792T>C		68.0	0.0		73.0	4.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.512	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
MAP4K3	8491	hgsc.bcm.edu	37	2	39535144	39535144	+	Silent	SNP	G	G	A	rs373302450		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:39535144G>A	ENST00000263881.3	-	15	1383	c.1059C>T	c.(1057-1059)ccC>ccT	p.P353P	MAP4K3_ENST00000341681.5_Intron|MAP4K3_ENST00000437545.1_Intron|MAP4K3_ENST00000536018.1_5'UTR	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	353					intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				CATCACTGTCGGGCTGTTTAG	0.368																																					p.P353P		Atlas-SNP	.											.	MAP4K3	109	.	0			c.C1059T						.	G		1,4405	2.1+/-5.4	0,1,2202	107.0	103.0	104.0		1059	5.8	1.0	2		104	0,8600		0,0,4300	no	coding-synonymous	MAP4K3	NM_003618.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		353/895	39535144	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8491	exon15			ACTGTCGGGCTGT	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1059C>T	chr2.hg19:g.39535144G>A		88.0	0.0		75.0	4.0	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	hg19	CCDS1803.1																																																																																			.	.		0.368	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
MSH6	2956	hgsc.bcm.edu	37	2	48027261	48027261	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:48027261T>C	ENST00000234420.5	+	4	2291	c.2139T>C	c.(2137-2139)gaT>gaC	p.D713D	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000540021.1_Silent_p.D583D|MSH6_ENST00000538136.1_Silent_p.D411D	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	713					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCCCTTGGATTCTGACACAG	0.403			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.D713D		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T2139C						.						105.0	104.0	104.0					2																	48027261		2203	4300	6503	SO:0001819	synonymous_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTTGGATTCTGAC	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2139T>C	chr2.hg19:g.48027261T>C		95.0	0.0		100.0	4.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	hg19	CCDS1836.1																																																																																			.	.		0.403	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
LHCGR	3973	hgsc.bcm.edu	37	2	48914978	48914978	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:48914978C>A	ENST00000294954.7	-	11	1979	c.1958G>T	c.(1957-1959)aGg>aTg	p.R653M	STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Missense_Mutation_p.R591M|LHCGR_ENST00000401907.1_3'UTR|LHCGR_ENST00000405626.1_Missense_Mutation_p.R626M|LHCGR_ENST00000403273.1_3'UTR	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	653					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	AAAATCTTTCCTTCTATAAAG	0.393																																					p.R653M		Atlas-SNP	.											.	LHCGR	154	.	0			c.G1958T						.						109.0	112.0	111.0					2																	48914978		2203	4300	6503	SO:0001583	missense	3973	exon11			TCTTTCCTTCTAT		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1958G>T	chr2.hg19:g.48914978C>A	ENSP00000294954:p.Arg653Met	121.0	0.0		113.0	5.0	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	C	5.943	0.358092	0.11239	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626	T;T;T	0.78126	-1.15;-0.98;-1.05	5.92	2.91	0.33838	.	0.308493	0.36591	N	0.002519	T	0.52853	0.1760	N	0.10809	0.05	0.30632	N	0.757415	B	0.16396	0.017	B	0.10450	0.005	T	0.42832	-0.9428	9	.	.	.	.	5.1548	0.15029	0.2953:0.5304:0.0:0.1743	.	653	P22888	LSHR_HUMAN	M	591;653;626	ENSP00000344301:R591M;ENSP00000294954:R653M;ENSP00000386033:R626M	.	R	-	2	0	LHCGR	48768482	0.639000	0.27234	1.000000	0.80357	0.547000	0.35210	1.482000	0.35486	0.853000	0.35312	0.585000	0.79938	AGG	.	.		0.393	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
EML6	400954	hgsc.bcm.edu	37	2	55194149	55194149	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:55194149C>T	ENST00000356458.6	+	38	6027	c.5507C>T	c.(5506-5508)gCc>gTc	p.A1836V	EML6_ENST00000490828.1_3'UTR	NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	1836						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						TCAACAGGTGCCTATAAGCGC	0.547																																					p.A1836V		Atlas-SNP	.											.	EML6	85	.	0			c.C5507T						.						68.0	69.0	69.0					2																	55194149		692	1591	2283	SO:0001583	missense	400954	exon38			CAGGTGCCTATAA		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.5507C>T	chr2.hg19:g.55194149C>T	ENSP00000348842:p.Ala1836Val	113.0	0.0		89.0	4.0	NM_001039753	A8MUB5|B6ZDG7	Missense_Mutation	SNP	ENST00000356458.6	hg19	CCDS46286.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.245378	0.59103	.	.	ENSG00000214595	ENST00000356458	T	0.36157	1.27	6.17	5.3	0.74995	WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.44664	0.1304	M	0.77616	2.38	0.33434	D	0.581464	B	0.15930	0.015	B	0.20184	0.028	T	0.56402	-0.7985	9	0.56958	D	0.05	.	15.7894	0.78343	0.0:0.935:0.0:0.065	.	1836	Q6ZMW3	EMAL6_HUMAN	V	1836	ENSP00000348842:A1836V	ENSP00000348842:A1836V	A	+	2	0	EML6	55047653	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.565000	0.60836	1.626000	0.50381	0.655000	0.94253	GCC	.	.		0.547	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
AFTPH	54812	hgsc.bcm.edu	37	2	64779485	64779485	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:64779485G>T	ENST00000422803.1	+	2	1191	c.877G>T	c.(877-879)Gga>Tga	p.G293*	AFTPH_ENST00000409183.1_5'Flank|AFTPH_ENST00000238855.7_Nonsense_Mutation_p.G293*|AFTPH_ENST00000409933.1_Nonsense_Mutation_p.G293*|AFTPH_ENST00000238856.4_Nonsense_Mutation_p.G293*			Q6ULP2	AFTIN_HUMAN	aftiphilin	293					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						AGACACTGATGGAGAGGATCA	0.373																																					p.G293X		Atlas-SNP	.											.	AFTPH	117	.	0			c.G877T						.						61.0	66.0	64.0					2																	64779485		2203	4300	6503	SO:0001587	stop_gained	54812	exon2			ACTGATGGAGAGG	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.877G>T	chr2.hg19:g.64779485G>T	ENSP00000397726:p.Gly293*	154.0	0.0		148.0	6.0	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Nonsense_Mutation	SNP	ENST00000422803.1	hg19		.	.	.	.	.	.	.	.	.	.	G	38	6.890172	0.97912	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933	.	.	.	5.78	1.55	0.23275	.	0.841047	0.10824	N	0.630138	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-0.2983	5.3584	0.16073	0.4928:0.1458:0.3615:0.0	.	.	.	.	X	293	.	ENSP00000238855:G293X	G	+	1	0	AFTPH	64632989	0.996000	0.38824	0.734000	0.30879	0.983000	0.72400	0.762000	0.26503	0.390000	0.25115	0.591000	0.81541	GGA	.	.		0.373	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657	
ALMS1	7840	hgsc.bcm.edu	37	2	73680043	73680043	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:73680043A>G	ENST00000264448.6	+	8	6497	c.6386A>G	c.(6385-6387)cAg>cGg	p.Q2129R	ALMS1_ENST00000377715.1_Missense_Mutation_p.Q2129R|ALMS1_ENST00000409009.1_Missense_Mutation_p.Q2087R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2129	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CCAGCTGGCCAGAAAACAGTA	0.403																																					p.Q2129R		Atlas-SNP	.											.	ALMS1	384	.	0			c.A6386G						.						50.0	48.0	48.0					2																	73680043		1850	4102	5952	SO:0001583	missense	7840	exon8			CTGGCCAGAAAAC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6386A>G	chr2.hg19:g.73680043A>G	ENSP00000264448:p.Gln2129Arg	94.0	0.0		99.0	4.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	8.519	0.868390	0.17250	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.15834	3.28;3.28;2.39	4.08	2.9	0.33743	.	0.203527	0.24597	N	0.037173	T	0.22360	0.0539	L	0.52573	1.65	0.09310	N	1	P;D;P	0.53745	0.952;0.962;0.952	P;P;P	0.53006	0.644;0.715;0.644	T	0.04065	-1.0980	10	0.35671	T	0.21	.	7.8479	0.29437	0.7902:0.2098:0.0:0.0	.	2129;2087;2129	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	2087;2129;2129	ENSP00000386627:Q2087R;ENSP00000264448:Q2129R;ENSP00000366944:Q2129R	ENSP00000264448:Q2129R	Q	+	2	0	ALMS1	73533551	0.183000	0.23186	0.083000	0.20561	0.041000	0.13682	1.650000	0.37292	0.860000	0.35481	0.533000	0.62120	CAG	.	.		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
C2orf81	388963	hgsc.bcm.edu	37	2	74643206	74643206	+	De_novo_Start_InFrame	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:74643206C>A	ENST00000517883.1	-	0	504				C2orf81_ENST00000290390.5_Missense_Mutation_p.G64W			A6NN90	CB081_HUMAN	chromosome 2 open reading frame 81											endometrium(3)|kidney(1)	4						AAGATGTCCCCTACGACGTCC	0.627																																					p.G64W		Atlas-SNP	.											.	C2orf81	23	.	0			c.G190T						.						34.0	42.0	39.0					2																	74643206		692	1591	2283			388963	exon2			TGTCCCCTACGAC	AC005041, CH471053		2p13.1	2012-08-07			ENSG00000159239	ENSG00000159239			34350	protein-coding gene	gene with protein product						15815621	Standard	NM_001145054		Approved	LOC388963, hCG40743	uc010yrq.1	A6NN90	OTTHUMG00000164184		chr2.hg19:g.74643206C>A		82.0	0.0		64.0	4.0	NM_001145054		Missense_Mutation	SNP	ENST00000517883.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.12	3.033153	0.54896	.	.	ENSG00000159239	ENST00000290390;ENST00000517896;ENST00000518401	.	.	.	5.52	5.52	0.82312	.	0.000000	0.45361	D	0.000366	T	0.78142	0.4237	M	0.66939	2.045	0.41080	D	0.985515	D	0.89917	1.0	D	0.91635	0.999	T	0.76083	-0.3089	9	0.39692	T	0.17	-43.0883	18.5729	0.91142	0.0:1.0:0.0:0.0	.	64	G3XAA6	.	W	64;64;89	.	ENSP00000290390:G64W	G	-	1	0	C2orf81	74496714	0.986000	0.35501	1.000000	0.80357	0.956000	0.61745	3.183000	0.50918	2.762000	0.94881	0.467000	0.42956	GGG	.	.		0.627	C2orf81-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000377683.1	NM_001145054	
CTNNA2	1496	hgsc.bcm.edu	37	2	80085187	80085187	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:80085187C>A	ENST00000402739.4	+	3	352	c.347C>A	c.(346-348)tCg>tAg	p.S116*	CTNNA2_ENST00000541047.1_Nonsense_Mutation_p.S116*|CTNNA2_ENST00000496558.1_Nonsense_Mutation_p.S116*|CTNNA2_ENST00000361291.4_Nonsense_Mutation_p.S150*|CTNNA2_ENST00000466387.1_Nonsense_Mutation_p.S116*|CTNNA2_ENST00000540488.1_Nonsense_Mutation_p.S116*	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	116					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GACCCTTGCTCGTCGGTAAAG	0.587																																					p.S116X		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C347A						.						99.0	96.0	97.0					2																	80085187		2061	4193	6254	SO:0001587	stop_gained	1496	exon4			CTTGCTCGTCGGT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.347C>A	chr2.hg19:g.80085187C>A	ENSP00000384638:p.Ser116*	102.0	0.0		96.0	4.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Nonsense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	C	37	6.135242	0.97315	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000409971;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	.	.	.	5.67	5.67	0.87782	.	0.070349	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.773	0.96379	0.0:1.0:0.0:0.0	.	.	.	.	X	116;116;116;150;116;116;116	.	ENSP00000355398:S150X	S	+	2	0	CTNNA2	79938695	1.000000	0.71417	0.947000	0.38551	0.965000	0.64279	7.818000	0.86416	2.677000	0.91161	0.655000	0.94253	TCG	.	.		0.587	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
CTNNA2	1496	hgsc.bcm.edu	37	2	80085274	80085274	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:80085274A>G	ENST00000402739.4	+	3	439	c.434A>G	c.(433-435)gAt>gGt	p.D145G	CTNNA2_ENST00000541047.1_Missense_Mutation_p.D145G|CTNNA2_ENST00000496558.1_Missense_Mutation_p.D145G|CTNNA2_ENST00000361291.4_Missense_Mutation_p.D179G|CTNNA2_ENST00000466387.1_Missense_Mutation_p.D145G|CTNNA2_ENST00000540488.1_Missense_Mutation_p.D145G	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	145					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GACATGGCAGATGTCATGAGA	0.493																																					p.D145G		Atlas-SNP	.											.	CTNNA2	462	.	0			c.A434G						.						68.0	68.0	68.0					2																	80085274		2029	4184	6213	SO:0001583	missense	1496	exon4			TGGCAGATGTCAT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.434A>G	chr2.hg19:g.80085274A>G	ENSP00000384638:p.Asp145Gly	88.0	0.0		72.0	4.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	A	32	5.172343	0.94807	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.70202	0.3197	M	0.89214	3.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.75283	-0.3372	10	0.51188	T	0.08	.	15.9204	0.79562	1.0:0.0:0.0:0.0	.	145;145;145	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	G	145;145;179;145;145;145	ENSP00000418191:D145G;ENSP00000419295:D145G;ENSP00000355398:D179G;ENSP00000384638:D145G;ENSP00000444675:D145G;ENSP00000441705:D145G	ENSP00000355398:D179G	D	+	2	0	CTNNA2	79938782	1.000000	0.71417	0.979000	0.43373	0.993000	0.82548	9.339000	0.96797	2.164000	0.68074	0.533000	0.62120	GAT	.	.		0.493	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
SEMA4C	54910	hgsc.bcm.edu	37	2	97529483	97529483	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:97529483A>G	ENST00000305476.5	-	12	1511	c.1379T>C	c.(1378-1380)cTg>cCg	p.L460P		NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	460	Dominant negative effect on myogenic differentiation. {ECO:0000250}.|Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell migration in hindbrain (GO:0021535)|cerebellum development (GO:0021549)|muscle cell differentiation (GO:0042692)|neural tube closure (GO:0001843)|positive regulation of stress-activated MAPK cascade (GO:0032874)|semaphorin-plexin signaling pathway (GO:0071526)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle membrane (GO:0030672)	receptor activity (GO:0004872)			NS(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	17						CTCCTCAATCAGGTGAACCCA	0.607																																					p.L460P		Atlas-SNP	.											.	SEMA4C	56	.	0			c.T1379C						.						74.0	76.0	75.0					2																	97529483		2203	4300	6503	SO:0001583	missense	54910	exon12			TCAATCAGGTGAA	AB051526	CCDS2029.1	2q11.2	2013-01-11			ENSG00000168758	ENSG00000168758		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10731	protein-coding gene	gene with protein product	"""M-Sema F"""	604462		SEMAI		7656991	Standard	NM_017789		Approved	Semacl1, Semaf	uc002sxh.4	Q9C0C4	OTTHUMG00000130535	ENST00000305476.5:c.1379T>C	chr2.hg19:g.97529483A>G	ENSP00000306844:p.Leu460Pro	92.0	0.0		72.0	4.0	NM_017789	Q32MJ3|Q7Z5X0	Missense_Mutation	SNP	ENST00000305476.5	hg19	CCDS2029.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.291916	0.80914	.	.	ENSG00000168758	ENST00000305476	T	0.12569	2.67	5.26	5.26	0.73747	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.443089	0.23081	N	0.052142	T	0.32255	0.0823	M	0.67625	2.065	0.80722	D	1	P;P	0.51240	0.943;0.943	P;P	0.59171	0.853;0.853	T	0.02581	-1.1138	10	0.87932	D	0	.	14.2933	0.66295	1.0:0.0:0.0:0.0	.	460;170	Q9C0C4;Q6P5A5	SEM4C_HUMAN;.	P	460	ENSP00000306844:L460P	ENSP00000306844:L460P	L	-	2	0	SEMA4C	96893210	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.146000	0.94640	2.208000	0.71279	0.533000	0.62120	CTG	.	.		0.607	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252957.1	NM_017789	
MAP4K4	9448	hgsc.bcm.edu	37	2	102486261	102486261	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:102486261T>C	ENST00000347699.4	+	20	2396		c.e20+2		MAP4K4_ENST00000324219.4_Splice_Site|MAP4K4_ENST00000302217.5_Splice_Site|MAP4K4_ENST00000413150.2_Splice_Site|MAP4K4_ENST00000456652.1_Splice_Site|MAP4K4_ENST00000350878.4_Splice_Site|MAP4K4_ENST00000425019.1_Splice_Site|MAP4K4_ENST00000498066.1_Splice_Site|MAP4K4_ENST00000350198.4_Splice_Site	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4						intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CAGAGCAGCGTCAGTCCCCGG	0.572																																					.		Atlas-SNP	.											.	MAP4K4	111	.	0			c.2306+2T>C						.						29.0	34.0	33.0					2																	102486261		2048	4187	6235	SO:0001630	splice_region_variant	9448	exon20			GCAGCGTCAGTCC	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2396+2T>C	chr2.hg19:g.102486261T>C		78.0	0.0		112.0	5.0	NM_145686	O75172|Q9NST7	Splice_Site	SNP	ENST00000347699.4	hg19	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190971	0.78789	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878;ENST00000421882	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0569	0.71921	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAP4K4	101852693	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.481000	0.81124	1.960000	0.56953	0.460000	0.39030	.	.	.		0.572	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	Intron
PTPN4	5775	hgsc.bcm.edu	37	2	120720202	120720202	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:120720202A>G	ENST00000263708.2	+	24	3062	c.2291A>G	c.(2290-2292)cAc>cGc	p.H764R	PTPN4_ENST00000544261.1_Missense_Mutation_p.H397R	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	764	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	GTTAAATGTCACCAATATTGG	0.308																																					p.H764R		Atlas-SNP	.											.	PTPN4	89	.	0			c.A2291G						.						44.0	39.0	41.0					2																	120720202		2203	4300	6503	SO:0001583	missense	5775	exon24			AATGTCACCAATA		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2291A>G	chr2.hg19:g.120720202A>G	ENSP00000263708:p.His764Arg	97.0	0.0		116.0	5.0	NM_002830	B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	hg19	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.148096	0.78001	.	.	ENSG00000088179	ENST00000263708;ENST00000544261	D;D	0.83163	-1.69;-1.69	5.51	5.51	0.81932	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.92980	0.7766	M	0.92970	3.365	0.80722	D	1	D	0.59357	0.985	D	0.74348	0.983	D	0.94565	0.7766	10	0.87932	D	0	.	15.6199	0.76799	1.0:0.0:0.0:0.0	.	764	P29074	PTN4_HUMAN	R	764;397	ENSP00000263708:H764R;ENSP00000445841:H397R	ENSP00000263708:H764R	H	+	2	0	PTPN4	120436672	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.976000	0.93442	2.095000	0.63458	0.377000	0.23210	CAC	.	.		0.308	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2		
ERCC3	2071	hgsc.bcm.edu	37	2	128051105	128051105	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:128051105G>A	ENST00000285398.2	-	2	312	c.218C>T	c.(217-219)tCc>tTc	p.S73F	ERCC3_ENST00000493187.2_Missense_Mutation_p.S9F	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	73					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GAGGGGCCTGGAGGTGTGGTC	0.592			"""Mis, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.S73F		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"""excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"""		E	.	ERCC3	73	.	0			c.C218T						.						77.0	68.0	71.0					2																	128051105		2203	4300	6503	SO:0001583	missense	2071	exon2	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGCCTGGAGGTGT	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	3435	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group B complementing"""	133510	"""excision repair cross-complementing rodent repair deficiency, complementation group 3"""			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.218C>T	chr2.hg19:g.128051105G>A	ENSP00000285398:p.Ser73Phe	174.0	0.0		172.0	54.0	NM_000122	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	hg19	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.721592	0.68959	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	T;T	0.66995	-0.24;-0.21	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.64702	0.2622	L	0.54323	1.7	0.80722	D	1	B;B	0.18013	0.025;0.025	B;B	0.20767	0.031;0.031	T	0.65483	-0.6157	10	0.62326	D	0.03	-17.7841	17.448	0.87584	0.0:0.0:1.0:0.0	.	73;73	A8K359;P19447	.;ERCC3_HUMAN	F	73;9	ENSP00000285398:S73F;ENSP00000444796:S9F	ENSP00000285398:S73F	S	-	2	0	ERCC3	127767575	1.000000	0.71417	0.159000	0.22649	0.969000	0.65631	8.939000	0.92951	2.347000	0.79759	0.655000	0.94253	TCC	.	.		0.592	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122	
MZT2A	653784	hgsc.bcm.edu	37	2	132249809	132249809	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:132249809C>A	ENST00000309451.6	-	1	186	c.141G>T	c.(139-141)gcG>gcT	p.A47A	AC093838.4_ENST00000438378.2_RNA|MIR4784_ENST00000579560.1_RNA|MZT2A_ENST00000410036.2_Intron	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A	47				EEMELYELAQAAGGGIDPDVFK -> LQGGGRAGRRGLTGP ASVPAR (in Ref. 2; AAI04651). {ECO:0000305}.		centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						TACCGCCGCCCGCCGCCTGAG	0.736																																					p.A47A		Atlas-SNP	.											.	MZT2A	6	.	0			c.G141T						.						7.0	12.0	10.0					2																	132249809		2146	4261	6407	SO:0001819	synonymous_variant	653784	exon1			GCCGCCCGCCGCC	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"""	613449	"""family with sequence similarity 128, member A"""	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.141G>T	chr2.hg19:g.132249809C>A		39.0	0.0		42.0	4.0	NM_001085365	Q3SWV8|Q8WVB2	Silent	SNP	ENST00000309451.6	hg19	CCDS42758.1																																																																																			.	.		0.736	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2		
TMEM163	81615	hgsc.bcm.edu	37	2	135308182	135308182	+	Silent	SNP	G	G	A	rs576374684		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:135308182G>A	ENST00000281924.6	-	4	481	c.417C>T	c.(415-417)taC>taT	p.Y139Y		NM_030923.4	NP_112185.1	Q8TC26	TM163_HUMAN	transmembrane protein 163	139						cell junction (GO:0030054)|early endosome membrane (GO:0031901)|integral component of synaptic vesicle membrane (GO:0030285)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.154)		CCGCGTTGCTGTAACGCCACA	0.522													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21293	0.0		0.0	False		,,,				2504	0.0				p.Y139Y		Atlas-SNP	.											.	TMEM163	34	.	0			c.C417T						.						124.0	118.0	120.0					2																	135308182		2203	4300	6503	SO:0001819	synonymous_variant	81615	exon4			GTTGCTGTAACGC		CCDS2172.1	2q21.3	2008-02-05			ENSG00000152128	ENSG00000152128			25380	protein-coding gene	gene with protein product						17623043	Standard	NM_030923		Approved	DKFZP566N034, SV31	uc002ttx.3	Q8TC26	OTTHUMG00000131713	ENST00000281924.6:c.417C>T	chr2.hg19:g.135308182G>A		119.0	0.0		100.0	4.0	NM_030923	Q53QM3|Q53SV7|Q69YH3|Q9UFG3	Silent	SNP	ENST00000281924.6	hg19	CCDS2172.1																																																																																			.	.		0.522	TMEM163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254631.2	NM_030923	
GALNT13	114805	hgsc.bcm.edu	37	2	155295139	155295139	+	Silent	SNP	C	C	A	rs182009673		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:155295139C>A	ENST00000392825.3	+	12	1998	c.1431C>A	c.(1429-1431)acC>acA	p.T477T	GALNT13_ENST00000487047.1_3'UTR|AC009227.2_ENST00000434635.1_RNA|GALNT13_ENST00000409237.1_Silent_p.T477T	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	477	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						AAATCCGAACCGATGACTTGT	0.343																																					p.T477T		Atlas-SNP	.											.	GALNT13	170	.	0			c.C1431A						.						124.0	123.0	124.0					2																	155295139		2203	4300	6503	SO:0001819	synonymous_variant	114805	exon12			CCGAACCGATGAC	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23242	protein-coding gene	gene with protein product	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13"", ""polypeptide GalNAc transferase 13"""	608369	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"""			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1431C>A	chr2.hg19:g.155295139C>A		141.0	0.0		117.0	5.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Silent	SNP	ENST00000392825.3	hg19	CCDS2199.1																																																																																			.	C|0.999;T|0.001		0.343	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917	
PKP4	8502	hgsc.bcm.edu	37	2	159519916	159519916	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:159519916T>C	ENST00000389759.3	+	15	2648	c.2536T>C	c.(2536-2538)Tct>Cct	p.S846P	AC005042.4_ENST00000342892.4_RNA|PKP4_ENST00000495123.1_3'UTR|PKP4_ENST00000389757.3_Missense_Mutation_p.S846P	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	846					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						CTTGGAAGGCTCTGCAGGGTC	0.488										HNSCC(62;0.18)																											p.S846P		Atlas-SNP	.											.	PKP4	133	.	0			c.T2536C						.						61.0	62.0	61.0					2																	159519916		2203	4300	6503	SO:0001583	missense	8502	exon15			GAAGGCTCTGCAG	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"""Armadillo repeat containing"""	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2536T>C	chr2.hg19:g.159519916T>C	ENSP00000374409:p.Ser846Pro	126.0	0.0		118.0	5.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.879990	0.72294	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.52295	0.67;0.67	5.76	4.59	0.56863	Armadillo-like helical (1);Armadillo-type fold (1);	0.122752	0.56097	D	0.000027	T	0.58133	0.2101	M	0.76574	2.34	0.54753	D	0.999986	D;P;P	0.56035	0.974;0.867;0.954	P;B;P	0.50754	0.649;0.439;0.649	T	0.63637	-0.6592	10	0.87932	D	0	-10.2313	13.0322	0.58848	0.0:0.0:0.1347:0.8653	.	801;846;846	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	P	846	ENSP00000374407:S846P;ENSP00000374409:S846P	ENSP00000374407:S846P	S	+	1	0	PKP4	159228162	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.167000	0.58209	0.978000	0.38470	0.533000	0.62120	TCT	.	.		0.488	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
MARCH7	64844	hgsc.bcm.edu	37	2	160605076	160605076	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:160605076A>G	ENST00000259050.4	+	5	1397	c.1275A>G	c.(1273-1275)agA>agG	p.R425R	MARCH7_ENST00000539065.1_Silent_p.R369R|MARCH7_ENST00000409591.1_Silent_p.R387R|MARCH7_ENST00000409175.1_Silent_p.R425R	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	425					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						ATATTTTTAGAAGAGAATCAA	0.438																																					p.R425R		Atlas-SNP	.											.	MARCH7	48	.	0			c.A1275G						.						76.0	80.0	79.0					2																	160605076		2203	4300	6503	SO:0001819	synonymous_variant	64844	exon5			TTTTAGAAGAGAA	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	17393	protein-coding gene	gene with protein product		613334	"""axotrophin"", ""membrane-associated ring finger (C3HC4) 7"""	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.1275A>G	chr2.hg19:g.160605076A>G		77.0	0.0		87.0	4.0	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Silent	SNP	ENST00000259050.4	hg19	CCDS2210.1																																																																																			.	.		0.438	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
SCN1A	6323	hgsc.bcm.edu	37	2	166900257	166900257	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:166900257A>G	ENST00000303395.4	-	11	1964	c.1965T>C	c.(1963-1965)ggT>ggC	p.G655G	AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Intron|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000423058.2_Silent_p.G655G|SCN1A_ENST00000375405.3_Silent_p.G655G			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	655					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTGAAGGTCCACCAACCAAGG	0.478																																					p.G655G		Atlas-SNP	.											.	SCN1A	641	.	0			c.T1965C						.						143.0	122.0	129.0					2																	166900257		2203	4300	6503	SO:0001819	synonymous_variant	6323	exon11			AGGTCCACCAACC	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1965T>C	chr2.hg19:g.166900257A>G		142.0	0.0		115.0	5.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.478	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
LRP2	4036	hgsc.bcm.edu	37	2	170104009	170104009	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:170104009A>G	ENST00000263816.3	-	20	3072	c.2787T>C	c.(2785-2787)acT>acC	p.T929T	LRP2_ENST00000443831.1_Silent_p.T792T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	929					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	GTCTCCAGTCAGTAAAAAATA	0.368																																					p.T929T		Atlas-SNP	.											.	LRP2	751	.	0			c.T2787C						.						87.0	85.0	86.0					2																	170104009		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon20			CCAGTCAGTAAAA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.2787T>C	chr2.hg19:g.170104009A>G		77.0	0.0		86.0	4.0	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.		0.368	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
GPR155	151556	hgsc.bcm.edu	37	2	175324698	175324698	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:175324698T>C	ENST00000392552.2	-	10	1917	c.1679A>G	c.(1678-1680)cAc>cGc	p.H560R	GPR155_ENST00000392551.2_Missense_Mutation_p.H560R|GPR155_ENST00000295500.4_Missense_Mutation_p.H560R	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	560					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						CACCACTTTGTGGCTCTGAGA	0.468																																					p.H560R		Atlas-SNP	.											.	GPR155	76	.	0			c.A1679G						.						108.0	97.0	101.0					2																	175324698		2203	4300	6503	SO:0001583	missense	151556	exon11			ACTTTGTGGCTCT	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1679A>G	chr2.hg19:g.175324698T>C	ENSP00000376335:p.His560Arg	81.0	0.0		78.0	4.0	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	hg19	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	T	5.161	0.215270	0.09810	.	.	ENSG00000163328	ENST00000392552;ENST00000510236;ENST00000392551;ENST00000295500	T;T;T	0.40756	1.02;1.02;1.02	5.89	-0.821	0.10822	.	0.761606	0.13610	N	0.375202	T	0.16685	0.0401	N	0.08118	0	0.09310	N	0.999991	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.26608	-1.0098	10	0.12766	T	0.61	-0.024	5.368	0.16125	0.0:0.4657:0.1864:0.3479	.	40;560	F5H464;Q7Z3F1	.;GP155_HUMAN	R	560;40;560;560	ENSP00000376335:H560R;ENSP00000376334:H560R;ENSP00000295500:H560R	ENSP00000295500:H560R	H	-	2	0	GPR155	175032944	0.801000	0.28930	0.494000	0.27515	0.805000	0.45488	0.506000	0.22658	0.153000	0.19213	0.459000	0.35465	CAC	.	.		0.468	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529	
OSBPL6	114880	hgsc.bcm.edu	37	2	179197627	179197627	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179197627G>T	ENST00000190611.4	+	8	892	c.516G>T	c.(514-516)tgG>tgT	p.W172C	OSBPL6_ENST00000359685.3_Missense_Mutation_p.W172C|OSBPL6_ENST00000357080.4_Missense_Mutation_p.W172C|OSBPL6_ENST00000315022.2_Missense_Mutation_p.W151C|OSBPL6_ENST00000409045.3_Missense_Mutation_p.W172C|OSBPL6_ENST00000409631.1_Missense_Mutation_p.W172C|OSBPL6_ENST00000392505.2_Missense_Mutation_p.W172C	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	172	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TTGATGCATGGGTCTCCAAAC	0.428																																					p.W172C		Atlas-SNP	.											.	OSBPL6	178	.	0			c.G516T						.						162.0	156.0	158.0					2																	179197627		2203	4300	6503	SO:0001583	missense	114880	exon8			TGCATGGGTCTCC	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.516G>T	chr2.hg19:g.179197627G>T	ENSP00000190611:p.Trp172Cys	126.0	0.0		122.0	5.0	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	hg19	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.775178	0.90108	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.58210	0.35;0.45;0.61;0.4;0.4;0.45;0.43	5.57	5.57	0.84162	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.83078	0.5176	H	0.96604	3.85	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;0.996;0.999;0.997;0.998	D	0.88211	0.2890	10	0.87932	D	0	-9.033	19.9215	0.97087	0.0:0.0:1.0:0.0	.	172;151;172;172;172;172	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	C	172;172;172;172;172;172;151	ENSP00000376293:W172C;ENSP00000352713:W172C;ENSP00000349591:W172C;ENSP00000387248:W172C;ENSP00000190611:W172C;ENSP00000386885:W172C;ENSP00000318723:W151C	ENSP00000190611:W172C	W	+	3	0	OSBPL6	178905873	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.813000	0.99286	2.785000	0.95823	0.655000	0.94253	TGG	.	.		0.428	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
TTN	7273	hgsc.bcm.edu	37	2	179399454	179399454	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179399454G>A	ENST00000591111.1	-	308	97189	c.96965C>T	c.(96964-96966)gCc>gTc	p.A32322V	TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A24898V|TTN_ENST00000589042.1_Missense_Mutation_p.A33963V|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A25090V|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A25023V|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A31395V|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32322	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCTGACGGGCTTGACCAAA	0.423																																					p.A33963V		Atlas-SNP	.											.	TTN	18412	.	0			c.C101888T						.						57.0	56.0	57.0					2																	179399454		1873	4114	5987	SO:0001583	missense	7273	exon358			TGACGGGCTTGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.96965C>T	chr2.hg19:g.179399454G>A	ENSP00000465570:p.Ala32322Val	153.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.8	4.201966	0.79127	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89312	0.6679	M	0.91972	3.26	0.58432	D	0.999994	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.65010	0.931;0.931;0.931;0.931	D	0.90503	0.4475	9	0.87932	D	0	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	24898;25023;25090;32322	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	31395;24898;25090;25023;24895	ENSP00000343764:A31395V;ENSP00000434586:A24898V;ENSP00000340554:A25090V;ENSP00000352154:A25023V	ENSP00000340554:A25090V	A	-	2	0	TTN	179107700	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.922000	0.87538	2.857000	0.98124	0.650000	0.86243	GCC	.	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179476169	179476169	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179476169T>C	ENST00000591111.1	-	219	46088	c.45864A>G	c.(45862-45864)agA>agG	p.R15288R	TTN_ENST00000460472.2_Silent_p.R7864R|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Silent_p.R16929R|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Silent_p.R8056R|TTN_ENST00000359218.5_Silent_p.R7989R|TTN_ENST00000342992.6_Silent_p.R14361R|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15288	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATTGACTGCTCTCACTCTCA	0.408																																					p.R16929R		Atlas-SNP	.											.	TTN	18412	.	0			c.A50787G						.						95.0	93.0	94.0					2																	179476169		2031	4192	6223	SO:0001819	synonymous_variant	7273	exon269			GACTGCTCTCACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45864A>G	chr2.hg19:g.179476169T>C		121.0	0.0		122.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179647564	179647564	+	Silent	SNP	G	G	T	rs371447978		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:179647564G>T	ENST00000591111.1	-	18	3293	c.3069C>A	c.(3067-3069)acC>acA	p.T1023T	TTN_ENST00000460472.2_Silent_p.T977T|TTN_ENST00000360870.5_Silent_p.T1023T|TTN_ENST00000589042.1_Silent_p.T1023T|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342175.6_Silent_p.T977T|TTN_ENST00000359218.5_Silent_p.T977T|TTN_ENST00000342992.6_Silent_p.T1023T			Q8WZ42	TITIN_HUMAN	titin	32576	Ig-like 3.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T1023T(3)|p.T977T(3)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTGCTGACGGTTCCAGCCT	0.498																																					p.T1023T		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,0,11	TTN	18412	.	6	Substitution - coding silent(6)	endometrium(6)	c.C3069A						.						88.0	73.0	78.0					2																	179647564		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon18			GCTGACGGTTCCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.3069C>A	chr2.hg19:g.179647564G>T		120.0	0.0		97.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZC3H15	55854	hgsc.bcm.edu	37	2	187366137	187366137	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:187366137G>A	ENST00000337859.6	+	4	654	c.427G>A	c.(427-429)Gaa>Aaa	p.E143K	ZC3H15_ENST00000468120.1_3'UTR|ZC3H15_ENST00000544130.1_Intron	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	143					cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			TGCAAGAGATGAAGAACTTGA	0.313																																					p.E143K		Atlas-SNP	.											.	ZC3H15	28	.	0			c.G427A						.						87.0	88.0	88.0					2																	187366137		1836	4072	5908	SO:0001583	missense	55854	exon4			AGAGATGAAGAAC		CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"""Zinc fingers, CCCH-type domain containing"""	29528	protein-coding gene	gene with protein product	"""likely ortholog of mouse immediate early response, erythropoietin 4"""					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.427G>A	chr2.hg19:g.187366137G>A	ENSP00000338788:p.Glu143Lys	78.0	0.0		125.0	5.0	NM_018471	B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Missense_Mutation	SNP	ENST00000337859.6	hg19	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	G	36	5.601878	0.96614	.	.	ENSG00000065548	ENST00000337859;ENST00000536434	T	0.33438	1.41	5.94	5.94	0.96194	.	0.089037	0.85682	D	0.000000	T	0.41026	0.1141	L	0.55017	1.72	0.80722	D	1	P	0.52316	0.952	P	0.47075	0.536	T	0.10177	-1.0641	10	0.48119	T	0.1	-9.3332	20.3736	0.98901	0.0:0.0:1.0:0.0	.	143	Q8WU90	ZC3HF_HUMAN	K	143	ENSP00000338788:E143K	ENSP00000338788:E143K	E	+	1	0	ZC3H15	187074382	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.496000	0.97967	2.820000	0.97059	0.650000	0.86243	GAA	.	.		0.313	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471	
SLC40A1	30061	hgsc.bcm.edu	37	2	190426883	190426883	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:190426883C>A	ENST00000261024.2	-	8	1863	c.1437G>T	c.(1435-1437)ttG>ttT	p.L479F		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	479					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			TTTCTTGCAGCAACTGTGTCA	0.313																																					p.L479F		Atlas-SNP	.											.	SLC40A1	51	.	0			c.G1437T						.						48.0	47.0	47.0					2																	190426883		2203	4300	6503	SO:0001583	missense	30061	exon8			TTGCAGCAACTGT	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"""Solute carriers"""	10909	protein-coding gene	gene with protein product	"""ferroportin 1"""	604653	"""solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"""	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.1437G>T	chr2.hg19:g.190426883C>A	ENSP00000261024:p.Leu479Phe	66.0	0.0		97.0	4.0	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.832574	0.71258	.	.	ENSG00000138449	ENST00000261024	D	0.82344	-1.6	5.92	5.03	0.67393	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.90133	0.6917	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90219	0.4270	10	0.72032	D	0.01	-21.1431	9.1175	0.36766	0.0:0.7512:0.1212:0.1276	.	479	Q9NP59	S40A1_HUMAN	F	479	ENSP00000261024:L479F	ENSP00000261024:L479F	L	-	3	2	SLC40A1	190135128	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.779000	0.26746	2.814000	0.96858	0.585000	0.79938	TTG	.	.		0.313	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2		
PMS1	5378	hgsc.bcm.edu	37	2	190656664	190656664	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:190656664A>G	ENST00000441310.2	+	2	362	c.129A>G	c.(127-129)aaA>aaG	p.K43K	PMS1_ENST00000418224.3_5'UTR|PMS1_ENST00000447232.2_Silent_p.K43K|PMS1_ENST00000409823.3_Silent_p.K43K|PMS1_ENST00000374826.4_Silent_p.K43K|PMS1_ENST00000432292.3_5'UTR|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000409985.1_Silent_p.K43K	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	43					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TAGATGTTAAACTGGTGAGTG	0.393			"""Mis, N"""			"""colorectal, endometrial, ovarian"""		Direct reversal of damage;Mismatch excision repair (MMR)																													p.K43K		Atlas-SNP	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.A129G						.						90.0	82.0	85.0					2																	190656664		2203	4300	6503	SO:0001819	synonymous_variant	5378	exon2			TGTTAAACTGGTG		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"""postmeiotic segregation increased (S. cerevisiae) 1"""	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.129A>G	chr2.hg19:g.190656664A>G		109.0	0.0		95.0	4.0	NM_001128143	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Silent	SNP	ENST00000441310.2	hg19	CCDS2302.1																																																																																			.	.		0.393	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2		
NAB1	4664	hgsc.bcm.edu	37	2	191548468	191548468	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:191548468G>T	ENST00000337386.5	+	7	1471	c.1010G>T	c.(1009-1011)gGg>gTg	p.G337V	AC006460.2_ENST00000411949.1_RNA|AC006460.2_ENST00000421437.1_RNA|NAB1_ENST00000357215.5_Intron|NAB1_ENST00000484774.1_3'UTR|NAB1_ENST00000409641.1_Missense_Mutation_p.G337V|AC006460.2_ENST00000428032.1_RNA|NAB1_ENST00000409581.1_Missense_Mutation_p.G337V|NAB1_ENST00000545490.1_Intron	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	337	Necessary for nuclear localization. {ECO:0000250}.				endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			CCACAGGATGGGTTTCCAGAT	0.358																																					p.G337V		Atlas-SNP	.											.	NAB1	31	.	0			c.G1010T						.						70.0	72.0	71.0					2																	191548468		2203	4300	6503	SO:0001583	missense	4664	exon7			AGGATGGGTTTCC		CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"""EGR1 binding protein 1"""	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.1010G>T	chr2.hg19:g.191548468G>T	ENSP00000336894:p.Gly337Val	91.0	0.0		80.0	5.0	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	hg19	CCDS2307.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.991187	0.54041	.	.	ENSG00000138386	ENST00000409581;ENST00000337386;ENST00000409641	.	.	.	5.14	5.14	0.70334	Nab1, C-terminal (1);	0.221327	0.47852	D	0.000218	T	0.56426	0.1984	L	0.27053	0.805	0.80722	D	1	P;P	0.37101	0.582;0.582	P;P	0.47299	0.543;0.543	T	0.59118	-0.7514	9	0.54805	T	0.06	-14.4149	15.9119	0.79479	0.0:0.0:1.0:0.0	.	337;337	B8ZZS2;Q13506	.;NAB1_HUMAN	V	337	.	ENSP00000336894:G337V	G	+	2	0	NAB1	191256713	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	6.179000	0.71974	2.675000	0.91044	0.650000	0.86243	GGG	.	.		0.358	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966	
UNC80	285175	hgsc.bcm.edu	37	2	210806147	210806147	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:210806147C>A	ENST00000439458.1	+	43	6731	c.6651C>A	c.(6649-6651)acC>acA	p.T2217T	UNC80_ENST00000272845.6_Silent_p.T2212T	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	2217					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T2217T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						TCATCAACACCGCGGTGCACT	0.547																																					p.T2217T		Atlas-SNP	.											UNC80_ENST00000439458,NS,carcinoma,0,1	UNC80	280	.	1	Substitution - coding silent(1)	endometrium(1)	c.C6651A						.						98.0	90.0	92.0					2																	210806147		692	1591	2283	SO:0001819	synonymous_variant	285175	exon43			CAACACCGCGGTG	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.6651C>A	chr2.hg19:g.210806147C>A		90.0	0.0		94.0	4.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Silent	SNP	ENST00000439458.1	hg19	CCDS46504.1																																																																																			.	.		0.547	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
LANCL1	10314	hgsc.bcm.edu	37	2	211341073	211341073	+	Silent	SNP	G	G	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:211341073G>C	ENST00000443314.1	-	1	390	c.48C>G	c.(46-48)tcC>tcG	p.S16S	LANCL1_ENST00000233714.4_Silent_p.S16S|LANCL1_ENST00000441020.3_Silent_p.S16S|CPS1_ENST00000430249.2_5'Flank|LANCL1_ENST00000431941.2_Silent_p.S16S|LANCL1_ENST00000450366.2_Silent_p.S16S			O43813	LANC1_HUMAN	LanC lantibiotic synthetase component C-like 1 (bacterial)	16					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|G-protein coupled receptor activity (GO:0004930)|glutathione binding (GO:0043295)|low-density lipoprotein particle receptor binding (GO:0050750)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)		CTTCGGCCAGGGATTTGTTAT	0.517																																					p.S16S		Atlas-SNP	.											.	LANCL1	23	.	0			c.C48G						.						53.0	51.0	52.0					2																	211341073		2203	4300	6503	SO:0001819	synonymous_variant	10314	exon2			GGCCAGGGATTTG	Y11395	CCDS2392.1	2q33-q35	2008-05-23	2001-12-04		ENSG00000115365	ENSG00000115365			6508	protein-coding gene	gene with protein product		604155	"""LanC (bacterial lantibiotic synthetase component C)-like 1"""	GPR69A		9512664	Standard	NM_001136574		Approved	p40	uc010zjh.2	O43813	OTTHUMG00000132991	ENST00000443314.1:c.48C>G	chr2.hg19:g.211341073G>C		374.0	0.0		322.0	163.0	NM_001136574		Silent	SNP	ENST00000443314.1	hg19	CCDS2392.1																																																																																			.	.		0.517	LANCL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336817.1	NM_006055	
CPS1	1373	hgsc.bcm.edu	37	2	211455601	211455601	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:211455601C>T	ENST00000233072.5	+	9	1114	c.918C>T	c.(916-918)gcC>gcT	p.A306A	CPS1_ENST00000451903.2_5'Flank|CPS1_ENST00000430249.2_Silent_p.A312A	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	306	Glutamine amidotransferase type-1.				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)	CTGCTGGTGCCAAAACCTACA	0.398																																					p.A312A		Atlas-SNP	.											.	CPS1	485	.	0			c.C936T						.						85.0	91.0	89.0					2																	211455601		2203	4300	6503	SO:0001819	synonymous_variant	1373	exon10			TGGTGCCAAAACC	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.918C>T	chr2.hg19:g.211455601C>T		53.0	0.0		70.0	4.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.398	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
ABCA12	26154	hgsc.bcm.edu	37	2	215797448	215797448	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:215797448G>T	ENST00000272895.7	-	53	7917	c.7698C>A	c.(7696-7698)gcC>gcA	p.A2566A	ABCA12_ENST00000389661.4_Silent_p.A2248A|AC072062.1_ENST00000607412.1_RNA	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2566					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCTGGTCTTTGGCAAAGTTGA	0.408																																					p.A2566A	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C7698A						.						112.0	107.0	109.0					2																	215797448		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon53			GTCTTTGGCAAAG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.7698C>A	chr2.hg19:g.215797448G>T		107.0	0.0		96.0	4.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.		0.408	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
TNS1	7145	hgsc.bcm.edu	37	2	218712394	218712394	+	Missense_Mutation	SNP	G	G	T	rs567400983		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:218712394G>T	ENST00000171887.4	-	17	2923	c.2471C>A	c.(2470-2472)cCg>cAg	p.P824Q	TNS1_ENST00000419504.1_Missense_Mutation_p.P824Q|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Missense_Mutation_p.P824Q	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	824					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.P824L(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GTGGGTGGTCGGAAGGAAGGC	0.582																																					p.P824Q		Atlas-SNP	.											TNS1,NS,carcinoma,0,2	TNS1	251	.	1	Substitution - Missense(1)	endometrium(1)	c.C2471A						.						86.0	69.0	75.0					2																	218712394		2203	4300	6503	SO:0001583	missense	7145	exon17			GTGGTCGGAAGGA	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.2471C>A	chr2.hg19:g.218712394G>T	ENSP00000171887:p.Pro824Gln	103.0	0.0		92.0	4.0	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	5.143	0.211988	0.09757	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930	D;D;D	0.91521	-2.84;-2.86;-2.85	3.77	3.77	0.43336	.	0.832278	0.10588	N	0.657099	T	0.80929	0.4718	N	0.14661	0.345	0.80722	D	1	B;B;P;P;P	0.39216	0.435;0.048;0.664;0.468;0.468	B;B;B;B;B	0.33042	0.112;0.011;0.157;0.109;0.157	T	0.75611	-0.3258	10	0.16896	T	0.51	.	13.9433	0.64069	0.0:0.0:1.0:0.0	.	824;878;824;824;824	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	Q	824	ENSP00000171887:P824Q;ENSP00000408724:P824Q;ENSP00000406016:P824Q	ENSP00000171887:P824Q	P	-	2	0	TNS1	218420639	0.892000	0.30473	0.893000	0.35052	0.213000	0.24496	0.912000	0.28597	2.093000	0.63338	0.455000	0.32223	CCG	.	.		0.582	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
PLCD4	84812	hgsc.bcm.edu	37	2	219480768	219480768	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:219480768G>A	ENST00000450993.2	+	3	503	c.164G>A	c.(163-165)gGc>gAc	p.G55D	PLCD4_ENST00000432688.1_Missense_Mutation_p.G55D|PLCD4_ENST00000417849.1_Missense_Mutation_p.G55D	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	55	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CAGGCCAGGGGCAGTGCCAAG	0.582																																					p.G55D		Atlas-SNP	.											PLCD4,NS,carcinoma,0,1	PLCD4	51	.	0			c.G164A						.						37.0	38.0	37.0					2																	219480768		2022	4189	6211	SO:0001583	missense	84812	exon3			CCAGGGGCAGTGC	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.164G>A	chr2.hg19:g.219480768G>A	ENSP00000388631:p.Gly55Asp	61.0	0.0		68.0	3.0	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	hg19	CCDS46516.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.147017	0.57151	.	.	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000457426;ENST00000417849;ENST00000415854;ENST00000432688	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.16	4.27	0.50696	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.400623	0.27495	N	0.019116	T	0.66025	0.2748	L	0.41124	1.26	0.22066	N	0.999383	D	0.56968	0.978	D	0.63113	0.911	T	0.57734	-0.7760	10	0.10111	T	0.7	.	14.4048	0.67075	0.0:0.1487:0.8513:0.0	.	55	Q9BRC7	PLCD4_HUMAN	D	55	ENSP00000388631:G55D;ENSP00000396942:G55D;ENSP00000391850:G55D;ENSP00000396185:G55D	ENSP00000251959:G55D	G	+	2	0	PLCD4	219189012	1.000000	0.71417	0.026000	0.17262	0.839000	0.47603	5.094000	0.64523	1.380000	0.46344	0.655000	0.94253	GGC	.	.		0.582	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		
SERPINE2	5270	hgsc.bcm.edu	37	2	224856708	224856708	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:224856708T>C	ENST00000258405.4	-	4	739	c.497A>G	c.(496-498)gAc>gGc	p.D166G	SERPINE2_ENST00000409304.1_Missense_Mutation_p.D166G|SERPINE2_ENST00000447280.2_Missense_Mutation_p.D178G|SERPINE2_ENST00000409840.3_Missense_Mutation_p.D166G	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	166					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CAGCAGATTGTCAATCATATC	0.488																																					p.D178G		Atlas-SNP	.											.	SERPINE2	103	.	0			c.A533G						.						58.0	51.0	54.0					2																	224856708		2203	4300	6503	SO:0001583	missense	5270	exon4			AGATTGTCAATCA	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.497A>G	chr2.hg19:g.224856708T>C	ENSP00000258405:p.Asp166Gly	55.0	0.0		59.0	4.0	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	hg19	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.468784	0.43839	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738	D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81	5.8	5.8	0.92144	Serpin domain (3);	0.205916	0.52532	D	0.000077	T	0.81602	0.4857	L	0.44542	1.39	0.47862	D	0.999539	P;P	0.38395	0.629;0.488	B;B	0.37731	0.257;0.257	T	0.81141	-0.1068	10	0.38643	T	0.18	.	16.1506	0.81618	0.0:0.0:0.0:1.0	.	178;166	B4DIF2;P07093	.;GDN_HUMAN	G	166;166;166;178;166	ENSP00000386412:D166G;ENSP00000258405:D166G;ENSP00000386969:D166G;ENSP00000415786:D178G;ENSP00000408452:D166G	ENSP00000258405:D166G	D	-	2	0	SERPINE2	224564952	1.000000	0.71417	0.852000	0.33557	0.932000	0.56968	5.130000	0.64745	2.206000	0.71126	0.528000	0.53228	GAC	.	.		0.488	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
DOCK10	55619	hgsc.bcm.edu	37	2	225652004	225652004	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:225652004T>C	ENST00000258390.7	-	49	5596	c.5529A>G	c.(5527-5529)caA>caG	p.Q1843Q	DOCK10_ENST00000409592.3_Silent_p.Q1837Q	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1843	DHR-2.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TGAAGTCTCGTTGTTTCTCAA	0.368																																					p.Q1843Q		Atlas-SNP	.											.	DOCK10	308	.	0			c.A5529G						.						137.0	132.0	134.0					2																	225652004		1911	4130	6041	SO:0001819	synonymous_variant	55619	exon49			GTCTCGTTGTTTC	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.5529A>G	chr2.hg19:g.225652004T>C		112.0	0.0		99.0	4.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	hg19	CCDS46528.1																																																																																			.	.		0.368	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
COL4A4	1286	hgsc.bcm.edu	37	2	227895215	227895215	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:227895215G>A	ENST00000396625.3	-	41	4124	c.3917C>T	c.(3916-3918)cCa>cTa	p.P1306L	COL4A4_ENST00000329662.7_Missense_Mutation_p.P1306L	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1306	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TGGAGGGCCTGGTGGGCCAGG	0.547																																					p.P1306L		Atlas-SNP	.											.	COL4A4	215	.	0			c.C3917T						.						113.0	112.0	112.0					2																	227895215		1913	4107	6020	SO:0001583	missense	1286	exon41			GGGCCTGGTGGGC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3917C>T	chr2.hg19:g.227895215G>A	ENSP00000379866:p.Pro1306Leu	77.0	0.0		72.0	4.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	hg19	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	G	8.997	0.979168	0.18812	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.95412	-3.7;-3.7	5.45	4.54	0.55810	.	.	.	.	.	D	0.96367	0.8815	M	0.72353	2.195	0.48087	D	0.999583	D	0.58620	0.983	P	0.58266	0.836	D	0.95538	0.8609	9	0.45353	T	0.12	.	11.9533	0.52966	0.0:0.1751:0.8249:0.0	.	1306	P53420	CO4A4_HUMAN	L	1306	ENSP00000379866:P1306L;ENSP00000328553:P1306L	ENSP00000328553:P1306L	P	-	2	0	COL4A4	227603459	0.963000	0.33076	0.903000	0.35520	0.304000	0.27724	0.954000	0.29175	1.255000	0.44051	0.609000	0.83330	CCA	.	.		0.547	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
SPHKAP	80309	hgsc.bcm.edu	37	2	228881550	228881550	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:228881550A>G	ENST00000392056.3	-	7	4066	c.4020T>C	c.(4018-4020)tcT>tcC	p.S1340S	SPHKAP_ENST00000344657.5_Silent_p.S1340S	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1340						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CTTGCGAGGGAGAGCCACCAG	0.517																																					p.S1340S		Atlas-SNP	.											.	SPHKAP	750	.	0			c.T4020C						.						99.0	87.0	91.0					2																	228881550		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			CGAGGGAGAGCCA		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4020T>C	chr2.hg19:g.228881550A>G		111.0	0.0		99.0	4.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.517	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
NPPC	4880	hgsc.bcm.edu	37	2	232790144	232790144	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:232790144C>T	ENST00000409852.1	-	2	525	c.372G>A	c.(370-372)ctG>ctA	p.L124L	NPPC_ENST00000295440.2_Silent_p.L124L	NM_024409.2	NP_077720.1	P23582	ANFC_HUMAN	natriuretic peptide C	124					cGMP biosynthetic process (GO:0006182)|growth plate cartilage chondrocyte differentiation (GO:0003418)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of vasodilation (GO:0045909)|post-embryonic development (GO:0009791)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood vessel size (GO:0050880)|regulation of cAMP metabolic process (GO:0030814)|regulation of cGMP metabolic process (GO:0030823)|regulation of multicellular organism growth (GO:0040014)|regulation of smooth muscle cell proliferation (GO:0048660)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|single organism reproductive process (GO:0044702)	extracellular space (GO:0005615)|secretory granule (GO:0030141)	receptor binding (GO:0005102)						all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;9.35e-14)|BRCA - Breast invasive adenocarcinoma(100;0.00119)|LUSC - Lung squamous cell carcinoma(224;0.00746)|Lung(119;0.00834)		ACTAACATCCCAGGCCGCTCA	0.701																																					p.L124L		Atlas-SNP	.											.	NPPC	3	.	0			c.G372A						.						30.0	37.0	34.0					2																	232790144		2192	4298	6490	SO:0001819	synonymous_variant	4880	exon2			ACATCCCAGGCCG		CCDS2489.1	2q37.1	2014-01-30	2010-11-09		ENSG00000163273	ENSG00000163273		"""Endogenous ligands"""	7941	protein-coding gene	gene with protein product		600296	"""natriuretic peptide precursor C"""			7698765, 8330189	Standard	NM_024409		Approved	CNP	uc002vsl.2	P23582	OTTHUMG00000133232	ENST00000409852.1:c.372G>A	chr2.hg19:g.232790144C>T		90.0	0.0		110.0	22.0	NM_024409	Q4ZG41	Silent	SNP	ENST00000409852.1	hg19	CCDS2489.1																																																																																			.	.		0.701	NPPC-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331011.1	NM_024409	
C2orf54	79919	hgsc.bcm.edu	37	2	241826548	241826548	+	Missense_Mutation	SNP	C	C	A	rs373154669		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:241826548C>A	ENST00000388934.4	-	5	1441	c.1283G>T	c.(1282-1284)cGg>cTg	p.R428L	C2orf54_ENST00000307486.8_Missense_Mutation_p.R279L|C2orf54_ENST00000402775.2_Missense_Mutation_p.R260L	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	428										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GGCAGAGATCCGGTCCTTATC	0.597																																					p.R428L		Atlas-SNP	.											.	C2orf54	14	.	0			c.G1283T						.						89.0	92.0	91.0					2																	241826548		1972	4172	6144	SO:0001583	missense	79919	exon5			GAGATCCGGTCCT	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.1283G>T	chr2.hg19:g.241826548C>A	ENSP00000373586:p.Arg428Leu	93.0	0.0		71.0	4.0	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Missense_Mutation	SNP	ENST00000388934.4	hg19	CCDS42839.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.322931	0.60634	.	.	ENSG00000172478	ENST00000402775;ENST00000307486;ENST00000388934	T;T;T	0.61040	0.14;0.67;0.67	4.55	4.55	0.56014	.	0.000000	0.47455	D	0.000224	T	0.65026	0.2652	L	0.34521	1.04	0.30073	N	0.809844	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.989;0.992;0.995	T	0.65191	-0.6228	10	0.87932	D	0	-4.9023	12.8318	0.57750	0.0:1.0:0.0:0.0	.	428;279;260	Q08AI8;B3KU29;Q08AI8-3	CB054_HUMAN;.;.	L	260;279;428	ENSP00000385338:R260L;ENSP00000302779:R279L;ENSP00000373586:R428L	ENSP00000302779:R279L	R	-	2	0	C2orf54	241475221	0.397000	0.25270	0.142000	0.22268	0.491000	0.33493	2.692000	0.47018	2.090000	0.63153	0.467000	0.42956	CGG	.	.		0.597	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
FARP2	9855	hgsc.bcm.edu	37	2	242432429	242432429	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:242432429T>C	ENST00000264042.3	+	25	3043	c.2873T>C	c.(2872-2874)tTg>tCg	p.L958S	STK25_ENST00000316586.4_3'UTR|STK25_ENST00000478403.1_5'Flank	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	958	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		AACTTCTGTTTGTTCTTCTAC	0.448																																					p.L958S		Atlas-SNP	.											.	FARP2	92	.	0			c.T2873C						.						127.0	120.0	122.0					2																	242432429		2203	4300	6503	SO:0001583	missense	9855	exon25			TCTGTTTGTTCTT	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.2873T>C	chr2.hg19:g.242432429T>C	ENSP00000264042:p.Leu958Ser	81.0	0.0		98.0	4.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	hg19	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.216431	0.79352	.	.	ENSG00000006607	ENST00000264042	T	0.46819	0.86	4.88	4.88	0.63580	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000007	T	0.74176	0.3682	M	0.94063	3.49	0.80722	D	1	D	0.63880	0.993	D	0.63113	0.911	T	0.82446	-0.0453	10	0.87932	D	0	.	14.8099	0.69985	0.0:0.0:0.0:1.0	.	958	O94887	FARP2_HUMAN	S	958	ENSP00000264042:L958S	ENSP00000264042:L958S	L	+	2	0	FARP2	242081102	1.000000	0.71417	0.552000	0.28243	0.957000	0.61999	7.770000	0.85390	1.962000	0.57031	0.533000	0.62120	TTG	.	.		0.448	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
NEU4	129807	hgsc.bcm.edu	37	2	242756144	242756144	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr2:242756144A>G	ENST00000391969.2	+	4	968	c.257A>G	c.(256-258)aAc>aGc	p.N86S	NEU4_ENST00000405370.1_Missense_Mutation_p.N86S|NEU4_ENST00000404257.1_Missense_Mutation_p.N98S|NEU4_ENST00000407683.1_Missense_Mutation_p.N86S|NEU4_ENST00000325935.6_Missense_Mutation_p.N99S	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	86					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CGGTCCATGAACCCCTGCCCT	0.677																																					p.N99S		Atlas-SNP	.											.	NEU4	39	.	0			c.A296G						.						43.0	42.0	43.0					2																	242756144		2203	4299	6502	SO:0001583	missense	129807	exon3			CCATGAACCCCTG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.257A>G	chr2.hg19:g.242756144A>G	ENSP00000375830:p.Asn86Ser	115.0	0.0		99.0	4.0	NM_001167599	A8K056|J3KNJ5|Q96D64	Missense_Mutation	SNP	ENST00000391969.2	hg19	CCDS54442.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.267201	0.59540	.	.	ENSG00000204099	ENST00000407683;ENST00000405370;ENST00000472793;ENST00000423583;ENST00000404257;ENST00000391969;ENST00000325935;ENST00000420288;ENST00000428592	D;D;D;D;D;D;D;D	0.92397	-3.03;-3.03;-3.03;-3.03;-3.03;-3.03;-3.03;-2.0	4.24	4.24	0.50183	Neuraminidase (2);	0.099000	0.64402	U	0.000003	D	0.95449	0.8522	M	0.78049	2.395	0.43527	D	0.9958	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.76575	0.988;0.98;0.98	D	0.95632	0.8690	10	0.62326	D	0.03	-22.5734	13.3204	0.60430	1.0:0.0:0.0:0.0	.	98;98;86	A8K211;Q8WWR8-2;Q8WWR8	.;.;NEUR4_HUMAN	S	86;86;96;86;98;86;99;86;127	ENSP00000385402:N86S;ENSP00000384804:N86S;ENSP00000397860:N86S;ENSP00000385149:N98S;ENSP00000375830:N86S;ENSP00000320318:N99S;ENSP00000388707:N86S;ENSP00000396197:N127S	ENSP00000320318:N99S	N	+	2	0	NEU4	242404817	1.000000	0.71417	0.996000	0.52242	0.567000	0.35839	6.152000	0.71812	1.546000	0.49388	0.379000	0.24179	AAC	.	.		0.677	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
SUMF1	285362	hgsc.bcm.edu	37	3	4458810	4458810	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:4458810A>G	ENST00000272902.5	-	6	876		c.e6+1		SUMF1_ENST00000534863.1_Splice_Site|SUMF1_ENST00000405420.2_Splice_Site|SUMF1_ENST00000383843.5_Splice_Site|SUMF1_ENST00000458465.2_Intron	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1						cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		CTCATTACTCACAGGCGCAGT	0.547																																					.		Atlas-SNP	.											.	SUMF1	23	.	0			c.765+2T>C						.						167.0	148.0	155.0					3																	4458810		2203	4300	6503	SO:0001630	splice_region_variant	285362	exon6			TTACTCACAGGCG	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.840+1T>C	chr3.hg19:g.4458810A>G		83.0	0.0		77.0	4.0	NM_001164674	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Splice_Site	SNP	ENST00000272902.5	hg19	CCDS2564.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.400217	0.83120	.	.	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000383843;ENST00000405420	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1525	0.72713	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SUMF1	4433810	1.000000	0.71417	0.999000	0.59377	0.853000	0.48598	8.263000	0.89864	2.217000	0.71921	0.533000	0.62120	.	.	.		0.547	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	Intron
SRGAP3	9901	hgsc.bcm.edu	37	3	9032408	9032408	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:9032408A>G	ENST00000383836.3	-	21	3101	c.2674T>C	c.(2674-2676)Tgc>Cgc	p.C892R	SRGAP3_ENST00000360413.3_Missense_Mutation_p.C868R	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	892					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CTGCTGGGGCAGGCAGCAGCC	0.692			T	RAF1	pilocytic astrocytoma																																p.C892R		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	SRGAP3,bladder,carcinoma,+1,1	SRGAP3	146	.	0			c.T2674C						.						10.0	13.0	12.0					3																	9032408		2184	4272	6456	SO:0001583	missense	9901	exon21			TGGGGCAGGCAGC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2674T>C	chr3.hg19:g.9032408A>G	ENSP00000373347:p.Cys892Arg	160.0	2.0		145.0	6.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	A	11.44	1.639155	0.29157	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.23950	1.88;2.28	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.17323	0.0416	N	0.16478	0.41	0.80722	D	1	D;P	0.53745	0.962;0.937	B;B	0.43536	0.423;0.243	T	0.05115	-1.0905	10	0.15066	T	0.55	.	14.6015	0.68445	1.0:0.0:0.0:0.0	.	868;892	O43295-2;O43295	.;SRGP2_HUMAN	R	892;868	ENSP00000373347:C892R;ENSP00000353587:C868R	ENSP00000353587:C868R	C	-	1	0	SRGAP3	9007408	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.697000	0.74603	1.938000	0.56188	0.533000	0.62120	TGC	.	.		0.692	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		
NUP210	23225	hgsc.bcm.edu	37	3	13364885	13364885	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:13364885G>A	ENST00000254508.5	-	34	4774	c.4692C>T	c.(4690-4692)ccC>ccT	p.P1564P		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1564					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TGGTCTGGATGGGGTGGAGGT	0.592																																					p.P1564P		Atlas-SNP	.											.	NUP210	182	.	0			c.C4692T						.						122.0	119.0	120.0					3																	13364885		2203	4300	6503	SO:0001819	synonymous_variant	23225	exon34			CTGGATGGGGTGG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.4692C>T	chr3.hg19:g.13364885G>A		89.0	0.0		89.0	4.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	hg19	CCDS33704.1																																																																																			.	.		0.592	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
KCNH8	131096	hgsc.bcm.edu	37	3	19575099	19575099	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:19575099T>C	ENST00000328405.2	+	16	3098	c.2832T>C	c.(2830-2832)taT>taC	p.Y944Y		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	944					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						GGGCTGCTTATACCCAAGCAC	0.552																																					p.Y944Y	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.T2832C						.						82.0	80.0	81.0					3																	19575099		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon16			TGCTTATACCCAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2832T>C	chr3.hg19:g.19575099T>C		125.0	0.0		120.0	5.0	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.		0.552	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
UBP1	7342	hgsc.bcm.edu	37	3	33444345	33444345	+	Missense_Mutation	SNP	G	G	T	rs373493970		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:33444345G>T	ENST00000283629.3	-	9	1508	c.979C>A	c.(979-981)Cca>Aca	p.P327T	UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Missense_Mutation_p.P291T|UBP1_ENST00000283628.5_Missense_Mutation_p.P327T	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	327					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						GTGGGCGCTGGGGAAGGGCTG	0.483																																					p.P327T		Atlas-SNP	.											.	UBP1	42	.	0			c.C979A						.	G	THR/PRO,THR/PRO,THR/PRO	0,4406		0,0,2203	84.0	68.0	73.0		871,979,979	-0.7	1.0	3		73	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	38,38,38	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign,benign,benign	291/505,327/541,327/541	33444345	1,13005	2203	4300	6503	SO:0001583	missense	7342	exon9			GCGCTGGGGAAGG	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.979C>A	chr3.hg19:g.33444345G>T	ENSP00000283629:p.Pro327Thr	184.0	0.0		173.0	7.0	NM_014517	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	hg19	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386906	0.42308	0.0	1.16E-4	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628	T;T;T	0.21543	2.0;2.17;2.0	6.17	-0.703	0.11261	.	0.377335	0.33327	N	0.005031	T	0.12220	0.0297	L	0.40543	1.245	0.37362	D	0.911274	B;B	0.14805	0.001;0.011	B;B	0.23852	0.002;0.049	T	0.27331	-1.0077	10	0.08599	T	0.76	0.0141	5.6838	0.17790	0.0738:0.3079:0.4747:0.1436	.	291;327	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	T	327;291;327	ENSP00000283629:P327T;ENSP00000395558:P291T;ENSP00000283628:P327T	ENSP00000283628:P327T	P	-	1	0	UBP1	33419349	0.998000	0.40836	0.986000	0.45419	0.961000	0.63080	0.409000	0.21082	-0.124000	0.11724	0.655000	0.94253	CCA	.	.		0.483	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517	
DLEC1	9940	hgsc.bcm.edu	37	3	38150965	38150965	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:38150965A>G	ENST00000308059.6	+	22	3193	c.3172A>G	c.(3172-3174)Atg>Gtg	p.M1058V	DLEC1_ENST00000452631.2_Missense_Mutation_p.M1058V|DLEC1_ENST00000346219.3_Missense_Mutation_p.M1058V					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CGTGTCAGGCATGAAGAAGCC	0.572																																					p.M1058V		Atlas-SNP	.											.	DLEC1	278	.	0			c.A3172G						.						102.0	102.0	102.0					3																	38150965		1930	4144	6074	SO:0001583	missense	9940	exon22			TCAGGCATGAAGA	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.3172A>G	chr3.hg19:g.38150965A>G	ENSP00000308597:p.Met1058Val	95.0	0.0		91.0	4.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	A	18.03	3.531539	0.64972	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.50548	0.74;0.74;0.74	5.2	2.79	0.32731	.	0.000000	0.85682	D	0.000000	T	0.64136	0.2571	M	0.77820	2.39	0.44380	D	0.997281	D;P;D;D	0.89917	1.0;0.955;1.0;1.0	D;P;D;D	0.87578	0.998;0.84;0.994;0.998	T	0.59773	-0.7391	10	0.34782	T	0.22	-20.4746	8.9095	0.35543	0.843:0.0:0.157:0.0	.	1058;1058;1058;1058	F8W6T4;B7ZW06;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	V	1058	ENSP00000308597:M1058V;ENSP00000315914:M1058V;ENSP00000410427:M1058V	ENSP00000308597:M1058V	M	+	1	0	DLEC1	38125969	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.002000	0.63952	0.313000	0.23062	0.533000	0.62120	ATG	.	.		0.572	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
XIRP1	165904	hgsc.bcm.edu	37	3	39229651	39229651	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:39229651G>T	ENST00000340369.3	-	2	1514	c.1286C>A	c.(1285-1287)cCc>cAc	p.P429H	XIRP1_ENST00000396251.1_Missense_Mutation_p.P429H|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	429					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		ATCCCTCTGGGGGGCACTCTG	0.562																																					p.P429H		Atlas-SNP	.											.	XIRP1	173	.	0			c.C1286A						.						147.0	158.0	154.0					3																	39229651		2203	4300	6503	SO:0001583	missense	165904	exon2			CTCTGGGGGGCAC	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1286C>A	chr3.hg19:g.39229651G>T	ENSP00000343140:p.Pro429His	68.0	0.0		86.0	4.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.497610	0.44455	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.05081	3.5;3.88	4.64	4.64	0.57946	.	0.652316	0.14310	N	0.327703	T	0.17704	0.0425	M	0.68317	2.08	0.46749	D	0.999181	D;D	0.69078	0.997;0.963	P;P	0.55667	0.781;0.735	T	0.00202	-1.1925	10	0.62326	D	0.03	.	13.2295	0.59933	0.0:0.0:1.0:0.0	.	429;429	Q702N8;Q702N8-2	XIRP1_HUMAN;.	H	429	ENSP00000379550:P429H;ENSP00000343140:P429H	ENSP00000343140:P429H	P	-	2	0	XIRP1	39204655	0.428000	0.25522	0.736000	0.30914	0.789000	0.44602	2.029000	0.41098	2.583000	0.87209	0.655000	0.94253	CCC	.	.		0.562	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
ULK4	54986	hgsc.bcm.edu	37	3	41860960	41860960	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:41860960A>G	ENST00000301831.4	-	19	2265	c.1803T>C	c.(1801-1803)gtT>gtC	p.V601V		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	601					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)		CAGCCAAGGGAACAGCCCAGC	0.443																																					p.V601V		Atlas-SNP	.											.	ULK4	150	.	0			c.T1803C						.						109.0	109.0	109.0					3																	41860960		1893	4115	6008	SO:0001819	synonymous_variant	54986	exon19			CAAGGGAACAGCC	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.1803T>C	chr3.hg19:g.41860960A>G		67.0	0.0		60.0	4.0	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Silent	SNP	ENST00000301831.4	hg19	CCDS43071.1																																																																																			.	.		0.443	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
ZNF35	7584	hgsc.bcm.edu	37	3	44700749	44700749	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:44700749A>G	ENST00000396056.2	+	4	1129	c.894A>G	c.(892-894)aaA>aaG	p.K298K	ZNF35_ENST00000542250.1_Silent_p.K138K|RP11-944L7.4_ENST00000457331.1_RNA|ZNF35_ENST00000296092.3_3'UTR	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	298					cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		TACATCAAAAAATCCACTCCT	0.403																																					p.K298K		Atlas-SNP	.											.	ZNF35	34	.	0			c.A894G						.						51.0	56.0	54.0					3																	44700749		2203	4300	6503	SO:0001819	synonymous_variant	7584	exon4			TCAAAAAATCCAC	X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"""Zinc fingers, C2H2-type"""	13099	protein-coding gene	gene with protein product		194533	"""zinc finger protein 35 (clone HF.10)"""			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.894A>G	chr3.hg19:g.44700749A>G		63.0	0.0		62.0	4.0	NM_003420	B2RBU6|Q53Y54|Q96D01	Silent	SNP	ENST00000396056.2	hg19	CCDS2718.2																																																																																			.	.		0.403	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420	
LIMD1	8994	hgsc.bcm.edu	37	3	45637017	45637017	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:45637017C>A	ENST00000273317.4	+	1	667	c.646C>A	c.(646-648)Cca>Aca	p.P216T	LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Missense_Mutation_p.P216T	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	216	Interaction with EGLN1/PHD2.				cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		GGGGAGTGACCCACCACTGCC	0.622																																					p.P216T		Atlas-SNP	.											.	LIMD1	34	.	0			c.C646A						.						65.0	69.0	68.0					3																	45637017		2203	4300	6503	SO:0001583	missense	8994	exon1			AGTGACCCACCAC	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.646C>A	chr3.hg19:g.45637017C>A	ENSP00000273317:p.Pro216Thr	66.0	0.0		61.0	4.0	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	hg19	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	C	7.101	0.574062	0.13623	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.56611	0.45;0.65	4.12	-1.31	0.09230	.	1.773090	0.03020	N	0.150555	T	0.31040	0.0784	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.04386	-1.0955	10	0.13108	T	0.6	.	1.218	0.01918	0.1341:0.3038:0.2872:0.2748	.	216	Q9UGP4	LIMD1_HUMAN	T	216	ENSP00000394537:P216T;ENSP00000273317:P216T	ENSP00000273317:P216T	P	+	1	0	LIMD1	45612021	0.000000	0.05858	0.000000	0.03702	0.327000	0.28475	0.984000	0.29565	-0.431000	0.07307	0.462000	0.41574	CCA	.	.		0.622	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	
CCR5	1234	hgsc.bcm.edu	37	3	46414949	46414949	+	Missense_Mutation	SNP	C	C	A	rs333|rs562091107|rs113869679	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:46414949C>A	ENST00000292303.4	+	2	702	c.556C>A	c.(556-558)Cag>Aag	p.Q186K	CCR5_ENST00000343801.4_Missense_Mutation_p.Q186K|RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000445772.1_Missense_Mutation_p.Q186K	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	186					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	TCCATACAGTCAGTATCAATT	0.453																																					p.Q186K		Atlas-SNP	.											CCR5,colon,carcinoma,0,1	CCR5	128	.	0			c.C556A						.						136.0	138.0	137.0					3																	46414949		2203	4271	6474	SO:0001583	missense	1234	exon3			TACAGTCAGTATC		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1606	protein-coding gene	gene with protein product		601373	"""chemokine (C-C motif) receptor 5"""	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.556C>A	chr3.hg19:g.46414949C>A	ENSP00000292303:p.Gln186Lys	80.0	1.0		125.0	6.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Missense_Mutation	SNP	ENST00000292303.4	hg19	CCDS2739.1	.	.	.	.	.	.	.	.	.	.	C	9.584	1.124440	0.20959	.	.	ENSG00000160791	ENST00000343801;ENST00000400886;ENST00000292303;ENST00000445772	T;T;T	0.36699	1.24;1.24;1.24	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39341	U	0.001383	T	0.32971	0.0847	L	0.45285	1.41	0.27965	N	0.936637	B	0.16166	0.016	B	0.22152	0.038	T	0.23332	-1.0191	10	0.51188	T	0.08	.	13.0639	0.59022	0.1602:0.8398:0.0:0.0	.	186	P51681	CCR5_HUMAN	K	186;166;186;186	ENSP00000343985:Q186K;ENSP00000292303:Q186K;ENSP00000404881:Q186K	ENSP00000292303:Q186K	Q	+	1	0	CCR5	46389953	0.000000	0.05858	0.065000	0.19835	0.019000	0.09904	0.810000	0.27183	2.470000	0.83445	0.561000	0.74099	CAG	.	.		0.453	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579	
SETD2	29072	hgsc.bcm.edu	37	3	47129614	47129614	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:47129614C>T	ENST00000409792.3	-	10	5308	c.5266G>A	c.(5266-5268)Gaa>Aaa	p.E1756K	snoU13_ENST00000516129.1_RNA	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1756					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.E1253*(1)|p.E1756*(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTATGAGTTCCAGACAGGTA	0.378			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.E1756K		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	721	.	2	Substitution - Nonsense(2)	lung(2)	c.G5266A						.						120.0	125.0	124.0					3																	47129614		2203	4300	6503	SO:0001583	missense	29072	exon10			TGAGTTCCAGACA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5266G>A	chr3.hg19:g.47129614C>T	ENSP00000386759:p.Glu1756Lys	43.0	0.0		49.0	2.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	2.797	-0.249982	0.05867	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.86297	-2.1	4.46	-4.26	0.03755	.	0.481780	0.18774	N	0.131531	T	0.53077	0.1774	N	0.00707	-1.245	0.20975	N	0.999818	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.60068	-0.7335	10	0.02654	T	1	.	8.4158	0.32670	0.0:0.4985:0.1305:0.3711	.	1756;1756	F2Z317;Q9BYW2	.;SETD2_HUMAN	K	1756	ENSP00000386759:E1756K	ENSP00000386759:E1756K	E	-	1	0	SETD2	47104618	0.947000	0.32204	0.005000	0.12908	0.920000	0.55202	0.827000	0.27421	-0.940000	0.03705	-0.355000	0.07637	GAA	.	.		0.378	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
CSPG5	10675	hgsc.bcm.edu	37	3	47618664	47618664	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:47618664A>G	ENST00000383738.2	-	2	2950	c.852T>C	c.(850-852)gaT>gaC	p.D284D	CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000456150.1_Silent_p.D146D|CSPG5_ENST00000264723.4_Silent_p.D284D	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	284	Interaction with TNC and TNR. {ECO:0000250}.				axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		catctttgtcatcctcctctt	0.507																																					p.D284D		Atlas-SNP	.											.	CSPG5	46	.	0			c.T852C						.						22.0	23.0	23.0					3																	47618664		2202	4300	6502	SO:0001819	synonymous_variant	10675	exon2			TTTGTCATCCTCC	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.852T>C	chr3.hg19:g.47618664A>G		84.0	0.0		82.0	4.0	NM_006574	Q71M39|Q71M40	Silent	SNP	ENST00000383738.2	hg19	CCDS56253.1																																																																																			.	.		0.507	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574	
ATRIP	84126	hgsc.bcm.edu	37	3	48502119	48502119	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:48502119C>T	ENST00000320211.3	+	8	1779	c.1666C>T	c.(1666-1668)Ctt>Ttt	p.L556F	ATRIP_ENST00000357105.6_Missense_Mutation_p.L429F|ATRIP_ENST00000346691.4_Missense_Mutation_p.L556F|ATRIP_ENST00000412052.1_Missense_Mutation_p.L463F	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	556					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)	22				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AACAGGTCACCTTCAAGCCAG	0.502								Other conserved DNA damage response genes																													p.L556F		Atlas-SNP	.											.	ATRIP	41	.	0			c.C1666T						.						77.0	73.0	74.0					3																	48502119		2203	4300	6503	SO:0001583	missense	84126	exon8			GGTCACCTTCAAG	AF451323	CCDS2767.1, CCDS2768.1, CCDS59449.1, CCDS59450.1	3p24.3-p22.1	2007-06-20			ENSG00000164053	ENSG00000164053			33499	protein-coding gene	gene with protein product		606605				11721054	Standard	NM_130384		Approved	FLJ12343, MGC20625, MGC21482, MGC26740	uc003ctf.2	Q8WXE1	OTTHUMG00000133532	ENST00000320211.3:c.1666C>T	chr3.hg19:g.48502119C>T	ENSP00000323099:p.Leu556Phe	105.0	0.0		87.0	5.0	NM_130384	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Missense_Mutation	SNP	ENST00000320211.3	hg19	CCDS2768.1	.	.	.	.	.	.	.	.	.	.	C	8.183	0.794282	0.16327	.	.	ENSG00000164053	ENST00000320211;ENST00000346691;ENST00000357105;ENST00000412052	T;T;T;T	0.65916	2.64;-0.18;2.64;2.64	6.08	3.05	0.35203	.	1.010300	0.07913	N	0.974673	T	0.51092	0.1654	L	0.35723	1.085	0.09310	N	1	B;B	0.17268	0.021;0.021	B;B	0.18263	0.021;0.021	T	0.36866	-0.9730	9	.	.	.	-1.0E-4	8.1825	0.31319	0.0:0.7642:0.0:0.2358	.	556;556	Q8WXE1-2;Q8WXE1	.;ATRIP_HUMAN	F	556;556;429;463	ENSP00000323099:L556F;ENSP00000302338:L556F;ENSP00000349620:L429F;ENSP00000400930:L463F	.	L	+	1	0	ATRIP	48477123	0.323000	0.24643	0.022000	0.16811	0.968000	0.65278	0.993000	0.29680	0.329000	0.23460	0.591000	0.81541	CTT	.	.		0.502	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384	
COL7A1	1294	hgsc.bcm.edu	37	3	48625362	48625362	+	Silent	SNP	T	T	C	rs201566458		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:48625362T>C	ENST00000328333.8	-	21	2828	c.2721A>G	c.(2719-2721)gaA>gaG	p.E907E	COL7A1_ENST00000454817.1_Silent_p.E907E	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	907	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCGGGACTGTTCCTGGCCAC	0.652																																					p.E907E		Atlas-SNP	.											.	COL7A1	320	.	0			c.A2721G						.						12.0	14.0	13.0					3																	48625362		2193	4288	6481	SO:0001819	synonymous_variant	1294	exon21			GGACTGTTCCTGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.2721A>G	chr3.hg19:g.48625362T>C		60.0	0.0		69.0	4.0	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.652	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
NCKIPSD	51517	hgsc.bcm.edu	37	3	48720411	48720411	+	Missense_Mutation	SNP	C	C	T	rs368902568		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:48720411C>T	ENST00000294129.2	-	2	325	c.206G>A	c.(205-207)cGg>cAg	p.R69Q	NCKIPSD_ENST00000416649.2_Missense_Mutation_p.R69Q|NCKIPSD_ENST00000341520.4_Missense_Mutation_p.R69Q	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	69					cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTCGATGGCCCGGTCAATGGC	0.632																																					p.R69Q		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.G206A						.	C	GLN/ARG,GLN/ARG	0,4328		0,0,2164	77.0	43.0	55.0		206,206	4.9	1.0	3		55	1,8411		0,1,4205	no	missense,missense	NCKIPSD	NM_016453.2,NM_184231.1	43,43	0,1,6369	TT,TC,CC		0.0119,0.0,0.0078	probably-damaging,probably-damaging	69/723,69/716	48720411	1,12739	2164	4206	6370	SO:0001583	missense	51517	exon2			ATGGCCCGGTCAA	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.206G>A	chr3.hg19:g.48720411C>T	ENSP00000294129:p.Arg69Gln	94.0	0.0		99.0	4.0	NM_184231	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	hg19	CCDS2776.1	.	.	.	.	.	.	.	.	.	.	C	35	5.459309	0.96240	0.0	1.19E-4	ENSG00000213672	ENST00000341520;ENST00000416649;ENST00000294129;ENST00000439518	T;T;T;T	0.52526	0.66;1.27;1.25;1.23	4.87	4.87	0.63330	.	0.000000	0.64402	U	0.000007	T	0.65709	0.2717	M	0.68952	2.095	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.997	T	0.61287	-0.7093	10	0.16896	T	0.51	.	18.0227	0.89259	0.0:1.0:0.0:0.0	.	69;69;69	C9JSC3;Q9NZQ3;Q9NZQ3-3	.;SPN90_HUMAN;.	Q	69	ENSP00000342621:R69Q;ENSP00000389059:R69Q;ENSP00000294129:R69Q;ENSP00000409675:R69Q	ENSP00000294129:R69Q	R	-	2	0	NCKIPSD	48695415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.811000	0.86092	2.258000	0.74832	0.591000	0.81541	CGG	.	.		0.632	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
DALRD3	55152	hgsc.bcm.edu	37	3	49053492	49053492	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:49053492T>C	ENST00000341949.4	-	10	1363	c.1357A>G	c.(1357-1359)Atc>Gtc	p.I453V	DALRD3_ENST00000441576.2_Splice_Site_p.Y444C|DALRD3_ENST00000440857.1_Missense_Mutation_p.I286V|DALRD3_ENST00000496568.1_5'Flank|DALRD3_ENST00000395462.4_Missense_Mutation_p.I286V|DALRD3_ENST00000313778.5_Missense_Mutation_p.I286V	NM_001009996.1	NP_001009996.1	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	453					arginyl-tRNA aminoacylation (GO:0006420)		arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)			breast(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AAGGGGAGGATACTGTTGAAG	0.592																																					p.I453V		Atlas-SNP	.											.	DALRD3	57	.	0			c.A1357G						.						58.0	63.0	61.0					3																	49053492		2203	4300	6503	SO:0001583	missense	55152	exon10			GGAGGATACTGTT	BC014099	CCDS2783.1, CCDS33754.1, CCDS63632.1	3p21.31	2005-01-10			ENSG00000178149	ENSG00000178149			25536	protein-coding gene	gene with protein product						12477932	Standard	NM_001009996		Approved	FLJ10496	uc003cvk.2	Q5D0E6	OTTHUMG00000156748	ENST00000341949.4:c.1357A>G	chr3.hg19:g.49053492T>C	ENSP00000344989:p.Ile453Val	93.0	0.0		88.0	4.0	NM_001009996	Q7Z5S7|Q86WY1|Q8N105|Q8NA89|Q9NVU8	Missense_Mutation	SNP	ENST00000341949.4	hg19	CCDS33754.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	2.342|2.342	-0.350941|-0.350941	0.05173|0.05173	.|.	.|.	ENSG00000178149|ENSG00000178149	ENST00000341949;ENST00000395462;ENST00000440857;ENST00000313778|ENST00000438585;ENST00000441576	T;T;T;T|T	0.77229|0.48836	-1.08;-1.08;-1.08;-1.08|0.8	5.48|5.48	-2.95|-2.95	0.05564|0.05564	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);DALR anticodon binding (2);|.	0.556527|.	0.19877|.	N|.	0.104049|.	T|T	0.33731|0.33731	0.0873|0.0873	L|L	0.45352|0.45352	1.415|1.415	0.09310|0.09310	N|N	0.999999|0.999999	B;B|B	0.13594|0.02656	0.008;0.004|0.0	B;B|B	0.13407|0.04013	0.007;0.009|0.001	T|T	0.28902|0.28902	-1.0029|-1.0029	10|8	0.13853|.	T|.	0.58|.	-13.1072|-13.1072	8.2195|8.2195	0.31532|0.31532	0.0:0.3099:0.1596:0.5304|0.0:0.3099:0.1596:0.5304	.|.	286;453|444	C9JJG6;Q5D0E6|Q5D0E6-2	.;DALD3_HUMAN|.	V|C	453;286;286;286|99;444	ENSP00000344989:I453V;ENSP00000378846:I286V;ENSP00000403770:I286V;ENSP00000323265:I286V|ENSP00000410623:Y444C	ENSP00000323265:I286V|.	I|Y	-|-	1|2	0|0	DALRD3|DALRD3	49028496|49028496	0.008000|0.008000	0.16893|0.16893	0.053000|0.053000	0.19242|0.19242	0.539000|0.539000	0.34962|0.34962	-0.019000|-0.019000	0.12546|0.12546	-0.208000|-0.208000	0.10171|0.10171	-0.451000|-0.451000	0.05528|0.05528	ATC|TAT	.	.		0.592	DALRD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345581.1	NM_018114	
DALRD3	55152	hgsc.bcm.edu	37	3	49053675	49053675	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:49053675C>A	ENST00000341949.4	-	9	1251	c.1245G>T	c.(1243-1245)gaG>gaT	p.E415D	DALRD3_ENST00000441576.2_Missense_Mutation_p.E415D|DALRD3_ENST00000440857.1_Missense_Mutation_p.E248D|DALRD3_ENST00000496568.1_5'Flank|DALRD3_ENST00000395462.4_Missense_Mutation_p.E248D|DALRD3_ENST00000313778.5_Missense_Mutation_p.E248D	NM_001009996.1	NP_001009996.1	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	415					arginyl-tRNA aminoacylation (GO:0006420)		arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)			breast(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		ACTTGTAACTCTCAAAGAGTG	0.502																																					p.E415D		Atlas-SNP	.											.	DALRD3	57	.	0			c.G1245T						.						100.0	93.0	95.0					3																	49053675		2203	4300	6503	SO:0001583	missense	55152	exon9			GTAACTCTCAAAG	BC014099	CCDS2783.1, CCDS33754.1, CCDS63632.1	3p21.31	2005-01-10			ENSG00000178149	ENSG00000178149			25536	protein-coding gene	gene with protein product						12477932	Standard	NM_001009996		Approved	FLJ10496	uc003cvk.2	Q5D0E6	OTTHUMG00000156748	ENST00000341949.4:c.1245G>T	chr3.hg19:g.49053675C>A	ENSP00000344989:p.Glu415Asp	78.0	0.0		81.0	4.0	NM_001009996	Q7Z5S7|Q86WY1|Q8N105|Q8NA89|Q9NVU8	Missense_Mutation	SNP	ENST00000341949.4	hg19	CCDS33754.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.124|9.124	1.009636|1.009636	0.19277|0.19277	.|.	.|.	ENSG00000178149|ENSG00000178149	ENST00000441576;ENST00000341949;ENST00000395462;ENST00000440857;ENST00000313778|ENST00000438585	T;T;T;T;T|.	0.77750|.	0.9;-1.12;-1.12;-1.08;-1.12|.	5.79|5.79	0.273|0.273	0.15650|0.15650	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);DALR anticodon binding (2);|.	0.325026|0.325026	0.37053|0.37053	N|N	0.002265|0.002265	T|.	0.13927|.	0.0337|.	N|N	0.16368|0.16368	0.405|0.405	0.26230|0.26230	N|N	0.979024|0.979024	B;B;B;B|.	0.17852|.	0.024;0.005;0.024;0.007|.	B;B;B;B|.	0.18561|.	0.019;0.007;0.019;0.022|.	T|.	0.09185|.	-1.0686|.	10|.	0.20046|0.11794	T|T	0.44|0.64	-17.7675|-17.7675	0.7964|0.7964	0.01067|0.01067	0.3878:0.2629:0.1297:0.2196|0.3878:0.2629:0.1297:0.2196	.|.	415;248;415;415|.	B7Z727;C9JJG6;Q5D0E6-2;Q5D0E6|.	.;.;.;DALD3_HUMAN|.	D|X	415;415;248;248;248|62	ENSP00000410623:E415D;ENSP00000344989:E415D;ENSP00000378846:E248D;ENSP00000403770:E248D;ENSP00000323265:E248D|.	ENSP00000323265:E248D|ENSP00000396650:E62X	E|E	-|-	3|1	2|0	DALRD3|DALRD3	49028679|49028679	0.812000|0.812000	0.29077|0.29077	0.477000|0.477000	0.27303|0.27303	0.965000|0.965000	0.64279|0.64279	0.264000|0.264000	0.18497|0.18497	0.332000|0.332000	0.23536|0.23536	0.561000|0.561000	0.74099|0.74099	GAG|GAG	.	.		0.502	DALRD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345581.1	NM_018114	
RNF123	63891	hgsc.bcm.edu	37	3	49735904	49735904	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:49735904C>T	ENST00000327697.6	+	8	659	c.515C>T	c.(514-516)gCc>gTc	p.A172V	RNF123_ENST00000432042.1_Missense_Mutation_p.A26V	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	172	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		AACTCCTATGCCTATGATGGC	0.572																																					p.A172V		Atlas-SNP	.											.	RNF123	100	.	0			c.C515T						.						82.0	74.0	77.0					3																	49735904		2203	4300	6503	SO:0001583	missense	63891	exon8			CCTATGCCTATGA	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.515C>T	chr3.hg19:g.49735904C>T	ENSP00000328287:p.Ala172Val	115.0	0.0		90.0	5.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	36	5.628320	0.96671	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.71103	-0.54;-0.54	4.96	4.96	0.65561	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.117675	0.56097	D	0.000030	D	0.84871	0.5568	M	0.80616	2.505	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.86731	0.1948	10	0.87932	D	0	-25.1749	17.731	0.88377	0.0:1.0:0.0:0.0	.	172	Q5XPI4	RN123_HUMAN	V	172;172;26	ENSP00000328287:A172V;ENSP00000392443:A26V	ENSP00000328287:A172V	A	+	2	0	RNF123	49710908	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.960000	0.76036	2.735000	0.93741	0.561000	0.74099	GCC	.	.		0.572	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
RBM5	10181	hgsc.bcm.edu	37	3	50154760	50154760	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:50154760G>T	ENST00000347869.3	+	24	2445	c.2270G>T	c.(2269-2271)cGg>cTg	p.R757L	RP11-493K19.3_ENST00000437204.1_RNA|RP11-493K19.3_ENST00000425674.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	757	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.|Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ATGGGCTGGCGGGAAGGCTCT	0.542																																					p.R757L		Atlas-SNP	.											.	RBM5	76	.	0			c.G2270T						.						164.0	158.0	160.0					3																	50154760		2203	4300	6503	SO:0001583	missense	10181	exon24			GCTGGCGGGAAGG	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.2270G>T	chr3.hg19:g.50154760G>T	ENSP00000343054:p.Arg757Leu	127.0	0.0		114.0	5.0	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Missense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.946746	0.73672	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	T	0.32272	1.46	5.48	4.6	0.57074	D111/G-patch (3);	0.247806	0.39909	N	0.001227	T	0.37348	0.1000	L	0.42581	1.335	0.80722	D	1	P;P	0.47962	0.903;0.616	P;P	0.53954	0.738;0.617	T	0.12941	-1.0528	10	0.56958	D	0.05	-14.1443	9.1131	0.36741	0.0734:0.0:0.7789:0.1477	.	447;757	Q59HE6;P52756	.;RBM5_HUMAN	L	757;756;447	ENSP00000343054:R757L	ENSP00000343054:R757L	R	+	2	0	RBM5	50129764	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.778000	0.62368	1.290000	0.44636	-0.188000	0.12872	CGG	.	.		0.542	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
DOCK3	1795	hgsc.bcm.edu	37	3	51297588	51297588	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:51297588C>A	ENST00000266037.9	+	23	2209	c.2186C>A	c.(2185-2187)gCc>gAc	p.A729D		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	729					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACTTTTCAGGCCTTGGAGTAC	0.443																																					p.A729D		Atlas-SNP	.											DOCK3_ENST00000266037,NS,carcinoma,0,2	DOCK3	397	.	0			c.C2186A						.						84.0	80.0	81.0					3																	51297588		1930	4149	6079	SO:0001630	splice_region_variant	1795	exon23			TTCAGGCCTTGGA	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.2185-1C>A	chr3.hg19:g.51297588C>A		193.0	0.0		182.0	8.0	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022119	0.93462	.	.	ENSG00000088538	ENST00000266037	T	0.68624	-0.34	5.93	5.05	0.67936	.	0.046361	0.85682	D	0.000000	T	0.81941	0.4929	M	0.89287	3.02	0.80722	D	1	D	0.54047	0.964	P	0.58391	0.838	D	0.84894	0.0838	10	0.66056	D	0.02	.	15.4007	0.74838	0.0:0.9326:0.0:0.0674	.	729	Q8IZD9	DOCK3_HUMAN	D	729	ENSP00000266037:A729D	ENSP00000266037:A729D	A	+	2	0	DOCK3	51272628	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	6.082000	0.71318	2.805000	0.96524	0.655000	0.94253	GCC	.	.		0.443	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	Missense_Mutation
VPRBP	9730	hgsc.bcm.edu	37	3	51456168	51456168	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:51456168A>G	ENST00000335891.5	-	8	2061	c.2052T>C	c.(2050-2052)tgT>tgC	p.C684C				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	1133					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CTGAGTTGTGACAGTTATAGC	0.493																																					p.C1080C		Atlas-SNP	.											.	VPRBP	107	.	0			c.T3240C						.						137.0	139.0	138.0					3																	51456168		2034	4196	6230	SO:0001819	synonymous_variant	9730	exon15			GTTGTGACAGTTA	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"""DDB1 and CUL4 associated factors"""	30911	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 1"""					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.2052T>C	chr3.hg19:g.51456168A>G		94.0	0.0		90.0	4.0	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Silent	SNP	ENST00000335891.5	hg19																																																																																				.	.		0.493	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	
ERC2	26059	hgsc.bcm.edu	37	3	56207475	56207475	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:56207475T>C	ENST00000288221.6	-	4	1403	c.1148A>G	c.(1147-1149)aAg>aGg	p.K383R		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	383						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		AGTTCCTACCTTCATTTCGAT	0.453																																					p.K383R		Atlas-SNP	.											.	ERC2	221	.	0			c.A1148G						.						89.0	92.0	91.0					3																	56207475		2104	4235	6339	SO:0001630	splice_region_variant	26059	exon4			CCTACCTTCATTT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.1149+1A>G	chr3.hg19:g.56207475T>C		89.0	0.0		93.0	4.0	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.32|18.32	3.597176|3.597176	0.66332|0.66332	.|.	.|.	ENSG00000187672|ENSG00000187672	ENST00000288221|ENST00000492584	T|.	0.56611|.	0.45|.	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	0.044301|.	0.85682|.	D|.	0.000000|.	T|T	0.77274|0.77274	0.4106|0.4106	M|M	0.81497|0.81497	2.545|2.545	0.47183|0.47183	D|D	0.999347|0.999347	D|.	0.57257|.	0.979|.	D|.	0.71414|.	0.973|.	T|T	0.79017|0.79017	-0.1975|-0.1975	10|5	0.56958|.	D|.	0.05|.	-28.8882|-28.8882	15.7711|15.7711	0.78170|0.78170	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	383|.	O15083|.	ERC2_HUMAN|.	R|G	383|22	ENSP00000288221:K383R|.	ENSP00000288221:K383R|.	K|R	-|-	2|1	0|2	ERC2|ERC2	56182515|56182515	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	7.553000|7.553000	0.82203|0.82203	2.182000|2.182000	0.69389|0.69389	0.455000|0.455000	0.32223|0.32223	AAG|AGG	.	.		0.453	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	Missense_Mutation
FAM208A	23272	hgsc.bcm.edu	37	3	56658883	56658883	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:56658883G>C	ENST00000493960.2	-	22	4301	c.4291C>G	c.(4291-4293)Cag>Gag	p.Q1431E	FAM208A_ENST00000355628.5_Missense_Mutation_p.Q1370E|FAM208A_ENST00000485156.1_Intron|FAM208A_ENST00000431842.2_Missense_Mutation_p.Q994E	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1431							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TGTCGTTGCTGTATGTTCTGA	0.383																																					p.Q1431E		Atlas-SNP	.											.	FAM208A	113	.	0			c.C4291G						.						127.0	125.0	126.0					3																	56658883		2203	4300	6503	SO:0001583	missense	23272	exon22			GTTGCTGTATGTT	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.4291C>G	chr3.hg19:g.56658883G>C	ENSP00000417509:p.Gln1431Glu	360.0	1.0		326.0	167.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279138	0.80692	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.53206	0.63;0.63;0.63	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000008	T	0.52613	0.1745	L	0.38838	1.175	0.47245	D	0.999367	P;B;D;B	0.61697	0.629;0.045;0.99;0.435	B;B;P;B	0.55011	0.382;0.094;0.766;0.104	T	0.54070	-0.8348	10	0.72032	D	0.01	-0.4466	14.6453	0.68756	0.0:0.0:0.8544:0.1456	.	1431;1370;994;1431	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	E	994;1431;1370	ENSP00000399410:Q994E;ENSP00000417509:Q1431E;ENSP00000347845:Q1370E	ENSP00000347845:Q1370E	Q	-	1	0	C3orf63	56633923	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.500000	0.81588	2.685000	0.91497	0.655000	0.94253	CAG	.	.		0.383	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
CADPS	8618	hgsc.bcm.edu	37	3	62459862	62459862	+	Missense_Mutation	SNP	C	C	T	rs368477906		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:62459862C>T	ENST00000383710.4	-	24	3812	c.3463G>A	c.(3463-3465)Gaa>Aaa	p.E1155K	CADPS_ENST00000357948.3_Missense_Mutation_p.E1076K|CADPS_ENST00000283269.9_Missense_Mutation_p.E1116K	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1155					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TGGCCCATTTCCATGCTGCAA	0.353																																					p.E1155K		Atlas-SNP	.											.	CADPS	387	.	0			c.G3463A						.	C	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	116.0	116.0	116.0		3463,3226,3346	6.0	1.0	3		116	1,8599		0,1,4299	no	missense,missense,missense	CADPS	NM_003716.3,NM_183393.2,NM_183394.2	56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	1155/1354,1076/1275,1116/1315	62459862	1,13005	2203	4300	6503	SO:0001583	missense	8618	exon24			CCATTTCCATGCT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3463G>A	chr3.hg19:g.62459862C>T	ENSP00000373215:p.Glu1155Lys	64.0	0.0		70.0	4.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	18.86|18.86|18.86	3.712760|3.712760|3.712760	0.68730|0.68730|0.68730	0.0|0.0|0.0	1.16E-4|1.16E-4|1.16E-4	ENSG00000163618|ENSG00000163618|ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269|ENST00000466621|ENST00000473635	T;T;T|.|.	0.30182|.|.	1.54;1.54;1.54|.|.	5.97|5.97|5.97	5.97|5.97|5.97	0.96955|0.96955|0.96955	.|.|.	0.095518|.|.	0.64402|.|.	D|.|.	0.000001|.|.	T|T|.	0.69187|0.69187|.	0.3083|0.3083|.	L|L|L	0.42245|0.42245|0.42245	1.32|1.32|1.32	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B;P;P|.|.	0.44521|.|.	0.016;0.449;0.799;0.837|.|.	B;B;B;P|.|.	0.47430|.|.	0.025;0.107;0.108;0.547|.|.	T|T|.	0.62358|0.62358|.	-0.6871|-0.6871|.	10|5|.	0.51188|.|.	T|.|.	0.08|.|.	.|.|.	20.428|20.428|20.428	0.99075|0.99075|0.99075	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	1076;1116;1155;1155|.|.	Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4|.|.	.;.;CAPS1_HUMAN;.|.|.	K|E|X	1155;1155;1076;1116|66|141	ENSP00000373215:E1155K;ENSP00000350632:E1076K;ENSP00000283269:E1116K|.|.	ENSP00000283269:E1116K|.|.	E|G|W	-|-|-	1|2|3	0|0|0	CADPS|CADPS|CADPS	62434902|62434902|62434902	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.818000|7.818000|7.818000	0.86416|0.86416|0.86416	2.837000|2.837000|2.837000	0.97791|0.97791|0.97791	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAA|GGA|TGG	.	.		0.353	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
PDZRN3	23024	hgsc.bcm.edu	37	3	73433257	73433257	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:73433257A>G	ENST00000263666.4	-	10	2574	c.2460T>C	c.(2458-2460)ccT>ccC	p.P820P	PDZRN3_ENST00000462146.2_Silent_p.P477P|PDZRN3_ENST00000466780.1_Silent_p.P477P|PDZRN3_ENST00000535920.1_Silent_p.P542P|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000479530.1_Silent_p.P537P	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	820					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GGCTATAGGTAGGGGTGCCCA	0.662																																					p.P820P		Atlas-SNP	.											.	PDZRN3	196	.	0			c.T2460C						.						52.0	58.0	56.0					3																	73433257		2203	4300	6503	SO:0001819	synonymous_variant	23024	exon10			ATAGGTAGGGGTG	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2460T>C	chr3.hg19:g.73433257A>G		82.0	0.0		73.0	4.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	hg19	CCDS33789.1																																																																																			.	.		0.662	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
CADM2	253559	hgsc.bcm.edu	37	3	85932567	85932567	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:85932567C>T	ENST00000407528.2	+	3	400	c.338C>T	c.(337-339)aCt>aTt	p.T113I	CADM2_ENST00000405615.2_Missense_Mutation_p.T115I|CADM2_ENST00000383699.3_Missense_Mutation_p.T122I	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	113	Ig-like V-type.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CCTGTCAAAACTTCCAAGGCA	0.403																																					p.T122I		Atlas-SNP	.											.	CADM2	195	.	0			c.C365T						.						97.0	81.0	87.0					3																	85932567		2203	4300	6503	SO:0001583	missense	253559	exon4			TCAAAACTTCCAA	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	29849	protein-coding gene	gene with protein product	"""nectin-like 3"""	609938	"""immunoglobulin superfamily, member 4D"""	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.338C>T	chr3.hg19:g.85932567C>T	ENSP00000384575:p.Thr113Ile	157.0	0.0		121.0	31.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.009951	0.54361	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.28454	1.61;1.61;1.61	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.043673	0.85682	D	0.000000	T	0.64023	0.2561	M	0.87547	2.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.988;0.998;0.999	T	0.68887	-0.5290	10	0.72032	D	0.01	.	19.8568	0.96762	0.0:1.0:0.0:0.0	.	115;122;113	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	I	122;113;115	ENSP00000373200:T122I;ENSP00000384575:T113I;ENSP00000384193:T115I	ENSP00000373200:T122I	T	+	2	0	CADM2	86015257	1.000000	0.71417	0.952000	0.39060	0.016000	0.09150	5.721000	0.68477	2.764000	0.94973	0.650000	0.86243	ACT	.	.		0.403	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
OR5K4	403278	hgsc.bcm.edu	37	3	98073598	98073598	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:98073598A>T	ENST00000354924.2	+	1	901	c.901A>T	c.(901-903)Att>Ttt	p.I301F	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TCTTAAAAAAATTATGAGGAA	0.249																																					p.I301F		Atlas-SNP	.											.,4	OR5K4	75	.	0			c.A901T						.						80.0	101.0	94.0					3																	98073598		2175	4254	6429	SO:0001583	missense	403278	exon1			AAAAAAATTATGA		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"""GPCR / Class A : Olfactory receptors"""	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.901A>T	chr3.hg19:g.98073598A>T	ENSP00000347003:p.Ile301Phe	22.0	0.0		42.0	5.0	NM_001005517		Missense_Mutation	SNP	ENST00000354924.2	hg19	CCDS33802.1	.	.	.	.	.	.	.	.	.	.	A	8.782	0.928577	0.18131	.	.	ENSG00000196098	ENST00000354924	T	0.38560	1.13	4.83	-4.36	0.03645	.	1.915270	0.03787	U	0.262255	T	0.23611	0.0571	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.19257	-1.0311	10	0.49607	T	0.09	-0.152	4.4994	0.11856	0.238:0.0:0.332:0.4299	.	301	A6NMS3	OR5K4_HUMAN	F	301	ENSP00000347003:I301F	ENSP00000347003:I301F	I	+	1	0	OR5K4	99556288	0.436000	0.25586	0.001000	0.08648	0.018000	0.09664	-0.189000	0.09629	-0.889000	0.03950	-0.461000	0.05368	ATT	.	.		0.249	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1		
PLCXD2	257068	hgsc.bcm.edu	37	3	111427204	111427204	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:111427204C>A	ENST00000477665.1	+	2	919	c.595C>A	c.(595-597)Ctg>Atg	p.L199M	PLCXD2_ENST00000393934.3_Missense_Mutation_p.L199M	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	199	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						AAGTTTGACGCTGCGAACTCT	0.512																																					p.L199M		Atlas-SNP	.											.	PLCXD2	36	.	0			c.C595A						.						63.0	62.0	62.0					3																	111427204		2203	4300	6503	SO:0001583	missense	257068	exon2			TTGACGCTGCGAA	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.595C>A	chr3.hg19:g.111427204C>A	ENSP00000420686:p.Leu199Met	141.0	0.0		118.0	5.0	NM_001185106	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	hg19	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.195817	0.38806	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.73	2.93	0.34026	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.79845	0.4516	M	0.88450	2.955	0.49915	D	0.999838	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81673	-0.0826	8	0.87932	D	0	-9.2257	10.3159	0.43736	0.0:0.768:0.0:0.232	.	199;199	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	M	199	.	ENSP00000377511:L199M	L	+	1	2	PLCXD2	112909894	0.992000	0.36948	0.030000	0.17652	0.135000	0.20990	2.953000	0.49105	0.881000	0.35993	0.655000	0.94253	CTG	.	.		0.512	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268	
SLC15A2	6565	hgsc.bcm.edu	37	3	121647383	121647383	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:121647383A>G	ENST00000489711.1	+	15	1710	c.1322A>G	c.(1321-1323)gAg>gGg	p.E441G	SLC15A2_ENST00000295605.2_Missense_Mutation_p.E410G|SLC15A2_ENST00000465060.1_3'UTR	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	441					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CTGTTGATAGAGTCCATCAAA	0.393																																					p.E441G		Atlas-SNP	.											.	SLC15A2	92	.	0			c.A1322G						.						168.0	176.0	173.0					3																	121647383		2203	4300	6503	SO:0001583	missense	6565	exon15			TGATAGAGTCCAT	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1322A>G	chr3.hg19:g.121647383A>G	ENSP00000417085:p.Glu441Gly	126.0	0.0		100.0	6.0	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	A	8.753	0.921676	0.17982	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.04454	3.62;3.62	5.65	4.48	0.54585	.	0.424514	0.28996	N	0.013477	T	0.05868	0.0153	L	0.50333	1.59	0.39041	D	0.960127	B;B	0.11235	0.004;0.0	B;B	0.16722	0.016;0.005	T	0.27020	-1.0086	10	0.30078	T	0.28	-3.7873	8.9241	0.35630	0.8349:0.0:0.0:0.165	.	410;441	B4E2A7;Q16348	.;S15A2_HUMAN	G	441;403;410	ENSP00000417085:E441G;ENSP00000295605:E410G	ENSP00000295605:E410G	E	+	2	0	SLC15A2	123130073	0.994000	0.37717	0.977000	0.42913	0.285000	0.27093	2.545000	0.45769	1.124000	0.41980	0.533000	0.62120	GAG	.	.		0.393	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
SEMA5B	54437	hgsc.bcm.edu	37	3	122646670	122646670	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:122646670G>T	ENST00000357599.3	-	8	1203	c.817C>A	c.(817-819)Cgc>Agc	p.R273S	SEMA5B_ENST00000195173.4_Missense_Mutation_p.R273S|SEMA5B_ENST00000451055.2_Missense_Mutation_p.R327S|AC078794.1_ENST00000408284.1_RNA	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	273	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TGGGCAGTGCGAAGCGGTGGC	0.627																																					p.R327S		Atlas-SNP	.											SEMA5B_ENST00000451055,bladder,carcinoma,0,4	SEMA5B	303	.	0			c.C979A						.						59.0	60.0	59.0					3																	122646670		2203	4300	6503	SO:0001583	missense	54437	exon8			CAGTGCGAAGCGG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.817C>A	chr3.hg19:g.122646670G>T	ENSP00000350215:p.Arg273Ser	54.0	0.0		75.0	3.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.039632	0.93630	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	5.53	5.53	0.82687	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.38026	0.1025	M	0.86573	2.825	0.80722	D	1	P;D;D	0.53885	0.954;0.963;0.963	P;P;P	0.58077	0.742;0.832;0.832	T	0.24297	-1.0164	10	0.87932	D	0	.	14.0515	0.64739	0.0:0.0:0.8397:0.1603	.	215;273;273	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	S	273;273;215;327;273	ENSP00000350215:R273S;ENSP00000195173:R273S;ENSP00000389588:R327S;ENSP00000377208:R273S	ENSP00000195173:R273S	R	-	1	0	SEMA5B	124129360	1.000000	0.71417	0.984000	0.44739	0.981000	0.71138	4.148000	0.58085	2.882000	0.98803	0.655000	0.94253	CGC	.	.		0.627	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
RHO	6010	hgsc.bcm.edu	37	3	129249881	129249881	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:129249881G>A	ENST00000296271.3	+	2	618	c.524G>A	c.(523-525)tGg>tAg	p.W175*		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	175					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	CTCGCCGGCTGGTCCAGGTAA	0.622																																					p.W175X	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.G524A						.						52.0	48.0	50.0					3																	129249881		2202	4300	6502	SO:0001587	stop_gained	6010	exon2			CCGGCTGGTCCAG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.524G>A	chr3.hg19:g.129249881G>A	ENSP00000296271:p.Trp175*	48.0	0.0		66.0	4.0	NM_000539	Q16414|Q2M249	Nonsense_Mutation	SNP	ENST00000296271.3	hg19	CCDS3063.1	.	.	.	.	.	.	.	.	.	.	G	33	5.253294	0.95336	.	.	ENSG00000163914	ENST00000296271	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8606	0.92270	0.0:0.0:1.0:0.0	.	.	.	.	X	175	.	ENSP00000296271:W175X	W	+	2	0	RHO	130732571	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	9.863000	0.99569	2.448000	0.82819	0.462000	0.41574	TGG	.	.		0.622	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	
ASTE1	28990	hgsc.bcm.edu	37	3	130735171	130735171	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:130735171A>G	ENST00000264992.3	-	5	1967	c.1526T>C	c.(1525-1527)cTg>cCg	p.L509P	ATP2C1_ENST00000504381.1_3'UTR|ATP2C1_ENST00000507488.2_3'UTR|ATP2C1_ENST00000422190.2_3'UTR|ATP2C1_ENST00000393221.4_3'UTR|ATP2C1_ENST00000359644.3_3'UTR|ATP2C1_ENST00000513801.1_3'UTR|ATP2C1_ENST00000533801.2_3'UTR|ATP2C1_ENST00000328560.8_3'UTR|ASTE1_ENST00000514044.1_Missense_Mutation_p.L509P	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	509					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						ATCTTCCTGCAGCTCTTCCTT	0.423																																					p.L509P		Atlas-SNP	.											.	ASTE1	67	.	0			c.T1526C						.						139.0	125.0	130.0					3																	130735171		2203	4300	6503	SO:0001583	missense	28990	exon5			TCCTGCAGCTCTT	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.1526T>C	chr3.hg19:g.130735171A>G	ENSP00000264992:p.Leu509Pro	119.0	0.0		119.0	5.0	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	hg19	CCDS3068.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.28|10.28	1.305458|1.305458	0.23736|0.23736	.|.	.|.	ENSG00000034533|ENSG00000034533	ENST00000505290|ENST00000514044;ENST00000264992	.|.	.|.	.|.	5.86|5.86	-1.11|-1.11	0.09840|0.09840	.|.	.|0.955177	.|0.08797	.|N	.|0.892355	T|T	0.29093|0.29093	0.0723|0.0723	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	0.999996|0.999996	.|B;B	.|0.10296	.|0.003;0.001	.|B;B	.|0.06405	.|0.002;0.002	T|T	0.25222|0.25222	-1.0138|-1.0138	5|9	.|0.33141	.|T	.|0.24	0.6471|0.6471	4.8709|4.8709	0.13631|0.13631	0.4424:0.0:0.3353:0.2223|0.4424:0.0:0.3353:0.2223	.|.	.|509;509	.|D6RG30;Q2TB18	.|.;ASTE1_HUMAN	R|P	86|509	.|.	.|ENSP00000264992:L509P	C|L	-|-	1|2	0|0	ASTE1|ASTE1	132217861|132217861	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.052000|0.052000	0.14988|0.14988	-1.149000|-1.149000	0.03182|0.03182	-0.118000|-0.118000	0.11851|0.11851	0.533000|0.533000	0.62120|0.62120	TGC|CTG	.	.		0.423	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065	
PRR23A	729627	hgsc.bcm.edu	37	3	138725110	138725110	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:138725110T>C	ENST00000383163.2	-	1	0	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	MRPS22_ENST00000495075.1_Intron	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	1										endometrium(3)|kidney(1)|lung(7)	11						CGGCTGCCCATAGCCTCGACG	0.697																																					p.M1V		Atlas-SNP	.											.	PRR23A	35	.	0			c.A1G						.						1.0	2.0	2.0					3																	138725110		348	1024	1372	SO:0001630	splice_region_variant	729627	exon1			TGCCCATAGCCTC		CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260			37172	protein-coding gene	gene with protein product							Standard	NM_001134659		Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.1-1A>G	chr3.hg19:g.138725110T>C		19.0	0.0		12.0	8.0	NM_001134659		Missense_Mutation	SNP	ENST00000383163.2	hg19	CCDS46923.1	.	.	.	.	.	.	.	.	.	.	T	7.219	0.597077	0.13875	.	.	ENSG00000206260	ENST00000383163	.	.	.	2.52	1.36	0.22044	.	1.434950	0.04639	N	0.405053	T	0.28566	0.0707	.	.	.	0.09310	N	1	B	0.24618	0.107	B	0.23716	0.048	T	0.22382	-1.0218	8	0.36615	T	0.2	.	4.0819	0.09931	0.0:0.1761:0.0:0.8239	.	1	A6NEV1	PR23A_HUMAN	V	1	.	ENSP00000372649:M1V	M	-	1	0	PRR23A	140207800	0.000000	0.05858	0.003000	0.11579	0.209000	0.24338	-0.245000	0.08890	0.407000	0.25591	0.379000	0.24179	ATG	.	.		0.697	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659	Missense_Mutation
ATR	545	hgsc.bcm.edu	37	3	142281918	142281918	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:142281918C>A	ENST00000350721.4	-	4	447	c.326G>T	c.(325-327)cGg>cTg	p.R109L	ATR_ENST00000383101.3_Missense_Mutation_p.R109L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	109					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R109L(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TGCTGCAATCCGCAGAAGTCT	0.308								Other conserved DNA damage response genes																													p.R109L		Atlas-SNP	.											.	ATR	285	.	1	Substitution - Missense(1)	lung(1)	c.G326T						.						89.0	102.0	98.0					3																	142281918		2143	4277	6420	SO:0001583	missense	545	exon4			GCAATCCGCAGAA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.326G>T	chr3.hg19:g.142281918C>A	ENSP00000343741:p.Arg109Leu	87.0	0.0		83.0	4.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.472384	0.63737	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.40476	1.03;1.03	5.62	5.62	0.85841	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65281	0.2676	M	0.65975	2.015	0.40605	D	0.981619	D	0.89917	1.0	D	0.81914	0.995	T	0.66532	-0.5900	10	0.59425	D	0.04	-12.9653	19.6544	0.95831	0.0:1.0:0.0:0.0	.	109	Q13535	ATR_HUMAN	L	109	ENSP00000343741:R109L;ENSP00000372581:R109L	ENSP00000343741:R109L	R	-	2	0	ATR	143764608	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.683000	0.74533	2.647000	0.89833	0.467000	0.42956	CGG	.	.		0.308	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
PLSCR1	5359	hgsc.bcm.edu	37	3	146246440	146246440	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:146246440A>G	ENST00000342435.4	-	4	683	c.273T>C	c.(271-273)ccT>ccC	p.P91P	PLSCR1_ENST00000448787.2_Intron|PLSCR1_ENST00000448205.1_Intron|PLSCR1_ENST00000487389.1_Silent_p.P84P	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	91					acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						AGTTTAATGGAGGCTGTGGCG	0.443																																					p.P91P		Atlas-SNP	.											.	PLSCR1	35	.	0			c.T273C						.						101.0	107.0	105.0					3																	146246440		2203	4300	6503	SO:0001819	synonymous_variant	5359	exon4			TAATGGAGGCTGT	AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.273T>C	chr3.hg19:g.146246440A>G		141.0	0.0		99.0	4.0	NM_021105	B2R8H8|B4DTE8	Silent	SNP	ENST00000342435.4	hg19	CCDS3135.1	.	.	.	.	.	.	.	.	.	.	A	1.765	-0.485865	0.04352	.	.	ENSG00000188313	ENST00000483300	.	.	.	4.03	2.75	0.32379	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.14504	-1.0470	4	.	.	.	.	4.1876	0.10405	0.6219:0.0:0.0924:0.2857	.	.	.	.	P	33	.	.	L	-	2	0	PLSCR1	147729130	0.056000	0.20664	0.115000	0.21578	0.341000	0.28922	0.487000	0.22356	1.784000	0.52394	0.402000	0.26972	CTC	.	.		0.443	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105	
HPS3	84343	hgsc.bcm.edu	37	3	148880655	148880655	+	Nonsense_Mutation	SNP	C	C	A	rs373037058		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:148880655C>A	ENST00000296051.2	+	13	2611	c.2471C>A	c.(2470-2472)tCg>tAg	p.S824*	HPS3_ENST00000460120.1_Nonsense_Mutation_p.S659*	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	824					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TTGCGAACATCGGAGGATCTG	0.363									Hermansky-Pudlak syndrome																												p.S824X		Atlas-SNP	.											.	HPS3	104	.	0			c.C2471A						.						98.0	96.0	96.0					3																	148880655		2203	4300	6503	SO:0001587	stop_gained	84343	exon13	Familial Cancer Database	HPS, HPS1-8	GAACATCGGAGGA	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2471C>A	chr3.hg19:g.148880655C>A	ENSP00000296051:p.Ser824*	74.0	0.0		79.0	4.0	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Nonsense_Mutation	SNP	ENST00000296051.2	hg19	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	C	36	5.970018	0.97156	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	.	.	.	5.87	5.87	0.94306	.	0.394049	0.29093	N	0.013172	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	-5.2168	20.2103	0.98287	0.0:1.0:0.0:0.0	.	.	.	.	X	824;659	.	ENSP00000296051:S824X	S	+	2	0	HPS3	150363345	0.743000	0.28239	0.116000	0.21606	0.010000	0.07245	5.958000	0.70330	2.780000	0.95670	0.563000	0.77884	TCG	.	.		0.363	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
WWTR1	25937	hgsc.bcm.edu	37	3	149243898	149243898	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:149243898G>A	ENST00000465804.1	-	7	1176	c.920C>T	c.(919-921)tCg>tTg	p.S307L	WWTR1_ENST00000360632.3_Missense_Mutation_p.S307L|WWTR1_ENST00000467467.1_Missense_Mutation_p.S307L|RNU6-1098P_ENST00000516772.1_RNA	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	307					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CTGCTCCCTCGAATGATATGG	0.453			T	CAMTA1	epitheliod hemangioendothelioma																																p.S307L		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	WWTR1,colon,carcinoma,0,1	WWTR1	42	.	0			c.C920T						.						105.0	95.0	98.0					3																	149243898		2203	4300	6503	SO:0001583	missense	25937	exon7			TCCCTCGAATGAT	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.920C>T	chr3.hg19:g.149243898G>A	ENSP00000419465:p.Ser307Leu	60.0	0.0		69.0	3.0	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000465804.1	hg19	CCDS3144.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119092	0.94385	.	.	ENSG00000018408	ENST00000465804;ENST00000360632;ENST00000467467;ENST00000472417	T;T;T	0.51071	0.72;0.72;0.72	5.56	5.56	0.83823	.	0.061015	0.64402	D	0.000002	T	0.66587	0.2804	M	0.77103	2.36	0.80722	D	1	D	0.69078	0.997	P	0.55965	0.788	T	0.71144	-0.4678	10	0.87932	D	0	-16.6941	19.5073	0.95124	0.0:0.0:1.0:0.0	.	307	Q9GZV5	WWTR1_HUMAN	L	307;307;307;165	ENSP00000419465:S307L;ENSP00000353847:S307L;ENSP00000419234:S307L	ENSP00000353847:S307L	S	-	2	0	WWTR1	150726588	1.000000	0.71417	0.454000	0.27019	0.942000	0.58702	9.467000	0.97671	2.606000	0.88127	0.563000	0.77884	TCG	.	.		0.453	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472	
MED12L	116931	hgsc.bcm.edu	37	3	151107911	151107911	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:151107911T>C	ENST00000474524.1	+	36	5529	c.5491T>C	c.(5491-5493)Tct>Cct	p.S1831P	MED12L_ENST00000273432.4_Missense_Mutation_p.S1691P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1831						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCAGAACCAATCTCTTACTCC	0.493																																					p.S1831P		Atlas-SNP	.											.	MED12L	271	.	0			c.T5491C						.						131.0	144.0	140.0					3																	151107911		2203	4300	6503	SO:0001583	missense	116931	exon36			AACCAATCTCTTA	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5491T>C	chr3.hg19:g.151107911T>C	ENSP00000417235:p.Ser1831Pro	52.0	0.0		55.0	4.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	T	2.556	-0.302968	0.05495	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.58797	0.56;0.31	5.75	0.525	0.17072	Mediator complex, subunit Med12, catenin-binding (1);	0.195620	0.46145	D	0.000309	T	0.25568	0.0622	N	0.08118	0	0.22562	N	0.998985	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.25779	-1.0122	10	0.05351	T	0.99	-7.3491	5.8181	0.18512	0.0:0.1291:0.5249:0.346	.	1691;1831	F8WAE6;Q86YW9	.;MD12L_HUMAN	P	1831;1691	ENSP00000417235:S1831P;ENSP00000273432:S1691P	ENSP00000273432:S1691P	S	+	1	0	MED12L	152590601	0.210000	0.23517	0.245000	0.24217	0.971000	0.66376	0.439000	0.21575	0.074000	0.16767	0.533000	0.62120	TCT	.	.		0.493	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
IGSF10	285313	hgsc.bcm.edu	37	3	151174848	151174848	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:151174848G>A	ENST00000282466.3	-	2	289	c.290C>T	c.(289-291)cCt>cTt	p.P97L		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	97					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGTCTTGTCAGGGATTGTGTG	0.468																																					p.P97L		Atlas-SNP	.											.	IGSF10	279	.	0			c.C290T						.						124.0	109.0	114.0					3																	151174848		2203	4300	6503	SO:0001583	missense	285313	exon2			TTGTCAGGGATTG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.290C>T	chr3.hg19:g.151174848G>A	ENSP00000282466:p.Pro97Leu	88.0	0.0		91.0	4.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.589048	0.46110	.	.	ENSG00000152580	ENST00000282466	T	0.60920	0.15	5.87	4.05	0.47172	.	0.670883	0.12960	N	0.425111	T	0.52322	0.1727	L	0.58428	1.81	0.37437	D	0.914269	P	0.39352	0.669	B	0.39904	0.313	T	0.57382	-0.7821	10	0.72032	D	0.01	.	4.9421	0.13971	0.0708:0.1336:0.5389:0.2567	.	97	Q6WRI0	IGS10_HUMAN	L	97	ENSP00000282466:P97L	ENSP00000282466:P97L	P	-	2	0	IGSF10	152657538	0.286000	0.24305	0.081000	0.20488	0.896000	0.52359	1.305000	0.33493	0.796000	0.33947	0.655000	0.94253	CCT	.	.		0.468	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
GFM1	85476	hgsc.bcm.edu	37	3	158364696	158364696	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:158364696C>A	ENST00000486715.1	+	4	889	c.532C>A	c.(532-534)Cga>Aga	p.R178R	GFM1_ENST00000264263.5_Silent_p.R178R|GFM1_ENST00000478576.1_Silent_p.R178R	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			CAAATTGGACCGAATGGGCTC	0.463																																					p.R178R		Atlas-SNP	.											.	GFM1	83	.	0			c.C532A						.						83.0	80.0	81.0					3																	158364696		2203	4300	6503	SO:0001819	synonymous_variant	85476	exon4			TTGGACCGAATGG	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"""G translation elongation factor, mitochondrial"""			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.532C>A	chr3.hg19:g.158364696C>A		93.0	0.0		92.0	4.0	NM_024996		Silent	SNP	ENST00000486715.1	hg19	CCDS33885.1																																																																																			.	.		0.463	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
OTOL1	131149	hgsc.bcm.edu	37	3	161221475	161221475	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:161221475T>C	ENST00000327928.4	+	4	1179	c.1179T>C	c.(1177-1179)caT>caC	p.H393H		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	393	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TTTCCTACCATATTACGGTGA	0.438																																					p.H393H		Atlas-SNP	.											.	OTOL1	63	.	0			c.T1179C						.						63.0	56.0	59.0					3																	161221475		1925	4126	6051	SO:0001819	synonymous_variant	131149	exon4			CTACCATATTACG		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1179T>C	chr3.hg19:g.161221475T>C		71.0	0.0		72.0	4.0	NM_001080440		Silent	SNP	ENST00000327928.4	hg19	CCDS46948.1																																																																																			.	.		0.438	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
LRRIQ4	344657	hgsc.bcm.edu	37	3	169546665	169546665	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:169546665G>T	ENST00000340806.6	+	2	1139	c.1139G>T	c.(1138-1140)gGg>gTg	p.G380V		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	380										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						TTATACATTGGGCAAGACCAG	0.438																																					p.G380V		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.G1139T						.						124.0	120.0	121.0					3																	169546665		1854	4100	5954	SO:0001583	missense	344657	exon2			ACATTGGGCAAGA		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"""leucine rich repeat containing 64"""						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.1139G>T	chr3.hg19:g.169546665G>T	ENSP00000342188:p.Gly380Val	69.0	0.0		88.0	4.0	NM_001080460		Missense_Mutation	SNP	ENST00000340806.6	hg19	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.189830	0.38707	.	.	ENSG00000188306	ENST00000340806	T	0.17054	2.3	5.77	4.89	0.63831	.	0.000000	0.64402	D	0.000002	T	0.38054	0.1026	L	0.60012	1.86	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.08106	-1.0738	10	0.39692	T	0.17	.	15.8421	0.78857	0.0:0.0:0.863:0.137	.	380	A6NIV6	LRIQ4_HUMAN	V	380	ENSP00000342188:G380V	ENSP00000342188:G380V	G	+	2	0	LRRIQ4	171029359	1.000000	0.71417	0.982000	0.44146	0.036000	0.12997	6.502000	0.73695	1.419000	0.47118	-0.182000	0.12963	GGG	.	.		0.438	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460	
MAP3K13	9175	hgsc.bcm.edu	37	3	185198180	185198180	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:185198180C>A	ENST00000265026.3	+	13	2996	c.2662C>A	c.(2662-2664)Ctg>Atg	p.L888M	TMEM41A_ENST00000475480.1_5'UTR|MAP3K13_ENST00000446828.1_Missense_Mutation_p.L681M|MAP3K13_ENST00000535426.1_Missense_Mutation_p.L744M|MAP3K13_ENST00000443863.1_Missense_Mutation_p.L744M|MAP3K13_ENST00000424227.1_Missense_Mutation_p.L888M	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			GCTAGACGACCTGCTGTCCCA	0.517																																					p.L888M		Atlas-SNP	.											.	MAP3K13	209	.	0			c.C2662A						.						114.0	102.0	106.0					3																	185198180		2203	4300	6503	SO:0001583	missense	9175	exon13			GACGACCTGCTGT	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6852	protein-coding gene	gene with protein product	"""leucine zipper-bearing kinase"""	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.2662C>A	chr3.hg19:g.185198180C>A	ENSP00000265026:p.Leu888Met	134.0	0.0		73.0	4.0	NM_004721		Missense_Mutation	SNP	ENST00000265026.3	hg19	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	C	11.64	1.697519	0.30142	.	.	ENSG00000073803	ENST00000446828;ENST00000424227;ENST00000443863;ENST00000535426;ENST00000265026	T;T;T;T;T	0.78246	-1.16;-1.11;-1.04;-1.04;-1.11	5.86	4.94	0.65067	.	0.086755	0.49305	D	0.000144	T	0.59959	0.2232	N	0.16656	0.425	0.80722	D	1	B;P;P	0.38195	0.204;0.622;0.488	B;B;B	0.34180	0.082;0.177;0.086	T	0.59311	-0.7478	10	0.13470	T	0.59	.	14.2652	0.66113	0.2188:0.7812:0.0:0.0	.	744;681;888	O43283-4;O43283-5;O43283	.;.;M3K13_HUMAN	M	681;888;744;744;888	ENSP00000411483:L681M;ENSP00000399910:L888M;ENSP00000409325:L744M;ENSP00000439257:L744M;ENSP00000265026:L888M	ENSP00000265026:L888M	L	+	1	2	MAP3K13	186680874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.613000	0.46351	2.773000	0.95371	0.655000	0.94253	CTG	.	.		0.517	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721	
LIPH	200879	hgsc.bcm.edu	37	3	185236957	185236957	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:185236957A>G	ENST00000296252.4	-	6	1000	c.859T>C	c.(859-861)Tca>Cca	p.S287P	LIPH_ENST00000424591.2_Missense_Mutation_p.S253P	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	287					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			TCTTTTTGTGACGTGCCGCAG	0.478																																					p.S287P		Atlas-SNP	.											.	LIPH	56	.	0			c.T859C						.						132.0	132.0	132.0					3																	185236957		2203	4300	6503	SO:0001583	missense	200879	exon6			TTTGTGACGTGCC	AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.859T>C	chr3.hg19:g.185236957A>G	ENSP00000296252:p.Ser287Pro	117.0	0.0		99.0	4.0	NM_139248	A2IBA7|Q8TEC7	Missense_Mutation	SNP	ENST00000296252.4	hg19	CCDS3272.1	.	.	.	.	.	.	.	.	.	.	A	10.59	1.392802	0.25118	.	.	ENSG00000163898	ENST00000296252;ENST00000424591	D;D	0.90844	-2.74;-2.74	5.01	-10.0	0.00425	Lipase, N-terminal (1);	1.076220	0.07157	N	0.850046	T	0.66944	0.2841	N	0.01417	-0.88	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.003;0.008	T	0.59467	-0.7449	10	0.33141	T	0.24	2.0167	5.2024	0.15273	0.3999:0.4034:0.114:0.0826	.	253;287	A2IBA6;Q8WWY8	.;LIPH_HUMAN	P	287;253	ENSP00000296252:S287P;ENSP00000396384:S253P	ENSP00000296252:S287P	S	-	1	0	LIPH	186719651	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.081000	0.11321	-1.587000	0.01630	-0.474000	0.04947	TCA	.	.		0.478	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1		
FETUB	26998	hgsc.bcm.edu	37	3	186358341	186358341	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:186358341T>C	ENST00000265029.3	+	1	193	c.92T>C	c.(91-93)cTg>cCg	p.L31P	FETUB_ENST00000382136.3_Missense_Mutation_p.L31P|FETUB_ENST00000450521.1_Missense_Mutation_p.L31P|FETUB_ENST00000382134.3_Missense_Mutation_p.L31P|FETUB_ENST00000539949.1_Intron|FETUB_ENST00000488561.1_3'UTR|RP11-134F2.2_ENST00000428501.1_RNA|RP11-134F2.2_ENST00000455926.1_RNA	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	31	Cystatin fetuin-B-type 1. {ECO:0000255|PROSITE-ProRule:PRU00862}.				binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		CCCTCGGCTCTGCTCTCCCGG	0.582																																					p.L31P		Atlas-SNP	.											.	FETUB	53	.	0			c.T92C						.						159.0	165.0	163.0					3																	186358341		2203	4300	6503	SO:0001583	missense	26998	exon1			CGGCTCTGCTCTC	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.92T>C	chr3.hg19:g.186358341T>C	ENSP00000265029:p.Leu31Pro	174.0	0.0		129.0	6.0	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Missense_Mutation	SNP	ENST00000265029.3	hg19	CCDS3279.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.531121	0.27387	.	.	ENSG00000090512	ENST00000450521;ENST00000265029;ENST00000382134;ENST00000382136	T;T;T;T	0.17213	2.69;2.69;2.9;2.29	4.17	0.513	0.17000	Proteinase inhibitor I25, cystatin (1);	1.282600	0.05444	N	0.548118	T	0.24661	0.0598	M	0.75447	2.3	0.09310	N	1	B;B;B	0.29481	0.105;0.005;0.245	B;B;B	0.35039	0.042;0.008;0.194	T	0.40739	-0.9547	10	0.87932	D	0	-0.575	6.0607	0.19837	0.0:0.3217:0.0:0.6783	.	31;31;31	E9PG06;E9PG08;Q9UGM5	.;.;FETUB_HUMAN	P	31	ENSP00000404288:L31P;ENSP00000265029:L31P;ENSP00000371569:L31P;ENSP00000371571:L31P	ENSP00000265029:L31P	L	+	2	0	FETUB	187841035	0.004000	0.15560	0.000000	0.03702	0.011000	0.07611	1.566000	0.36396	0.087000	0.17167	0.533000	0.62120	CTG	.	.		0.582	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375	
LRRC15	131578	hgsc.bcm.edu	37	3	194080638	194080638	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:194080638G>A	ENST00000347624.3	-	2	1220	c.1135C>T	c.(1135-1137)Cag>Tag	p.Q379*	LRRC15_ENST00000439944.2_Nonsense_Mutation_p.Q385*|LRRC15_ENST00000428839.1_Nonsense_Mutation_p.Q385*	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	379					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		CCTGGGAGCTGTCTGAGGCGG	0.582																																					p.Q385X		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1153T						.						59.0	58.0	58.0					3																	194080638		2203	4300	6503	SO:0001587	stop_gained	131578	exon3			GGAGCTGTCTGAG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1135C>T	chr3.hg19:g.194080638G>A	ENSP00000306276:p.Gln379*	117.0	0.0		91.0	4.0	NM_001135057	Q495Q6|Q7RTN7	Nonsense_Mutation	SNP	ENST00000347624.3	hg19	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643587	0.87859	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	.	.	.	5.2	2.19	0.27852	.	1.169430	0.06219	N	0.686472	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	2.6203	0.04914	0.1546:0.4506:0.24:0.1548	.	.	.	.	X	379;385;385	.	ENSP00000306276:Q379X	Q	-	1	0	LRRC15	195561933	.	.	0.887000	0.34795	0.979000	0.70002	.	.	1.318000	0.45170	0.655000	0.94253	CAG	.	.		0.582	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
MUC4	4585	hgsc.bcm.edu	37	3	195517320	195517320	+	Silent	SNP	G	G	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:195517320G>C	ENST00000463781.3	-	2	1590	c.1131C>G	c.(1129-1131)acC>acG	p.T377T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T377T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	382					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGGGGATGAGGTGGTTGTTT	0.458																																					p.T377T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C1131G						.						225.0	207.0	213.0					3																	195517320		1956	4143	6099	SO:0001819	synonymous_variant	4585	exon2			GGATGAGGTGGTT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.1131C>G	chr3.hg19:g.195517320G>C		394.0	0.0		377.0	117.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	hg19	CCDS54700.1																																																																																			.	.		0.458	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMEM175	84286	hgsc.bcm.edu	37	4	951958	951958	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:951958G>A	ENST00000264771.4	+	11	1374	c.1189G>A	c.(1189-1191)Gcg>Acg	p.A397T	TMEM175_ENST00000508204.1_Missense_Mutation_p.A315T|TMEM175_ENST00000515740.1_Missense_Mutation_p.A281T	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	397						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GTGGACCACGGCGCTGCTGCA	0.677																																					p.A397T		Atlas-SNP	.											.	TMEM175	44	.	0			c.G1189A						.						30.0	30.0	30.0					4																	951958		2198	4295	6493	SO:0001583	missense	84286	exon11			ACCACGGCGCTGC	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.1189G>A	chr4.hg19:g.951958G>A	ENSP00000264771:p.Ala397Thr	112.0	0.0		91.0	4.0	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	hg19	CCDS3341.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.39|15.39	2.819061|2.819061	0.50633|0.50633	.|.	.|.	ENSG00000127419|ENSG00000127419	ENST00000264771;ENST00000515740;ENST00000508204|ENST00000505148	T;T;T|.	0.53206|.	1.14;1.21;0.63|.	4.65|4.65	3.81|3.81	0.43845|0.43845	.|.	0.064516|.	0.64402|.	N|.	0.000009|.	T|T	0.65354|0.65354	0.2683|0.2683	M|M	0.70275|0.70275	2.135|2.135	0.47737|0.47737	D|D	0.999509|0.999509	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.996;0.996|.	T|T	0.63844|0.63844	-0.6545|-0.6545	10|5	0.72032|.	D|.	0.01|.	-8.2942|-8.2942	10.4562|10.4562	0.44553|0.44553	0.0973:0.0:0.9027:0.0|0.0973:0.0:0.9027:0.0	.|.	315;397|.	D3DVN5;Q9BSA9|.	.;TM175_HUMAN|.	T|D	397;281;315|233	ENSP00000264771:A397T;ENSP00000427039:A281T;ENSP00000423669:A315T|.	ENSP00000264771:A397T|.	A|G	+|+	1|2	0|0	TMEM175|TMEM175	941958|941958	1.000000|1.000000	0.71417|0.71417	0.690000|0.690000	0.30148|0.30148	0.002000|0.002000	0.02628|0.02628	8.944000|8.944000	0.92980|0.92980	0.954000|0.954000	0.37851|0.37851	-0.339000|-0.339000	0.08088|0.08088	GCG|GGC	.	.		0.677	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326	
TACC3	10460	hgsc.bcm.edu	37	4	1725265	1725265	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:1725265A>G	ENST00000313288.4	+	2	223	c.117A>G	c.(115-117)tcA>tcG	p.S39S	TMEM129_ENST00000382936.3_5'Flank|TMEM129_ENST00000303277.2_5'Flank|TMEM129_ENST00000536901.1_5'Flank	NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	39					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			TTCGTGTGTCACAGAAAGAAA	0.463																																					p.S39S	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.A117G						.						64.0	64.0	64.0					4																	1725265		2203	4298	6501	SO:0001819	synonymous_variant	10460	exon2			TGTGTCACAGAAA	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.117A>G	chr4.hg19:g.1725265A>G		155.0	0.0		99.0	4.0	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	hg19	CCDS3352.1																																																																																			.	.		0.463	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
JAKMIP1	152789	hgsc.bcm.edu	37	4	6087187	6087187	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:6087187G>T	ENST00000282924.5	-	4	1279	c.794C>A	c.(793-795)cCg>cAg	p.P265Q	JAKMIP1_ENST00000409831.1_Missense_Mutation_p.P265Q|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.P100Q|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.P265Q|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.P100Q	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	265	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GATCCCGGGCGGGAGCTCTCT	0.612																																					p.P265Q		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.C794A						.						50.0	52.0	52.0					4																	6087187		2203	4300	6503	SO:0001583	missense	152789	exon4			CCGGGCGGGAGCT	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.794C>A	chr4.hg19:g.6087187G>T	ENSP00000282924:p.Pro265Gln	95.0	0.0		63.0	4.0	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	hg19	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.672284	0.47781	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000007	T	0.51449	0.1675	M	0.73217	2.22	0.39418	D	0.966877	D;D;D;D;D	0.63880	0.993;0.983;0.98;0.98;0.983	P;P;P;P;P	0.61132	0.774;0.884;0.838;0.838;0.884	T	0.60193	-0.7311	10	0.72032	D	0.01	.	15.9279	0.79635	0.0:0.0:1.0:0.0	.	100;265;100;265;265	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	Q	265;100;265;265;157;265;265;100	ENSP00000386711:P265Q;ENSP00000387042:P100Q;ENSP00000282924:P265Q;ENSP00000386925:P265Q;ENSP00000386745:P100Q	ENSP00000282924:P265Q	P	-	2	0	JAKMIP1	6138088	1.000000	0.71417	0.902000	0.35471	0.201000	0.24016	5.460000	0.66691	2.239000	0.73571	0.655000	0.94253	CCG	.	.		0.612	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720	
KIAA0232	9778	hgsc.bcm.edu	37	4	6882546	6882546	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:6882546A>G	ENST00000307659.5	+	10	4496	c.4041A>G	c.(4039-4041)ggA>ggG	p.G1347G	KIAA0232_ENST00000425103.1_Silent_p.G1347G	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	1347							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						GATGTACAGGAGAGAGAGATT	0.458																																					p.G1347G		Atlas-SNP	.											.	KIAA0232	102	.	0			c.A4041G						.						78.0	79.0	79.0					4																	6882546		1895	4125	6020	SO:0001819	synonymous_variant	9778	exon10			TACAGGAGAGAGA	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.4041A>G	chr4.hg19:g.6882546A>G		89.0	0.0		78.0	4.0	NM_014743	A7E2D2	Silent	SNP	ENST00000307659.5	hg19	CCDS43209.1																																																																																			.	.		0.458	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743	
SORCS2	57537	hgsc.bcm.edu	37	4	7719906	7719906	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:7719906A>G	ENST00000507866.2	+	18	2529	c.2420A>G	c.(2419-2421)gAg>gGg	p.E807G	SORCS2_ENST00000329016.9_Missense_Mutation_p.E635G	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	807	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						GTGCGGCAGGAGCAGGTGAGT	0.697																																					p.E807G		Atlas-SNP	.											SORCS2,colon,carcinoma,0,1	SORCS2	98	.	0			c.A2420G						.						21.0	25.0	24.0					4																	7719906		2095	4200	6295	SO:0001583	missense	57537	exon18			GGCAGGAGCAGGT	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2420A>G	chr4.hg19:g.7719906A>G	ENSP00000422185:p.Glu807Gly	153.0	2.0		82.0	5.0	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880370	0.72294	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.65916	-0.18;-0.18	4.41	4.41	0.53225	PKD/Chitinase domain (1);PKD domain (3);	0.229367	0.35040	N	0.003495	T	0.73079	0.3541	M	0.62723	1.935	0.80722	D	1	P;P	0.43314	0.803;0.803	P;P	0.56865	0.755;0.808	T	0.76386	-0.2978	10	0.72032	D	0.01	.	13.8152	0.63287	1.0:0.0:0.0:0.0	.	635;807	B5MED8;Q96PQ0	.;SORC2_HUMAN	G	807;635	ENSP00000422185:E807G;ENSP00000329124:E635G	ENSP00000329124:E635G	E	+	2	0	SORCS2	7770806	1.000000	0.71417	1.000000	0.80357	0.424000	0.31475	7.762000	0.85270	1.852000	0.53769	0.533000	0.62120	GAG	.	.		0.697	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
BOD1L1	259282	hgsc.bcm.edu	37	4	13602619	13602619	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:13602619T>C	ENST00000040738.5	-	10	6040	c.5905A>G	c.(5905-5907)Aca>Gca	p.T1969A		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1969						nucleus (GO:0005634)	DNA binding (GO:0003677)										GGAACTGGTGTCACTTCATCC	0.463																																					p.T1969A		Atlas-SNP	.											.	.	.	.	0			c.A5905G						.						147.0	141.0	143.0					4																	13602619		2203	4300	6503	SO:0001583	missense	259282	exon10			CTGGTGTCACTTC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5905A>G	chr4.hg19:g.13602619T>C	ENSP00000040738:p.Thr1969Ala	99.0	0.0		63.0	4.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.957397	0.00465	.	.	ENSG00000038219	ENST00000040738	T	0.05580	3.42	5.28	2.29	0.28610	.	0.728860	0.12720	N	0.444822	T	0.01800	0.0057	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46679	-0.9174	10	0.02654	T	1	-0.033	5.1288	0.14899	0.0:0.4699:0.2731:0.257	.	1969	Q8NFC6	BOD1L_HUMAN	A	1969	ENSP00000040738:T1969A	ENSP00000040738:T1969A	T	-	1	0	BOD1L	13211717	0.000000	0.05858	0.003000	0.11579	0.476000	0.33039	0.733000	0.26087	0.105000	0.17753	0.379000	0.24179	ACA	.	.		0.463	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
CPEB2	132864	hgsc.bcm.edu	37	4	15005655	15005655	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:15005655T>C	ENST00000507071.1	+	1	134	c.47T>C	c.(46-48)cTg>cCg	p.L16P	CPEB2_ENST00000382401.3_Missense_Mutation_p.L16P|CPEB2_ENST00000345451.3_Missense_Mutation_p.L16P|CPEB2_ENST00000541112.1_Missense_Mutation_p.L453P|CPEB2_ENST00000442003.2_Missense_Mutation_p.L453P|CPEB2_ENST00000382395.3_Missense_Mutation_p.L16P|RP11-665G4.1_ENST00000513384.1_RNA|RP11-665G4.1_ENST00000502344.1_RNA|CPEB2_ENST00000538197.1_Missense_Mutation_p.L453P|CPEB2_ENST00000259997.5_Missense_Mutation_p.L16P			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2	16	Pro-rich.				cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						TACCCCGGGCTGCCGTCGTCC	0.751																																					p.L453P		Atlas-SNP	.											.	CPEB2	77	.	0			c.T1358C						.						11.0	11.0	11.0					4																	15005655		1756	3492	5248	SO:0001583	missense	132864	exon1			CCGGGCTGCCGTC	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"""RNA binding motif (RRM) containing"""	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.47T>C	chr4.hg19:g.15005655T>C	ENSP00000424084:p.Leu16Pro	119.0	0.0		79.0	5.0	NM_001177381	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Missense_Mutation	SNP	ENST00000507071.1	hg19		.	.	.	.	.	.	.	.	.	.	t	17.12	3.308889	0.60305	.	.	ENSG00000137449	ENST00000538197;ENST00000541112;ENST00000442003;ENST00000507071;ENST00000345451;ENST00000382395;ENST00000382401;ENST00000259997;ENST00000382391	T;T;T;T;T;T;T;T	0.52983	0.68;0.68;0.64;0.83;0.77;0.77;0.78;0.82	1.96	0.266	0.15617	.	0.352702	0.23680	U	0.045626	T	0.24890	0.0604	N	0.22421	0.69	0.53005	D	0.999962	B;B;B;B;B;B	0.33637	0.289;0.289;0.191;0.42;0.289;0.296	B;B;B;B;B;B	0.26614	0.045;0.045;0.02;0.071;0.045;0.032	T	0.05869	-1.0859	10	0.59425	D	0.04	.	4.7864	0.13227	0.2749:0.0:0.0:0.7251	.	16;16;453;453;16;16	Q7Z5Q1-4;Q7Z5Q1-6;E7EPM3;F5H160;Q7Z5Q1-5;Q7Z5Q1	.;.;.;.;.;CPEB2_HUMAN	P	453;453;453;16;16;16;16;16;16	ENSP00000443985:L453P;ENSP00000437884:L453P;ENSP00000414270:L453P;ENSP00000424084:L16P;ENSP00000334058:L16P;ENSP00000371832:L16P;ENSP00000371838:L16P;ENSP00000259997:L16P	ENSP00000259997:L16P	L	+	2	0	CPEB2	14614753	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.610000	0.46325	0.610000	0.30035	0.333000	0.21579	CTG	.	.		0.751	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607	
SLIT2	9353	hgsc.bcm.edu	37	4	20618726	20618726	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:20618726G>T	ENST00000504154.1	+	35	4293	c.4041G>T	c.(4039-4041)caG>caT	p.Q1347H	SLIT2_ENST00000503823.1_Missense_Mutation_p.Q1339H|SLIT2_ENST00000503837.1_Missense_Mutation_p.Q1343H|SLIT2_ENST00000273739.5_Missense_Mutation_p.Q1360H	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1347	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GCACATGCCAGCCCAGCAGCC	0.577																																					p.Q1347H		Atlas-SNP	.											.	SLIT2	290	.	0			c.G4041T						.						56.0	55.0	55.0					4																	20618726		2203	4300	6503	SO:0001583	missense	9353	exon35			ATGCCAGCCCAGC	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.4041G>T	chr4.hg19:g.20618726G>T	ENSP00000422591:p.Gln1347His	100.0	0.0		79.0	4.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921298	0.33908	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.80824	-1.4;-1.42;-1.33;-1.38	5.94	3.07	0.35406	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.321839	0.36555	N	0.002537	T	0.61553	0.2356	N	0.12920	0.275	0.34239	D	0.677448	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.001	T	0.61564	-0.7037	10	0.30078	T	0.28	.	6.7824	0.23654	0.0689:0.2964:0.5169:0.1178	.	1339;1347	O94813-3;O94813	.;SLIT2_HUMAN	H	1339;1347;1360;1343;1343	ENSP00000427548:Q1339H;ENSP00000422591:Q1347H;ENSP00000273739:Q1360H;ENSP00000422261:Q1343H	ENSP00000273739:Q1360H	Q	+	3	2	SLIT2	20227824	0.990000	0.36364	1.000000	0.80357	0.993000	0.82548	0.278000	0.18753	1.512000	0.48834	0.650000	0.86243	CAG	.	.		0.577	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
SLC34A2	10568	hgsc.bcm.edu	37	4	25664190	25664190	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:25664190G>A	ENST00000382051.3	+	2	118	c.68G>A	c.(67-69)gGt>gAt	p.G23D	SLC34A2_ENST00000503434.1_Missense_Mutation_p.G23D|SLC34A2_ENST00000504570.1_Missense_Mutation_p.G23D	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	23					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				GGGGCCGCAGGTCAGCAGCCC	0.547			T	ROS1	NSCLC																																p.G23D		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"""solute carrier family 34 (sodium phosphate), member 2"""		E	.	SLC34A2	93	.	0			c.G68A						.						69.0	70.0	70.0					4																	25664190		2203	4300	6503	SO:0001583	missense	10568	exon2			CCGCAGGTCAGCA	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"""Solute carriers"""	11020	protein-coding gene	gene with protein product		604217	"""solute carrier family 34 (sodium phosphate), member 2"""			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.68G>A	chr4.hg19:g.25664190G>A	ENSP00000371483:p.Gly23Asp	124.0	0.0		90.0	4.0	NM_001177998	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	hg19	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	G	6.559	0.471493	0.12461	.	.	ENSG00000157765	ENST00000513204;ENST00000504570;ENST00000382051;ENST00000503434;ENST00000507530	T;T;T;T;T	0.54071	0.59;2.0;2.0;2.0;0.59	5.25	-2.44	0.06502	.	2.205720	0.01628	N	0.023400	T	0.43919	0.1269	L	0.44542	1.39	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.22836	-1.0205	10	0.35671	T	0.21	1.0696	7.1731	0.25728	0.3183:0.3219:0.3598:0.0	.	23;23	O95436-2;O95436	.;NPT2B_HUMAN	D	23	ENSP00000423038:G23D;ENSP00000425501:G23D;ENSP00000371483:G23D;ENSP00000423021:G23D;ENSP00000424266:G23D	ENSP00000371483:G23D	G	+	2	0	SLC34A2	25273288	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.130000	0.10498	-0.372000	0.07992	-0.165000	0.13383	GGT	.	.		0.547	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424	
SEL1L3	23231	hgsc.bcm.edu	37	4	25849271	25849271	+	Silent	SNP	G	G	T	rs200467510	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:25849271G>T	ENST00000399878.3	-	2	500	c.378C>A	c.(376-378)ccC>ccA	p.P126P	SEL1L3_ENST00000513364.1_Intron|SEL1L3_ENST00000502949.1_5'UTR|SEL1L3_ENST00000264868.5_Silent_p.P91P	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	126						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TTTTGTACACGGGAATGCTAC	0.393																																					p.P126P		Atlas-SNP	.											.	SEL1L3	62	.	0			c.C378A						.						109.0	100.0	103.0					4																	25849271		1878	4117	5995	SO:0001819	synonymous_variant	23231	exon2			GTACACGGGAATG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.378C>A	chr4.hg19:g.25849271G>T		172.0	0.0		97.0	4.0	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Silent	SNP	ENST00000399878.3	hg19	CCDS47037.1																																																																																			.	G|0.996;A|0.004		0.393	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
PDS5A	23244	hgsc.bcm.edu	37	4	39910134	39910134	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:39910134G>T	ENST00000303538.8	-	11	1653	c.1114C>A	c.(1114-1116)Cca>Aca	p.P372T	PDS5A_ENST00000503396.1_Missense_Mutation_p.P372T	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GCTTCTTCTGGATCATGTGAT	0.358																																					p.P372T		Atlas-SNP	.											.	PDS5A	114	.	0			c.C1114A						.						118.0	109.0	111.0					4																	39910134		1838	4087	5925	SO:0001583	missense	23244	exon11			CTTCTGGATCATG	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1114C>A	chr4.hg19:g.39910134G>T	ENSP00000303427:p.Pro372Thr	92.0	0.0		68.0	4.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.451583	0.26074	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T;T	0.68331	-0.13;-0.32	4.93	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77329	0.4114	L	0.46741	1.465	0.80722	D	1	B;D	0.89917	0.328;1.0	B;D	0.97110	0.155;1.0	T	0.76083	-0.3089	9	.	.	.	-8.9094	18.1354	0.89617	0.0:0.0:1.0:0.0	.	372;372	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	T	372	ENSP00000303427:P372T;ENSP00000426749:P372T	.	P	-	1	0	PDS5A	39586529	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.843000	0.99491	2.285000	0.76669	0.557000	0.71058	CCA	.	.		0.358	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
RBM47	54502	hgsc.bcm.edu	37	4	40439926	40439926	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:40439926T>C	ENST00000381793.2	-	3	1381	c.985A>G	c.(985-987)Aag>Gag	p.K329E	RBM47_ENST00000319592.4_Missense_Mutation_p.K329E|RBM47_ENST00000514014.1_Missense_Mutation_p.K291E|RBM47_ENST00000295971.7_Missense_Mutation_p.K329E|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000381795.6_Missense_Mutation_p.K329E			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	329					hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CTGGCTGCCTTCTGGTAGCGC	0.652																																					p.K329E		Atlas-SNP	.											.	RBM47	146	.	0			c.A985G						.						41.0	39.0	40.0					4																	40439926		2203	4300	6503	SO:0001583	missense	54502	exon4			CTGCCTTCTGGTA	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.985A>G	chr4.hg19:g.40439926T>C	ENSP00000371212:p.Lys329Glu	135.0	0.0		97.0	4.0	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	hg19	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.239228	0.58995	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	5.58	5.58	0.84498	Nucleotide-binding, alpha-beta plait (1);	0.096829	0.64402	D	0.000001	T	0.72374	0.3452	M	0.62723	1.935	0.80722	D	1	P;B	0.47106	0.89;0.142	P;B	0.45881	0.496;0.103	T	0.71833	-0.4473	10	0.05351	T	0.99	-29.902	15.7506	0.77983	0.0:0.0:0.0:1.0	.	329;329	A0AV96-2;A0AV96	.;RBM47_HUMAN	E	329;329;329;329;291	ENSP00000320108:K329E;ENSP00000371212:K329E;ENSP00000371214:K329E;ENSP00000295971:K329E;ENSP00000423243:K291E	ENSP00000295971:K329E	K	-	1	0	RBM47	40134683	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.916000	0.69981	2.125000	0.65367	0.379000	0.24179	AAG	.	.		0.652	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027	
RBM47	54502	hgsc.bcm.edu	37	4	40440443	40440443	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:40440443G>A	ENST00000381793.2	-	3	864	c.468C>T	c.(466-468)ggC>ggT	p.G156G	RBM47_ENST00000319592.4_Silent_p.G156G|RBM47_ENST00000514014.1_Silent_p.G118G|RBM47_ENST00000295971.7_Silent_p.G156G|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000381795.6_Silent_p.G156G			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	156	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						TGGGGATCCCGCCGATGAAGA	0.647																																					p.G156G		Atlas-SNP	.											RBM47_ENST00000381793,NS,carcinoma,0,3	RBM47	146	.	0			c.C468T						.						45.0	42.0	43.0					4																	40440443		2201	4292	6493	SO:0001819	synonymous_variant	54502	exon4			GATCCCGCCGATG	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.468C>T	chr4.hg19:g.40440443G>A		52.0	0.0		40.0	2.0	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Silent	SNP	ENST00000381793.2	hg19	CCDS43223.1																																																																																			.	.		0.647	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027	
NSUN7	79730	hgsc.bcm.edu	37	4	40762502	40762502	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:40762502C>T	ENST00000381782.2	+	3	845	c.350C>T	c.(349-351)aCc>aTc	p.T117I	NSUN7_ENST00000316607.5_Missense_Mutation_p.T117I	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	117							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						TTCCCAAGTACCACAATAGTA	0.313																																					p.T117I		Atlas-SNP	.											.	NSUN7	70	.	0			c.C350T						.						104.0	103.0	103.0					4																	40762502		2203	4300	6503	SO:0001583	missense	79730	exon3			CAAGTACCACAAT	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"""NOP2/Sun domain containing"""	25857	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family, member 7"""			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.350C>T	chr4.hg19:g.40762502C>T	ENSP00000371201:p.Thr117Ile	124.0	0.0		94.0	4.0	NM_024677	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	hg19	CCDS3461.2	.	.	.	.	.	.	.	.	.	.	C	10.78	1.447320	0.25987	.	.	ENSG00000179299	ENST00000381782;ENST00000316607	T;T	0.38560	1.13;1.13	5.68	4.61	0.57282	.	0.564882	0.19101	N	0.122720	T	0.32823	0.0842	M	0.65975	2.015	0.28396	N	0.91885	P;P;P	0.36086	0.536;0.529;0.529	B;B;B	0.29077	0.045;0.098;0.098	T	0.30357	-0.9981	10	0.32370	T	0.25	-7.528	4.7215	0.12920	0.2082:0.6638:0.0:0.128	.	117;117;117	Q8NE18;Q8NE18-2;Q8NE18-3	NSUN7_HUMAN;.;.	I	117	ENSP00000371201:T117I;ENSP00000319127:T117I	ENSP00000319127:T117I	T	+	2	0	NSUN7	40457259	0.938000	0.31826	1.000000	0.80357	0.977000	0.68977	1.526000	0.35964	2.835000	0.97688	0.650000	0.86243	ACC	.	.		0.313	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677	
BEND4	389206	hgsc.bcm.edu	37	4	42127600	42127600	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:42127600C>T	ENST00000502486.1	-	4	1725	c.1146G>A	c.(1144-1146)gaG>gaA	p.E382E	BEND4_ENST00000504360.1_Splice_Site_p.E378E	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	382										NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						AGAGACCTACCTCTGTCGGCT	0.453																																					p.E382E		Atlas-SNP	.											.	BEND4	67	.	0			c.G1146A						.						101.0	105.0	104.0					4																	42127600		1933	4128	6061	SO:0001630	splice_region_variant	389206	exon4			ACCTACCTCTGTC	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"""BEN domain containing"""	23815	protein-coding gene	gene with protein product			"""coiled-coil domain containing 4"""	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.1146+1G>A	chr4.hg19:g.42127600C>T		137.0	0.0		78.0	4.0	NM_001159547	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Silent	SNP	ENST00000502486.1	hg19	CCDS47048.1																																																																																			.	.		0.453	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406	Silent
DCUN1D4	23142	hgsc.bcm.edu	37	4	52740446	52740446	+	Missense_Mutation	SNP	G	G	T	rs142966675		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:52740446G>T	ENST00000334635.5	+	4	326	c.146G>T	c.(145-147)cGg>cTg	p.R49L	DCUN1D4_ENST00000451288.2_Missense_Mutation_p.R93L|DCUN1D4_ENST00000381437.4_5'UTR|DCUN1D4_ENST00000381441.3_Missense_Mutation_p.R49L|DCUN1D4_ENST00000513800.1_3'UTR	NM_001040402.1	NP_001035492.1	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 4	49						nucleus (GO:0005634)		p.R49P(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	9			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)			GGAAGTCTGCGGTCTTGCAGT	0.383													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17024	0.0		0.0	False		,,,				2504	0.0				p.R49L		Atlas-SNP	.											DCUN1D4,NS,carcinoma,0,1	DCUN1D4	26	.	1	Substitution - Missense(1)	ovary(1)	c.G146T						.	G	LEU/ARG,LEU/ARG	1,4405	2.1+/-5.4	0,1,2202	125.0	122.0	123.0		146,146	4.3	1.0	4	dbSNP_134	123	0,8600		0,0,4300	no	missense,missense	DCUN1D4	NM_001040402.1,NM_015115.2	102,102	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	49/293,49/258	52740446	1,13005	2203	4300	6503	SO:0001583	missense	23142	exon4			GTCTGCGGTCTTG	D87466	CCDS3487.2, CCDS33982.1, CCDS75123.1	4q11	2013-06-10	2013-06-10		ENSG00000109184	ENSG00000109184			28998	protein-coding gene	gene with protein product		612977	"""DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)"""			15988528	Standard	XM_005265731		Approved	KIAA0276	uc003gze.3	Q92564	OTTHUMG00000128700	ENST00000334635.5:c.146G>T	chr4.hg19:g.52740446G>T	ENSP00000334625:p.Arg49Leu	39.0	0.0		32.0	4.0	NM_015115	B4DH25|Q7Z3F3|Q7Z6B8	Missense_Mutation	SNP	ENST00000334635.5	hg19	CCDS33982.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.077896	0.76528	2.27E-4	0.0	ENSG00000109184	ENST00000334635;ENST00000381441;ENST00000505403;ENST00000451288	.	.	.	5.18	4.34	0.51931	.	0.394763	0.26971	N	0.021575	T	0.40743	0.1129	N	0.22421	0.69	0.80722	D	1	P;P;P	0.42785	0.499;0.79;0.473	B;B;B	0.43838	0.072;0.433;0.122	T	0.13899	-1.0492	9	0.25751	T	0.34	-8.7843	11.2283	0.48897	0.0843:0.0:0.9157:0.0	.	93;49;49	B4DH25;Q92564-2;Q92564	.;.;DCNL4_HUMAN	L	49;49;93;93	.	ENSP00000334625:R49L	R	+	2	0	DCUN1D4	52435203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.188000	0.77739	1.194000	0.43101	0.651000	0.88453	CGG	.	G|1.000;T|0.000		0.383	DCUN1D4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250599.2	NM_015115	
SPATA18	132671	hgsc.bcm.edu	37	4	52917894	52917894	+	Silent	SNP	G	G	A	rs151044158		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:52917894G>A	ENST00000295213.4	+	1	398	c.24G>A	c.(22-24)ctG>ctA	p.L8L	SPATA18_ENST00000506829.1_3'UTR|SPATA18_ENST00000419395.2_Silent_p.L8L	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	8					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TGAAAAGACTGGTCTCAAACG	0.582																																					p.L8L		Atlas-SNP	.											SPATA18_ENST00000295213,NS,carcinoma,0,2	SPATA18	222	.	0			c.G24A						.						132.0	127.0	129.0					4																	52917894		2203	4300	6503	SO:0001819	synonymous_variant	132671	exon1			AAGACTGGTCTCA	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"""spermatogenesis associated 18 homolog (rat)"""			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.24G>A	chr4.hg19:g.52917894G>A		60.0	0.0		41.0	2.0	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Silent	SNP	ENST00000295213.4	hg19	CCDS3489.1																																																																																			.	G|1.000;C|0.000		0.582	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263	
UBA6	55236	hgsc.bcm.edu	37	4	68534270	68534270	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:68534270C>A	ENST00000322244.5	-	9	851	c.792G>T	c.(790-792)acG>acT	p.T264T	UBA6_ENST00000420827.2_Splice_Site_p.T264T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	264					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						TTGACTTACCCGTTATTTGTT	0.338																																					p.T264T		Atlas-SNP	.											.	UBA6	98	.	0			c.G792T						.						114.0	111.0	112.0					4																	68534270		2202	4300	6502	SO:0001630	splice_region_variant	55236	exon9			CTTACCCGTTATT	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.793+1G>T	chr4.hg19:g.68534270C>A		153.0	0.0		114.0	5.0	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	hg19	CCDS3516.1																																																																																			.	.		0.338	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	Silent
UGT2A1	10941	hgsc.bcm.edu	37	4	70504773	70504773	+	Intron	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:70504773G>T	ENST00000503640.1	-	1	771				UGT2A1_ENST00000512704.1_Intron|UGT2A1_ENST00000286604.4_Intron|UGT2A1_ENST00000514019.1_Missense_Mutation_p.P397T|UGT2A2_ENST00000457664.2_Missense_Mutation_p.P196T	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus						cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						ACTGGTGCTGGGATTTTCCCA	0.428																																					p.P397T		Atlas-SNP	.											.	UGT2A1	131	.	0			c.C1189A						.						54.0	56.0	56.0					4																	70504773		1971	4172	6143	SO:0001627	intron_variant	10941	exon3			GTGCTGGGATTTT	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"""UDP glucuronosyltransferases"""	12542	protein-coding gene	gene with protein product		604716	"""UDP glycosyltransferase 2 family, polypeptide A1"", ""UDP glucuronosyltransferase 2 family, polypeptide A1"""			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.715+7874C>A	chr4.hg19:g.70504773G>T		195.0	0.0		100.0	4.0	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	hg19	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510468	0.64522	.	.	ENSG00000173610	ENST00000457664;ENST00000514019	T;T	0.65364	-0.15;-0.15	5.98	5.98	0.97165	.	.	.	.	.	D	0.83501	0.5268	M	0.90759	3.145	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85693	0.1308	8	0.66056	D	0.02	.	17.9458	0.89038	0.0:0.0:1.0:0.0	.	397;196	E9PDM7;Q9Y4X1-2	.;.	T	196;397	ENSP00000387888:P196T;ENSP00000425497:P397T	ENSP00000387888:P196T	P	-	1	0	UGT2A1	70539362	1.000000	0.71417	0.993000	0.49108	0.558000	0.35554	9.004000	0.93583	2.838000	0.97847	0.591000	0.81541	CCA	.	.		0.428	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
ADAMTS3	9508	hgsc.bcm.edu	37	4	73179418	73179418	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:73179418C>A	ENST00000286657.4	-	12	1757	c.1721G>T	c.(1720-1722)aGa>aTa	p.R574I		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	574	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R574K(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CTGGCGTGTTCTGAAACGAAC	0.388																																					p.R574I	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											ADAMTS3,NS,carcinoma,0,1	ADAMTS3	164	.	1	Substitution - Missense(1)	endometrium(1)	c.G1721T						.						115.0	90.0	98.0					4																	73179418		2203	4300	6503	SO:0001583	missense	9508	exon12			CGTGTTCTGAAAC	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.1721G>T	chr4.hg19:g.73179418C>A	ENSP00000286657:p.Arg574Ile	117.0	0.0		68.0	3.0	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	34	5.379997	0.95945	.	.	ENSG00000156140	ENST00000286657	T	0.80909	-1.43	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	D	0.94272	0.8160	H	0.98133	4.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95070	0.8203	10	0.56958	D	0.05	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	574	O15072	ATS3_HUMAN	I	574	ENSP00000286657:R574I	ENSP00000286657:R574I	R	-	2	0	ADAMTS3	73398282	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.857000	0.98124	0.650000	0.86243	AGA	.	.		0.388	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
CCDC158	339965	hgsc.bcm.edu	37	4	77255317	77255317	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:77255317A>G	ENST00000388914.3	-	18	2820	c.2668T>C	c.(2668-2670)Tct>Cct	p.S890P		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	890										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						GCTTTTGTAGAGTGCTGAGTT	0.373																																					p.S890P		Atlas-SNP	.											.	CCDC158	114	.	0			c.T2668C						.						153.0	145.0	148.0					4																	77255317		1891	4122	6013	SO:0001583	missense	339965	exon18			TTGTAGAGTGCTG	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.2668T>C	chr4.hg19:g.77255317A>G	ENSP00000373566:p.Ser890Pro	174.0	0.0		124.0	5.0	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	hg19	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	A	6.993	0.553351	0.13374	.	.	ENSG00000163749	ENST00000388914	T	0.33216	1.42	5.19	4.01	0.46588	.	0.308471	0.23670	N	0.045733	T	0.13628	0.0330	N	0.08118	0	0.80722	D	1	B	0.14805	0.011	B	0.13407	0.009	T	0.10497	-1.0627	10	0.26408	T	0.33	.	6.204	0.20591	0.8875:0.0:0.1125:0.0	.	890	Q5M9N0	CD158_HUMAN	P	890	ENSP00000373566:S890P	ENSP00000373566:S890P	S	-	1	0	CCDC158	77474341	0.998000	0.40836	0.982000	0.44146	0.035000	0.12851	1.977000	0.40589	2.188000	0.69820	0.533000	0.62120	TCT	.	.		0.373	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
SHROOM3	57619	hgsc.bcm.edu	37	4	77660862	77660862	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:77660862T>C	ENST00000296043.6	+	5	2489	c.1536T>C	c.(1534-1536)gcT>gcC	p.A512A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	512					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			ACAAGATGGCTACCATTGATG	0.537																																					p.A512A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T1536C						.						119.0	120.0	119.0					4																	77660862		2203	4300	6503	SO:0001819	synonymous_variant	57619	exon5			GATGGCTACCATT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1536T>C	chr4.hg19:g.77660862T>C		93.0	0.0		54.0	4.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.		0.537	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
FRAS1	80144	hgsc.bcm.edu	37	4	79284759	79284759	+	Missense_Mutation	SNP	G	G	T	rs199918192		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:79284759G>T	ENST00000325942.6	+	21	2955	c.2515G>T	c.(2515-2517)Ggg>Tgg	p.G839W	FRAS1_ENST00000264895.6_Missense_Mutation_p.G839W	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	839					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CCTGCTGCTCGGGGACCACTG	0.572																																					p.G839W		Atlas-SNP	.											.	FRAS1	779	.	0			c.G2515T						.						43.0	43.0	43.0					4																	79284759		2074	4209	6283	SO:0001583	missense	80144	exon21			CTGCTCGGGGACC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.2515G>T	chr4.hg19:g.79284759G>T	ENSP00000326330:p.Gly839Trp	134.0	0.0		77.0	4.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134900	0.56828	.	.	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.32988	1.43;2.5	5.12	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.66557	0.2801	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.75260	-0.3380	10	0.72032	D	0.01	.	10.6501	0.45642	0.1542:0.0:0.8458:0.0	.	839;839	E9PHH6;A2RRR8	.;.	W	839	ENSP00000326330:G839W;ENSP00000264895:G839W	ENSP00000264895:G839W	G	+	1	0	FRAS1	79503783	1.000000	0.71417	0.378000	0.26068	0.725000	0.41563	4.170000	0.58229	1.163000	0.42636	0.585000	0.79938	GGG	.	.		0.572	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
FRAS1	80144	hgsc.bcm.edu	37	4	79455681	79455681	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:79455681C>A	ENST00000264895.6	+	71	11444	c.11004C>A	c.(11002-11004)ctC>ctA	p.L3668L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3664					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AATTTCAGCTCTGCAATAATG	0.418																																					p.L3668L		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11004A						.						169.0	153.0	158.0					4																	79455681		1907	4119	6026	SO:0001819	synonymous_variant	80144	exon71			TCAGCTCTGCAAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11004C>A	chr4.hg19:g.79455681C>A		140.0	0.0		79.0	4.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	8.382	0.837726	0.16891	.	.	ENSG00000138759	ENST00000512123	T	0.66995	-0.24	5.29	1.07	0.20283	.	0.000000	0.64402	D	0.000003	T	0.69744	0.3145	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69339	-0.5171	7	0.87932	D	0	.	7.3831	0.26868	0.1098:0.4326:0.3864:0.0711	.	.	.	.	M	1897	ENSP00000422834:L1897M	ENSP00000422834:L1897M	L	+	1	2	FRAS1	79674705	0.945000	0.32115	1.000000	0.80357	0.995000	0.86356	0.050000	0.14120	0.542000	0.28846	0.591000	0.81541	CTG	.	.		0.418	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CDS1	1040	hgsc.bcm.edu	37	4	85562071	85562071	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:85562071A>G	ENST00000295887.5	+	10	1383	c.960A>G	c.(958-960)gaA>gaG	p.E320E		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		TCGTGACAGAATGTGAGCCCT	0.413																																					p.E320E		Atlas-SNP	.											.	CDS1	58	.	0			c.A960G						.						161.0	149.0	153.0					4																	85562071		2203	4300	6503	SO:0001819	synonymous_variant	1040	exon10			GACAGAATGTGAG	U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.960A>G	chr4.hg19:g.85562071A>G		167.0	0.0		98.0	4.0	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000295887.5	hg19	CCDS3608.1																																																																																			.	.		0.413	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2		
KLHL8	57563	hgsc.bcm.edu	37	4	88098001	88098001	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:88098001A>G	ENST00000273963.5	-	6	1457	c.1116T>C	c.(1114-1116)ggT>ggC	p.G372G	KLHL8_ENST00000512111.1_Silent_p.G372G|KLHL8_ENST00000498875.2_Silent_p.G296G|KLHL8_ENST00000425278.2_Silent_p.G189G|KLHL8_ENST00000545252.1_Silent_p.G21G	NM_020803.3	NP_065854.3	Q9P2G9	KLHL8_HUMAN	kelch-like family member 8	372					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		CATCATGTCCACCTACTGCAT	0.313																																					p.G372G		Atlas-SNP	.											.	KLHL8	51	.	0			c.T1116C						.						203.0	183.0	190.0					4																	88098001		2203	4300	6503	SO:0001819	synonymous_variant	57563	exon6			ATGTCCACCTACT	AB037799	CCDS3617.1, CCDS75163.1	4q21.3	2013-01-30	2013-01-30		ENSG00000145332	ENSG00000145332		"""Kelch-like"", ""BTB/POZ domain containing"""	18644	protein-coding gene	gene with protein product		611967	"""kelch-like 8 (Drosophila)"""				Standard	XM_005263153		Approved	KIAA1378	uc003hql.1	Q9P2G9	OTTHUMG00000130593	ENST00000273963.5:c.1116T>C	chr4.hg19:g.88098001A>G		156.0	0.0		97.0	4.0	NM_020803	Q53XA3|Q6N018	Silent	SNP	ENST00000273963.5	hg19	CCDS3617.1																																																																																			.	.		0.313	KLHL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253040.1		
HERC3	8916	hgsc.bcm.edu	37	4	89591124	89591124	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:89591124T>C	ENST00000402738.1	+	15	1986	c.1747T>C	c.(1747-1749)Ttt>Ctt	p.F583L	HERC3_ENST00000543130.1_Missense_Mutation_p.F27L|HERC3_ENST00000264345.3_Missense_Mutation_p.F583L	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	583					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TCCCGTACTGTTTAACAATTA	0.418																																					p.F583L		Atlas-SNP	.											.	HERC3	82	.	0			c.T1747C						.						115.0	116.0	116.0					4																	89591124		2203	4300	6503	SO:0001583	missense	8916	exon15			GTACTGTTTAACA	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"""hect domain and RLD 3"""			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1747T>C	chr4.hg19:g.89591124T>C	ENSP00000385684:p.Phe583Leu	136.0	0.0		81.0	4.0	NM_014606	A8K1S5|Q8IXX3	Missense_Mutation	SNP	ENST00000402738.1	hg19	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.956114	0.53293	.	.	ENSG00000138641	ENST00000402738;ENST00000264345;ENST00000543130	T;T;T	0.38401	1.14;1.14;1.36	5.08	5.08	0.68730	.	0.111220	0.64402	D	0.000005	T	0.24198	0.0586	N	0.19112	0.55	0.43471	D	0.995686	B	0.14805	0.011	B	0.17979	0.02	T	0.06826	-1.0805	10	0.12103	T	0.63	.	15.313	0.74048	0.0:0.0:0.0:1.0	.	583	Q15034	HERC3_HUMAN	L	583;583;27	ENSP00000385684:F583L;ENSP00000264345:F583L;ENSP00000441703:F27L	ENSP00000264345:F583L	F	+	1	0	HERC3	89810147	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.509000	0.45459	2.261000	0.74972	0.533000	0.62120	TTT	.	.		0.418	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606	
NAP1L5	266812	hgsc.bcm.edu	37	4	89618533	89618533	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:89618533C>T	ENST00000323061.5	-	1	853	c.373G>A	c.(373-375)Ggc>Agc	p.G125S	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000402738.1_Intron|HERC3_ENST00000264345.3_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	125	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		TCCATCTCGCCGGTGAGCTCT	0.517																																					p.G125S		Atlas-SNP	.											.	NAP1L5	23	.	0			c.G373A						.						64.0	67.0	66.0					4																	89618533		2203	4300	6503	SO:0001583	missense	266812	exon1			TCTCGCCGGTGAG	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.373G>A	chr4.hg19:g.89618533C>T	ENSP00000320488:p.Gly125Ser	173.0	0.0		100.0	4.0	NM_153757		Missense_Mutation	SNP	ENST00000323061.5	hg19	CCDS3632.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.474854	0.43942	.	.	ENSG00000177432	ENST00000323061;ENST00000539293	T	0.23147	1.92	3.61	1.12	0.20585	.	.	.	.	.	T	0.23410	0.0566	M	0.85197	2.74	0.22317	N	0.999202	P	0.42757	0.789	B	0.29440	0.102	T	0.20107	-1.0285	9	0.33141	T	0.24	-8.3765	5.2981	0.15764	0.0:0.6275:0.0:0.3725	.	125	Q96NT1	NP1L5_HUMAN	S	125	ENSP00000320488:G125S	ENSP00000320488:G125S	G	-	1	0	NAP1L5	89837556	0.740000	0.28207	0.921000	0.36526	0.994000	0.84299	0.735000	0.26115	0.328000	0.23435	0.446000	0.29264	GGC	.	.		0.517	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757	
CCSER1	401145	hgsc.bcm.edu	37	4	91230222	91230222	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:91230222T>C	ENST00000509176.1	+	2	1075	c.787T>C	c.(787-789)Ttg>Ctg	p.L263L	CCSER1_ENST00000333691.8_Silent_p.L263L|CCSER1_ENST00000432775.2_Silent_p.L263L	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	263																	ATTTTTAGCCTTGACTGAAGA	0.433																																					p.L263L		Atlas-SNP	.											.	.	.	.	0			c.T787C						.						151.0	140.0	143.0					4																	91230222		1859	4119	5978	SO:0001819	synonymous_variant	401145	exon2			TTAGCCTTGACTG		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.787T>C	chr4.hg19:g.91230222T>C		46.0	0.0		31.0	4.0	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	hg19	CCDS47099.1																																																																																			.	.		0.433	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
TSPAN5	10098	hgsc.bcm.edu	37	4	99408000	99408000	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:99408000G>T	ENST00000305798.3	-	3	570	c.168C>A	c.(166-168)ctC>ctA	p.L56L	TSPAN5_ENST00000505184.1_5'UTR|TSPAN5_ENST00000509168.1_5'UTR	NM_005723.3	NP_005714.2	P62079	TSN5_HUMAN	tetraspanin 5	56					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)	p.L56L(1)		kidney(2)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		CAAAGCCGCCGAGATCGGTGA	0.512																																					p.L56L		Atlas-SNP	.											TSPAN5,NS,carcinoma,0,1	TSPAN5	32	.	1	Substitution - coding silent(1)	lung(1)	c.C168A						.						142.0	139.0	140.0					4																	99408000		2203	4300	6503	SO:0001819	synonymous_variant	10098	exon3			GCCGCCGAGATCG		CCDS3646.1	4q22.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000168785	ENSG00000168785		"""Tetraspanins"""	17753	protein-coding gene	gene with protein product		613136	"""transmembrane 4 superfamily member 9"""	TM4SF9			Standard	NM_005723		Approved	Tspan-5, NET-4	uc003hub.3	P62079	OTTHUMG00000131008	ENST00000305798.3:c.168C>A	chr4.hg19:g.99408000G>T		122.0	0.0		92.0	4.0	NM_005723	B2RDY2|O60628|O60746|Q6FHE5|Q9JLY1	Silent	SNP	ENST00000305798.3	hg19	CCDS3646.1																																																																																			.	.		0.512	TSPAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253641.2	NM_005723	
DAPP1	27071	hgsc.bcm.edu	37	4	100756811	100756811	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:100756811G>T	ENST00000512369.1	+	2	201	c.133G>T	c.(133-135)Gct>Tct	p.A45S	DAPP1_ENST00000296414.7_Missense_Mutation_p.A45S	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	45	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		ACGCCATGCTGCTGAAGCTCT	0.552																																					p.A45S		Atlas-SNP	.											.	DAPP1	47	.	0			c.G133T						.						147.0	146.0	146.0					4																	100756811		2096	4222	6318	SO:0001583	missense	27071	exon2			CATGCTGCTGAAG	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.133G>T	chr4.hg19:g.100756811G>T	ENSP00000423602:p.Ala45Ser	124.0	0.0		100.0	5.0	NM_014395	Q8TCK5|Q9UHF2	Missense_Mutation	SNP	ENST00000512369.1	hg19	CCDS47112.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399565	0.62177	.	.	ENSG00000070190	ENST00000296414;ENST00000512369	D;D	0.92099	-2.97;-2.97	5.9	5.9	0.94986	SH2 motif (5);	0.051911	0.85682	D	0.000000	D	0.95059	0.8400	L	0.59967	1.855	0.80722	D	1	P;D;D	0.76494	0.905;0.999;0.991	P;D;P	0.65443	0.751;0.935;0.876	D	0.93983	0.7260	10	0.44086	T	0.13	-0.2833	19.8893	0.96923	0.0:0.0:1.0:0.0	.	45;45;45	B4DW38;Q9UN19-2;Q9UN19	.;.;DAPP1_HUMAN	S	45	ENSP00000296414:A45S;ENSP00000423602:A45S	ENSP00000296414:A45S	A	+	1	0	DAPP1	100975834	1.000000	0.71417	0.060000	0.19600	0.017000	0.09413	8.816000	0.91979	2.788000	0.95919	0.650000	0.86243	GCT	.	.		0.552	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1		
TBCK	93627	hgsc.bcm.edu	37	4	107154107	107154107	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:107154107C>T	ENST00000273980.5	-	18	2074	c.1627G>A	c.(1627-1629)Gtg>Atg	p.V543M	TBCK_ENST00000361687.4_Missense_Mutation_p.V480M|TBCK_ENST00000394706.3_Missense_Mutation_p.V504M|TBCK_ENST00000394708.2_Missense_Mutation_p.V543M|TBCK_ENST00000432496.2_Missense_Mutation_p.V543M					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TGCCAATACACAAGATCAGGA	0.353																																					p.V543M		Atlas-SNP	.											.	TBCK	89	.	0			c.G1627A						.						117.0	113.0	115.0					4																	107154107		2203	4300	6503	SO:0001583	missense	93627	exon17			AATACACAAGATC		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1627G>A	chr4.hg19:g.107154107C>T	ENSP00000273980:p.Val543Met	195.0	0.0		87.0	4.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953603	0.92660	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708	T;T;T;T;T	0.04156	3.69;3.69;3.69;3.69;3.69	5.46	5.46	0.80206	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.29321	0.0730	M	0.88241	2.94	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.986;0.998	T	0.10245	-1.0638	10	0.87932	D	0	.	19.3032	0.94151	0.0:1.0:0.0:0.0	.	543;504;480	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	M	543;543;480;504;543	ENSP00000273980:V543M;ENSP00000405847:V543M;ENSP00000355338:V480M;ENSP00000378196:V504M;ENSP00000378198:V543M	ENSP00000273980:V543M	V	-	1	0	TBCK	107373556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.656000	0.83736	2.563000	0.86464	0.655000	0.94253	GTG	.	.		0.353	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
PAPSS1	9061	hgsc.bcm.edu	37	4	108576006	108576006	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:108576006C>T	ENST00000265174.4	-	8	1218	c.946G>A	c.(946-948)Gat>Aat	p.D316N	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	316					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		CTCTCTTTATCTTCATGAGTC	0.468																																					p.D316N		Atlas-SNP	.											.	PAPSS1	57	.	0			c.G946A						.						98.0	101.0	100.0					4																	108576006		2203	4300	6503	SO:0001583	missense	9061	exon8			CTTTATCTTCATG	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.946G>A	chr4.hg19:g.108576006C>T	ENSP00000265174:p.Asp316Asn	151.0	0.0		95.0	4.0	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	hg19	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377210	0.42105	.	.	ENSG00000138801	ENST00000265174	T	0.24151	1.87	5.72	5.72	0.89469	Sulphate adenylyltransferase (2);PUA-like domain (1);	0.130031	0.64402	D	0.000002	T	0.33177	0.0854	L	0.58583	1.82	0.80722	D	1	B	0.21309	0.054	B	0.26864	0.074	T	0.05954	-1.0854	10	0.51188	T	0.08	-19.2517	19.8968	0.96969	0.0:1.0:0.0:0.0	.	316	O43252	PAPS1_HUMAN	N	316	ENSP00000265174:D316N	ENSP00000265174:D316N	D	-	1	0	PAPSS1	108795455	1.000000	0.71417	0.734000	0.30879	0.071000	0.16799	3.445000	0.52921	2.691000	0.91804	0.655000	0.94253	GAT	.	.		0.468	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		
SEC24B	10427	hgsc.bcm.edu	37	4	110384380	110384380	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:110384380T>C	ENST00000265175.5	+	2	512	c.457T>C	c.(457-459)Tcc>Ccc	p.S153P	SEC24B_ENST00000504968.2_Missense_Mutation_p.S184P|SEC24B_ENST00000399100.2_Missense_Mutation_p.S153P	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	153					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CCAACCATACTCCTCTTTTGT	0.498																																					p.S153P		Atlas-SNP	.											.	SEC24B	186	.	0			c.T457C						.						267.0	257.0	260.0					4																	110384380		2045	4185	6230	SO:0001583	missense	10427	exon2			CCATACTCCTCTT	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.457T>C	chr4.hg19:g.110384380T>C	ENSP00000265175:p.Ser153Pro	140.0	0.0		103.0	5.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	T	13.36	2.213861	0.39102	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;D;T	0.82619	-1.18;-1.63;-1.38	4.5	0.453	0.16639	.	0.891618	0.09768	N	0.758401	T	0.67411	0.2890	N	0.24115	0.695	0.41022	D	0.985088	B;B;B;B	0.15141	0.001;0.012;0.002;0.007	B;B;B;B	0.09377	0.002;0.004;0.004;0.004	T	0.55860	-0.8074	10	0.30854	T	0.27	-3.8125	3.5609	0.07882	0.163:0.1809:0.0:0.656	.	103;184;153;153	B4DTM6;B7ZKM8;O95487-2;O95487	.;.;.;SC24B_HUMAN	P	184;153;153	ENSP00000428564:S184P;ENSP00000382051:S153P;ENSP00000265175:S153P	ENSP00000265175:S153P	S	+	1	0	SEC24B	110603829	0.954000	0.32549	0.988000	0.46212	0.993000	0.82548	0.162000	0.16501	0.163000	0.19507	0.260000	0.18958	TCC	.	.		0.498	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		
SEC24B	10427	hgsc.bcm.edu	37	4	110453794	110453794	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:110453794G>T	ENST00000265175.5	+	21	3445		c.e21-1		SEC24B_ENST00000504968.2_Splice_Site|SEC24B_ENST00000399100.2_Splice_Site	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		TTTCTTTTCAGGGTGCAGTAC	0.398																																					.		Atlas-SNP	.											.	SEC24B	186	.	0			c.3391-1G>T						.						111.0	102.0	105.0					4																	110453794		1892	4113	6005	SO:0001630	splice_region_variant	10427	exon21			TTTTCAGGGTGCA	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"""SEC24 (S. cerevisiae) related gene family, member B"", ""SEC24 family, member B (S. cerevisiae)"""			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.3391-1G>T	chr4.hg19:g.110453794G>T		85.0	0.0		49.0	4.0	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Splice_Site	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323452	0.81580	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6544	0.95831	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEC24B	110673243	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	9.244000	0.95423	2.647000	0.89833	0.467000	0.42956	.	.	.		0.398	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2		Intron
AP1AR	55435	hgsc.bcm.edu	37	4	113174413	113174413	+	Splice_Site	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:113174413G>A	ENST00000274000.5	+	2	487		c.e2+1		AP1AR_ENST00000309703.6_Splice_Site	NM_018569.4	NP_061039.3	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated regulatory protein						cellular protein localization (GO:0034613)|negative regulation of cell motility (GO:2000146)|negative regulation of receptor recycling (GO:0001920)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|protein transport (GO:0015031)|regulation of Arp2/3 complex-mediated actin nucleation (GO:0034315)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|transport vesicle (GO:0030133)	AP-1 adaptor complex binding (GO:0035650)|kinesin binding (GO:0019894)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	9						AACAATAGAGGTAAGTAGTCC	0.353																																					.		Atlas-SNP	.											.	AP1AR	25	.	0			c.132+1G>A						.						62.0	64.0	63.0					4																	113174413		2203	4299	6502	SO:0001630	splice_region_variant	55435	exon2			ATAGAGGTAAGTA	AL136628	CCDS3696.1, CCDS47125.1	4q25	2009-09-28	2009-09-25	2009-09-25	ENSG00000138660	ENSG00000138660			28808	protein-coding gene	gene with protein product	"""gamma1-adaptin brefeldin A resistance"""	610851	"""chromosome 4 open reading frame 16"""	C4orf16		15775984	Standard	NM_018569		Approved	PRO0971, 2C18, gamma-BAR	uc003iaj.4	Q63HQ0	OTTHUMG00000132849	ENST00000274000.5:c.132+1G>A	chr4.hg19:g.113174413G>A		126.0	0.0		83.0	5.0	NM_001128426	B2RCV7|Q96GG6|Q9H0V0|Q9P1L4	Splice_Site	SNP	ENST00000274000.5	hg19	CCDS3696.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416841	0.83449	.	.	ENSG00000138660	ENST00000274000;ENST00000309703	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2417	0.93887	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AP1AR	113393862	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.582000	0.82546	2.619000	0.88677	0.650000	0.86243	.	.	.		0.353	AP1AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256323.2	NM_018569	Intron
ALPK1	80216	hgsc.bcm.edu	37	4	113360847	113360847	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:113360847A>G	ENST00000458497.1	+	14	3636	c.3357A>G	c.(3355-3357)ttA>ttG	p.L1119L	ALPK1_ENST00000177648.9_Silent_p.L1119L|ALPK1_ENST00000504176.2_Silent_p.L1041L	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	1119	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TTCAGATTTTAGAGGACAAGA	0.373																																					p.L1119L		Atlas-SNP	.											.	ALPK1	125	.	0			c.A3357G						.						92.0	82.0	86.0					4																	113360847		2202	4300	6502	SO:0001819	synonymous_variant	80216	exon14			GATTTTAGAGGAC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.3357A>G	chr4.hg19:g.113360847A>G		148.0	0.0		89.0	4.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	hg19	CCDS3697.1																																																																																			.	.		0.373	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
ANK2	287	hgsc.bcm.edu	37	4	114095576	114095576	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:114095576A>G	ENST00000357077.4	+	2	142	c.89A>G	c.(88-90)gAc>gGc	p.D30G	ANK2_ENST00000506722.1_Missense_Mutation_p.D9G|ANK2_ENST00000264366.6_Missense_Mutation_p.D30G|ANK2_ENST00000394537.3_Missense_Mutation_p.D30G	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	30					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TCGCAGTCTGACAGCAATGCA	0.408																																					p.D30G		Atlas-SNP	.											.	ANK2	576	.	0			c.A89G						.						59.0	54.0	56.0					4																	114095576		2203	4300	6503	SO:0001583	missense	287	exon2			AGTCTGACAGCAA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.89A>G	chr4.hg19:g.114095576A>G	ENSP00000349588:p.Asp30Gly	200.0	0.0		95.0	4.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502551	0.85176	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000508613;ENST00000511380;ENST00000343056	T;T;T;T;T;T;T;T;T	0.69685	1.82;-0.13;-0.38;-0.32;-0.38;-0.41;-0.42;-0.38;-0.38	5.54	5.54	0.83059	Ankyrin repeat-containing domain (2);	0.000000	0.53938	D	0.000052	T	0.81004	0.4733	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.996	D;D;D;D;D	0.91635	0.998;0.999;0.999;0.998;0.987	T	0.83334	-0.0011	10	0.87932	D	0	.	15.3587	0.74453	1.0:0.0:0.0:0.0	.	30;30;30;9;9	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	G	9;9;9;45;30;30;30;45;47;9	ENSP00000423799:D9G;ENSP00000421011:D9G;ENSP00000421067:D9G;ENSP00000424722:D45G;ENSP00000378044:D30G;ENSP00000349588:D30G;ENSP00000264366:D30G;ENSP00000422900:D45G;ENSP00000425775:D47G	ENSP00000264366:D30G	D	+	2	0	ANK2	114315025	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	9.067000	0.93955	2.098000	0.63641	0.533000	0.62120	GAC	.	.		0.408	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
ANK2	287	hgsc.bcm.edu	37	4	114279607	114279607	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:114279607C>A	ENST00000357077.4	+	38	9886	c.9833C>A	c.(9832-9834)cCa>cAa	p.P3278Q	ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.P3245Q|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3278					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GATTCTTCCCCAGAAGAACAG	0.443																																					p.P3278Q		Atlas-SNP	.											.	ANK2	576	.	0			c.C9833A						.						101.0	98.0	99.0					4																	114279607		2203	4300	6503	SO:0001583	missense	287	exon38			CTTCCCCAGAAGA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.9833C>A	chr4.hg19:g.114279607C>A	ENSP00000349588:p.Pro3278Gln	146.0	0.0		116.0	6.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980398	0.74474	.	.	ENSG00000145362	ENST00000357077;ENST00000264366;ENST00000505342	T;T;D	0.96265	-0.33;-0.34;-3.96	5.71	5.71	0.89125	.	0.000000	0.56097	D	0.000024	D	0.97854	0.9295	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96981	0.9715	10	0.32370	T	0.25	.	19.8625	0.96789	0.0:1.0:0.0:0.0	.	3245;3278	Q01484;Q01484-4	ANK2_HUMAN;.	Q	3278;3245;288	ENSP00000349588:P3278Q;ENSP00000264366:P3245Q;ENSP00000422498:P288Q	ENSP00000264366:P3245Q	P	+	2	0	ANK2	114499056	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.487000	0.81328	2.689000	0.91719	0.655000	0.94253	CCA	.	.		0.443	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
PRSS12	8492	hgsc.bcm.edu	37	4	119203115	119203115	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:119203115C>A	ENST00000296498.3	-	13	2886	c.2604G>T	c.(2602-2604)tgG>tgT	p.W868C	PRSS12_ENST00000510903.1_5'Flank|SNHG8_ENST00000384096.1_lincRNA	NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	868	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						CACTTTTTATCCAAGGTACAA	0.448																																					p.W868C		Atlas-SNP	.											.	PRSS12	71	.	0			c.G2604T						.						94.0	96.0	96.0					4																	119203115		2203	4300	6503	SO:0001583	missense	8492	exon13			TTTTATCCAAGGT	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"""Serine peptidases / Serine peptidases"""	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.2604G>T	chr4.hg19:g.119203115C>A	ENSP00000296498:p.Trp868Cys	81.0	0.0		64.0	4.0	NM_003619	Q9UP16	Missense_Mutation	SNP	ENST00000296498.3	hg19	CCDS3709.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.676123	0.88445	.	.	ENSG00000164099	ENST00000296498	D	0.99121	-5.45	6.17	6.17	0.99709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.99616	0.9860	H	0.97186	3.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97998	1.0358	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	868	P56730	NETR_HUMAN	C	868	ENSP00000296498:W868C	ENSP00000296498:W868C	W	-	3	0	PRSS12	119422563	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.941000	0.99782	0.655000	0.94253	TGG	.	.		0.448	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2		
SEC24D	9871	hgsc.bcm.edu	37	4	119666159	119666159	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:119666159T>C	ENST00000280551.6	-	14	2002	c.1764A>G	c.(1762-1764)gaA>gaG	p.E588E	SEC24D_ENST00000511481.1_Silent_p.E219E|SEC24D_ENST00000429811.2_Silent_p.E144E|SEC24D_ENST00000505134.1_5'UTR|SEC24D_ENST00000419654.2_Silent_p.E144E|SEC24D_ENST00000379735.5_Silent_p.E589E			O94855	SC24D_HUMAN	SEC24 family member D	588					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)|in utero embryonic development (GO:0001701)|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(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						TCCCTGGTGCTTCAGCAGTTG	0.388																																					p.E588E		Atlas-SNP	.											.	SEC24D	96	.	0			c.A1764G						.						124.0	130.0	128.0					4																	119666159		2203	4300	6503	SO:0001819	synonymous_variant	9871	exon14			TGGTGCTTCAGCA	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.1764A>G	chr4.hg19:g.119666159T>C		252.0	0.0		170.0	7.0	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	hg19	CCDS3710.1																																																																																			.	.		0.388	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
MYOZ2	51778	hgsc.bcm.edu	37	4	120079175	120079175	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:120079175A>G	ENST00000307128.5	+	4	459		c.e4-1			NM_016599.4	NP_057683.1			myozenin 2											endometrium(1)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						GATTAAATACAGCACAGTATT	0.378																																					.		Atlas-SNP	.											.	MYOZ2	34	.	0			c.247-2A>G						.						101.0	102.0	102.0					4																	120079175		2203	4300	6503	SO:0001630	splice_region_variant	51778	exon4			AAATACAGCACAG	AF249873	CCDS3711.1	4q26-q27	2014-09-17	2002-01-07	2002-01-11	ENSG00000172399	ENSG00000172399			1330	protein-coding gene	gene with protein product		605602	"""chromosome 4 open reading frame 5"""	C4orf5		8619474, 9110174	Standard	NM_016599		Approved	CS-1	uc003icp.4	Q9NPC6	OTTHUMG00000132968	ENST00000307128.5:c.247-1A>G	chr4.hg19:g.120079175A>G		146.0	0.0		75.0	4.0	NM_016599		Splice_Site	SNP	ENST00000307128.5	hg19	CCDS3711.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592099	0.66219	.	.	ENSG00000172399	ENST00000307128	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9541	0.79871	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MYOZ2	120298623	1.000000	0.71417	0.997000	0.53966	0.806000	0.45545	5.215000	0.65241	2.163000	0.67991	0.533000	0.62120	.	.	.		0.378	MYOZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256526.2		Intron
KIAA1109	84162	hgsc.bcm.edu	37	4	123280777	123280777	+	Missense_Mutation	SNP	G	G	T	rs368229897		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:123280777G>T	ENST00000264501.4	+	85	15074	c.14701G>T	c.(14701-14703)Gac>Tac	p.D4901Y	KIAA1109_ENST00000388738.3_Missense_Mutation_p.D4901Y			Q2LD37	K1109_HUMAN	KIAA1109	4901					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TATACATGACGACAATTCCTC	0.348																																					p.D4901Y		Atlas-SNP	.											KIAA1109,colon,carcinoma,0,1	KIAA1109	424	.	0			c.G14701T						.	G	TYR/ASP	0,3686		0,0,1843	127.0	113.0	118.0		14701	5.9	1.0	4		118	1,8177		0,1,4088	no	missense	KIAA1109	NM_015312.3	160	0,1,5931	TT,TG,GG		0.0122,0.0,0.0084	possibly-damaging	4901/5006	123280777	1,11863	1843	4089	5932	SO:0001583	missense	84162	exon83			CATGACGACAATT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14701G>T	chr4.hg19:g.123280777G>T	ENSP00000264501:p.Asp4901Tyr	136.0	0.0		70.0	3.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.443890	0.83993	0.0	1.22E-4	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755	T;T;T	0.48836	0.8;0.8;0.8	5.94	5.94	0.96194	Fragile site-associated protein, C-terminal (1);	0.334301	0.34879	N	0.003608	T	0.49949	0.1587	N	0.19112	0.55	0.80722	D	1	P;P	0.46512	0.693;0.879	P;P	0.52267	0.47;0.694	T	0.49799	-0.8901	10	0.56958	D	0.05	.	20.3731	0.98895	0.0:0.0:1.0:0.0	.	4900;4901	Q2LD37-4;Q2LD37	.;K1109_HUMAN	Y	4901;4901;1570;502	ENSP00000264501:D4901Y;ENSP00000373390:D4901Y;ENSP00000410874:D1570Y	ENSP00000264501:D4901Y	D	+	1	0	KIAA1109	123500227	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.271000	0.72569	2.829000	0.97493	0.650000	0.86243	GAC	.	.		0.348	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
FAT4	79633	hgsc.bcm.edu	37	4	126328107	126328107	+	Nonsense_Mutation	SNP	G	G	T	rs200789529		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:126328107G>T	ENST00000394329.3	+	3	5393	c.5380G>T	c.(5380-5382)Gga>Tga	p.G1794*	FAT4_ENST00000335110.5_Nonsense_Mutation_p.G92*	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1794	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCCAGAATCCGGAGATCTGAT	0.473																																					p.G1794X		Atlas-SNP	.											FAT4_ENST00000394329,caecum,carcinoma,0,2	FAT4	1752	.	0			c.G5380T						.						130.0	123.0	125.0					4																	126328107		2203	4300	6503	SO:0001587	stop_gained	79633	exon3			GAATCCGGAGATC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5380G>T	chr4.hg19:g.126328107G>T	ENSP00000377862:p.Gly1794*	164.0	1.0		94.0	4.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Nonsense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	46	12.534214	0.99675	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	.	.	.	5.28	5.28	0.74379	.	0.000000	0.33610	U	0.004730	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.2767	0.94034	0.0:0.0:1.0:0.0	.	.	.	.	X	1794;92	.	ENSP00000335169:G92X	G	+	1	0	FAT4	126547557	1.000000	0.71417	0.990000	0.47175	0.597000	0.36814	9.365000	0.97139	2.622000	0.88805	0.585000	0.79938	GGA	.	.		0.473	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
ELF2	1998	hgsc.bcm.edu	37	4	139981781	139981781	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:139981781A>G	ENST00000394235.2	-	9	1320	c.818T>C	c.(817-819)cTt>cCt	p.L273P	ELF2_ENST00000265495.4_Missense_Mutation_p.L273P|ELF2_ENST00000515489.1_5'Flank|ELF2_ENST00000510408.1_Missense_Mutation_p.L213P|ELF2_ENST00000358635.3_Missense_Mutation_p.L225P|ELF2_ENST00000379550.1_Missense_Mutation_p.L285P|ELF2_ENST00000379549.2_Missense_Mutation_p.L196P	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					CTGATATACAAGCCTCTGTCC	0.368																																					p.H225P		Atlas-SNP	.											.	ELF2	43	.	0			c.A674C						.						105.0	106.0	105.0					4																	139981781		2203	4300	6503	SO:0001583	missense	1998	exon6			TATACAAGCCTCT	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.818T>C	chr4.hg19:g.139981781A>G	ENSP00000377782:p.Leu273Pro	154.0	0.0		96.0	4.0	NM_006874		Missense_Mutation	SNP	ENST00000394235.2	hg19	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.707552	0.89018	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000540754;ENST00000510408;ENST00000420916;ENST00000512627	T;T;T;T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.60715	0.2290	M	0.91972	3.26	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.992;1.0;0.999;0.992	D;D;D;D;D	0.91635	0.995;0.945;0.994;0.999;0.945	T	0.70378	-0.4888	9	.	.	.	.	16.0102	0.80396	1.0:0.0:0.0:0.0	.	88;273;196;213;225	B7Z8R4;Q15723-1;E9PCX3;B7Z720;Q15723-3	.;.;.;.;.	P	225;273;285;273;196;88;213;196;184	ENSP00000351458:L225P;ENSP00000377782:L273P;ENSP00000368868:L285P;ENSP00000265495:L273P;ENSP00000368867:L196P;ENSP00000426997:L213P;ENSP00000397796:L196P;ENSP00000426087:L184P	.	L	-	2	0	ELF2	140201231	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.336000	0.96533	2.190000	0.69967	0.533000	0.62120	CTT	.	.		0.368	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874	
USP38	84640	hgsc.bcm.edu	37	4	144135131	144135131	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:144135131A>G	ENST00000307017.4	+	9	2508	c.2002A>G	c.(2002-2004)Atc>Gtc	p.I668V	USP38_ENST00000510377.1_Missense_Mutation_p.I668V	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	668	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					AGCTGCCTTCATCTGTGACTC	0.418																																					p.I668V		Atlas-SNP	.											USP38,NS,carcinoma,0,1	USP38	92	.	0			c.A2002G						.						141.0	154.0	150.0					4																	144135131		2203	4299	6502	SO:0001583	missense	84640	exon9			GCCTTCATCTGTG	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"""Ubiquitin-specific peptidases"""	20067	protein-coding gene	gene with protein product			"""ubiquitin specific protease 38"""			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2002A>G	chr4.hg19:g.144135131A>G	ENSP00000303434:p.Ile668Val	92.0	1.0		66.0	3.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	A	3.162	-0.171904	0.06421	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.07567	3.18;3.19	5.52	3.71	0.42584	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.432949	0.23521	N	0.047300	T	0.02230	0.0069	N	0.00621	-1.32	0.20403	N	0.999903	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42716	-0.9435	10	0.27785	T	0.31	-8.4565	6.1744	0.20434	0.1693:0.0:0.6825:0.1482	.	668;668	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	V	668	ENSP00000427647:I668V;ENSP00000303434:I668V	ENSP00000303434:I668V	I	+	1	0	USP38	144354581	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	3.018000	0.49625	0.602000	0.29896	0.477000	0.44152	ATC	.	.		0.418	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
MMAA	166785	hgsc.bcm.edu	37	4	146575291	146575291	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:146575291C>A	ENST00000281317.5	+	6	2175	c.965C>A	c.(964-966)cCa>cAa	p.P322Q	MMAA_ENST00000541599.1_Missense_Mutation_p.P41Q	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	322					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTCTGGAAACCAAAGGTAAGC	0.398																																					p.P322Q		Atlas-SNP	.											.	MMAA	46	.	0			c.C965A						.						125.0	116.0	119.0					4																	146575291		2203	4300	6503	SO:0001583	missense	166785	exon6			GGAAACCAAAGGT	AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"""methylmalonic aciduria (cobalamin deficiency) type A"""			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.965C>A	chr4.hg19:g.146575291C>A	ENSP00000281317:p.Pro322Gln	94.0	0.0		76.0	4.0	NM_172250	B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	hg19	CCDS3766.1	.	.	.	.	.	.	.	.	.	.	C	32	5.176237	0.94846	.	.	ENSG00000151611	ENST00000281317;ENST00000537246;ENST00000541599	D;D	0.92805	-3.11;-3.11	5.49	5.49	0.81192	.	0.050420	0.85682	D	0.000000	D	0.97195	0.9083	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97864	1.0282	10	0.87932	D	0	-14.0752	19.3608	0.94436	0.0:1.0:0.0:0.0	.	322	Q8IVH4	MMAA_HUMAN	Q	322;322;41	ENSP00000281317:P322Q;ENSP00000442284:P41Q	ENSP00000281317:P322Q	P	+	2	0	MMAA	146794741	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.456000	0.80751	2.572000	0.86782	0.650000	0.86243	CCA	.	.		0.398	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2		
ZNF827	152485	hgsc.bcm.edu	37	4	146744660	146744660	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:146744660T>C	ENST00000508784.1	-	8	2524	c.2297A>G	c.(2296-2298)gAc>gGc	p.D766G	ZNF827_ENST00000379448.4_Missense_Mutation_p.D766G|ZNF827_ENST00000513320.1_Missense_Mutation_p.D416G			Q17R98	ZN827_HUMAN	zinc finger protein 827	766					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					TCTAAATGTGTCTTCTGAAAA	0.443																																					p.D766G		Atlas-SNP	.											.	ZNF827	102	.	0			c.A2297G						.						128.0	131.0	130.0					4																	146744660		2203	4300	6503	SO:0001583	missense	152485	exon8			AATGTGTCTTCTG	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"""Zinc fingers, C2H2-type"""	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2297A>G	chr4.hg19:g.146744660T>C	ENSP00000421863:p.Asp766Gly	99.0	0.0		83.0	4.0	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.27	3.346311	0.61073	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280	T;T;T	0.08008	3.18;3.14;3.22	5.52	5.52	0.82312	.	0.135755	0.64402	D	0.000003	T	0.16128	0.0388	N	0.24115	0.695	0.47819	D	0.999528	P;D;P	0.63880	0.906;0.993;0.906	B;D;P	0.68192	0.418;0.956;0.52	T	0.02232	-1.1191	10	0.72032	D	0.01	-20.9382	13.1743	0.59617	0.0:0.0:0.0:1.0	.	416;766;766	G5E9Z1;Q17R98;Q17R98-2	.;ZN827_HUMAN;.	G	766;416;766;765;416	ENSP00000421863:D766G;ENSP00000423130:D416G;ENSP00000368761:D766G	ENSP00000281318:D765G	D	-	2	0	ZNF827	146964110	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	4.529000	0.60588	2.096000	0.63516	0.397000	0.26171	GAC	.	.		0.443	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835	
GATB	5188	hgsc.bcm.edu	37	4	152679945	152679945	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:152679945T>C	ENST00000515812.1	-	2	322	c.306A>G	c.(304-306)gcA>gcG	p.A102A	PET112_ENST00000263985.6_Silent_p.A102A|PET112_ENST00000512306.1_Silent_p.A102A|PET112_ENST00000508611.1_Silent_p.A102A																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						CAGGTAGAGATGCATCAAAAA	0.323																																					p.A102A		Atlas-SNP	.											.	PET112	43	.	0			c.A306G						.						89.0	95.0	93.0					4																	152679945		2203	4300	6503	SO:0001819	synonymous_variant	5188	exon2			TAGAGATGCATCA																												ENST00000515812.1:c.306A>G	chr4.hg19:g.152679945T>C		100.0	0.0		89.0	4.0	NM_004564		Silent	SNP	ENST00000515812.1	hg19																																																																																				.	.		0.323	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
KIAA0922	23240	hgsc.bcm.edu	37	4	154524546	154524546	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:154524546A>G	ENST00000409663.3	+	24	2780	c.2728A>G	c.(2728-2730)Agc>Ggc	p.S910G	KIAA0922_ENST00000440693.1_Missense_Mutation_p.S827G|KIAA0922_ENST00000409959.3_Missense_Mutation_p.S911G	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	910	Poly-Ser.					integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				GCAAAATGCTAGCTCCTCTTC	0.438																																					p.S911G		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A2731G						.						168.0	154.0	159.0					4																	154524546		2203	4300	6503	SO:0001583	missense	23240	exon24			AATGCTAGCTCCT	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.2728A>G	chr4.hg19:g.154524546A>G	ENSP00000386574:p.Ser910Gly	247.0	0.0		171.0	147.0	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	A	10.73	1.433805	0.25813	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.19250	2.42;2.16;2.42;2.16	6.17	0.976	0.19727	.	0.397804	0.34853	N	0.003640	T	0.13072	0.0317	L	0.36672	1.1	0.09310	N	1	B;B;B	0.15719	0.014;0.002;0.001	B;B;B	0.12837	0.008;0.006;0.002	T	0.24012	-1.0172	10	0.26408	T	0.33	-3.2992	5.69	0.17825	0.6965:0.0:0.1887:0.1148	.	827;911;910	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	G	910;827;911;688	ENSP00000386574:S910G;ENSP00000409663:S827G;ENSP00000386787:S911G;ENSP00000240487:S688G	ENSP00000240487:S688G	S	+	1	0	KIAA0922	154743996	0.986000	0.35501	0.018000	0.16275	0.871000	0.50021	2.084000	0.41625	-0.033000	0.13736	0.533000	0.62120	AGC	.	.		0.438	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
KLHL2	11275	hgsc.bcm.edu	37	4	166226800	166226800	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:166226800G>T	ENST00000226725.6	+	9	1221	c.962G>T	c.(961-963)cGg>cTg	p.R321L	KLHL2_ENST00000514860.1_Missense_Mutation_p.R325L|KLHL2_ENST00000421009.2_Missense_Mutation_p.R224L|KLHL2_ENST00000509028.1_Intron|KLHL2_ENST00000506761.1_Missense_Mutation_p.R155L|KLHL2_ENST00000538127.1_Missense_Mutation_p.R233L	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	321					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		AAGGCTATCCGGAGTGTGGAA	0.458																																					p.R325L		Atlas-SNP	.											.	KLHL2	42	.	0			c.G974T						.						173.0	166.0	168.0					4																	166226800		2203	4300	6503	SO:0001583	missense	11275	exon9			CTATCCGGAGTGT	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"""Kelch-like"", ""BTB/POZ domain containing"""	6353	protein-coding gene	gene with protein product	"""mayven"""	605774	"""kelch (Drosophila)-like 2 (Mayven)"", ""kelch-like 2, Mayven (Drosophila)"""			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.962G>T	chr4.hg19:g.166226800G>T	ENSP00000226725:p.Arg321Leu	152.0	0.0		99.0	4.0	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	hg19	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294774	0.95546	.	.	ENSG00000109466	ENST00000226725;ENST00000514860;ENST00000538127;ENST00000421009;ENST00000506761	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	5.6	5.6	0.85130	Galactose oxidase, beta-propeller (1);	0.058050	0.64402	D	0.000001	D	0.83774	0.5327	M	0.68317	2.08	0.80722	D	1	D;D	0.54601	0.967;0.967	P;P	0.52793	0.709;0.709	D	0.83359	0.0001	10	0.44086	T	0.13	.	19.6107	0.95606	0.0:0.0:1.0:0.0	.	325;321	B4DFH7;O95198	.;KLHL2_HUMAN	L	321;325;233;224;155	ENSP00000226725:R321L;ENSP00000424198:R325L;ENSP00000437526:R233L;ENSP00000408974:R224L;ENSP00000424108:R155L	ENSP00000226725:R321L	R	+	2	0	KLHL2	166446250	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.869000	0.99810	2.648000	0.89879	0.655000	0.94253	CGG	.	.		0.458	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1		
AADAT	51166	hgsc.bcm.edu	37	4	170999725	170999725	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:170999725T>C	ENST00000337664.4	-	4	655	c.379A>G	c.(379-381)Atg>Gtg	p.M127V	AADAT_ENST00000353187.2_Missense_Mutation_p.M127V|AADAT_ENST00000509167.1_Missense_Mutation_p.M131V|AADAT_ENST00000515480.1_Missense_Mutation_p.M127V	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	127					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		TTAATGATCATTTCAAACACC	0.373																																					p.M127V		Atlas-SNP	.											.	AADAT	28	.	0			c.A379G						.						105.0	102.0	103.0					4																	170999725		2203	4300	6503	SO:0001583	missense	51166	exon5			TGATCATTTCAAA	AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"""kynurenine aminotransferase II"", ""L kynurenine/alpha aminoadipate aminotransferase"""	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.379A>G	chr4.hg19:g.170999725T>C	ENSP00000336808:p.Met127Val	102.0	0.0		67.0	4.0	NM_182662	B3KP84|Q9UL02	Missense_Mutation	SNP	ENST00000337664.4	hg19	CCDS3814.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.254043	0.59212	.	.	ENSG00000109576	ENST00000337664;ENST00000515480;ENST00000509167;ENST00000353187;ENST00000510340;ENST00000507375;ENST00000502392	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.42	5.42	0.78866	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.84678	0.5525	L	0.42744	1.35	0.58432	D	0.999998	P;P	0.47302	0.554;0.893	B;B	0.42593	0.272;0.392	T	0.82583	-0.0385	10	0.10636	T	0.68	-26.7196	15.7937	0.78388	0.0:0.0:0.0:1.0	.	131;127	Q8N5Z0-2;Q8N5Z0	.;AADAT_HUMAN	V	127;127;131;127;118;127;127	ENSP00000336808:M127V;ENSP00000423341:M127V;ENSP00000423190:M131V;ENSP00000226840:M127V;ENSP00000425067:M118V;ENSP00000421389:M127V;ENSP00000423843:M127V	ENSP00000336808:M127V	M	-	1	0	AADAT	171236300	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.211000	0.77933	2.188000	0.69820	0.528000	0.53228	ATG	.	.		0.373	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228	
HPGD	3248	hgsc.bcm.edu	37	4	175443106	175443106	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr4:175443106T>C	ENST00000296522.6	-	2	652	c.206A>G	c.(205-207)cAa>cGa	p.Q69R	HPGD_ENST00000422112.2_Missense_Mutation_p.Q69R|HPGD_ENST00000541923.1_5'UTR|RP11-440I14.2_ENST00000515178.1_lincRNA|HPGD_ENST00000296521.7_Missense_Mutation_p.Q69R|HPGD_ENST00000542498.1_Missense_Mutation_p.Q69R|HPGD_ENST00000510901.1_5'UTR|HPGD_ENST00000504433.1_Missense_Mutation_p.Q69R	NM_000860.5|NM_001145816.2|NM_001256301.1|NM_001256307.1	NP_000851.2|NP_001139288.1|NP_001243230.1|NP_001243236.1	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	69					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|ductus arteriosus closure (GO:0097070)|female pregnancy (GO:0007565)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|ovulation (GO:0030728)|parturition (GO:0007567)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|thrombin receptor signaling pathway (GO:0070493)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|catalytic activity (GO:0003824)|NAD binding (GO:0051287)|NAD+ binding (GO:0070403)|prostaglandin E receptor activity (GO:0004957)|protein homodimerization activity (GO:0042803)			kidney(1)|lung(3)|prostate(3)	7		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)		TCTCAGTTGTTGCTGGTCAGC	0.537																																					p.Q69R		Atlas-SNP	.											.	HPGD	19	.	0			c.A206G						.						175.0	175.0	175.0					4																	175443106		2203	4300	6503	SO:0001583	missense	3248	exon2			AGTTGTTGCTGGT		CCDS3821.1, CCDS54821.1, CCDS58933.1, CCDS58934.1, CCDS58935.1	4q34-q35	2011-09-14			ENSG00000164120	ENSG00000164120	1.1.1.141	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	5154	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 36C, member 1"""	601688				19027726	Standard	NM_000860		Approved	SDR36C1	uc003itu.3	P15428	OTTHUMG00000160772	ENST00000296522.6:c.206A>G	chr4.hg19:g.175443106T>C	ENSP00000296522:p.Gln69Arg	85.0	0.0		57.0	4.0	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Missense_Mutation	SNP	ENST00000296522.6	hg19	CCDS3821.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.103285	0.37145	.	.	ENSG00000164120	ENST00000296522;ENST00000296521;ENST00000422112;ENST00000542498;ENST00000504433	T;D;T;D;D	0.87729	-1.35;-1.76;-1.35;-2.29;-2.29	5.39	2.86	0.33363	NAD(P)-binding domain (1);	0.454373	0.27744	N	0.018032	T	0.74619	0.3740	N	0.16233	0.39	0.26141	N	0.980274	B;B;B;B;B;B	0.13145	0.001;0.0;0.007;0.0;0.0;0.0	B;B;B;B;B;B	0.11329	0.006;0.0;0.005;0.0;0.0;0.001	T	0.62163	-0.6912	10	0.40728	T	0.16	.	7.3943	0.26927	0.0:0.077:0.144:0.779	.	69;69;69;69;69;69	E7EV11;O00749;E9PBZ2;Q12998;B4DV57;P15428	.;.;.;.;.;PGDH_HUMAN	R	69	ENSP00000296522:Q69R;ENSP00000296521:Q69R;ENSP00000398720:Q69R;ENSP00000443644:Q69R;ENSP00000420892:Q69R	ENSP00000296521:Q69R	Q	-	2	0	HPGD	175679681	0.997000	0.39634	0.811000	0.32455	0.891000	0.51852	3.014000	0.49590	0.326000	0.23384	0.379000	0.24179	CAA	.	.		0.537	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3		
SLC12A7	10723	hgsc.bcm.edu	37	5	1088466	1088466	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:1088466T>C	ENST00000264930.5	-	5	542	c.499A>G	c.(499-501)Acc>Gcc	p.T167A		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	167					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GAAATGGCGGTCAGCATTGTC	0.582																																					p.T167A		Atlas-SNP	.											.	SLC12A7	97	.	0			c.A499G						.						58.0	51.0	54.0					5																	1088466		2183	4290	6473	SO:0001583	missense	10723	exon5			TGGCGGTCAGCAT	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.499A>G	chr5.hg19:g.1088466T>C	ENSP00000264930:p.Thr167Ala	100.0	0.0		122.0	5.0	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.005794	0.54254	.	.	ENSG00000113504	ENST00000264930;ENST00000343658	D	0.98807	-5.15	3.48	3.48	0.39840	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99251	0.9739	H	0.94658	3.565	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.99110	1.0846	10	0.87932	D	0	.	11.0972	0.48152	0.0:0.0:0.0:1.0	.	167	Q9Y666	S12A7_HUMAN	A	167	ENSP00000264930:T167A	ENSP00000264930:T167A	T	-	1	0	SLC12A7	1141466	1.000000	0.71417	0.955000	0.39395	0.238000	0.25445	7.198000	0.77823	1.363000	0.46019	0.379000	0.24179	ACC	.	.		0.582	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
ICE1	23379	hgsc.bcm.edu	37	5	5489287	5489287	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:5489287A>G	ENST00000296564.7	+	19	6867	c.6645A>G	c.(6643-6645)gcA>gcG	p.A2215A		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		2215					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TACAGTTAGCAGCCGTGTATG	0.413																																					p.A2215A		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A6645G						.						53.0	53.0	53.0					5																	5489287		1857	4108	5965	SO:0001819	synonymous_variant	23379	exon19			GTTAGCAGCCGTG																												ENST00000296564.7:c.6645A>G	chr5.hg19:g.5489287A>G		76.0	0.0		83.0	4.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.413	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
RICTOR	253260	hgsc.bcm.edu	37	5	38950476	38950476	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:38950476T>A	ENST00000357387.3	-	31	3504	c.3474A>T	c.(3472-3474)caA>caT	p.Q1158H	RICTOR_ENST00000296782.5_Missense_Mutation_p.Q1158H	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					AAGTCTCTAATTGTAATGTTT	0.373																																					p.Q1158H		Atlas-SNP	.											.	RICTOR	182	.	0			c.A3474T						.						168.0	171.0	170.0					5																	38950476		2203	4300	6503	SO:0001583	missense	253260	exon31			CTCTAATTGTAAT		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3474A>T	chr5.hg19:g.38950476T>A	ENSP00000349959:p.Gln1158His	309.0	1.0		427.0	190.0	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.634307	0.29068	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.44881	0.91;0.91	5.86	-0.886	0.10590	.	0.193901	0.53938	D	0.000058	T	0.19725	0.0474	N	0.08118	0	0.22684	N	0.99886	B;B	0.28584	0.216;0.216	B;B	0.31337	0.128;0.128	T	0.17440	-1.0369	10	0.87932	D	0	-15.0279	6.2372	0.20770	0.0:0.3467:0.2363:0.417	.	1158;1158	Q6R327;Q6R327-3	RICTR_HUMAN;.	H	1158	ENSP00000349959:Q1158H;ENSP00000296782:Q1158H	ENSP00000296782:Q1158H	Q	-	3	2	RICTOR	38986233	0.995000	0.38212	0.994000	0.49952	0.994000	0.84299	0.143000	0.16115	-0.010000	0.14271	0.528000	0.53228	CAA	.	.		0.373	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
ITGA2	3673	hgsc.bcm.edu	37	5	52376343	52376343	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:52376343A>G	ENST00000296585.5	+	25	3074	c.2931A>G	c.(2929-2931)gtA>gtG	p.V977V		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	977					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				CTACATAGGTAACAACAGGAA	0.438																																					p.V977V		Atlas-SNP	.											.	ITGA2	211	.	0			c.A2931G						.						145.0	135.0	139.0					5																	52376343		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon25			ATAGGTAACAACA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2931A>G	chr5.hg19:g.52376343A>G		92.0	0.0		99.0	4.0	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	hg19	CCDS3957.1																																																																																			.	.		0.438	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
IL31RA	133396	hgsc.bcm.edu	37	5	55164685	55164685	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:55164685G>A	ENST00000447346.2	+	3	286	c.221G>A	c.(220-222)tGg>tAg	p.W74*	IL31RA_ENST00000359040.5_Nonsense_Mutation_p.W74*|IL31RA_ENST00000297015.3_Intron|IL31RA_ENST00000396836.2_Nonsense_Mutation_p.W74*|IL31RA_ENST00000354961.4_Nonsense_Mutation_p.W55*|IL31RA_ENST00000396834.1_Nonsense_Mutation_p.W55*|IL31RA_ENST00000490985.1_5'UTR	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	42	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				ACCTGCACTTGGAGTCCAGGA	0.418																																					p.W74X		Atlas-SNP	.											.	IL31RA	84	.	0			c.G221A						.						104.0	108.0	106.0					5																	55164685		2203	4300	6503	SO:0001587	stop_gained	133396	exon3			GCACTTGGAGTCC	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.221G>A	chr5.hg19:g.55164685G>A	ENSP00000415900:p.Trp74*	66.0	0.0		81.0	4.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Nonsense_Mutation	SNP	ENST00000447346.2	hg19	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	G	22.5	4.304348	0.81136	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000354961	.	.	.	3.95	3.95	0.45737	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8596	11.6914	0.51519	0.0:0.0:1.0:0.0	.	.	.	.	X	74;55;74;74;55	.	ENSP00000347047:W55X	W	+	2	0	IL31RA	55200442	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.519000	0.60517	2.201000	0.70794	0.655000	0.94253	TGG	.	.		0.418	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628300	60628301	+	Missense_Mutation	DNP	GC	GC	TT			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:60628300_60628301GC>TT	ENST00000252744.5	+	1	201_202	c.201_202GC>TT	c.(199-204)ccGCcg>ccTTcg	p.P68S		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	68	Gly-rich.				neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						GGTTGCTGCCGCCGGGCAAGAC	0.777																																					p.P67P|p.P68S		Atlas-SNP	.											.	ZSWIM6	51	.	0			c.G201T|c.C202T						.																																			SO:0001583	missense	57688	exon1			GCTGCCGCCGGGC|CTGCCGCCGGGCA	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	Exception_encountered	chr5.hg19:g.60628300_60628301delinsTT	ENSP00000252744:p.Pro68Ser	18.0	0.0		25.0|27.0	17.0	NM_020928		Silent|Missense_Mutation	SNP	ENST00000252744.5	hg19	CCDS47215.1																																																																																			.	.		0.777	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628341	60628341	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:60628341C>T	ENST00000252744.5	+	1	242	c.242C>T	c.(241-243)gCg>gTg	p.A81V		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	81	Gly-rich.				neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						CTGGACATCGCGGCGCGCAGG	0.751																																					p.A81V		Atlas-SNP	.											.	ZSWIM6	51	.	0			c.C242T						.						3.0	6.0	5.0					5																	60628341		596	1443	2039	SO:0001583	missense	57688	exon1			ACATCGCGGCGCG	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.242C>T	chr5.hg19:g.60628341C>T	ENSP00000252744:p.Ala81Val	74.0	0.0		95.0	4.0	NM_020928		Missense_Mutation	SNP	ENST00000252744.5	hg19	CCDS47215.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.359803	0.24598	.	.	ENSG00000130449	ENST00000252744	T	0.32988	1.43	2.08	1.18	0.20946	.	.	.	.	.	T	0.31827	0.0809	M	0.70595	2.14	0.26541	N	0.974087	B	0.25390	0.125	B	0.16722	0.016	T	0.26849	-1.0091	9	0.72032	D	0.01	.	9.8988	0.41335	0.0:0.7886:0.2114:0.0	.	81	Q9HCJ5	ZSWM6_HUMAN	V	81	ENSP00000252744:A81V	ENSP00000252744:A81V	A	+	2	0	ZSWIM6	60664098	1.000000	0.71417	0.983000	0.44433	0.033000	0.12548	2.062000	0.41413	0.089000	0.17243	-1.244000	0.01528	GCG	.	.		0.751	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
MAP1B	4131	hgsc.bcm.edu	37	5	71492350	71492350	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:71492350T>C	ENST00000296755.7	+	5	3466	c.3168T>C	c.(3166-3168)ggT>ggC	p.G1056G		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1056					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CAGAGGCTGGTGGTGCCGAGG	0.517																																					p.G1056G	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T3168C						.						111.0	114.0	113.0					5																	71492350		2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			GGCTGGTGGTGCC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3168T>C	chr5.hg19:g.71492350T>C		100.0	0.0		78.0	4.0	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.517	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163834	73163834	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:73163834C>T	ENST00000426542.2	+	18	2306	c.2286C>T	c.(2284-2286)acC>acT	p.T762T	ARHGEF28_ENST00000545377.1_Silent_p.T762T|ARHGEF28_ENST00000287898.5_Silent_p.T762T|ARHGEF28_ENST00000296794.6_Silent_p.T762T|ARHGEF28_ENST00000296799.4_Silent_p.T449T|ARHGEF28_ENST00000437974.1_Silent_p.T762T|ARHGEF28_ENST00000513042.2_Silent_p.T762T			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	762					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TTCCAGGCACCACCTTGGAAA	0.537																																					p.T762T		Atlas-SNP	.											.	.	.	.	0			c.C2286T						.						96.0	92.0	93.0					5																	73163834		1957	4142	6099	SO:0001819	synonymous_variant	64283	exon19			AGGCACCACCTTG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2286C>T	chr5.hg19:g.73163834C>T		103.0	0.0		93.0	4.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	hg19	CCDS54870.1																																																																																			.	.		0.537	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
PAPD4	167153	hgsc.bcm.edu	37	5	78938677	78938677	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:78938677A>G	ENST00000296783.3	+	8	994	c.695A>G	c.(694-696)aAg>aGg	p.K232R	PAPD4_ENST00000428308.2_Missense_Mutation_p.K232R|PAPD4_ENST00000504233.1_Missense_Mutation_p.K232R|PAPD4_ENST00000423041.2_Missense_Mutation_p.K228R|PAPD4_ENST00000453514.1_Missense_Mutation_p.K232R			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	232					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)			biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		GTAAATCAGAAGACTGAAGCA	0.323																																					p.K232R		Atlas-SNP	.											.	PAPD4	51	.	0			c.A695G						.						97.0	87.0	90.0					5																	78938677		2203	4300	6503	SO:0001583	missense	167153	exon8			ATCAGAAGACTGA	AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"""TUTase2"""	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.695A>G	chr5.hg19:g.78938677A>G	ENSP00000296783:p.Lys232Arg	121.0	0.0		125.0	5.0	NM_173797	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	hg19	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	A	9.732	1.162472	0.21538	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T	0.56103	0.48;0.95;0.48;0.48	5.88	5.88	0.94601	.	0.230281	0.52532	D	0.000076	T	0.32585	0.0834	N	0.13003	0.285	0.45295	D	0.998291	B;B;B	0.25719	0.007;0.027;0.132	B;B;B	0.18871	0.01;0.023;0.017	T	0.25398	-1.0133	10	0.02654	T	1	-10.5102	16.275	0.82640	1.0:0.0:0.0:0.0	.	232;228;232	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	R	232;228;232;232;232	ENSP00000397563:K232R;ENSP00000393412:K228R;ENSP00000396861:K232R;ENSP00000296783:K232R	ENSP00000296783:K232R	K	+	2	0	PAPD4	78974433	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.706000	0.61845	2.248000	0.74166	0.477000	0.44152	AAG	.	.		0.323	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797	
VCAN	1462	hgsc.bcm.edu	37	5	82849183	82849183	+	Splice_Site	SNP	A	A	G	rs13184139		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:82849183A>G	ENST00000265077.3	+	11	10059	c.9494A>G	c.(9493-9495)gAt>gGt	p.D3165G	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000343200.5_Splice_Site_p.D2178G|VCAN_ENST00000512590.2_Splice_Site_p.D1363G|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Splice_Site_p.D424G|VCAN_ENST00000342785.4_Splice_Site_p.D1411G	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3165					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TTCTTCTCAGATACCGAGACA	0.493																																					p.D3165G		Atlas-SNP	.											.	VCAN	498	.	0			c.A9494G						.						105.0	93.0	97.0					5																	82849183		2203	4300	6503	SO:0001630	splice_region_variant	1462	exon11			TCTCAGATACCGA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.9494-1A>G	chr5.hg19:g.82849183A>G		52.0	0.0		59.0	4.0	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018909	0.75275	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	6.06	6.06	0.98353	C-type lectin-like (1);	0.000000	0.64402	D	0.000007	T	0.38241	0.1033	L	0.49256	1.55	0.58432	D	0.999998	D;D;B;D	0.89917	1.0;1.0;0.318;1.0	D;D;P;D	0.91635	0.999;0.998;0.64;0.999	T	0.05451	-1.0884	10	0.62326	D	0.03	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	1411;424;2178;3165	P13611-3;P13611-4;P13611-2;P13611	.;.;.;CSPG2_HUMAN	G	3165;2178;1411;1363;424	ENSP00000265077:D3165G;ENSP00000340062:D2178G;ENSP00000342768:D1411G;ENSP00000425959:D1363G;ENSP00000421362:D424G	ENSP00000265077:D3165G	D	+	2	0	VCAN	82884939	1.000000	0.71417	1.000000	0.80357	0.297000	0.27493	9.339000	0.96797	2.324000	0.78689	0.533000	0.62120	GAT	.	A|1.000;|0.000		0.493	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	Missense_Mutation
PAM	5066	hgsc.bcm.edu	37	5	102237061	102237061	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:102237061C>A	ENST00000438793.3	+	3	682	c.212C>A	c.(211-213)tCc>tAc	p.S71Y	PAM_ENST00000304400.7_Splice_Site_p.S71Y|PAM_ENST00000274392.9_Intron|PAM_ENST00000346918.2_Splice_Site_p.S71Y|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000348126.2_Splice_Site_p.S71Y|PAM_ENST00000455264.2_Splice_Site_p.S71Y	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	71	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TTTTAATAGTCCGATACATAC	0.353																																					p.S71Y		Atlas-SNP	.											.	PAM	180	.	0			c.C212A						.						98.0	100.0	99.0					5																	102237061		2203	4300	6503	SO:0001630	splice_region_variant	5066	exon3			AATAGTCCGATAC	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"""peptidyl-alpha-hydroxyglycine alpha-amidating lyase"", ""peptidylglycine alpha-hydroxylating monooxygenase"""	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.211-1C>A	chr5.hg19:g.102237061C>A		380.0	1.0		382.0	137.0	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592299	0.66219	.	.	ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.39	5.39	0.77823	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.000000	0.85682	D	0.000000	T	0.61362	0.2341	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;0.998	D;D;P;D;D	0.91635	0.999;0.998;0.892;0.998;0.943	T	0.63001	-0.6734	10	0.72032	D	0.01	.	19.5261	0.95208	0.0:1.0:0.0:0.0	.	71;71;71;71;71	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	Y	71	ENSP00000396493:S71Y;ENSP00000282992:S71Y;ENSP00000314638:S71Y;ENSP00000306100:S71Y;ENSP00000403461:S71Y	ENSP00000306100:S71Y	S	+	2	0	PAM	102264960	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	5.307000	0.65762	2.668000	0.90789	0.650000	0.86243	TCC	.	.		0.353	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919	Missense_Mutation
SEMA6A	57556	hgsc.bcm.edu	37	5	115823894	115823894	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:115823894T>C	ENST00000343348.6	-	9	1443		c.e9-2		SEMA6A_ENST00000510263.1_Splice_Site|SEMA6A_ENST00000257414.8_Splice_Site|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000503962.1_5'Flank|CTB-118N6.3_ENST00000510682.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A						apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		AGTATGGTTCTGTAGACAAAC	0.383																																					.		Atlas-SNP	.											.	SEMA6A	93	.	0			c.656-2A>G						.						77.0	70.0	72.0					5																	115823894		1863	4111	5974	SO:0001630	splice_region_variant	57556	exon10			TGGTTCTGTAGAC	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.656-2A>G	chr5.hg19:g.115823894T>C		126.0	0.0		139.0	6.0	NM_020796	Q9P2H9	Splice_Site	SNP	ENST00000343348.6	hg19	CCDS47256.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.609553	0.46527	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000510263	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2215	0.82262	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA6A	115851793	1.000000	0.71417	0.999000	0.59377	0.446000	0.32137	7.997000	0.88414	2.367000	0.80283	0.528000	0.53228	.	.	.		0.383	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	Intron
SRFBP1	153443	hgsc.bcm.edu	37	5	121309963	121309963	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:121309963C>A	ENST00000339397.4	+	2	181	c.109C>A	c.(109-111)Cga>Aga	p.R37R		NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		GAGTGTTGGCCGACTGAAGTC	0.313																																					p.R37R		Atlas-SNP	.											.	SRFBP1	47	.	0			c.C109A						.						70.0	65.0	67.0					5																	121309963		1816	4073	5889	SO:0001819	synonymous_variant	153443	exon2			GTTGGCCGACTGA	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"""BUD22 homolog (S. cerevisiae)"""	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.109C>A	chr5.hg19:g.121309963C>A		135.0	0.0		115.0	5.0	NM_152546		Silent	SNP	ENST00000339397.4	hg19	CCDS43354.1																																																																																			.	.		0.313	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
FBN2	2201	hgsc.bcm.edu	37	5	127704892	127704892	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:127704892C>T	ENST00000508053.1	-	22	3205	c.2231G>A	c.(2230-2232)tGc>tAc	p.C744Y	FBN2_ENST00000508989.1_Missense_Mutation_p.C711Y|FBN2_ENST00000262464.4_Missense_Mutation_p.C744Y|Y_RNA_ENST00000384560.1_RNA|FBN2_ENST00000511489.1_5'UTR			P35556	FBN2_HUMAN	fibrillin 2	744	TB 3.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TTTTGCAGGGCATGGCTGGCA	0.463																																					p.C744Y		Atlas-SNP	.											.	FBN2	858	.	0			c.G2231A						.						108.0	101.0	103.0					5																	127704892		2203	4300	6503	SO:0001583	missense	2201	exon16			GCAGGGCATGGCT	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.2231G>A	chr5.hg19:g.127704892C>T	ENSP00000424571:p.Cys744Tyr	42.0	0.0		39.0	15.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466836	0.84425	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.99875	-7.4;-7.4;-7.4	4.57	4.57	0.56435	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.64402	D	0.000001	D	0.99880	0.9943	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.996	D	0.96462	0.9342	10	0.72032	D	0.01	.	18.667	0.91493	0.0:1.0:0.0:0.0	.	711;744	D6RJI3;P35556	.;FBN2_HUMAN	Y	744;744;711	ENSP00000262464:C744Y;ENSP00000424571:C744Y;ENSP00000425596:C711Y	ENSP00000262464:C744Y	C	-	2	0	FBN2	127732791	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.609000	0.82925	2.824000	0.97209	0.655000	0.94253	TGC	.	.		0.463	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
PCDHB11	56125	hgsc.bcm.edu	37	5	140579924	140579924	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:140579924G>T	ENST00000354757.3	+	1	577	c.577G>T	c.(577-579)Gag>Tag	p.E193*	PCDHB11_ENST00000536699.1_Intron	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	193	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E193Q(1)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAAATACCCCGAGTTAGTTCT	0.463																																					p.E193X		Atlas-SNP	.											PCDHB11,NS,NS,0,1	PCDHB11	162	.	1	Substitution - Missense(1)	NS(1)	c.G577T						.						62.0	65.0	64.0					5																	140579924		2203	4300	6503	SO:0001587	stop_gained	56125	exon1			TACCCCGAGTTAG	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.577G>T	chr5.hg19:g.140579924G>T	ENSP00000346802:p.Glu193*	196.0	0.0		262.0	123.0	NM_018931	B4DSF7|Q2M223	Nonsense_Mutation	SNP	ENST00000354757.3	hg19	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	G	34	5.355734	0.95854	.	.	ENSG00000197479	ENST00000354757	.	.	.	2.7	2.7	0.31948	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.3974	0.60861	0.0:0.0:1.0:0.0	.	.	.	.	X	193	.	ENSP00000346802:E193X	E	+	1	0	PCDHB11	140560108	1.000000	0.71417	0.739000	0.30968	0.889000	0.51656	9.162000	0.94745	1.496000	0.48567	0.467000	0.42956	GAG	.	.		0.463	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626597	140626597	+	Missense_Mutation	SNP	C	C	G	rs532029427		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:140626597C>G	ENST00000231173.3	+	1	1451	c.1451C>G	c.(1450-1452)gCc>gGc	p.A484G		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	484	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCACCAACGCCCAGGTCACC	0.647																																					p.A484G		Atlas-SNP	.											.	PCDHB15	138	.	0			c.C1451G						.						61.0	73.0	68.0					5																	140626597		2203	4296	6499	SO:0001583	missense	56121	exon1			CCAACGCCCAGGT	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1451C>G	chr5.hg19:g.140626597C>G	ENSP00000231173:p.Ala484Gly	240.0	0.0		277.0	125.0	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.304160	0.60305	.	.	ENSG00000113248	ENST00000231173	T	0.51574	0.7	4.52	4.52	0.55395	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.41903	0.1179	N	0.17800	0.525	0.38899	D	0.957276	P	0.36125	0.538	B	0.43838	0.433	T	0.52034	-0.8629	9	0.72032	D	0.01	.	14.1287	0.65238	0.0:0.8486:0.1514:0.0	.	484	Q9Y5E8	PCDBF_HUMAN	G	484	ENSP00000231173:A484G	ENSP00000231173:A484G	A	+	2	0	PCDHB15	140606781	0.398000	0.25279	1.000000	0.80357	0.980000	0.70556	0.978000	0.29488	2.251000	0.74343	0.485000	0.47835	GCC	.	.		0.647	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735864	140735864	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:140735864T>C	ENST00000571252.1	+	1	1097	c.1097T>C	c.(1096-1098)aTt>aCt	p.I366T	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	366	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTACAGTAATTGCACTTTTC	0.453																																					p.I366T		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.T1097C						.						30.0	29.0	30.0					5																	140735864		1968	4109	6077	SO:0001583	missense	56111	exon1			CAGTAATTGCACT	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1097T>C	chr5.hg19:g.140735864T>C	ENSP00000458570:p.Ile366Thr	91.0	0.0		114.0	45.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.453	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
ARHGEF37	389337	hgsc.bcm.edu	37	5	148980735	148980735	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:148980735G>T	ENST00000333677.6	+	3	414	c.251G>T	c.(250-252)aGa>aTa	p.R84I		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	84	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GTGAACAGCAGATTCCTCCAT	0.468																																					p.R84I		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.G251T						.						106.0	107.0	107.0					5																	148980735		1971	4174	6145	SO:0001583	missense	389337	exon3			ACAGCAGATTCCT	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.251G>T	chr5.hg19:g.148980735G>T	ENSP00000328083:p.Arg84Ile	85.0	0.0		89.0	4.0	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	hg19	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196217	0.58126	.	.	ENSG00000183111	ENST00000505810;ENST00000333677	T;T	0.64803	-0.12;-0.12	5.4	1.71	0.24356	Dbl homology (DH) domain (5);	0.132397	0.30742	U	0.008966	T	0.57110	0.2031	L	0.41906	1.305	0.48185	D	0.999602	P	0.47106	0.89	P	0.50490	0.642	T	0.51787	-0.8661	10	0.46703	T	0.11	.	7.4622	0.27302	0.3404:0.0:0.6596:0.0	.	84	A1IGU5	ARH37_HUMAN	I	84	ENSP00000425621:R84I;ENSP00000328083:R84I	ENSP00000328083:R84I	R	+	2	0	ARHGEF37	148960928	0.998000	0.40836	0.986000	0.45419	0.556000	0.35491	0.781000	0.26774	0.134000	0.18681	0.561000	0.74099	AGA	.	.		0.468	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
MYOZ3	91977	hgsc.bcm.edu	37	5	150056368	150056368	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:150056368T>C	ENST00000520112.1	+	2	546	c.436T>C	c.(436-438)Tct>Cct	p.S146P	MYOZ3_ENST00000297130.4_Silent_p.R229R|MYOZ3_ENST00000456566.2_3'UTR|MYOZ3_ENST00000517768.1_Silent_p.R229R					myozenin 3											large_intestine(2)|lung(1)|skin(2)	5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AACTCCTCCGTCTCAGACCCA	0.637																																					p.R229R		Atlas-SNP	.											.	MYOZ3	21	.	0			c.T687C						.						60.0	68.0	65.0					5																	150056368		2203	4300	6503	SO:0001583	missense	91977	exon7			CCTCCGTCTCAGA	AF480443	CCDS4309.1	5q33.2	2008-07-18			ENSG00000164591	ENSG00000164591			18565	protein-coding gene	gene with protein product	"""calsarcin 3"", ""FATZ related protein 3"""	610735				11842093	Standard	NM_001122853		Approved	CS-3, CS3, FRP3	uc003lsr.3	Q8TDC0	OTTHUMG00000130077	ENST00000520112.1:c.436T>C	chr5.hg19:g.150056368T>C	ENSP00000429439:p.Ser146Pro	77.0	0.0		82.0	4.0	NM_001122853		Silent	SNP	ENST00000520112.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.96	1.794993	0.31777	.	.	ENSG00000164591	ENST00000520112	.	.	.	5.2	-0.127	0.13510	.	.	.	.	.	T	0.55689	0.1936	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54820	-0.8236	5	0.87932	D	0	-26.3218	3.1134	0.06366	0.3182:0.4096:0.0:0.2722	.	.	.	.	P	146	.	ENSP00000429439:S146P	S	+	1	0	MYOZ3	150036561	0.041000	0.20044	0.994000	0.49952	0.976000	0.68499	-0.244000	0.08903	-0.040000	0.13580	-0.132000	0.14878	TCT	.	.		0.637	MYOZ3-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000374429.1	NM_001122853	
RARS	5917	hgsc.bcm.edu	37	5	167945066	167945066	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:167945066T>C	ENST00000231572.3	+	14	1926	c.1872T>C	c.(1870-1872)acT>acC	p.T624T	RARS_ENST00000538719.1_Splice_Site_p.T418T	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	624					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		ATAGACAGACTGGTGAGTGTC	0.403																																					p.T624T		Atlas-SNP	.											.	RARS	58	.	0			c.T1872C						.						36.0	36.0	36.0					5																	167945066		2203	4300	6503	SO:0001630	splice_region_variant	5917	exon14			ACAGACTGGTGAG	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1873+1T>C	chr5.hg19:g.167945066T>C		69.0	0.0		84.0	5.0	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	hg19	CCDS4367.1																																																																																			.	.		0.403	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	Silent
NPM1	4869	hgsc.bcm.edu	37	5	170827199	170827199	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr5:170827199A>G	ENST00000296930.5	+	7	868	c.567A>G	c.(565-567)aaA>aaG	p.K189K	NPM1_ENST00000517671.1_Silent_p.K189K|NPM1_ENST00000351986.6_Silent_p.K189K|NPM1_ENST00000393820.2_Silent_p.K189K	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	189					cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)		NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ctgaagaAAAAGCGCCAGTGA	0.333			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																p.K189K		Atlas-SNP	.		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	.	NPM1	5003	.	0			c.A567G						.						110.0	103.0	106.0					5																	170827199		2203	4300	6503	SO:0001819	synonymous_variant	4869	exon7			AGAAAAAGCGCCA	M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.567A>G	chr5.hg19:g.170827199A>G		137.0	0.0		125.0	5.0	NM_199185	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Silent	SNP	ENST00000296930.5	hg19	CCDS4376.1																																																																																			.	.		0.333	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252858.2	NM_002520	
FAM217A	222826	hgsc.bcm.edu	37	6	4070154	4070154	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:4070154C>A	ENST00000274673.3	-	7	706	c.303G>T	c.(301-303)agG>agT	p.R101S	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	101																	TTTTGAATTCCCtttaaaaaa	0.284																																					p.R101S		Atlas-SNP	.											.	.	.	.	0			c.G303T						.						18.0	19.0	19.0					6																	4070154		2192	4267	6459	SO:0001630	splice_region_variant	222826	exon7			GAATTCCCTTTAA	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 146"""	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.303-1G>T	chr6.hg19:g.4070154C>A		68.0	0.0		100.0	4.0	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	hg19	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535360	0.45176	.	.	ENSG00000145975	ENST00000274673;ENST00000470599;ENST00000498677	T	0.18016	2.24	5.54	4.66	0.58398	.	0.153207	0.43919	D	0.000515	T	0.05090	0.0136	N	0.24115	0.695	0.33064	D	0.534462	B	0.31931	0.347	B	0.31751	0.135	T	0.14504	-1.0470	10	0.87932	D	0	.	9.3285	0.38008	0.0:0.9029:0.0:0.0971	.	101	Q8IXS0	CF146_HUMAN	S	101;229;38	ENSP00000274673:R101S	ENSP00000274673:R101S	R	-	3	2	C6orf146	4015153	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.640000	0.37186	1.546000	0.49388	0.650000	0.86243	AGG	.	.		0.284	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	Missense_Mutation
JARID2	3720	hgsc.bcm.edu	37	6	15497298	15497298	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:15497298C>T	ENST00000341776.2	+	7	2086	c.1842C>T	c.(1840-1842)atC>atT	p.I614I	JARID2_ENST00000541660.1_Silent_p.I576I|JARID2_ENST00000397311.3_Silent_p.I442I	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	614					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TTCAGCACATCCACAAGCTGG	0.622																																					p.I614I		Atlas-SNP	.											.	JARID2	135	.	0			c.C1842T						.						29.0	24.0	25.0					6																	15497298		2203	4298	6501	SO:0001819	synonymous_variant	3720	exon7			GCACATCCACAAG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1842C>T	chr6.hg19:g.15497298C>T		155.0	0.0		156.0	67.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	hg19	CCDS4533.1																																																																																			.	.		0.622	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
LRRC16A	55604	hgsc.bcm.edu	37	6	25529110	25529110	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:25529110A>G	ENST00000329474.6	+	24	2424	c.2056A>G	c.(2056-2058)Acc>Gcc	p.T686A		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	686					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.T686P(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						TGTCACCAGCACCACCCAGCA	0.473																																					p.T686A		Atlas-SNP	.											LRRC16A,colon,carcinoma,0,1	LRRC16A	168	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2056G						.						22.0	26.0	25.0					6																	25529110		1971	4163	6134	SO:0001583	missense	55604	exon24			ACCAGCACCACCC	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.2056A>G	chr6.hg19:g.25529110A>G	ENSP00000331983:p.Thr686Ala	60.0	0.0		30.0	3.0	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	hg19	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.561053	0.86335	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.46063	0.88	5.69	5.69	0.88448	.	0.045312	0.85682	D	0.000000	T	0.44644	0.1303	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.999;0.998	D;D;D;D	0.85130	0.993;0.996;0.997;0.993	T	0.42599	-0.9442	10	0.44086	T	0.13	.	15.6029	0.76639	1.0:0.0:0.0:0.0	.	686;686;686;686	Q5VZK9;B2RTQ5;Q5VZK9-2;B8X1J0	LR16A_HUMAN;.;.;.	A	686	ENSP00000331983:T686A	ENSP00000331983:T686A	T	+	1	0	LRRC16A	25637089	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.554000	0.90689	2.157000	0.67596	0.533000	0.62120	ACC	.	.		0.473	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
ZNF311	282890	hgsc.bcm.edu	37	6	28967374	28967374	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:28967374T>C	ENST00000377179.3	-	5	712	c.200A>G	c.(199-201)gAg>gGg	p.E67G	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						AGCTACATCCTCAAATGTCAC	0.438																																					p.E67G		Atlas-SNP	.											.	ZNF311	59	.	0			c.A200G						.						137.0	99.0	112.0					6																	28967374		1511	2709	4220	SO:0001583	missense	282890	exon5			ACATCCTCAAATG	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"""Zinc fingers, C2H2-type"", ""-"""	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.200A>G	chr6.hg19:g.28967374T>C	ENSP00000366384:p.Glu67Gly	84.0	0.0		91.0	4.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Missense_Mutation	SNP	ENST00000377179.3	hg19	CCDS34357.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.858953	0.51376	.	.	ENSG00000197935	ENST00000377179	T	0.02216	4.39	3.48	2.34	0.29019	Krueppel-associated box (4);	.	.	.	.	T	0.03434	0.0099	M	0.63169	1.94	0.25543	N	0.987162	D	0.69078	0.997	D	0.67900	0.954	T	0.41052	-0.9530	9	0.72032	D	0.01	-19.7298	6.3444	0.21341	0.0:0.125:0.0:0.875	.	67	Q5JNZ3	ZN311_HUMAN	G	67	ENSP00000366384:E67G	ENSP00000366384:E67G	E	-	2	0	ZNF311	29075353	0.874000	0.30092	0.995000	0.50966	0.597000	0.36814	1.099000	0.31013	1.532000	0.49169	0.477000	0.44152	GAG	.	.		0.438	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581	
OR2B3	442184	hgsc.bcm.edu	37	6	29054566	29054566	+	Missense_Mutation	SNP	C	C	A	rs369975513		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:29054566C>A	ENST00000377173.2	-	1	524	c.460G>T	c.(460-462)Ggc>Tgc	p.G154C		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						ACTGAGTTGCCGAAACCAATG	0.488																																					p.G154C		Atlas-SNP	.											.	OR2B3	44	.	0			c.G460T						.						63.0	58.0	60.0					6																	29054566		2203	4300	6503	SO:0001583	missense	442184	exon1			AGTTGCCGAAACC		CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"""GPCR / Class A : Olfactory receptors"""	8238	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 3 pseudogene"""	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.460G>T	chr6.hg19:g.29054566C>A	ENSP00000366378:p.Gly154Cys	72.0	0.0		102.0	5.0	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	hg19	CCDS34358.1	.	.	.	.	.	.	.	.	.	.	C	6.722	0.501960	0.12822	.	.	ENSG00000204703	ENST00000377173	T	0.37411	1.2	3.83	-0.243	0.13035	GPCR, rhodopsin-like superfamily (1);	0.341386	0.21456	U	0.074252	T	0.18087	0.0434	N	0.16368	0.405	0.09310	N	1	D	0.57899	0.981	D	0.63877	0.919	T	0.09952	-1.0651	10	0.62326	D	0.03	.	5.5456	0.17061	0.0:0.39:0.2112:0.3988	.	154	O76000	OR2B3_HUMAN	C	154	ENSP00000366378:G154C	ENSP00000366378:G154C	G	-	1	0	OR2B3	29162545	0.000000	0.05858	0.001000	0.08648	0.118000	0.20060	-3.800000	0.00363	-0.342000	0.08363	-0.409000	0.06214	GGC	.	.		0.488	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2		
TRIM10	10107	hgsc.bcm.edu	37	6	30121749	30121749	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:30121749G>T	ENST00000449742.2	-	7	1518	c.1443C>A	c.(1441-1443)tcC>tcA	p.S481S	TRIM10_ENST00000376704.3_Intron	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	481	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						CTCCTTCTCAGGAGCTCAGGG	0.532																																					p.S481S		Atlas-SNP	.											.	TRIM10	65	.	0			c.C1443A						.						90.0	98.0	95.0					6																	30121749		1509	2708	4217	SO:0001819	synonymous_variant	10107	exon7			TTCTCAGGAGCTC	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10072	protein-coding gene	gene with protein product		605701	"""tripartite motif-containing 10"""	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.1443C>A	chr6.hg19:g.30121749G>T		96.0	0.0		95.0	4.0	NM_006778	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Silent	SNP	ENST00000449742.2	hg19	CCDS34375.1																																																																																			.	.		0.532	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1		
TRIM10	10107	hgsc.bcm.edu	37	6	30121896	30121896	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:30121896C>A	ENST00000449742.2	-	7	1371	c.1296G>T	c.(1294-1296)agG>agT	p.R432S	TRIM10_ENST00000376704.3_Intron	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	432	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						CAAGAGACACCCTCACCTGCC	0.622																																					p.R432S		Atlas-SNP	.											.	TRIM10	65	.	0			c.G1296T						.						48.0	43.0	45.0					6																	30121896		1510	2708	4218	SO:0001583	missense	10107	exon7			AGACACCCTCACC	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10072	protein-coding gene	gene with protein product		605701	"""tripartite motif-containing 10"""	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.1296G>T	chr6.hg19:g.30121896C>A	ENSP00000397073:p.Arg432Ser	72.0	0.0		93.0	4.0	NM_006778	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	hg19	CCDS34375.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.478151	0.26511	.	.	ENSG00000204613	ENST00000449742;ENST00000376706	T	0.68765	-0.35	6.01	0.57	0.17347	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.122378	0.37012	N	0.002293	T	0.55386	0.1917	M	0.79475	2.455	0.80722	D	1	P	0.40000	0.698	P	0.48368	0.575	T	0.56727	-0.7931	10	0.54805	T	0.06	.	2.8201	0.05469	0.349:0.4022:0.1057:0.1431	.	432	Q9UDY6	TRI10_HUMAN	S	432	ENSP00000397073:R432S	ENSP00000365896:R432S	R	-	3	2	TRIM10	30229875	0.000000	0.05858	0.998000	0.56505	0.959000	0.62525	-1.892000	0.01610	0.132000	0.18615	0.643000	0.83706	AGG	.	.		0.622	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1		
DDR1	780	hgsc.bcm.edu	37	6	30862315	30862315	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:30862315G>T	ENST00000324771.8	+	13	1928	c.1380G>T	c.(1378-1380)acG>acT	p.T460T	DDR1_ENST00000513240.1_Silent_p.T460T|DDR1_ENST00000452441.1_Silent_p.T460T|DDR1_ENST00000376575.3_Silent_p.T460T|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000361741.4_Intron|DDR1_ENST00000376568.3_Silent_p.T460T|DDR1_ENST00000454612.2_Silent_p.T460T|DDR1_ENST00000376569.3_Silent_p.T460T|DDR1_ENST00000508312.1_Silent_p.T478T|DDR1_ENST00000418800.2_Silent_p.T460T|DDR1_ENST00000376567.2_Silent_p.T460T|DDR1_ENST00000376570.4_Silent_p.T460T			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	460					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T460T(2)|p.T459T(1)		central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	AGGAGCTGACGGTTCACCTCT	0.627																																					p.T478T		Atlas-SNP	.											DDR1_ENST00000376575,NS,carcinoma,0,6	DDR1	213	.	3	Substitution - coding silent(3)	lung(3)	c.G1434T						.						142.0	124.0	130.0					6																	30862315		2203	4300	6503	SO:0001819	synonymous_variant	780	exon11			GCTGACGGTTCAC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1380G>T	chr6.hg19:g.30862315G>T		57.0	0.0		64.0	3.0	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	hg19	CCDS34385.1																																																																																			.	.		0.627	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
BAG6	7917	hgsc.bcm.edu	37	6	31608658	31608658	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:31608658C>T	ENST00000375964.6	-	20	3068	c.2755G>A	c.(2755-2757)Gga>Aga	p.G919R	BAG6_ENST00000375976.4_Missense_Mutation_p.G913R|BAG6_ENST00000211379.5_Missense_Mutation_p.G913R|BAG6_ENST00000362049.6_Missense_Mutation_p.G913R|BAG6_ENST00000404765.2_Missense_Mutation_p.G949R|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000439687.2_Missense_Mutation_p.G787R	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	919					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						AGCCTCAGTCCCATCATAGTG	0.547																																					p.G919R		Atlas-SNP	.											.	BAG6	73	.	0			c.G2755A						.						83.0	66.0	72.0					6																	31608658		1511	2709	4220	SO:0001583	missense	7917	exon20			TCAGTCCCATCAT	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.2755G>A	chr6.hg19:g.31608658C>T	ENSP00000365131:p.Gly919Arg	61.0	0.0		83.0	4.0	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	hg19	CCDS47403.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.33|16.33	3.092130|3.092130	0.55968|0.55968	.|.	.|.	ENSG00000204463|ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049|ENST00000422948;ENST00000441793	T;T;T;T;T;T|.	0.45668|.	1.55;1.55;1.55;1.56;0.89;1.55|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.168112|.	0.51477|.	D|.	0.000086|.	T|.	0.21307|.	0.0513|.	N|N	0.22421|0.22421	0.69|0.69	0.34548|0.34548	D|D	0.711047|0.711047	D;D;D;D|.	0.76494|.	0.967;0.999;0.999;0.999|.	P;D;D;D|.	0.76071|.	0.71;0.951;0.973;0.987|.	T|.	0.07309|.	-1.0779|.	10|.	0.25106|.	T|.	0.35|.	.|.	6.615|6.615	0.22773|0.22773	0.1798:0.7312:0.0:0.0889|0.1798:0.7312:0.0:0.0889	.|.	787;913;919;913|.	E7EMZ4;F8VXY4;P46379;P46379-2|.	.;.;BAG6_HUMAN;.|.	R|X	913;919;913;949;787;913|19;61	ENSP00000365143:G913R;ENSP00000365131:G919R;ENSP00000211379:G913R;ENSP00000384494:G949R;ENSP00000402856:G787R;ENSP00000354875:G913R|.	ENSP00000211379:G913R|.	G|W	-|-	1|3	0|0	BAG6|BAG6	31716637|31716637	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.169000|1.169000	0.31871|0.31871	2.753000|2.753000	0.94483|0.94483	0.650000|0.650000	0.86243|0.86243	GGA|TGG	.	.		0.547	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	
ANKS1A	23294	hgsc.bcm.edu	37	6	35047653	35047653	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:35047653A>G	ENST00000360359.3	+	16	2630	c.2492A>G	c.(2491-2493)gAc>gGc	p.D831G	ANKS1A_ENST00000535627.1_Intron|ANKS1A_ENST00000470698.1_3'UTR	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	831	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						TCCCTCGCAGACAGACCGTAC	0.602																																					p.D831G		Atlas-SNP	.											.	ANKS1A	123	.	0			c.A2492G						.						24.0	23.0	23.0					6																	35047653		2194	4287	6481	SO:0001583	missense	23294	exon16			TCGCAGACAGACC	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2492A>G	chr6.hg19:g.35047653A>G	ENSP00000353518:p.Asp831Gly	71.0	0.0		91.0	4.0	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	hg19	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.620170	0.87460	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.06449	3.3	5.66	5.66	0.87406	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);	0.000000	0.51477	D	0.000083	T	0.09069	0.0224	L	0.31420	0.93	0.80722	D	1	B;B;P	0.49635	0.212;0.004;0.926	P;B;D	0.63381	0.7;0.102;0.914	T	0.10543	-1.0625	10	0.72032	D	0.01	-11.983	15.8895	0.79286	1.0:0.0:0.0:0.0	.	157;157;831	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	G	831;157	ENSP00000353518:D831G	ENSP00000353518:D831G	D	+	2	0	ANKS1A	35155631	1.000000	0.71417	0.953000	0.39169	0.842000	0.47809	9.315000	0.96313	2.153000	0.67306	0.459000	0.35465	GAC	.	.		0.602	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	
PNPLA1	285848	hgsc.bcm.edu	37	6	36270243	36270243	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:36270243C>T	ENST00000394571.2	+	6	1381	c.1381C>T	c.(1381-1383)Caa>Taa	p.Q461*	PNPLA1_ENST00000388715.3_Nonsense_Mutation_p.Q366*|PNPLA1_ENST00000312917.5_Nonsense_Mutation_p.Q375*	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	461					lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						AGAACAGCCCCAAGGTATGGA	0.572											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q461X		Atlas-SNP	.											.	PNPLA1	92	.	0			c.C1381T						.						104.0	109.0	107.0					6																	36270243		2203	4300	6503	SO:0001587	stop_gained	285848	exon6			CAGCCCCAAGGTA		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1381C>T	chr6.hg19:g.36270243C>T	ENSP00000378072:p.Gln461*	57.0	0.0	861	79.0	4.0	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Nonsense_Mutation	SNP	ENST00000394571.2	hg19	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078915	0.76528	.	.	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	.	.	.	4.35	2.53	0.30540	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	0.7404	5.2586	0.15561	0.2022:0.6918:0.0:0.106	.	.	.	.	X	366;375;462;461	.	ENSP00000321116:Q375X	Q	+	1	0	PNPLA1	36378221	0.009000	0.17119	0.080000	0.20451	0.193000	0.23685	0.665000	0.25083	0.563000	0.29222	0.650000	0.86243	CAA	.	.		0.572	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
TSPO2	222642	hgsc.bcm.edu	37	6	41011697	41011697	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:41011697C>T	ENST00000373161.1	+	4	579	c.334C>T	c.(334-336)Ctg>Ttg	p.L112L	TSPO2_ENST00000470917.1_Silent_p.L112L|TSPO2_ENST00000373158.2_Silent_p.C64C	NM_001010873.2	NP_001010873.1	Q5TGU0	TSPO2_HUMAN	translocator protein 2	112					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)			breast(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GCACCTGCTGCTGCTGTATGG	0.627																																					p.L112L		Atlas-SNP	.											.	TSPO2	26	.	0			c.C334T						.						78.0	57.0	64.0					6																	41011697		2203	4300	6503	SO:0001819	synonymous_variant	222642	exon4			CTGCTGCTGCTGT		CCDS34444.1	6p21.1	2009-09-18	2009-09-04	2009-09-04	ENSG00000112212	ENSG00000112212			21256	protein-coding gene	gene with protein product	"""similar to RIKEN cDNA 2510027D20"""		"""benzodiazapine receptor (peripheral)-like 1"""	BZRPL1		19729679	Standard	NM_001010873		Approved	dJ34B21.2	uc003opj.3	Q5TGU0	OTTHUMG00000014666	ENST00000373161.1:c.334C>T	chr6.hg19:g.41011697C>T		89.0	0.0		68.0	4.0	NM_001010873	B2RPR2|B7ZMN8|Q3SX82	Silent	SNP	ENST00000373161.1	hg19	CCDS34444.1																																																																																			.	.		0.627	TSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040493.1	NM_001010873.2	
UBR2	23304	hgsc.bcm.edu	37	6	42573470	42573470	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:42573470A>G	ENST00000372899.1	+	6	932	c.674A>G	c.(673-675)gAc>gGc	p.D225G	UBR2_ENST00000372903.2_Missense_Mutation_p.D225G|UBR2_ENST00000372901.1_Missense_Mutation_p.D225G	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	225					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GAGAAGAGTGACACCTACTAT	0.328																																					p.D225G		Atlas-SNP	.											.	UBR2	134	.	0			c.A674G						.						102.0	102.0	102.0					6																	42573470		2203	4299	6502	SO:0001583	missense	23304	exon6			AGAGTGACACCTA	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.674A>G	chr6.hg19:g.42573470A>G	ENSP00000361990:p.Asp225Gly	94.0	0.0		98.0	4.0	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210388	0.79240	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.74526	-0.85;0.08;0.08	5.22	5.22	0.72569	Adaptor protein ClpS, core (1);Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like (2);	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	L	0.42245	1.32	0.80722	D	1	B;P	0.39847	0.385;0.691	B;B	0.40038	0.178;0.317	T	0.65578	-0.6134	10	0.46703	T	0.11	-12.8997	15.1076	0.72332	1.0:0.0:0.0:0.0	.	225;225	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	G	225	ENSP00000361994:D225G;ENSP00000361990:D225G;ENSP00000361992:D225G	ENSP00000361990:D225G	D	+	2	0	UBR2	42681448	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.299000	0.78831	1.980000	0.57719	0.455000	0.32223	GAC	.	.		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
CUL7	9820	hgsc.bcm.edu	37	6	43010877	43010877	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:43010877G>T	ENST00000265348.3	-	18	3482	c.3397C>A	c.(3397-3399)Cgg>Agg	p.R1133R	CUL7_ENST00000535468.1_Silent_p.R1217R|CUL7_ENST00000478630.1_5'Flank			Q14999	CUL7_HUMAN	cullin 7	1133					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGAAGGCCCCGGGTAGCCAAG	0.622																																					p.R1217R		Atlas-SNP	.											.	CUL7	133	.	0			c.C3649A						.						53.0	52.0	52.0					6																	43010877		2203	4300	6503	SO:0001819	synonymous_variant	9820	exon18			GGCCCCGGGTAGC	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3397C>A	chr6.hg19:g.43010877G>T		47.0	0.0		59.0	4.0	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	hg19	CCDS4881.1																																																																																			.	.		0.622	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
XPO5	57510	hgsc.bcm.edu	37	6	43515423	43515423	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:43515423A>G	ENST00000265351.7	-	19	2292	c.2082T>C	c.(2080-2082)gcT>gcC	p.A694A		NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	694					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			ACGCAATGAAAGCATCAACAT	0.478																																					p.A694A		Atlas-SNP	.											.	XPO5	79	.	0			c.T2082C						.						100.0	96.0	97.0					6																	43515423		1969	4163	6132	SO:0001819	synonymous_variant	57510	exon19			AATGAAAGCATCA	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2082T>C	chr6.hg19:g.43515423A>G		85.0	0.0		103.0	5.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.478	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
TFAP2D	83741	hgsc.bcm.edu	37	6	50740456	50740456	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:50740456C>T	ENST00000008391.3	+	8	1466	c.1238C>T	c.(1237-1239)aCt>aTt	p.T413I		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					GAAAAACACACTACTCACAAG	0.512																																					p.T413I		Atlas-SNP	.											.	TFAP2D	144	.	0			c.C1238T						.						66.0	65.0	65.0					6																	50740456		2203	4300	6503	SO:0001583	missense	83741	exon8			AACACACTACTCA	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"""	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.1238C>T	chr6.hg19:g.50740456C>T	ENSP00000008391:p.Thr413Ile	85.0	0.0		120.0	43.0	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	hg19	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.688160	0.29962	.	.	ENSG00000008197	ENST00000008391	D	0.96885	-4.16	5.31	4.45	0.53987	Transcription factor AP-2, C-terminal (1);	0.155858	0.43579	D	0.000551	D	0.89132	0.6628	N	0.08118	0	0.44149	D	0.996941	B	0.19583	0.037	B	0.34346	0.18	D	0.85696	0.1310	10	0.66056	D	0.02	-8.3512	16.1801	0.81892	0.0:0.8665:0.1335:0.0	.	413	Q7Z6R9	AP2D_HUMAN	I	413	ENSP00000008391:T413I	ENSP00000008391:T413I	T	+	2	0	TFAP2D	50848415	1.000000	0.71417	0.987000	0.45799	0.690000	0.40134	7.487000	0.81328	1.258000	0.44101	-0.355000	0.07637	ACT	.	.		0.512	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238	
DST	667	hgsc.bcm.edu	37	6	56346864	56346864	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56346864A>G	ENST00000361203.3	-	85	20562	c.20555T>C	c.(20554-20556)cTc>cCc	p.L6852P	DST_ENST00000370769.4_Missense_Mutation_p.L6963P|DST_ENST00000370754.5_Missense_Mutation_p.L7141P|DST_ENST00000244364.6_Missense_Mutation_p.L4549P|DST_ENST00000421834.2_Missense_Mutation_p.L4875P|DST_ENST00000370788.2_Missense_Mutation_p.L4766P|DST_ENST00000446842.2_Missense_Mutation_p.L6637P|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	6853					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGATCAATGAGAGTCCGGAG	0.453																																					p.L4549P		Atlas-SNP	.											.	DST	1427	.	0			c.T13646C						.						40.0	42.0	41.0					6																	56346864		1944	4136	6080	SO:0001583	missense	667	exon71			TCAATGAGAGTCC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20555T>C	chr6.hg19:g.56346864A>G	ENSP00000354508:p.Leu6852Pro	30.0	0.0		71.0	4.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.38	3.107436	0.56291	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08	5.86	5.86	0.93980	.	0.000000	0.48286	D	0.000184	T	0.71204	0.3312	M	0.74881	2.28	0.35649	D	0.811618	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.996	D;D;D;D;D	0.97110	1.0;1.0;0.999;0.982;0.946	T	0.73404	-0.3993	9	0.52906	T	0.07	.	16.5602	0.84551	1.0:0.0:0.0:0.0	.	4875;6963;7141;6961;4549	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	P	4549;7141;6963;4875;6637;4766;6852	ENSP00000244364:L4549P;ENSP00000359790:L7141P;ENSP00000359805:L6963P;ENSP00000400883:L4875P;ENSP00000393645:L6637P;ENSP00000359824:L4766P;ENSP00000354508:L6852P	ENSP00000244364:L4549P	L	-	2	0	DST	56454823	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.412000	0.80091	2.367000	0.80283	0.528000	0.53228	CTC	.	.		0.453	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
DST	667	hgsc.bcm.edu	37	6	56358808	56358808	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56358808T>C	ENST00000361203.3	-	78	19441	c.19434A>G	c.(19432-19434)aaA>aaG	p.K6478K	DST_ENST00000370769.4_Splice_Site_p.K6589K|DST_ENST00000370754.5_Splice_Site_p.K6767K|DST_ENST00000244364.6_Splice_Site_p.K4175K|DST_ENST00000421834.2_Splice_Site_p.K4501K|DST_ENST00000370788.2_Splice_Site_p.K4392K|DST_ENST00000446842.2_Splice_Site_p.K6263K|DST_ENST00000312431.6_3'UTR|DST_ENST00000340834.4_5'Flank			Q03001	DYST_HUMAN	dystonin	6478					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AAGCACATACTTTCCTTTCAT	0.348																																					p.K4175K		Atlas-SNP	.											.	DST	1427	.	0			c.A12525G						.						136.0	119.0	124.0					6																	56358808		1823	4087	5910	SO:0001630	splice_region_variant	667	exon64			ACATACTTTCCTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.19434+1A>G	chr6.hg19:g.56358808T>C		121.0	0.0		138.0	6.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.348	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	Silent
DST	667	hgsc.bcm.edu	37	6	56436957	56436957	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56436957A>G	ENST00000361203.3	-	49	13036	c.13029T>C	c.(13027-13029)ctT>ctC	p.L4343L	DST_ENST00000370769.4_Silent_p.L4345L|DST_ENST00000370754.5_Silent_p.L4523L|DST_ENST00000244364.6_Silent_p.L1931L|DST_ENST00000421834.2_Silent_p.L2257L|DST_ENST00000370788.2_Silent_p.L2257L|DST_ENST00000446842.2_Silent_p.L4019L|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	4343					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTGTTTTTTCAAGGACCAAAG	0.303																																					p.L1931L		Atlas-SNP	.											.	DST	1427	.	0			c.T5793C						.						47.0	42.0	44.0					6																	56436957		1798	4055	5853	SO:0001819	synonymous_variant	667	exon34			TTTTTCAAGGACC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.13029T>C	chr6.hg19:g.56436957A>G		40.0	0.0		54.0	4.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.		0.303	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
KIAA1586	57691	hgsc.bcm.edu	37	6	56917800	56917800	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:56917800G>T	ENST00000370733.4	+	4	710	c.503G>T	c.(502-504)cGg>cTg	p.R168L	KIAA1586_ENST00000488682.1_3'UTR|KIAA1586_ENST00000545356.1_Missense_Mutation_p.R141L	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	168							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TCAGCAGTTCGGCATTTGGGA	0.363																																					p.R168L		Atlas-SNP	.											.	KIAA1586	59	.	0			c.G503T						.						92.0	88.0	89.0					6																	56917800		2203	4300	6503	SO:0001583	missense	57691	exon4			CAGTTCGGCATTT	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.503G>T	chr6.hg19:g.56917800G>T	ENSP00000359768:p.Arg168Leu	75.0	0.0		97.0	4.0	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	hg19	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	g	10.92	1.487165	0.26686	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.32023	1.47;1.47	3.7	-1.16	0.09678	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.20074	N	0.999935	B;B	0.26483	0.15;0.15	B;B	0.23018	0.043;0.043	T	0.39840	-0.9594	9	0.32370	T	0.25	.	3.7093	0.08413	0.4506:0.1941:0.3553:0.0	.	141;168	F5H2N6;Q9HCI6	.;K1586_HUMAN	L	168;141	ENSP00000359768:R168L;ENSP00000445507:R141L	ENSP00000359768:R168L	R	+	2	0	KIAA1586	57025759	0.044000	0.20184	0.755000	0.31263	0.980000	0.70556	-0.274000	0.08537	-0.113000	0.11958	0.467000	0.42956	CGG	.	.		0.363	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
BAI3	577	hgsc.bcm.edu	37	6	69684659	69684659	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:69684659T>C	ENST00000370598.1	+	9	2351	c.1530T>C	c.(1528-1530)ccT>ccC	p.P510P		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	510					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TTGCAGCACCTTATGAAATAT	0.413																																					p.P510P		Atlas-SNP	.											.	BAI3	451	.	0			c.T1530C						.						100.0	96.0	97.0					6																	69684659		2203	4300	6503	SO:0001819	synonymous_variant	577	exon9			AGCACCTTATGAA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1530T>C	chr6.hg19:g.69684659T>C		112.0	0.0		147.0	6.0	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	hg19	CCDS4968.1																																																																																			.	.		0.413	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
PRSS35	167681	hgsc.bcm.edu	37	6	84234261	84234261	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:84234261T>C	ENST00000369700.3	+	2	1278	c.1101T>C	c.(1099-1101)atT>atC	p.I367I	PRSS35_ENST00000536636.1_Silent_p.I367I	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	367	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		GCAAAATCATTGCGGTCTACT	0.522																																					p.I367I		Atlas-SNP	.											.	PRSS35	60	.	0			c.T1101C						.						76.0	71.0	73.0					6																	84234261		2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			AATCATTGCGGTC	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.1101T>C	chr6.hg19:g.84234261T>C		59.0	0.0		87.0	4.0	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	hg19	CCDS4999.1																																																																																			.	.		0.522	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
SPACA1	81833	hgsc.bcm.edu	37	6	88768538	88768538	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:88768538C>A	ENST00000237201.1	+	4	589	c.472C>A	c.(472-474)Caa>Aaa	p.Q158K		NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	158					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		AAGACAAGACCAAGTGAGTAA	0.333																																					p.Q158K		Atlas-SNP	.											.	SPACA1	49	.	0			c.C472A						.						69.0	69.0	69.0					6																	88768538		2203	4300	6503	SO:0001583	missense	81833	exon4			CAAGACCAAGTGA	AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.472C>A	chr6.hg19:g.88768538C>A	ENSP00000237201:p.Gln158Lys	91.0	0.0		89.0	5.0	NM_030960		Missense_Mutation	SNP	ENST00000237201.1	hg19	CCDS5014.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.146618	0.57044	.	.	ENSG00000118434	ENST00000237201	T	0.23147	1.92	5.77	5.77	0.91146	.	0.088226	0.49916	D	0.000136	T	0.21921	0.0528	L	0.55103	1.725	0.33206	D	0.552773	P	0.40970	0.734	P	0.46510	0.519	T	0.04579	-1.0941	10	0.44086	T	0.13	-16.1234	13.8419	0.63444	0.1525:0.8475:0.0:0.0	.	158	Q9HBV2	SACA1_HUMAN	K	158	ENSP00000237201:Q158K	ENSP00000237201:Q158K	Q	+	1	0	SPACA1	88825257	0.996000	0.38824	0.991000	0.47740	0.643000	0.38383	2.284000	0.43478	2.733000	0.93635	0.585000	0.79938	CAA	.	.		0.333	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1		
MDN1	23195	hgsc.bcm.edu	37	6	90368429	90368429	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:90368429T>G	ENST00000369393.3	-	89	15036	c.14921A>C	c.(14920-14922)gAa>gCa	p.E4974A	MDN1_ENST00000428876.1_Missense_Mutation_p.E4974A			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4974					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTCAGAGTGTTCTTCAGGATG	0.542																																					p.E4974A		Atlas-SNP	.											.	MDN1	478	.	0			c.A14921C						.						294.0	256.0	269.0					6																	90368429		2203	4300	6503	SO:0001583	missense	23195	exon89			GAGTGTTCTTCAG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14921A>C	chr6.hg19:g.90368429T>G	ENSP00000358400:p.Glu4974Ala	319.0	1.0		314.0	149.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.495882	0.26774	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03889	3.77;3.77	5.09	3.93	0.45458	.	0.395777	0.24470	N	0.038257	T	0.01222	0.0040	N	0.16478	0.41	0.33461	D	0.584991	B	0.10296	0.003	B	0.11329	0.006	T	0.46748	-0.9169	10	0.35671	T	0.21	.	9.9126	0.41415	0.0:0.0818:0.0:0.9182	.	4974	Q9NU22	MDN1_HUMAN	A	4974	ENSP00000358400:E4974A;ENSP00000413970:E4974A	ENSP00000358400:E4974A	E	-	2	0	MDN1	90425150	1.000000	0.71417	0.514000	0.27761	0.007000	0.05969	4.247000	0.58750	0.897000	0.36392	0.454000	0.30748	GAA	.	.		0.542	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
MDN1	23195	hgsc.bcm.edu	37	6	90428309	90428309	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:90428309T>C	ENST00000369393.3	-	43	6474	c.6359A>G	c.(6358-6360)aAg>aGg	p.K2120R	MDN1_ENST00000428876.1_Missense_Mutation_p.K2120R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2120					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCCCTCCACCTTCTCTAGCAG	0.463																																					p.K2120R		Atlas-SNP	.											.	MDN1	478	.	0			c.A6359G						.						110.0	100.0	104.0					6																	90428309		2203	4300	6503	SO:0001583	missense	23195	exon43			TCCACCTTCTCTA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.6359A>G	chr6.hg19:g.90428309T>C	ENSP00000358400:p.Lys2120Arg	71.0	0.0		78.0	4.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	7.537	0.659870	0.14645	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03272	3.99;3.99	5.91	4.75	0.60458	ATPase, AAA+ type, core (1);	0.159044	0.56097	D	0.000038	T	0.00936	0.0031	N	0.13235	0.315	0.32896	D	0.512502	B	0.06786	0.001	B	0.17979	0.02	T	0.49652	-0.8917	10	0.22109	T	0.4	.	11.7235	0.51696	0.0:0.0685:0.0:0.9315	.	2120	Q9NU22	MDN1_HUMAN	R	2120	ENSP00000358400:K2120R;ENSP00000413970:K2120R	ENSP00000358400:K2120R	K	-	2	0	MDN1	90485030	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	2.403000	0.44530	1.067000	0.40740	0.528000	0.53228	AAG	.	.		0.463	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
SIM1	6492	hgsc.bcm.edu	37	6	100898180	100898180	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:100898180A>G	ENST00000369208.3	-	4	1093	c.311T>C	c.(310-312)aTc>aCc	p.I104T	SIM1_ENST00000262901.4_Missense_Mutation_p.I104T			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	104	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		TGTCTCTGAGATGTACATGAT	0.537																																					p.I104T		Atlas-SNP	.											.	SIM1	173	.	0			c.T311C						.						178.0	161.0	167.0					6																	100898180		2203	4300	6503	SO:0001583	missense	6492	exon3			TCTGAGATGTACA	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.311T>C	chr6.hg19:g.100898180A>G	ENSP00000358210:p.Ile104Thr	57.0	0.0		90.0	4.0	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	hg19	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.493368	0.84962	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.18502	2.21;2.21	4.99	4.99	0.66335	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.34337	0.0894	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.28364	-1.0046	10	0.87932	D	0	.	14.6886	0.69068	1.0:0.0:0.0:0.0	.	104	P81133	SIM1_HUMAN	T	104	ENSP00000358210:I104T;ENSP00000262901:I104T	ENSP00000262901:I104T	I	-	2	0	SIM1	101004901	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.932000	0.92897	1.885000	0.54596	0.459000	0.35465	ATC	.	.		0.537	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
SMPD2	6610	hgsc.bcm.edu	37	6	109764241	109764241	+	Missense_Mutation	SNP	A	A	G	rs145532915	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:109764241A>G	ENST00000258052.3	+	8	1045	c.686A>G	c.(685-687)aAg>aGg	p.K229R	PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	229					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		CAGGAGCTGAAGCCATTTCCC	0.502																																					p.K229R		Atlas-SNP	.											.	SMPD2	25	.	0			c.A686G						.						96.0	88.0	91.0					6																	109764241		2203	4300	6503	SO:0001583	missense	6610	exon8			AGCTGAAGCCATT	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.686A>G	chr6.hg19:g.109764241A>G	ENSP00000258052:p.Lys229Arg	105.0	0.0		124.0	6.0	NM_003080	Q5TED1|Q9BWR3	Missense_Mutation	SNP	ENST00000258052.3	hg19	CCDS5075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.731|1.731	-0.494046|-0.494046	0.04322|0.04322	.|.	.|.	ENSG00000135587|ENSG00000135587	ENST00000258052|ENST00000458487	T|.	0.32272|.	1.46|.	5.95|5.95	0.512|0.512	0.16994|0.16994	Endonuclease/exonuclease/phosphatase (2);|.	1.230960|.	0.05155|.	N|.	0.496721|.	T|T	0.12263|0.12263	0.0298|0.0298	N|N	0.21282|0.21282	0.65|0.65	0.09310|0.09310	N|N	1|1	B|.	0.21821|.	0.061|.	B|.	0.22152|.	0.038|.	T|T	0.33240|0.33240	-0.9876|-0.9876	10|5	0.13470|.	T|.	0.59|.	-0.2032|-0.2032	8.7389|8.7389	0.34545|0.34545	0.5746:0.0:0.4254:0.0|0.5746:0.0:0.4254:0.0	.|.	229|.	O60906|.	NSMA_HUMAN|.	R|G	229|126	ENSP00000258052:K229R|.	ENSP00000258052:K229R|.	K|S	+|+	2|1	0|0	SMPD2|SMPD2	109870934|109870934	0.030000|0.030000	0.19436|0.19436	0.001000|0.001000	0.08648|0.08648	0.147000|0.147000	0.21601|0.21601	0.364000|0.364000	0.20325|0.20325	0.077000|0.077000	0.16863|0.16863	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.	A|0.999;T|0.001		0.502	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1		
LAMA2	3908	hgsc.bcm.edu	37	6	129722435	129722435	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:129722435A>G	ENST00000421865.2	+	38	5561	c.5512A>G	c.(5512-5514)Ata>Gta	p.I1838V		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1838	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGGCAATGACATACTCGATGA	0.388																																					p.I1838V		Atlas-SNP	.											.	LAMA2	481	.	0			c.A5512G						.						141.0	137.0	139.0					6																	129722435		2203	4300	6503	SO:0001583	missense	3908	exon38			AATGACATACTCG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.5512A>G	chr6.hg19:g.129722435A>G	ENSP00000400365:p.Ile1838Val	111.0	0.0		97.0	4.0	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	hg19	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.378577	0.24944	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.09723	2.95	5.28	1.41	0.22369	Laminin I (1);	0.261499	0.38492	N	0.001671	T	0.01627	0.0052	L	0.29908	0.895	0.30704	N	0.75001	B;B	0.11235	0.004;0.004	B;B	0.20184	0.026;0.028	T	0.47674	-0.9099	10	0.06891	T	0.86	.	6.3007	0.21111	0.6158:0.2486:0.1356:0.0	.	1838;1838	A6NF00;P24043	.;LAMA2_HUMAN	V	1838	ENSP00000400365:I1838V	ENSP00000346769:I1838V	I	+	1	0	LAMA2	129764128	1.000000	0.71417	0.933000	0.37362	0.848000	0.48234	1.173000	0.31920	0.059000	0.16252	0.533000	0.62120	ATA	.	.		0.388	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
ECT2L	345930	hgsc.bcm.edu	37	6	139135640	139135640	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:139135640A>G	ENST00000423192.1	+	3	240	c.79A>G	c.(79-81)Aga>Gga	p.R27G	ECT2L_ENST00000541398.1_5'Flank|ECT2L_ENST00000367682.2_Missense_Mutation_p.R27G			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	27							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						CTTTCAGGAAAGAGTGGCTCT	0.378			"""N, Splice, Mis"""		ETP ALL																																p.R27G		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A79G						.						72.0	70.0	71.0					6																	139135640		1844	4092	5936	SO:0001583	missense	345930	exon3			CAGGAAAGAGTGG		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.79A>G	chr6.hg19:g.139135640A>G	ENSP00000387388:p.Arg27Gly	66.0	0.0		65.0	4.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	19.22	3.784984	0.70222	.	.	ENSG00000203734	ENST00000423192;ENST00000401414;ENST00000367682	T;T;T	0.69175	-0.18;-0.38;-0.18	5.43	4.22	0.49857	.	.	.	.	.	T	0.71643	0.3364	M	0.62723	1.935	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.75525	-0.3287	9	0.87932	D	0	.	10.4461	0.44495	0.8373:0.1627:0.0:0.0	.	27	Q008S8	ECT2L_HUMAN	G	27	ENSP00000387388:R27G;ENSP00000385187:R27G;ENSP00000356655:R27G	ENSP00000356655:R27G	R	+	1	2	ECT2L	139177333	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.000000	0.57039	2.066000	0.61787	0.533000	0.62120	AGA	.	.		0.378	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	
PLAGL1	5325	hgsc.bcm.edu	37	6	144263706	144263706	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:144263706T>C	ENST00000360537.2	-	5	2160	c.247A>G	c.(247-249)Acc>Gcc	p.T83A	PLAGL1_ENST00000437412.1_Missense_Mutation_p.T31A|PLAGL1_ENST00000354765.2_Missense_Mutation_p.T83A|PLAGL1_ENST00000429150.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000392307.1_Missense_Mutation_p.T31A|PLAGL1_ENST00000367571.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000416623.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000367572.1_Missense_Mutation_p.T31A|PLAGL1_ENST00000444202.1_Missense_Mutation_p.T83A|PLAGL1_ENST00000392309.1_Missense_Mutation_p.T83A			Q9UM63	PLAL1_HUMAN	pleiomorphic adenoma gene-like 1	83					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(3)|stomach(2)	13				OV - Ovarian serous cystadenocarcinoma(155;5.74e-07)|GBM - Glioblastoma multiforme(68;0.0885)		GGGTCGTGGGTCTGGAGGTGG	0.542											OREG0017707	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T83A		Atlas-SNP	.											.	PLAGL1	33	.	0			c.A247G						.						124.0	114.0	118.0					6																	144263706		2203	4300	6503	SO:0001583	missense	5325	exon7			CGTGGGTCTGGAG	U81992	CCDS5202.1, CCDS5203.1	6q24-q25	2013-01-08			ENSG00000118495	ENSG00000118495		"""Zinc fingers, C2H2-type"""	9046	protein-coding gene	gene with protein product		603044				9722527, 9671765	Standard	NM_006718		Approved	ZAC, LOT1	uc003qkf.3	Q9UM63	OTTHUMG00000015738	ENST00000360537.2:c.247A>G	chr6.hg19:g.144263706T>C	ENSP00000353734:p.Thr83Ala	43.0	0.0	1685	55.0	4.0	NM_001080953	B2RBA4|B2RCM8|E1P595|E1P597|O76019|Q7Z3V8|Q92981|Q96JR9|Q9UIZ0	Missense_Mutation	SNP	ENST00000360537.2	hg19	CCDS5202.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.021705	0.75275	.	.	ENSG00000118495	ENST00000360537;ENST00000354765;ENST00000444202;ENST00000429150;ENST00000392309;ENST00000416623;ENST00000437412;ENST00000392307;ENST00000367572;ENST00000367571;ENST00000417959	T;T;T;T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;2.73;2.73;2.73;1.55;2.73	6.16	3.75	0.43078	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.082393	0.52532	N	0.000071	T	0.27454	0.0674	L	0.45285	1.41	0.40727	D	0.982711	D	0.65815	0.995	P	0.62184	0.899	T	0.08411	-1.0723	10	0.72032	D	0.01	-23.0055	7.8278	0.29326	0.1236:0.0665:0.0:0.8099	.	83	Q9UM63	PLAL1_HUMAN	A	83;83;83;83;83;83;31;31;31;83;31	ENSP00000353734:T83A;ENSP00000346810:T83A;ENSP00000400929:T83A;ENSP00000398409:T83A;ENSP00000376125:T83A;ENSP00000400060:T83A;ENSP00000392418:T31A;ENSP00000376124:T31A;ENSP00000356544:T31A;ENSP00000356543:T83A;ENSP00000395960:T31A	ENSP00000346810:T83A	T	-	1	0	PLAGL1	144305399	1.000000	0.71417	0.754000	0.31244	0.990000	0.78478	7.977000	0.88081	0.547000	0.28938	0.528000	0.53228	ACC	.	.		0.542	PLAGL1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042541.1		
TCP10	6953	hgsc.bcm.edu	37	6	167789461	167789461	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:167789461T>C	ENST00000397829.4	-	6	848	c.681A>G	c.(679-681)agA>agG	p.R227R	TCP10_ENST00000366827.2_Silent_p.R227R	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	254						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CACCAGCTCCTCTGGCTGCTG	0.572																																					p.R227R		Atlas-SNP	.											.	TCP10	35	.	0			c.A681G						.						20.0	24.0	22.0					6																	167789461		1985	4167	6152	SO:0001819	synonymous_variant	6953	exon6			AGCTCCTCTGGCT	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"""t-complex 10 (a murine tcp homolog)"", ""t-complex 10 (mouse)"", ""t-complex 10 homolog (mouse)"""			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.681A>G	chr6.hg19:g.167789461T>C		113.0	0.0		120.0	5.0	NM_004610	Q5JR60|Q6P4F4	Silent	SNP	ENST00000397829.4	hg19	CCDS43527.1																																																																																			.	.		0.572	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610	
TBP	6908	hgsc.bcm.edu	37	6	170871004	170871004	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43.0	45.0	44.0					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		58.0	0.0		73.0	4.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
TNRC18	84629	hgsc.bcm.edu	37	7	5427683	5427683	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:5427683T>A	ENST00000430969.1	-	5	2120	c.1772A>T	c.(1771-1773)tAc>tTc	p.Y591F	TNRC18_ENST00000399537.4_Missense_Mutation_p.Y591F	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	591							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCTGCCACTGTACTTTATAAG	0.682																																					p.Y591F		Atlas-SNP	.											.	TNRC18	311	.	0			c.A1772T						.						6.0	8.0	7.0					7																	5427683		1928	4082	6010	SO:0001583	missense	84629	exon5			CCACTGTACTTTA	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.1772A>T	chr7.hg19:g.5427683T>A	ENSP00000395538:p.Tyr591Phe	70.0	0.0		55.0	4.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	t	15.00	2.703990	0.48412	.	.	ENSG00000182095	ENST00000399537;ENST00000430969	T;T	0.33216	1.43;1.42	4.83	4.83	0.62350	.	.	.	.	.	T	0.52191	0.1719	M	0.63843	1.955	0.40329	D	0.978904	D	0.76494	0.999	D	0.78314	0.991	T	0.56998	-0.7886	9	0.62326	D	0.03	.	14.419	0.67171	0.0:0.0:0.0:1.0	.	591	O15417	TNC18_HUMAN	F	591	ENSP00000382452:Y591F;ENSP00000395538:Y591F	ENSP00000382452:Y591F	Y	-	2	0	TNRC18	5394209	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.390000	0.66261	1.804000	0.52760	0.454000	0.30748	TAC	.	.		0.682	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
MPP6	51678	hgsc.bcm.edu	37	7	24690104	24690104	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:24690104G>T	ENST00000222644.5	+	5	674	c.424G>T	c.(424-426)Ggt>Tgt	p.G142C	MPP6_ENST00000409761.1_Splice_Site_p.G30C|MPP6_ENST00000396475.2_Splice_Site_p.G142C			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						TTTTTCATAGGGTGTGACATT	0.323																																					p.G142C		Atlas-SNP	.											.	MPP6	62	.	0			c.G424T						.						50.0	53.0	52.0					7																	24690104		2202	4299	6501	SO:0001630	splice_region_variant	51678	exon6			TCATAGGGTGTGA	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.424-1G>T	chr7.hg19:g.24690104G>T		108.0	0.0		84.0	5.0	NM_016447	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	hg19	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354341	0.82243	.	.	ENSG00000105926	ENST00000432190;ENST00000222644;ENST00000409761;ENST00000396475;ENST00000430180	D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92	6.06	6.06	0.98353	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000018	D	0.95604	0.8571	H	0.97611	4.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96542	0.9401	9	.	.	.	.	18.8014	0.92018	0.0:0.0:1.0:0.0	.	142	Q9NZW5	MPP6_HUMAN	C	142;142;30;142;142	ENSP00000395859:G142C;ENSP00000222644:G142C;ENSP00000386262:G30C;ENSP00000379737:G142C;ENSP00000391020:G142C	.	G	+	1	0	MPP6	24656629	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	9.130000	0.94437	2.882000	0.98803	0.655000	0.94253	GGT	.	.		0.323	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4		Missense_Mutation
OSBPL3	26031	hgsc.bcm.edu	37	7	24870476	24870476	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:24870476G>T	ENST00000313367.2	-	16	2246	c.1795C>A	c.(1795-1797)Cga>Aga	p.R599R	OSBPL3_ENST00000396431.1_Silent_p.R568R|OSBPL3_ENST00000431825.2_Silent_p.R532R|OSBPL3_ENST00000352860.1_Silent_p.R568R|OSBPL3_ENST00000396429.1_Silent_p.R563R|OSBPL3_ENST00000353930.1_Silent_p.R563R|OSBPL3_ENST00000409069.1_Silent_p.R532R	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	599					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CTTCCAGCTCGGTAGTAGCTA	0.428																																					p.R599R		Atlas-SNP	.											.	OSBPL3	100	.	0			c.C1795A						.						124.0	130.0	128.0					7																	24870476		2203	4300	6503	SO:0001819	synonymous_variant	26031	exon16			CAGCTCGGTAGTA	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1795C>A	chr7.hg19:g.24870476G>T		119.0	0.0		80.0	4.0	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Silent	SNP	ENST00000313367.2	hg19	CCDS5390.1																																																																																			.	.		0.428	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
HOXA11	3207	hgsc.bcm.edu	37	7	27222608	27222608	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:27222608T>C	ENST00000006015.3	-	2	820	c.749A>G	c.(748-750)aAg>aGg	p.K250R	HOXA11-AS_ENST00000520360.1_RNA|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000522674.1_RNA|HOXA10_ENST00000396344.4_5'Flank|HOXA11-AS_ENST00000520395.1_RNA|RP1-170O19.20_ENST00000470747.4_5'Flank	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	250					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						GATCTGGTACTTGGTATAGGG	0.572			T	NUP98	CML																																p.K250R		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.A749G						.						89.0	86.0	87.0					7																	27222608		2203	4300	6503	SO:0001583	missense	3207	exon2			TGGTACTTGGTAT		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"""Homeoboxes / ANTP class : HOXL subclass"""	5101	protein-coding gene	gene with protein product		142958	"""homeo box A11"""	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.749A>G	chr7.hg19:g.27222608T>C	ENSP00000006015:p.Lys250Arg	102.0	0.0		72.0	4.0	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	hg19	CCDS5411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.7|28.7	4.946108|4.946108	0.92593|0.92593	.|.	.|.	ENSG00000005073|ENSG00000005073	ENST00000006015|ENST00000517402	D|.	0.96334|.	-3.98|.	5.91|5.91	5.91|5.91	0.95273|0.95273	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60779|0.60779	0.2295|0.2295	L|L	0.39245|0.39245	1.2|1.2	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.56739|0.56739	-0.7929|-0.7929	10|5	0.87932|.	D|.	0|.	.|.	16.3512|16.3512	0.83208|0.83208	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	250|.	P31270|.	HXA11_HUMAN|.	R|G	250|220	ENSP00000006015:K250R|.	ENSP00000006015:K250R|.	K|S	-|-	2|1	0|0	HOXA11|HOXA11	27189133|27189133	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	8.040000|8.040000	0.89188|0.89188	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	AAG|AGT	.	.		0.572	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1		
CRHR2	1395	hgsc.bcm.edu	37	7	30728894	30728894	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:30728894C>A	ENST00000348438.4	-	2	166	c.97G>T	c.(97-99)Ggg>Tgg	p.G33W	CRHR2_ENST00000462882.1_5'UTR|CRHR2_ENST00000341843.4_5'Flank	NM_001202475.1|NM_001202481.1	NP_001189404.1|NP_001189410.1	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	0					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TGGCTCTGCCCGGCTGCCTAG	0.582																																					p.G33W		Atlas-SNP	.											.	CRHR2	104	.	0			c.G97T						.																																			SO:0001583	missense	1395	exon2			TCTGCCCGGCTGC		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000348438.4:c.97G>T	chr7.hg19:g.30728894C>A	ENSP00000340943:p.Gly33Trp	148.0	0.0		95.0	4.0	NM_001202475	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000348438.4	hg19	CCDS56478.1	.	.	.	.	.	.	.	.	.	.	C	3.235	-0.156537	0.06544	.	.	ENSG00000106113	ENST00000348438;ENST00000445981	T	0.54071	0.59	4.1	-2.52	0.06346	.	1.265650	0.05704	N	0.594609	T	0.66117	0.2757	.	.	.	0.09310	N	1	D;D;D	0.89917	1.0;1.0;0.969	D;D;P	0.91635	0.999;0.987;0.737	T	0.57653	-0.7774	9	0.87932	D	0	.	5.6559	0.17642	0.0:0.2575:0.4937:0.2488	.	33;33;33	F2Z2M6;C9JZM9;Q13324-2	.;.;.	W	33	ENSP00000340943:G33W	ENSP00000340943:G33W	G	-	1	0	CRHR2	30695419	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.788000	0.04614	-0.435000	0.07264	0.455000	0.32223	GGG	.	.		0.582	CRHR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327785.1		
YAE1D1	57002	hgsc.bcm.edu	37	7	39610225	39610225	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:39610225A>G	ENST00000223273.2	+	2	293	c.250A>G	c.(250-252)Agt>Ggt	p.S84G	YAE1D1_ENST00000432096.2_Splice_Site_p.R84G|YAE1D1_ENST00000448268.1_Splice_Site_p.S84G	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	84																	AGGAACATTGAGGTAATTTTT	0.358																																					p.S84G		Atlas-SNP	.											.	YAE1D1	2	.	0			c.A250G						.						103.0	106.0	105.0					7																	39610225		2203	4300	6503	SO:0001630	splice_region_variant	57002	exon2			ACATTGAGGTAAT	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 36"""	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.251+1A>G	chr7.hg19:g.39610225A>G		102.0	0.0		75.0	4.0	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Missense_Mutation	SNP	ENST00000223273.2	hg19	CCDS5459.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.73|14.73	2.622666|2.622666	0.46840|0.46840	.|.	.|.	ENSG00000241127|ENSG00000241127	ENST00000432096|ENST00000223273;ENST00000448268	T|T;T	0.46819|0.53857	0.86|0.6;0.68	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	.|0.078660	.|0.85682	.|D	.|0.000000	T|T	0.69620|0.69620	0.3131|0.3131	M|M	0.74467|0.74467	2.265|2.265	0.22511|0.22511	N|N	0.999035|0.999035	.|D	.|0.76494	.|0.999	.|P	.|0.61070	.|0.883	T|T	0.66705|0.66705	-0.5856|-0.5856	6|10	.|0.66056	.|D	.|0.02	-12.0254|-12.0254	15.1131|15.1131	0.72375|0.72375	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|84	.|Q9NRH1	.|CG036_HUMAN	G|G	84|84	ENSP00000395777:R84G|ENSP00000223273:S84G;ENSP00000400511:S84G	.|ENSP00000223273:S84G	R|S	+|+	1|1	2|0	C7orf36|C7orf36	39576750|39576750	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.390000|0.390000	0.30446|0.30446	6.415000|6.415000	0.73328|0.73328	2.304000|2.304000	0.77564|0.77564	0.528000|0.528000	0.53228|0.53228	AGG|AGT	.	.		0.358	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192	Missense_Mutation
YKT6	10652	hgsc.bcm.edu	37	7	44250697	44250697	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:44250697A>G	ENST00000223369.2	+	6	622	c.535A>G	c.(535-537)Aca>Gca	p.T179A	YKT6_ENST00000447123.1_3'UTR|YKT6_ENST00000496112.1_Intron	NM_006555.3	NP_006546.1	O15498	YKT6_HUMAN	YKT6 v-SNARE homolog (S. cerevisiae)	179	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				ER to Golgi vesicle-mediated transport (GO:0006888)|metabolic process (GO:0008152)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle docking involved in exocytosis (GO:0006904)|vesicle targeting (GO:0006903)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|SNARE complex (GO:0031201)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7						GGTGCTGGGAACACAGTCTAA	0.502																																					p.T179A		Atlas-SNP	.											.	YKT6	12	.	0			c.A535G						.						94.0	91.0	92.0					7																	44250697		2203	4300	6503	SO:0001583	missense	10652	exon6			CTGGGAACACAGT	BC007319	CCDS5482.1	7p13	2006-07-07			ENSG00000106636	ENSG00000106636			16959	protein-coding gene	gene with protein product	"""R-SNARE"""	606209				15479160, 15544955	Standard	NM_006555		Approved		uc003tkm.3	O15498	OTTHUMG00000129089	ENST00000223369.2:c.535A>G	chr7.hg19:g.44250697A>G	ENSP00000223369:p.Thr179Ala	146.0	0.0		99.0	4.0	NM_006555	B4DR94|Q53F01|Q6FGU9|Q6IB15	Missense_Mutation	SNP	ENST00000223369.2	hg19	CCDS5482.1	.	.	.	.	.	.	.	.	.	.	A	2.683	-0.274933	0.05679	.	.	ENSG00000106636	ENST00000223369	T	0.39787	1.06	5.27	1.61	0.23674	Synaptobrevin (2);	0.653853	0.16508	N	0.211353	T	0.14270	0.0345	N	0.02865	-0.47	0.23893	N	0.996549	B	0.02656	0.0	B	0.01281	0.0	T	0.32929	-0.9888	10	0.02654	T	1	-0.7788	7.4757	0.27374	0.7474:0.0:0.2526:0.0	.	179	O15498	YKT6_HUMAN	A	179	ENSP00000223369:T179A	ENSP00000223369:T179A	T	+	1	0	YKT6	44217222	0.103000	0.21917	0.025000	0.17156	0.979000	0.70002	2.011000	0.40922	0.040000	0.15660	0.533000	0.62120	ACA	.	.		0.502	YKT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251125.2	NM_006555	
ABCA13	154664	hgsc.bcm.edu	37	7	48312768	48312768	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:48312768A>G	ENST00000435803.1	+	17	3529	c.3505A>G	c.(3505-3507)Atg>Gtg	p.M1169V		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1169					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TAAGTTTGACATGAATGTTTT	0.383																																					p.M1169V		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A3505G						.						95.0	91.0	92.0					7																	48312768		1843	4092	5935	SO:0001583	missense	154664	exon17			TTTGACATGAATG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.3505A>G	chr7.hg19:g.48312768A>G	ENSP00000411096:p.Met1169Val	113.0	0.0		97.0	5.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	1.760	-0.487001	0.04352	.	.	ENSG00000179869	ENST00000435803	D	0.84442	-1.85	5.64	-7.85	0.01192	.	1.722330	0.03242	N	0.180484	T	0.73273	0.3566	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55560	-0.8122	9	.	.	.	.	1.7537	0.02977	0.2465:0.1869:0.3627:0.2039	.	1169	Q86UQ4	ABCAD_HUMAN	V	1169	ENSP00000411096:M1169V	.	M	+	1	0	ABCA13	48283314	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.146000	0.03191	-1.461000	0.01909	-1.783000	0.00646	ATG	.	.		0.383	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ZPBP	11055	hgsc.bcm.edu	37	7	50070900	50070900	+	Missense_Mutation	SNP	C	C	T	rs368593046	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:50070900C>T	ENST00000046087.2	-	5	563	c.494G>A	c.(493-495)cGt>cAt	p.R165H	ZPBP_ENST00000491129.1_Intron|ZPBP_ENST00000419417.1_Missense_Mutation_p.R164H	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	165					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					ATGAGGCTCACGATAAGCTGT	0.279													C|||	3	0.000599042	0.0	0.0	5008	,	,		16839	0.003		0.0	False		,,,				2504	0.0				p.R165H		Atlas-SNP	.											ZPBP,caecum,carcinoma,0,1	ZPBP	65	.	0			c.G494A						.	C	HIS/ARG,HIS/ARG	0,4404		0,0,2202	22.0	23.0	23.0		491,494	3.3	1.0	7		23	1,8591		0,1,4295	no	missense,missense	ZPBP	NM_001159878.1,NM_007009.2	29,29	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	164/351,165/352	50070900	1,12995	2202	4296	6498	SO:0001583	missense	11055	exon5			GGCTCACGATAAG	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.494G>A	chr7.hg19:g.50070900C>T	ENSP00000046087:p.Arg165His	35.0	0.0		35.0	2.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Missense_Mutation	SNP	ENST00000046087.2	hg19	CCDS5509.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472613	0.43942	0.0	1.16E-4	ENSG00000042813	ENST00000046087;ENST00000419417	T;T	0.57752	0.38;0.38	5.25	3.33	0.38152	.	0.539928	0.18189	N	0.148884	T	0.45074	0.1324	M	0.69823	2.125	0.30181	N	0.800381	P;P	0.35944	0.529;0.529	B;B	0.29785	0.107;0.107	T	0.50499	-0.8821	9	.	.	.	-19.0611	8.0263	0.30438	0.1451:0.5656:0.2893:0.0	.	164;165	C9JPU1;Q9BS86	.;ZPBP1_HUMAN	H	165;164	ENSP00000046087:R165H;ENSP00000402071:R164H	.	R	-	2	0	ZPBP	50041446	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.170000	0.31883	2.604000	0.88044	0.655000	0.94253	CGT	.	.		0.279	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009	
EGFR	1956	hgsc.bcm.edu	37	7	55224338	55224338	+	Silent	SNP	G	G	T	rs2302536	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:55224338G>T	ENST00000275493.2	+	9	1296	c.1119G>T	c.(1117-1119)ccG>ccT	p.P373P	EGFR_ENST00000342916.3_Silent_p.P373P|EGFR_ENST00000344576.2_Silent_p.P373P|EGFR_ENST00000420316.2_Silent_p.P373P|EGFR_ENST00000442591.1_Silent_p.P373P|EGFR_ENST00000454757.2_Silent_p.P320P|EGFR_ENST00000455089.1_Silent_p.P328P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	373					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.P373P(2)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	ACATCCTGCCGGTGGCATTTA	0.408		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.P373P		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	EGFR_ENST00000344576,colon,carcinoma,0,2	EGFR	20426	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1119T						.						80.0	82.0	82.0					7																	55224338		2203	4300	6503	SO:0001819	synonymous_variant	1956	exon9	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CCTGCCGGTGGCA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1119G>T	chr7.hg19:g.55224338G>T		162.0	0.0		120.0	5.0	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	G|0.997;A|0.003		0.408	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
EGFR	1956	hgsc.bcm.edu	37	7	55272980	55272980	+	Silent	SNP	C	C	A	rs55796214	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:55272980C>A	ENST00000275493.2	+	28	3480	c.3303C>A	c.(3301-3303)ccC>ccA	p.P1101P	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Silent_p.P1048P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	1101					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCAAAAGGCCCGCTGGCTCTG	0.542		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.P1101P		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	EGFR,colon,carcinoma,0,1	EGFR	20426	.	0			c.C3303A						.						68.0	65.0	66.0					7																	55272980		2203	4300	6503	SO:0001819	synonymous_variant	1956	exon28	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	AAGGCCCGCTGGC		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.3303C>A	chr7.hg19:g.55272980C>A		92.0	0.0		55.0	3.0	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	C|1.000;G|0.000		0.542	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
GUSB	2990	hgsc.bcm.edu	37	7	65429376	65429376	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:65429376G>T	ENST00000304895.4	-	11	1853	c.1723C>A	c.(1723-1725)Caa>Aaa	p.Q575K	GUSB_ENST00000421103.1_Missense_Mutation_p.Q429K|GUSB_ENST00000345660.6_Missense_Mutation_p.Q524K	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	575					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)	p.Q575*(1)		breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						CTGCGTTTTTGATCCAGACCC	0.443																																					p.Q575K		Atlas-SNP	.											GUSB,NS,carcinoma,0,1	GUSB	52	.	1	Substitution - Nonsense(1)	lung(1)	c.C1723A						.						84.0	70.0	75.0					7																	65429376		2203	4297	6500	SO:0001583	missense	2990	exon11			GTTTTTGATCCAG	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1723C>A	chr7.hg19:g.65429376G>T	ENSP00000302728:p.Gln575Lys	99.0	0.0		42.0	2.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Missense_Mutation	SNP	ENST00000304895.4	hg19	CCDS5530.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432249	0.43122	.	.	ENSG00000169919	ENST00000304895;ENST00000421103;ENST00000345660	D;D;D	0.95137	-3.62;-3.62;-3.62	5.39	1.37	0.22104	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 2, TIM barrel (1);	0.364416	0.35124	N	0.003433	D	0.86628	0.5978	N	0.20685	0.6	0.39059	D	0.960485	B;B	0.12630	0.006;0.002	B;B	0.17433	0.018;0.004	T	0.74783	-0.3548	10	0.15499	T	0.54	.	9.5261	0.39165	0.0:0.2243:0.3974:0.3783	.	429;575	E9PCV0;P08236	.;BGLR_HUMAN	K	575;429;524	ENSP00000302728:Q575K;ENSP00000391390:Q429K;ENSP00000340734:Q524K	ENSP00000302728:Q575K	Q	-	1	0	GUSB	65066811	1.000000	0.71417	0.119000	0.21687	0.227000	0.25037	1.842000	0.39250	0.067000	0.16545	-0.188000	0.12872	CAA	.	.		0.443	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
KCTD7	154881	hgsc.bcm.edu	37	7	66098342	66098342	+	Silent	SNP	C	C	T	rs150589535		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:66098342C>T	ENST00000275532.3	+	2	409	c.225C>T	c.(223-225)acC>acT	p.T75T	KCTD7_ENST00000443322.1_Silent_p.T75T	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	75	BTB.				cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						ACGAAGACACCATGTTGGCAG	0.562																																					p.T75T		Atlas-SNP	.											.	KCTD7	26	.	0			c.C225T						.						131.0	97.0	108.0					7																	66098342		2203	4300	6503	SO:0001819	synonymous_variant	154881	exon2			AGACACCATGTTG	AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"""potassium channel tetramerisation domain containing 7"""			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.225C>T	chr7.hg19:g.66098342C>T		116.0	0.0		75.0	4.0	NM_001167961	A4D2M4|Q8IVR0	Silent	SNP	ENST00000275532.3	hg19	CCDS5534.1																																																																																			.	C|1.000;G|0.000		0.562	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033	
SEMA3C	10512	hgsc.bcm.edu	37	7	80433423	80433423	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:80433423G>T	ENST00000265361.3	-	8	1361	c.800C>A	c.(799-801)cCt>cAt	p.P267H	SEMA3C_ENST00000419255.2_Splice_Site_p.P267H|SEMA3C_ENST00000536800.1_Splice_Site_p.P119H|SEMA3C_ENST00000544525.1_Splice_Site_p.P285H	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	267	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						AATACTTACAGGACATATTCG	0.328																																					p.P267H		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C800A						.						143.0	135.0	138.0					7																	80433423		2203	4300	6503	SO:0001630	splice_region_variant	10512	exon8			CTTACAGGACATA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.801+1C>A	chr7.hg19:g.80433423G>T		154.0	0.0		120.0	5.0	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763294	0.69763	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525;ENST00000536800	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.62	4.71	0.59529	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.097572	0.64402	D	0.000001	T	0.41026	0.1141	L	0.51422	1.61	0.80722	D	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.74674	0.871;0.973;0.984	T	0.15809	-1.0424	10	0.59425	D	0.04	.	16.6279	0.84984	0.0:0.1295:0.8705:0.0	.	119;285;267	B4DRL8;F5H1Z7;Q99985	.;.;SEM3C_HUMAN	H	267;267;285;119	ENSP00000265361:P267H;ENSP00000411193:P267H;ENSP00000445649:P285H;ENSP00000438258:P119H	ENSP00000265361:P267H	P	-	2	0	SEMA3C	80271359	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.783000	0.75078	2.637000	0.89404	0.585000	0.79938	CCT	.	.		0.328	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	Missense_Mutation
GRM3	2913	hgsc.bcm.edu	37	7	86415661	86415661	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:86415661G>C	ENST00000361669.2	+	3	1652	c.553G>C	c.(553-555)Gat>Cat	p.D185H	AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000536043.1_Missense_Mutation_p.D57H|GRM3_ENST00000546348.1_Intron|GRM3_ENST00000394720.2_Missense_Mutation_p.D183H|AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000439827.1_Missense_Mutation_p.D185H	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	185					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					GTCGCGCTATGATTACTTTGC	0.567																																					p.D185H	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.G553C						.						132.0	126.0	128.0					7																	86415661		2203	4300	6503	SO:0001583	missense	2913	exon3			CGCTATGATTACT		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.553G>C	chr7.hg19:g.86415661G>C	ENSP00000355316:p.Asp185His	294.0	0.0		224.0	89.0	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	hg19	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.565840	0.86439	.	.	ENSG00000198822	ENST00000361669;ENST00000454217;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17	5.83	5.83	0.93111	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.93993	0.8076	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.94127	0.7385	10	0.87932	D	0	.	19.122	0.93367	0.0:0.0:1.0:0.0	.	57;185;185	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	H	185;57;57;185;183	ENSP00000355316:D185H;ENSP00000405427:D57H;ENSP00000441407:D57H;ENSP00000398767:D185H;ENSP00000378209:D183H	ENSP00000355316:D185H	D	+	1	0	GRM3	86253597	1.000000	0.71417	0.994000	0.49952	0.968000	0.65278	9.756000	0.98918	2.770000	0.95276	0.655000	0.94253	GAT	.	.		0.567	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
CDK14	5218	hgsc.bcm.edu	37	7	90747440	90747440	+	Missense_Mutation	SNP	G	G	T	rs74839397	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:90747440G>T	ENST00000380050.3	+	14	1486	c.1355G>T	c.(1354-1356)cGg>cTg	p.R452L	CDK14_ENST00000265741.3_Missense_Mutation_p.R434L|CDK14_ENST00000436577.2_Missense_Mutation_p.R323L|CDK14_ENST00000406263.1_Missense_Mutation_p.R406L			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	452					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						GAAAGCATGCGGGCCTTTGGG	0.403																																					p.R434L	GBM(83;1228 1256 8311 16577 31299)	Atlas-SNP	.											.	CDK14	153	.	0			c.G1301T						.						84.0	85.0	85.0					7																	90747440		2203	4300	6503	SO:0001583	missense	5218	exon13			GCATGCGGGCCTT		CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"""Cyclin-dependent kinases"""	8883	protein-coding gene	gene with protein product		610679	"""PFTAIRE protein kinase 1"""	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.1355G>T	chr7.hg19:g.90747440G>T	ENSP00000369390:p.Arg452Leu	115.0	0.0		93.0	4.0	NM_012395	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Missense_Mutation	SNP	ENST00000380050.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.57	1.976929	0.34848	.	.	ENSG00000058091	ENST00000380050;ENST00000265741;ENST00000406263;ENST00000436577	T;T;T;T	0.71934	-0.5;-0.52;-0.5;-0.61	5.87	5.87	0.94306	.	0.063724	0.64402	D	0.000009	T	0.56934	0.2019	L	0.29908	0.895	0.42726	D	0.993693	B;P;B	0.41748	0.18;0.761;0.18	B;B;B	0.35278	0.03;0.199;0.018	T	0.57985	-0.7716	10	0.31617	T	0.26	-12.2164	14.7159	0.69269	0.069:0.0:0.931:0.0	.	323;434;452	E7EUK8;O94921-2;O94921	.;.;CDK14_HUMAN	L	452;434;406;323	ENSP00000369390:R452L;ENSP00000265741:R434L;ENSP00000385034:R406L;ENSP00000398936:R323L	ENSP00000265741:R434L	R	+	2	0	CDK14	90585376	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.148000	0.64857	2.941000	0.99782	0.655000	0.94253	CGG	.	G|0.999;A|0.001		0.403	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395	
AKAP9	10142	hgsc.bcm.edu	37	7	91712764	91712764	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:91712764C>A	ENST00000359028.2	+	34	8702	c.8477C>A	c.(8476-8478)tCa>tAa	p.S2826*	AKAP9_ENST00000356239.3_Nonsense_Mutation_p.S2814*|AKAP9_ENST00000358100.2_Nonsense_Mutation_p.S2826*			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2826					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAATGTTCCTCAGAAGAAGTT	0.353			T	BRAF	papillary thyroid																																p.S2814X		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C8441A						.						45.0	46.0	46.0					7																	91712764		2202	4300	6502	SO:0001587	stop_gained	10142	exon33			GTTCCTCAGAAGA	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.8477C>A	chr7.hg19:g.91712764C>A	ENSP00000351922:p.Ser2826*	118.0	0.0		73.0	4.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Nonsense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	C	51	17.537519	0.99888	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	.	.	.	4.47	3.56	0.40772	.	0.893166	0.09107	N	0.847544	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4215	0.61001	0.1633:0.8367:0.0:0.0	.	.	.	.	X	2814;2826;2826;2818;660	.	ENSP00000348573:S2814X	S	+	2	0	AKAP9	91550700	0.985000	0.35326	0.784000	0.31847	0.948000	0.59901	3.785000	0.55424	1.046000	0.40249	0.591000	0.81541	TCA	.	.		0.353	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
COL1A2	1278	hgsc.bcm.edu	37	7	94043018	94043018	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:94043018A>G	ENST00000297268.6	+	27	2045	c.1574A>G	c.(1573-1575)gAt>gGt	p.D525G		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	525					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CCAGGTCCTGATGGAAACAAT	0.458										HNSCC(75;0.22)																											p.D525G		Atlas-SNP	.											.	COL1A2	240	.	0			c.A1574G						.						109.0	103.0	105.0					7																	94043018		2203	4300	6503	SO:0001583	missense	1278	exon27			GTCCTGATGGAAA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1574A>G	chr7.hg19:g.94043018A>G	ENSP00000297268:p.Asp525Gly	119.0	0.0		59.0	4.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962792	0.74016	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93189	-3.18	5.4	5.4	0.78164	.	0.054395	0.64402	D	0.000001	D	0.94676	0.8283	L	0.46819	1.47	0.80722	D	1	P	0.47253	0.892	P	0.58820	0.846	D	0.95208	0.8323	10	0.72032	D	0.01	.	15.7429	0.77914	1.0:0.0:0.0:0.0	.	525	P08123	CO1A2_HUMAN	G	525;526	ENSP00000297268:D525G	ENSP00000297268:D525G	D	+	2	0	COL1A2	93880954	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	9.292000	0.96076	2.181000	0.69327	0.533000	0.62120	GAT	.	.		0.458	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
PPP1R9A	55607	hgsc.bcm.edu	37	7	94540701	94540701	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:94540701G>T	ENST00000433881.1	+	2	1808	c.1276G>T	c.(1276-1278)Gat>Tat	p.D426Y	PPP1R9A_ENST00000424654.1_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.D426Y|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.D426Y			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	426	Interacts with protein phosphatase 1. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			TGAGGAGGAAGATAGTGATGA	0.423										HNSCC(28;0.073)																											p.D426Y		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.G1276T						.						73.0	66.0	68.0					7																	94540701		2203	4300	6503	SO:0001583	missense	55607	exon2			GAGGAAGATAGTG	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Sterile alpha motif (SAM) domain containing"""	14946	protein-coding gene	gene with protein product		602468	"""protein phosphatase 1, regulatory (inhibitor) subunit 9A"""			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.1276G>T	chr7.hg19:g.94540701G>T	ENSP00000398870:p.Asp426Tyr	127.0	0.0		92.0	4.0	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	hg19	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.324299	0.60634	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.17854	2.25;2.3;2.29;2.3;2.29;2.29	5.55	5.55	0.83447	.	0.188618	0.45867	D	0.000331	T	0.42131	0.1189	M	0.63428	1.95	0.53688	D	0.999978	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.981;0.995;0.997;0.98;0.972	T	0.03249	-1.1056	9	.	.	.	.	19.8905	0.96928	0.0:0.0:1.0:0.0	.	426;426;426;426;426	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	Y	426	ENSP00000405514:D426Y;ENSP00000344524:D426Y;ENSP00000411342:D426Y;ENSP00000398870:D426Y;ENSP00000289495:D426Y;ENSP00000402893:D426Y	.	D	+	1	0	PPP1R9A	94378637	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	7.964000	0.87933	2.789000	0.95967	0.655000	0.94253	GAT	.	.		0.423	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160	
SLC25A13	10165	hgsc.bcm.edu	37	7	95820553	95820553	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:95820553C>A	ENST00000265631.5	-	7	758	c.622G>T	c.(622-624)Gga>Tga	p.G208*	SLC25A13_ENST00000416240.2_Nonsense_Mutation_p.G208*|SLC25A13_ENST00000542654.1_Nonsense_Mutation_p.G100*			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	208					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	GTGGTACCTCCAGCAGCCTCA	0.323																																					p.G208X		Atlas-SNP	.											.	SLC25A13	131	.	0			c.G622T						.						72.0	72.0	72.0					7																	95820553		2203	4300	6503	SO:0001587	stop_gained	10165	exon7			TACCTCCAGCAGC	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.622G>T	chr7.hg19:g.95820553C>A	ENSP00000265631:p.Gly208*	91.0	0.0		74.0	4.0	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Nonsense_Mutation	SNP	ENST00000265631.5	hg19	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	C	37	6.412669	0.97546	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	.	.	.	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-17.1499	19.2746	0.94026	0.0:1.0:0.0:0.0	.	.	.	.	X	208;208;100	.	ENSP00000265631:G208X	G	-	1	0	SLC25A13	95658489	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.879000	0.69690	2.868000	0.98415	0.557000	0.71058	GGA	.	.		0.323	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
BHLHA15	168620	hgsc.bcm.edu	37	7	97842082	97842082	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:97842082A>G	ENST00000609256.1	+	2	587	c.461A>G	c.(460-462)cAg>cGg	p.Q154R	BHLHA15_ENST00000314018.2_Missense_Mutation_p.Q154R			Q7RTS1	BHA15_HUMAN	basic helix-loop-helix family, member a15	154					calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|Golgi organization (GO:0007030)|intracellular distribution of mitochondria (GO:0048312)|mitochondrial calcium ion transport (GO:0006851)	nucleus (GO:0005634)	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)										CAGCACTACCAGCAGCAGCAG	0.662																																					p.Q154R		Atlas-SNP	.											.	BHLHA15	11	.	0			c.A461G						.						9.0	9.0	9.0					7																	97842082		2125	4180	6305	SO:0001583	missense	168620	exon1			ACTACCAGCAGCA	BK000276	CCDS5655.1	7q21.3	2009-01-12	2009-01-12	2009-01-12	ENSG00000180535	ENSG00000180535		"""Basic helix-loop-helix proteins"""	22265	protein-coding gene	gene with protein product		608606	"""basic helix-loop-helix domain containing, class B, 8"""	BHLHB8		14516699, 18557763	Standard	NM_177455		Approved	MIST1, bHLHa15	uc003upf.1	Q7RTS1	OTTHUMG00000154289	ENST00000609256.1:c.461A>G	chr7.hg19:g.97842082A>G	ENSP00000476312:p.Gln154Arg	100.0	0.0		73.0	4.0	NM_177455	A4D271|Q14DE4	Missense_Mutation	SNP	ENST00000609256.1	hg19	CCDS5655.1	.	.	.	.	.	.	.	.	.	.	A	17.37	3.373778	0.61624	.	.	ENSG00000180535	ENST00000314018	D	0.93763	-3.28	3.33	3.33	0.38152	Helix-loop-helix DNA-binding (1);	0.499336	0.18937	U	0.127043	D	0.92427	0.7596	L	0.27053	0.805	0.58432	D	0.999997	D	0.71674	0.998	D	0.75484	0.986	D	0.88226	0.2900	10	0.14252	T	0.57	-9.3665	11.1497	0.48451	1.0:0.0:0.0:0.0	.	154	Q7RTS1	BHA15_HUMAN	R	154	ENSP00000326391:Q154R	ENSP00000326391:Q154R	Q	+	2	0	BHLHA15	97680018	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	5.744000	0.68664	1.270000	0.44297	0.402000	0.26972	CAG	.	.		0.662	BHLHA15-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472733.1	NM_177455	
TRRAP	8295	hgsc.bcm.edu	37	7	98545947	98545947	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:98545947G>T	ENST00000359863.4	+	33	4840	c.4631G>T	c.(4630-4632)cGg>cTg	p.R1544L	TRRAP_ENST00000446306.3_Missense_Mutation_p.R1525L|TRRAP_ENST00000355540.3_Missense_Mutation_p.R1526L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1544					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AAAACGGAGCGGGCGATGCTG	0.498																																					p.R1544L		Atlas-SNP	.											.	TRRAP	863	.	0			c.G4631T						.						85.0	77.0	80.0					7																	98545947		2203	4300	6503	SO:0001583	missense	8295	exon33			CGGAGCGGGCGAT	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.4631G>T	chr7.hg19:g.98545947G>T	ENSP00000352925:p.Arg1544Leu	112.0	0.0		99.0	4.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.2|21.2	4.108936|4.108936	0.77096|0.77096	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000456197|ENST00000359863;ENST00000355540;ENST00000446306	.|T;T	.|0.66995	.|-0.24;-0.24	5.74|5.74	5.74|5.74	0.90152|0.90152	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65123|0.65123	0.2661|0.2661	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.48911	.|0.917;0.65;0.79	.|P;B;B	.|0.45406	.|0.479;0.147;0.306	T|T	0.65557|0.65557	-0.6139|-0.6139	5|10	.|0.48119	.|T	.|0.1	.|.	20.2825|20.2825	0.98528|0.98528	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1526;1265;1544	.|Q9Y4A5-2;Q59FH1;Q9Y4A5	.|.;.;TRRAP_HUMAN	W|L	1266|1544;1526;1524	.|ENSP00000352925:R1544L;ENSP00000347733:R1526L	.|ENSP00000347733:R1526L	G|R	+|+	1|2	0|0	TRRAP|TRRAP	98383883|98383883	1.000000|1.000000	0.71417|0.71417	0.727000|0.727000	0.30756|0.30756	0.205000|0.205000	0.24178|0.24178	9.420000|9.420000	0.97426|0.97426	2.873000|2.873000	0.98535|0.98535	0.561000|0.561000	0.74099|0.74099	GGG|CGG	.	.		0.498	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
SMURF1	57154	hgsc.bcm.edu	37	7	98645414	98645414	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:98645414C>T	ENST00000361125.1	-	11	1442	c.1123G>A	c.(1123-1125)Gaa>Aaa	p.E375K	AC004893.11_ENST00000482799.2_RNA|SMURF1_ENST00000361368.2_Missense_Mutation_p.E349K|AC004893.11_ENST00000468960.2_RNA	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	375					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			AGATCTCTTTCGTATCTCTGG	0.562																																					p.E375K		Atlas-SNP	.											SMURF1,colon,carcinoma,0,3	SMURF1	58	.	0			c.G1123A						.						150.0	148.0	148.0					7																	98645414		2203	4300	6503	SO:0001583	missense	57154	exon11			CTCTTTCGTATCT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.1123G>A	chr7.hg19:g.98645414C>T	ENSP00000354621:p.Glu375Lys	67.0	0.0		67.0	3.0	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	hg19	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735783	0.49045	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.40756	1.33;1.02	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.15825	0.0381	N	0.00746	-1.225	0.80722	D	1	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.09377	0.002;0.004;0.001	T	0.33471	-0.9867	10	0.02654	T	1	.	19.2699	0.94004	0.0:1.0:0.0:0.0	.	349;375;349	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	K	349;375	ENSP00000355326:E349K;ENSP00000354621:E375K	ENSP00000354621:E375K	E	-	1	0	SMURF1	98483350	0.999000	0.42202	0.284000	0.24805	0.965000	0.64279	4.069000	0.57541	2.527000	0.85204	0.563000	0.77884	GAA	.	.		0.562	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
KPNA7	402569	hgsc.bcm.edu	37	7	98792707	98792707	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:98792707A>G	ENST00000327442.6	-	4	578	c.539T>C	c.(538-540)cTt>cCt	p.L180P		NM_001145715.1	NP_001139187.1	A9QM74	IMA8_HUMAN	karyopherin alpha 7 (importin alpha 8)	180					cytokine-mediated signaling pathway (GO:0019221)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(3)|endometrium(2)|kidney(1)|prostate(1)|skin(1)	8						TATATTACCAAGAGCCCACAC	0.552																																					p.L180P		Atlas-SNP	.											.	KPNA7	31	.	0			c.T539C						.						38.0	35.0	36.0					7																	98792707		692	1591	2283	SO:0001583	missense	402569	exon4			TTACCAAGAGCCC		CCDS47651.1	7q22.1	2013-02-14			ENSG00000185467	ENSG00000185467		"""Importins"", ""Armadillo repeat containing"""	21839	protein-coding gene	gene with protein product		614107					Standard	NM_001145715		Approved		uc010lft.2	A9QM74	OTTHUMG00000154412	ENST00000327442.6:c.539T>C	chr7.hg19:g.98792707A>G	ENSP00000330878:p.Leu180Pro	129.0	0.0		73.0	4.0	NM_001145715	A4D277	Missense_Mutation	SNP	ENST00000327442.6	hg19	CCDS47651.1	.	.	.	.	.	.	.	.	.	.	A	19.69	3.874312	0.72180	.	.	ENSG00000185467	ENST00000327442	D	0.85955	-2.05	5.58	4.38	0.52667	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.93838	0.8029	H	0.94886	3.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94927	0.8079	10	0.87932	D	0	-18.4739	12.113	0.53850	0.8572:0.1428:0.0:0.0	.	180	A9QM74	IMA8_HUMAN	P	180	ENSP00000330878:L180P	ENSP00000330878:L180P	L	-	2	0	KPNA7	98630643	1.000000	0.71417	0.524000	0.27887	0.951000	0.60555	7.387000	0.79785	2.134000	0.65973	0.459000	0.35465	CTT	.	.		0.552	KPNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335118.1	NM_001145715	
PTCD1	26024	hgsc.bcm.edu	37	7	99032620	99032620	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99032620G>A	ENST00000292478.4	-	2	496	c.246C>T	c.(244-246)gaC>gaT	p.D82D	ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000555673.1_Silent_p.D131D|ATP5J2-PTCD1_ENST00000413834.1_Silent_p.D131D|PTCD1_ENST00000485746.1_5'UTR	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	82					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CCTCCTCCTCGTCTTCTTCCT	0.612																																					p.D131D		Atlas-SNP	.											PTCD1,colon,carcinoma,0,1	.	.	.	0			c.C393T						.						63.0	67.0	66.0					7																	99032620		2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon3			CTCCTCGTCTTCT	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.246C>T	chr7.hg19:g.99032620G>A		114.0	0.0		83.0	4.0	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	hg19	CCDS34691.1																																																																																			.	.		0.612	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
ZNF655	79027	hgsc.bcm.edu	37	7	99170201	99170201	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99170201A>G	ENST00000394163.2	+	3	653	c.470A>G	c.(469-471)gAt>gGt	p.D157G	ZNF655_ENST00000425063.1_3'UTR|ZNF655_ENST00000419215.2_3'UTR|GS1-259H13.10_ENST00000455905.1_Intron|ZNF655_ENST00000252713.4_Missense_Mutation_p.D157G|ZNF655_ENST00000493277.1_Missense_Mutation_p.D192G|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000424881.1_Missense_Mutation_p.D192G	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	157					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					CAGAATACCGATGACAATGAT	0.378																																					p.D192G		Atlas-SNP	.											.	ZNF655	75	.	0			c.A575G						.						65.0	65.0	65.0					7																	99170201		2203	4300	6503	SO:0001583	missense	79027	exon4			ATACCGATGACAA	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"""Zinc fingers, C2H2-type"", ""-"""	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.470A>G	chr7.hg19:g.99170201A>G	ENSP00000377718:p.Asp157Gly	60.0	0.0		44.0	5.0	NM_001085368	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Missense_Mutation	SNP	ENST00000394163.2	hg19	CCDS5669.1	.	.	.	.	.	.	.	.	.	.	A	4.079	0.012634	0.07912	.	.	ENSG00000197343	ENST00000252713;ENST00000493277;ENST00000424881;ENST00000394163	T;T;T;T	0.06294	3.39;3.32;3.32;3.39	4.56	4.56	0.56223	.	0.000000	0.46145	D	0.000320	T	0.17023	0.0409	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.00205	-1.1922	10	0.87932	D	0	-7.711	10.6033	0.45379	1.0:0.0:0.0:0.0	.	192;157	Q8N720-3;Q8N720	.;ZN655_HUMAN	G	157;192;192;157	ENSP00000252713:D157G;ENSP00000419135:D192G;ENSP00000393876:D192G;ENSP00000377718:D157G	ENSP00000252713:D157G	D	+	2	0	ZNF655	99008137	0.026000	0.19158	0.985000	0.45067	0.077000	0.17291	2.941000	0.49011	2.275000	0.75901	0.528000	0.53228	GAT	.	.		0.378	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494	
MCM7	4176	hgsc.bcm.edu	37	7	99691801	99691801	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99691801C>T	ENST00000303887.5	-	13	2488	c.1843G>A	c.(1843-1845)Gct>Act	p.A615T	MIR106B_ENST00000385301.1_RNA|MIR93_ENST00000385024.1_RNA|MCM7_ENST00000343023.6_Intron|MIR25_ENST00000384816.1_RNA|MCM7_ENST00000354230.3_Missense_Mutation_p.A439T	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	615	Interaction with ATRIP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTTACCAGAGCAGTGGAAAGG	0.582																																					p.A615T		Atlas-SNP	.											.	MCM7	136	.	0			c.G1843A						.						99.0	96.0	97.0					7																	99691801		2203	4300	6503	SO:0001583	missense	4176	exon13			CCAGAGCAGTGGA		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 104"""	600592	"""minichromosome maintenance deficient (S. cerevisiae) 7"", ""MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"""	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1843G>A	chr7.hg19:g.99691801C>T	ENSP00000307288:p.Ala615Thr	91.0	0.0		75.0	4.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.679838	0.88542	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.18338	2.22;2.22	5.21	5.21	0.72293	.	0.060985	0.64402	D	0.000004	T	0.59838	0.2223	H	0.98507	4.25	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.76252	-0.3027	10	0.87932	D	0	-17.0029	16.289	0.82738	0.0:1.0:0.0:0.0	.	615	P33993	MCM7_HUMAN	T	615;552;508;439	ENSP00000307288:A615T;ENSP00000346171:A439T	ENSP00000307288:A615T	A	-	1	0	MCM7	99529737	1.000000	0.71417	1.000000	0.80357	0.699000	0.40488	7.227000	0.78070	2.716000	0.92895	0.561000	0.74099	GCT	.	.		0.582	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3		
AP4M1	9179	hgsc.bcm.edu	37	7	99701748	99701748	+	Nonsense_Mutation	SNP	G	G	T	rs387906838		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99701748G>T	ENST00000359593.4	+	7	735	c.577G>T	c.(577-579)Gag>Tag	p.E193*	AP4M1_ENST00000429084.1_Nonsense_Mutation_p.E200*|MCM7_ENST00000303887.5_5'Flank|MCM7_ENST00000343023.6_5'Flank|AP4M1_ENST00000422582.1_Nonsense_Mutation_p.E65*|AP4M1_ENST00000421755.1_Nonsense_Mutation_p.E193*	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	193	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGATGTGGTCGAGAGATTGTC	0.453																																					p.E193X	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.G577T						.						127.0	112.0	117.0					7																	99701748		2203	4300	6503	SO:0001587	stop_gained	9179	exon7			GTGGTCGAGAGAT	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"""mu-adaptin-related protein-2"", ""mu subunit of AP-4"", ""AP-4 adapter complex mu subunit"", ""adaptor-related protein complex AP-4 mu4 subunit"""	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.577G>T	chr7.hg19:g.99701748G>T	ENSP00000352603:p.Glu193*	121.0	0.0		84.0	4.0	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Nonsense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.746250	0.89663	.	.	ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000439416;ENST00000421755;ENST00000422582	.	.	.	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-9.649	15.2786	0.73764	0.0:0.0:1.0:0.0	.	.	.	.	X	125;200;193;149;193;65	.	ENSP00000352603:E193X	E	+	1	0	AP4M1	99539684	1.000000	0.71417	0.884000	0.34674	0.971000	0.66376	7.136000	0.77285	2.455000	0.83008	0.561000	0.74099	GAG	.	.		0.453	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	
PILRA	29992	hgsc.bcm.edu	37	7	99971978	99971978	+	Silent	SNP	C	C	A	rs141936238		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:99971978C>A	ENST00000198536.2	+	2	588	c.376C>A	c.(376-378)Cga>Aga	p.R126R	PILRA_ENST00000350573.2_Silent_p.R126R|PILRA_ENST00000394000.2_Silent_p.R126R|PILRA_ENST00000474013.1_3'UTR|PILRA_ENST00000453419.1_Silent_p.R126R	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	126	Ig-like V-type.				signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTATTTCTGCCGAGTTGAGCT	0.577																																					p.R126R		Atlas-SNP	.											.	PILRA	28	.	0			c.C376A						.						103.0	104.0	103.0					7																	99971978		2203	4300	6503	SO:0001819	synonymous_variant	29992	exon2			TTCTGCCGAGTTG	AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"""Immunoglobulin superfamily / V-set domain containing"""	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.376C>A	chr7.hg19:g.99971978C>A		98.0	0.0		89.0	4.0	NM_013439	Q8NHI1	Silent	SNP	ENST00000198536.2	hg19	CCDS5691.1																																																																																			.	C|1.000;G|0.000		0.577	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439	
TFR2	7036	hgsc.bcm.edu	37	7	100226878	100226878	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:100226878T>C	ENST00000462107.1	-	11	1675	c.1388A>G	c.(1387-1389)aAc>aGc	p.N463S	TFR2_ENST00000223051.3_Missense_Mutation_p.N463S|TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000544242.1_Missense_Mutation_p.N4S			Q9UP52	TFR2_HUMAN	transferrin receptor 2	463					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	GACCTTACCGTTGCTCACCAT	0.662																																					p.N463S		Atlas-SNP	.											.	TFR2	53	.	0			c.A1388G						.						95.0	89.0	91.0					7																	100226878		2203	4300	6503	SO:0001583	missense	7036	exon10			TTACCGTTGCTCA	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1388A>G	chr7.hg19:g.100226878T>C	ENSP00000420525:p.Asn463Ser	62.0	0.0		30.0	4.0	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	hg19	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.631235	0.46944	.	.	ENSG00000106327	ENST00000223051;ENST00000462107;ENST00000544242	T;T;T	0.46819	0.86;0.86;0.86	4.54	3.35	0.38373	Peptidase M28 (1);	0.273448	0.38837	N	0.001546	T	0.28466	0.0704	N	0.17922	0.545	0.80722	D	1	B	0.22800	0.075	B	0.23018	0.043	T	0.05131	-1.0904	10	0.25751	T	0.34	-26.323	6.9773	0.24683	0.0:0.1054:0.0:0.8946	.	463	Q9UP52	TFR2_HUMAN	S	463;463;4	ENSP00000223051:N463S;ENSP00000420525:N463S;ENSP00000443656:N4S	ENSP00000223051:N463S	N	-	2	0	TFR2	100064814	0.999000	0.42202	0.994000	0.49952	0.916000	0.54674	3.319000	0.51983	0.736000	0.32559	0.459000	0.35465	AAC	.	.		0.662	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227	
LRRC17	10234	hgsc.bcm.edu	37	7	102584705	102584705	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:102584705A>G	ENST00000339431.4	+	4	1272	c.977A>G	c.(976-978)aAc>aGc	p.N326S	FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000379305.3_Intron|LRRC17_ENST00000485478.1_3'UTR|LRRC17_ENST00000249377.4_3'UTR	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	326					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						TTATCAAACAACAGTCTGCAA	0.353																																					p.N326S		Atlas-SNP	.											.	LRRC17	45	.	0			c.A977G						.						98.0	105.0	103.0					7																	102584705		2203	4299	6502	SO:0001583	missense	10234	exon4			CAAACAACAGTCT	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.977A>G	chr7.hg19:g.102584705A>G	ENSP00000344242:p.Asn326Ser	110.0	0.0		78.0	33.0	NM_001031692	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	hg19	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.800116	0.90538	.	.	ENSG00000128606	ENST00000339431	T	0.68025	-0.3	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000004	D	0.87018	0.6073	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90545	0.4505	10	0.87932	D	0	-37.8037	16.3943	0.83563	1.0:0.0:0.0:0.0	.	326	Q8N6Y2	LRC17_HUMAN	S	326	ENSP00000344242:N326S	ENSP00000344242:N326S	N	+	2	0	LRRC17	102371941	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.281000	0.76405	0.533000	0.62120	AAC	.	.		0.353	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824	
ORC5	5001	hgsc.bcm.edu	37	7	103808900	103808900	+	Intron	SNP	T	T	C	rs34022264		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:103808900T>C	ENST00000297431.4	-	9	1020				ORC5_ENST00000545943.1_Intron|ORC5_ENST00000447452.2_Missense_Mutation_p.T300A	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5						DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						CCGGTAACTGTCTCAATACTT	0.353																																					p.T300A		Atlas-SNP	.											.	ORC5	48	.	0			c.A898G						.						116.0	112.0	113.0					7																	103808900		2203	4300	6503	SO:0001627	intron_variant	5001	exon9			TAACTGTCTCAAT		CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 117"""	602331	"""origin recognition complex, subunit 5 (yeast homolog)-like"", ""origin recognition complex, subunit 5-like (yeast)"", ""origin recognition complex, subunit 5 homolog (yeast)"""	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.877+20A>G	chr7.hg19:g.103808900T>C		112.0	0.0		80.0	4.0	NM_181747	A4D0P8|O60590|O95268	Missense_Mutation	SNP	ENST00000297431.4	hg19	CCDS5734.1	.	.	.	.	.	.	.	.	.	.	T	6.855	0.527054	0.13066	.	.	ENSG00000164815	ENST00000447452	T	0.22539	1.95	5.64	0.546	0.17196	.	.	.	.	.	T	0.07007	0.0178	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39901	-0.9591	8	0.06365	T	0.9	.	3.8006	0.08757	0.2442:0.2226:0.0:0.5332	.	300	O43913-2	.	A	300	ENSP00000395747:T300A	ENSP00000395747:T300A	T	-	1	0	ORC5	103596136	0.002000	0.14202	0.064000	0.19789	0.170000	0.22686	0.412000	0.21131	0.105000	0.17753	-1.304000	0.01323	ACA	.	.		0.353	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553	
CDHR3	222256	hgsc.bcm.edu	37	7	105621574	105621574	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:105621574C>A	ENST00000317716.9	+	3	490	c.410C>A	c.(409-411)gCa>gAa	p.A137E	CDHR3_ENST00000343407.5_5'UTR|CDHR3_ENST00000478080.1_Missense_Mutation_p.A49E|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000542731.1_Missense_Mutation_p.A137E|CDHR3_ENST00000541203.1_Missense_Mutation_p.A137E	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	137	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GGCAACTTGGCAGAAGGTAGG	0.502																																					p.A137E		Atlas-SNP	.											.	CDHR3	153	.	0			c.C410A						.						69.0	63.0	65.0					7																	105621574		2020	4176	6196	SO:0001583	missense	222256	exon3			ACTTGGCAGAAGG	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.410C>A	chr7.hg19:g.105621574C>A	ENSP00000325954:p.Ala137Glu	128.0	0.0		83.0	4.0	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	hg19	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.277273	0.59758	.	.	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080;ENST00000541203	T;T;T;T	0.57107	0.44;0.44;0.42;1.0	5.02	4.12	0.48240	Cadherin (1);	0.078618	0.52532	D	0.000061	T	0.67832	0.2935	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.989;0.997	T	0.65734	-0.6096	10	0.13470	T	0.59	-12.075	14.5236	0.67870	0.0:0.8518:0.1482:0.0	.	124;137	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	E	137;137;49;137	ENSP00000439766:A137E;ENSP00000325954:A137E;ENSP00000417771:A49E;ENSP00000443733:A137E	ENSP00000325954:A137E	A	+	2	0	CDHR3	105408810	0.991000	0.36638	0.881000	0.34555	0.540000	0.34992	2.119000	0.41958	1.442000	0.47568	0.561000	0.74099	GCA	.	.		0.502	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
MDFIC	29969	hgsc.bcm.edu	37	7	114619590	114619590	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:114619590A>G	ENST00000393486.1	+	4	837	c.247A>G	c.(247-249)Act>Gct	p.T83A	MDFIC_ENST00000257724.3_Missense_Mutation_p.T192A	NM_001166345.1|NM_199072.4	NP_001159817.1|NP_951038.1			MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						TCAGCTTCAGACTTCAGCCCA	0.423																																					p.T192A		Atlas-SNP	.											.	MDFIC	30	.	0			c.A574G						.						65.0	64.0	64.0					7																	114619590		2203	4300	6503	SO:0001583	missense	29969	exon4			CTTCAGACTTCAG	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000393486.1:c.247A>G	chr7.hg19:g.114619590A>G	ENSP00000377126:p.Thr83Ala	140.0	0.0		87.0	4.0	NM_199072		Missense_Mutation	SNP	ENST00000393486.1	hg19	CCDS55155.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.338646	0.41398	.	.	ENSG00000135272	ENST00000257724;ENST00000393486;ENST00000427207;ENST00000498196	.	.	.	5.98	0.822	0.18806	.	0.572336	0.18522	N	0.138727	T	0.42810	0.1219	M	0.66506	2.035	0.33700	D	0.61444	B	0.10296	0.003	B	0.08055	0.003	T	0.39981	-0.9587	9	0.17832	T	0.49	0.0133	5.9591	0.19289	0.5295:0.2302:0.2403:0.0	.	83	Q9P1T7	MDFIC_HUMAN	A	192;83;69;28	.	ENSP00000257724:T192A	T	+	1	0	MDFIC	114406826	0.937000	0.31787	0.005000	0.12908	0.893000	0.52053	0.472000	0.22116	-0.078000	0.12730	0.482000	0.46254	ACT	.	.		0.423	MDFIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059968.4	NM_199072	
ST7	7982	hgsc.bcm.edu	37	7	116759658	116759658	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:116759658T>C	ENST00000393446.2	+	3	581	c.278T>C	c.(277-279)aTt>aCt	p.I93T	ST7-AS2_ENST00000434993.1_RNA|ST7-AS2_ENST00000442719.1_RNA|ST7_ENST00000465133.1_Missense_Mutation_p.I50T|ST7_ENST00000393449.1_Missense_Mutation_p.I93T|ST7-AS2_ENST00000432541.1_RNA|ST7_ENST00000323984.3_Missense_Mutation_p.I93T|ST7_ENST00000422922.1_Missense_Mutation_p.I47T|ST7_ENST00000432298.1_Missense_Mutation_p.I47T|ST7_ENST00000393451.3_Missense_Mutation_p.I93T|ST7_ENST00000393444.3_Missense_Mutation_p.I50T|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393447.4_Missense_Mutation_p.I50T|ST7_ENST00000393443.1_Missense_Mutation_p.I43T|ST7_ENST00000265437.5_Missense_Mutation_p.I93T			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		ACTTCATTCATTGAACAAGTC	0.408																																					p.I93T		Atlas-SNP	.											.	ST7	64	.	0			c.T278C						.						127.0	121.0	123.0					7																	116759658		2203	4300	6503	SO:0001583	missense	7982	exon3			CATTCATTGAACA	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.278T>C	chr7.hg19:g.116759658T>C	ENSP00000377092:p.Ile93Thr	133.0	0.0		100.0	4.0	NM_018412	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000393446.2	hg19		.	.	.	.	.	.	.	.	.	.	T	27.0	4.787341	0.90367	.	.	ENSG00000004866	ENST00000393446;ENST00000265437;ENST00000393451;ENST00000323984;ENST00000393449;ENST00000417919;ENST00000446490;ENST00000421345;ENST00000432298;ENST00000422922;ENST00000449366;ENST00000393443;ENST00000465133;ENST00000477742;ENST00000393447;ENST00000393444;ENST00000420755;ENST00000490039	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.56202	0.1969	M	0.83603	2.65	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.987;1.0;0.987;1.0;1.0;0.984;1.0	D;D;D;D;D;D;D	0.97110	0.979;1.0;0.979;0.999;0.999;0.964;0.999	T	0.61753	-0.6998	10	0.87932	D	0	-13.1569	16.2903	0.82747	0.0:0.0:0.0:1.0	.	41;50;93;43;47;93;93	C9JU30;B7Z4L1;B7Z573;Q9NRC1-6;B7Z4U3;Q9NRC1-2;Q9NRC1	.;.;.;.;.;.;ST7_HUMAN	T	93;93;93;93;93;43;93;41;47;47;43;43;50;41;50;50;41;41	ENSP00000377092:I93T;ENSP00000265437:I93T;ENSP00000377097:I93T;ENSP00000325673:I93T;ENSP00000377095:I93T;ENSP00000391444:I43T;ENSP00000402934:I93T;ENSP00000416858:I41T;ENSP00000411118:I47T;ENSP00000414031:I47T;ENSP00000413601:I43T;ENSP00000377089:I43T;ENSP00000420052:I50T;ENSP00000419715:I41T;ENSP00000377093:I50T;ENSP00000377090:I50T;ENSP00000388698:I41T;ENSP00000419516:I41T	ENSP00000265437:I93T	I	+	2	0	ST7	116546894	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.326000	0.78906	0.533000	0.62120	ATT	.	.		0.408	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908	
FLNC	2318	hgsc.bcm.edu	37	7	128477572	128477572	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:128477572A>G	ENST00000325888.8	+	4	1081	c.820A>G	c.(820-822)Aac>Gac	p.N274D	FLNC_ENST00000346177.6_Missense_Mutation_p.N274D	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	274					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CAAGCAGCTGAACCCCAAGAA	0.597																																					p.N274D		Atlas-SNP	.											.	FLNC	339	.	0			c.A820G						.						115.0	126.0	122.0					7																	128477572		2155	4282	6437	SO:0001583	missense	2318	exon4			CAGCTGAACCCCA	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.820A>G	chr7.hg19:g.128477572A>G	ENSP00000327145:p.Asn274Asp	121.0	0.0		69.0	4.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830803	0.71258	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	T;T	0.58506	0.33;0.33	5.03	3.86	0.44501	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.235147	0.41396	D	0.000886	T	0.36826	0.0981	N	0.13098	0.295	0.31065	N	0.713702	B;B	0.28636	0.218;0.0	B;B	0.28305	0.088;0.023	T	0.39078	-0.9631	10	0.54805	T	0.06	.	6.7381	0.23421	0.6885:0.1591:0.0:0.1523	.	274;274	Q14315-2;Q14315	.;FLNC_HUMAN	D	274	ENSP00000327145:N274D;ENSP00000344002:N274D	ENSP00000327145:N274D	N	+	1	0	FLNC	128264808	0.988000	0.35896	1.000000	0.80357	0.997000	0.91878	0.692000	0.25482	0.745000	0.32763	0.533000	0.62120	AAC	.	.		0.597	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
LRGUK	136332	hgsc.bcm.edu	37	7	133876488	133876488	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:133876488T>C	ENST00000285928.2	+	12	1485	c.1416T>C	c.(1414-1416)gaT>gaC	p.D472D		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	472	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						ACGTTTTTGATGAAATGGTGA	0.338																																					p.D472D		Atlas-SNP	.											.	LRGUK	113	.	0			c.T1416C						.						130.0	121.0	124.0					7																	133876488		2203	4300	6503	SO:0001819	synonymous_variant	136332	exon12			TTTTGATGAAATG	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1416T>C	chr7.hg19:g.133876488T>C		154.0	0.0		87.0	4.0	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	hg19	CCDS5830.1																																																																																			.	.		0.338	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
ZC3HAV1L	92092	hgsc.bcm.edu	37	7	138719329	138719329	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:138719329C>A	ENST00000275766.1	-	2	472	c.461G>T	c.(460-462)cGg>cTg	p.R154L		NM_080660.3	NP_542391.2	Q96H79	ZCCHL_HUMAN	zinc finger CCCH-type, antiviral 1-like	154										NS(2)|endometrium(2)|large_intestine(1)|lung(4)|skin(1)	10						AAGCAGGATCCGAAGCTGGTT	0.453																																					p.R154L		Atlas-SNP	.											.	ZC3HAV1L	15	.	0			c.G461T						.						112.0	109.0	110.0					7																	138719329		2203	4300	6503	SO:0001583	missense	92092	exon2			AGGATCCGAAGCT	BC008842	CCDS5850.1	7q34	2006-07-03	2006-07-03	2006-07-03	ENSG00000146858	ENSG00000146858			22423	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 39"""	C7orf39			Standard	NM_080660		Approved	MGC14289	uc003vum.1	Q96H79	OTTHUMG00000157229	ENST00000275766.1:c.461G>T	chr7.hg19:g.138719329C>A	ENSP00000275766:p.Arg154Leu	93.0	0.0		80.0	4.0	NM_080660	Q8WUD9	Missense_Mutation	SNP	ENST00000275766.1	hg19	CCDS5850.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.862521	0.51482	.	.	ENSG00000146858	ENST00000275766	T	0.38560	1.13	5.86	1.96	0.26148	.	0.356873	0.20743	N	0.086485	T	0.30355	0.0762	L	0.52573	1.65	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.17137	-1.0379	10	0.33940	T	0.23	.	3.2547	0.06827	0.1435:0.56:0.1392:0.1573	.	154	Q96H79	ZCCHL_HUMAN	L	154	ENSP00000275766:R154L	ENSP00000275766:R154L	R	-	2	0	ZC3HAV1L	138369869	0.024000	0.19004	0.009000	0.14445	0.941000	0.58515	0.569000	0.23638	0.461000	0.27071	0.650000	0.86243	CGG	.	.		0.453	ZC3HAV1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348090.1	NM_080660	
SLC37A3	84255	hgsc.bcm.edu	37	7	140069457	140069457	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:140069457G>T	ENST00000326232.9	-	4	427	c.224C>A	c.(223-225)cCc>cAc	p.P75H	SLC37A3_ENST00000340308.3_Missense_Mutation_p.P75H|RNA5SP247_ENST00000411181.1_RNA|SLC37A3_ENST00000461089.1_5'UTR|SLC37A3_ENST00000447932.2_Missense_Mutation_p.P75H|SLC37A3_ENST00000429996.2_Missense_Mutation_p.P75H	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	75					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					CTCTGCACTGGGGAACAAATG	0.483																																					p.P75H	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C224A						.						99.0	87.0	91.0					7																	140069457		2203	4300	6503	SO:0001583	missense	84255	exon4			GCACTGGGGAACA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.224C>A	chr7.hg19:g.140069457G>T	ENSP00000321498:p.Pro75His	44.0	0.0		47.0	4.0	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	hg19	CCDS5859.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.798989	0.50208	.	.	ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232;ENST00000429996;ENST00000539816;ENST00000469193	T;T;T;T;T	0.47869	2.15;2.45;2.45;0.83;0.85	5.2	5.2	0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.335918	0.31199	N	0.008065	T	0.60599	0.2281	M	0.63843	1.955	0.46416	D	0.999031	P;P;P;P;P	0.43578	0.743;0.708;0.565;0.811;0.619	P;P;B;P;P	0.53401	0.683;0.554;0.43;0.725;0.566	T	0.61048	-0.7141	10	0.49607	T	0.09	-24.2852	16.5098	0.84281	0.0:0.0:1.0:0.0	.	75;75;75;75;75	B4DKF5;F5H743;Q8NCC5-2;Q8NCC5-3;Q8NCC5	.;.;.;.;SPX3_HUMAN	H	75	ENSP00000343358:P75H;ENSP00000397481:P75H;ENSP00000321498:P75H;ENSP00000412208:P75H;ENSP00000419024:P75H	ENSP00000321498:P75H	P	-	2	0	SLC37A3	139715926	1.000000	0.71417	0.643000	0.29450	0.204000	0.24138	3.508000	0.53378	2.435000	0.82474	0.591000	0.81541	CCC	.	.		0.483	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
ADCK2	90956	hgsc.bcm.edu	37	7	140373468	140373468	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:140373468T>C	ENST00000072869.4	+	1	516	c.338T>C	c.(337-339)cTc>cCc	p.L113P	ADCK2_ENST00000476491.1_Missense_Mutation_p.L113P	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	113						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					TTCTTCCCCCTCCTACTCCTC	0.657																																					p.L113P		Atlas-SNP	.											.	ADCK2	37	.	0			c.T338C						.						82.0	92.0	89.0					7																	140373468		2203	4300	6503	SO:0001583	missense	90956	exon1			TCCCCCTCCTACT	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.338T>C	chr7.hg19:g.140373468T>C	ENSP00000072869:p.Leu113Pro	83.0	0.0		68.0	4.0	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	hg19	CCDS5861.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.446707	0.84101	.	.	ENSG00000133597	ENST00000072869;ENST00000476491	T;T	0.55413	0.52;0.52	4.63	4.63	0.57726	.	0.000000	0.64402	D	0.000002	T	0.66376	0.2783	L	0.49778	1.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	T	0.70040	-0.4981	10	0.87932	D	0	0.0817	14.0644	0.64819	0.0:0.0:0.0:1.0	.	113;113	C9JE15;Q7Z695	.;ADCK2_HUMAN	P	113	ENSP00000072869:L113P;ENSP00000420512:L113P	ENSP00000072869:L113P	L	+	2	0	ADCK2	140019937	1.000000	0.71417	0.806000	0.32338	0.806000	0.45545	5.782000	0.68973	1.736000	0.51660	0.459000	0.35465	CTC	.	.		0.657	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
WEE2	494551	hgsc.bcm.edu	37	7	141414139	141414139	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:141414139T>C	ENST00000397541.2	+	2	879	c.473T>C	c.(472-474)tTc>tCc	p.F158S	WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000465110.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	158					female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					ATTAATCCCTTCACTCCAGAG	0.423																																					p.F158S		Atlas-SNP	.											.	WEE2	59	.	0			c.T473C						.						80.0	75.0	76.0					7																	141414139		1839	4097	5936	SO:0001583	missense	494551	exon2			ATCCCTTCACTCC	AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.473T>C	chr7.hg19:g.141414139T>C	ENSP00000380675:p.Phe158Ser	83.0	0.0		43.0	4.0	NM_001105558		Missense_Mutation	SNP	ENST00000397541.2	hg19	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179199	0.78564	.	.	ENSG00000214102	ENST00000397541	T	0.48201	0.82	5.03	3.87	0.44632	.	0.000000	0.64402	U	0.000001	T	0.67468	0.2896	M	0.82323	2.585	0.58432	D	0.999992	D	0.76494	0.999	D	0.69307	0.963	T	0.71059	-0.4702	10	0.87932	D	0	.	10.802	0.46493	0.0:0.0747:0.0:0.9252	.	158	P0C1S8	WEE2_HUMAN	S	158	ENSP00000380675:F158S	ENSP00000380675:F158S	F	+	2	0	WEE2	141060608	1.000000	0.71417	0.989000	0.46669	0.979000	0.70002	6.539000	0.73856	0.932000	0.37266	0.477000	0.44152	TTC	.	.		0.423	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558	
CLCN1	1180	hgsc.bcm.edu	37	7	143016896	143016896	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:143016896G>A	ENST00000343257.2	+	2	316	c.229G>A	c.(229-231)Ggg>Agg	p.G77R		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	77					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					GCAGGACATAGGGATGCCCAA	0.443																																					p.G77R		Atlas-SNP	.											.	CLCN1	141	.	0			c.G229A						.						192.0	160.0	171.0					7																	143016896		2203	4300	6503	SO:0001583	missense	1180	exon2			GACATAGGGATGC	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.229G>A	chr7.hg19:g.143016896G>A	ENSP00000339867:p.Gly77Arg	91.0	0.0		88.0	39.0	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	.	7.643	0.681360	0.14907	.	.	ENSG00000188037	ENST00000343257	D	0.84800	-1.9	5.45	3.66	0.41972	.	0.651527	0.15301	N	0.269603	T	0.77212	0.4097	L	0.47716	1.5	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.59337	-0.7473	10	0.16420	T	0.52	.	7.5381	0.27723	0.2616:0.0:0.7384:0.0	.	77	P35523	CLCN1_HUMAN	R	77	ENSP00000339867:G77R	ENSP00000339867:G77R	G	+	1	0	CLCN1	142727018	0.000000	0.05858	0.162000	0.22713	0.249000	0.25844	0.554000	0.23407	0.705000	0.31890	0.650000	0.86243	GGG	.	.		0.443	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	
NOBOX	135935	hgsc.bcm.edu	37	7	144096261	144096261	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:144096261C>T	ENST00000467773.1	-	8	1250	c.1251G>A	c.(1249-1251)atG>atA	p.M417I	NOBOX_ENST00000223140.5_Missense_Mutation_p.M300I|NOBOX_ENST00000483238.1_Missense_Mutation_p.M385I	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	417	Pro-rich.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|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)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					AAGTCAGCAGCATGGGGGGCT	0.592																																					p.M417I		Atlas-SNP	.											.	NOBOX	130	.	0			c.G1251A						.						14.0	15.0	14.0					7																	144096261		1965	4106	6071	SO:0001583	missense	135935	exon8			CAGCAGCATGGGG			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1251G>A	chr7.hg19:g.144096261C>T	ENSP00000419457:p.Met417Ile	99.0	0.0		61.0	4.0	NM_001080413	A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.76	1.441820	0.25900	.	.	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140	D;D;D	0.93189	-2.85;-3.18;-2.86	4.92	0.389	0.16269	.	1.413510	0.03906	N	0.281122	D	0.87458	0.6182	L	0.40543	1.245	0.19945	N	0.999947	B	0.20671	0.047	B	0.15870	0.014	T	0.70651	-0.4813	10	0.18276	T	0.48	-2.8092	1.6801	0.02830	0.1449:0.4316:0.142:0.2816	.	417	O60393	NOBOX_HUMAN	I	385;417;300	ENSP00000419565:M385I;ENSP00000419457:M417I;ENSP00000223140:M300I	ENSP00000223140:M300I	M	-	3	0	NOBOX	143727194	0.404000	0.25328	0.950000	0.38849	0.982000	0.71751	0.294000	0.19047	0.133000	0.18654	0.561000	0.74099	ATG	.	.		0.592	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
GIMAP8	155038	hgsc.bcm.edu	37	7	150171349	150171349	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:150171349A>G	ENST00000307271.3	+	4	1506	c.932A>G	c.(931-933)aAc>aGc	p.N311S		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	311	AIG1-type G 2.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TCTTTAAAGAACATTGACTCA	0.458																																					p.N311S		Atlas-SNP	.											.	GIMAP8	136	.	0			c.A932G						.						73.0	80.0	77.0					7																	150171349		2203	4300	6503	SO:0001583	missense	155038	exon4			TAAAGAACATTGA	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.932A>G	chr7.hg19:g.150171349A>G	ENSP00000305107:p.Asn311Ser	85.0	0.0		94.0	4.0	NM_175571		Missense_Mutation	SNP	ENST00000307271.3	hg19	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	A	7.642	0.681042	0.14907	.	.	ENSG00000171115	ENST00000307271	T	0.60920	0.15	4.47	-4.25	0.03766	AIG1 (1);	1.311810	0.05394	N	0.539498	T	0.29028	0.0721	N	0.11064	0.09	0.09310	N	1	B	0.18610	0.029	B	0.15870	0.014	T	0.09100	-1.0690	10	0.16896	T	0.51	.	2.0799	0.03632	0.2938:0.1806:0.3872:0.1384	.	311	Q8ND71	GIMA8_HUMAN	S	311	ENSP00000305107:N311S	ENSP00000305107:N311S	N	+	2	0	GIMAP8	149802282	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.199000	0.03032	-0.661000	0.05345	0.528000	0.53228	AAC	.	.		0.458	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
ASIC3	9311	hgsc.bcm.edu	37	7	150747908	150747908	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr7:150747908C>G	ENST00000349064.5	+	4	1075	c.877C>G	c.(877-879)Cca>Gca	p.P293A	ASIC3_ENST00000357922.4_Missense_Mutation_p.P293A|ASIC3_ENST00000297512.8_Missense_Mutation_p.P293A	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3	293					cation transmembrane transport (GO:0098655)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ion transmembrane transport (GO:0034220)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|response to heat (GO:0009408)|sensory perception (GO:0007600)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|enterobactin transporter activity (GO:0042931)|ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)										CAACTATGAGCCAGAGCCCTC	0.647																																					p.P293A		Atlas-SNP	.											.	.	.	.	0			c.C877G						.						29.0	33.0	32.0					7																	150747908		2203	4300	6503	SO:0001583	missense	9311	exon4			TATGAGCCAGAGC	AB010575	CCDS5914.1, CCDS5915.1, CCDS5916.1	7q35	2012-02-23	2012-02-22	2012-02-22	ENSG00000213199	ENSG00000213199		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	101	protein-coding gene	gene with protein product	"""testis sodium channel 1"""	611741	"""amiloride-sensitive cation channel 3, testis"", ""amiloride-sensitive cation channel 3"""	ACCN3		9571199, 9744806	Standard	NM_004769		Approved	TNaC1, DRASIC	uc003wio.3	Q9UHC3	OTTHUMG00000158685	ENST00000349064.5:c.877C>G	chr7.hg19:g.150747908C>G	ENSP00000344838:p.Pro293Ala	64.0	0.0		66.0	15.0	NM_020322	B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Missense_Mutation	SNP	ENST00000349064.5	hg19	CCDS5916.1	.	.	.	.	.	.	.	.	.	.	C	0.305	-0.971659	0.02215	.	.	ENSG00000213199	ENST00000357922;ENST00000349064;ENST00000297512	T;T;T	0.61859	0.07;0.07;0.07	4.84	0.71	0.18157	.	972.779000	0.00855	N	0.001860	T	0.47875	0.1469	L	0.54323	1.7	0.09310	N	1	B;B;B	0.28128	0.114;0.039;0.201	B;B;B	0.24701	0.053;0.023;0.055	T	0.05616	-1.0874	10	0.15952	T	0.53	-1.1147	1.8255	0.03119	0.139:0.4629:0.1363:0.2617	.	293;293;293	Q9UHC3-2;Q9UHC3-3;Q9UHC3	.;.;ACCN3_HUMAN	A	293	ENSP00000350600:P293A;ENSP00000344838:P293A;ENSP00000297512:P293A	ENSP00000297512:P293A	P	+	1	0	ACCN3	150378841	0.068000	0.21057	0.014000	0.15608	0.027000	0.11550	0.424000	0.21330	0.201000	0.20466	0.650000	0.86243	CCA	.	.		0.647	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769	
CSMD1	64478	hgsc.bcm.edu	37	8	2949044	2949044	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:2949044A>G	ENST00000520002.1	-	49	7837	c.7282T>C	c.(7282-7284)Tat>Cat	p.Y2428H	CSMD1_ENST00000602723.1_Missense_Mutation_p.Y2428H|CSMD1_ENST00000400186.3_Missense_Mutation_p.Y2428H|CSMD1_ENST00000542608.1_Missense_Mutation_p.Y2427H|CSMD1_ENST00000602557.1_Missense_Mutation_p.Y2428H|CSMD1_ENST00000537824.1_Missense_Mutation_p.Y2427H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2428	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTACCTGCATAGCGAATCTTG	0.303																																					p.Y2427H		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T7279C						.						110.0	103.0	105.0					8																	2949044		1831	4081	5912	SO:0001583	missense	64478	exon48			CTGCATAGCGAAT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7282T>C	chr8.hg19:g.2949044A>G	ENSP00000430733:p.Tyr2428His	92.0	0.0		76.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.7|22.7	4.321693|4.321693	0.81580|0.81580	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	.|T;T;T;T	.|0.57107	.|0.42;0.42;0.42;0.42	5.78|5.78	5.78|5.78	0.91487|0.91487	.|CUB (5);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.78020|0.78020	0.4218|0.4218	M|M	0.92649|0.92649	3.33|3.33	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.999;1.0;0.999	T|T	0.79524|0.79524	-0.1768|-0.1768	5|10	.|0.24483	.|T	.|0.36	.|.	16.0976|16.0976	0.81139|0.81139	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|2428;2428;2427	.|E5RIG2;Q96PZ7;F5H2I8	.|.;CSMD1_HUMAN;.	P|H	1844|2428;2428;2289;2427;2427	.|ENSP00000383047:Y2428H;ENSP00000430733:Y2428H;ENSP00000441462:Y2427H;ENSP00000446243:Y2427H	.|ENSP00000320445:Y2289H	L|Y	-|-	2|1	0|0	CSMD1|CSMD1	2936451|2936451	1.000000|1.000000	0.71417|0.71417	0.093000|0.093000	0.20910|0.20910	0.878000|0.878000	0.50629|0.50629	9.011000|9.011000	0.93618|0.93618	2.198000|2.198000	0.70561|0.70561	0.443000|0.443000	0.29094|0.29094	CTA|TAT	.	.		0.303	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
TNKS	8658	hgsc.bcm.edu	37	8	9623750	9623750	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:9623750T>C	ENST00000310430.6	+	25	3581	c.3555T>C	c.(3553-3555)ggT>ggC	p.G1185G	TNKS_ENST00000518281.1_Splice_Site_p.G948G	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	1185	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		TATTTCTAGGTTCTCCTTTCA	0.378																																					p.G1185G		Atlas-SNP	.											.	TNKS	198	.	0			c.T3555C						.						75.0	76.0	76.0					8																	9623750		2203	4300	6503	SO:0001630	splice_region_variant	8658	exon25			TCTAGGTTCTCCT	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.3554-1T>C	chr8.hg19:g.9623750T>C		61.0	0.0		71.0	4.0	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	hg19	CCDS5974.1																																																																																			.	.		0.378	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	Silent
RP1L1	94137	hgsc.bcm.edu	37	8	10469337	10469337	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:10469337A>G	ENST00000382483.3	-	4	2494	c.2271T>C	c.(2269-2271)gcT>gcC	p.A757A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	757					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CGGCAGAGGGAGCGTTGTGCG	0.642																																					p.A757A		Atlas-SNP	.											.	RP1L1	453	.	0			c.T2271C						.						47.0	54.0	52.0					8																	10469337		1976	4157	6133	SO:0001819	synonymous_variant	94137	exon4			AGAGGGAGCGTTG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2271T>C	chr8.hg19:g.10469337A>G		105.0	0.0		125.0	5.0	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	.		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
WHSC1L1	54904	hgsc.bcm.edu	37	8	38173035	38173035	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:38173035G>T	ENST00000317025.8	-	11	2531	c.2014C>A	c.(2014-2016)Cct>Act	p.P672T	WHSC1L1_ENST00000525081.1_5'Flank|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.P672T|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.P672T	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	672					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			GTAGCTGAAGGGCTATCTACT	0.393			T	NUP98	AML																																p.P672T		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.C2014A						.						139.0	127.0	131.0					8																	38173035		1892	4119	6011	SO:0001583	missense	54904	exon11			CTGAAGGGCTATC	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.2014C>A	chr8.hg19:g.38173035G>T	ENSP00000313983:p.Pro672Thr	83.0	0.0		95.0	4.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.626784	0.87560	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502	D;D;D	0.96104	-3.91;-3.91;-3.91	6.01	6.01	0.97437	Zinc finger, FYVE/PHD-type (1);	0.000000	0.48286	U	0.000194	D	0.97542	0.9195	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	D	0.97609	1.0128	10	0.87932	D	0	.	20.5211	0.99222	0.0:0.0:1.0:0.0	.	672;672;672	B7ZL11;Q9BZ95-2;Q9BZ95	.;.;NSD3_HUMAN	T	672;672;609;672	ENSP00000393284:P672T;ENSP00000313983:P672T;ENSP00000434730:P672T	ENSP00000313983:P672T	P	-	1	0	WHSC1L1	38292192	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.861000	0.98227	0.650000	0.86243	CCT	.	.		0.393	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
ADAM18	8749	hgsc.bcm.edu	37	8	39495084	39495084	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:39495084T>C	ENST00000265707.5	+	9	734	c.689T>C	c.(688-690)aTa>aCa	p.I230T	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.I206T	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	230	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TTGACTGTTATACTGTCTTCC	0.303																																					p.I230T		Atlas-SNP	.											.	ADAM18	169	.	0			c.T689C						.						84.0	80.0	81.0					8																	39495084		2203	4299	6502	SO:0001583	missense	8749	exon9			CTGTTATACTGTC	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.689T>C	chr8.hg19:g.39495084T>C	ENSP00000265707:p.Ile230Thr	173.0	0.0		182.0	81.0	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	T	8.687	0.906443	0.17833	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.63096	-0.02;-0.02	5.18	-0.21	0.13176	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	1.402720	0.04412	N	0.366199	T	0.50051	0.1593	L	0.35487	1.065	0.09310	N	1	B;B	0.26445	0.149;0.087	B;B	0.30572	0.111;0.117	T	0.39099	-0.9630	10	0.49607	T	0.09	.	3.0133	0.06051	0.304:0.1712:0.0:0.5247	.	206;230	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	T	230;206;162	ENSP00000265707:I230T;ENSP00000369195:I206T	ENSP00000265707:I230T	I	+	2	0	ADAM18	39614241	0.051000	0.20477	0.001000	0.08648	0.842000	0.47809	0.209000	0.17435	-0.154000	0.11118	-0.256000	0.11100	ATA	.	.		0.303	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
HOOK3	84376	hgsc.bcm.edu	37	8	42819578	42819578	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:42819578T>C	ENST00000307602.4	+	9	940	c.740T>C	c.(739-741)cTc>cCc	p.L247P		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	247					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			CATTTGCAGCTCCAGACTCAA	0.348			T	RET	papillary thyroid																																p.L247P		Atlas-SNP	.		Dom	yes		8	8p11.21	84376	hook homolog 3		E	.	HOOK3	71	.	0			c.T740C						.						87.0	86.0	86.0					8																	42819578		2203	4300	6503	SO:0001583	missense	84376	exon9			TGCAGCTCCAGAC	AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"""hook homolog 3 (Drosophila)"""			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.740T>C	chr8.hg19:g.42819578T>C	ENSP00000305699:p.Leu247Pro	86.0	0.0		91.0	4.0	NM_032410	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	hg19	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477781	0.84640	.	.	ENSG00000168172	ENST00000307602	T	0.26810	1.71	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.55657	0.1934	M	0.82323	2.585	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.78314	0.991;0.951	T	0.61598	-0.7030	10	0.72032	D	0.01	-0.4757	16.2274	0.82306	0.0:0.0:0.0:1.0	.	247;247	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	P	247	ENSP00000305699:L247P	ENSP00000305699:L247P	L	+	2	0	HOOK3	42938735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.642000	0.83385	2.229000	0.72834	0.528000	0.53228	CTC	.	.		0.348	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410	
HGSNAT	138050	hgsc.bcm.edu	37	8	43054663	43054663	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:43054663T>C	ENST00000458501.2	+	18	1943	c.1943T>C	c.(1942-1944)gTg>gCg	p.V648A	HGSNAT_ENST00000297798.7_Missense_Mutation_p.V352A|HGSNAT_ENST00000379644.4_Missense_Mutation_p.V620A|HGSNAT_ENST00000521576.1_Missense_Mutation_p.V337A			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	648					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GCCCTCTGGGTGCTCATTGCC	0.507																																					p.V620A		Atlas-SNP	.											.	HGSNAT	85	.	0			c.T1859C						.						50.0	52.0	51.0					8																	43054663		2200	4299	6499	SO:0001583	missense	138050	exon18			TCTGGGTGCTCAT		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"""transmembrane protein 76"""	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.1943T>C	chr8.hg19:g.43054663T>C	ENSP00000389524:p.Val648Ala	70.0	0.0		87.0	4.0	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.27	3.347366	0.61183	.	.	ENSG00000165102	ENST00000458501;ENST00000379644;ENST00000521576;ENST00000297798	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	5.29	5.29	0.74685	.	0.309598	0.29239	N	0.012723	T	0.75027	0.3794	M	0.75150	2.29	0.50039	D	0.999842	B	0.28439	0.212	B	0.25987	0.065	T	0.70934	-0.4737	10	0.17369	T	0.5	-11.1733	13.1833	0.59668	0.0:0.0:0.0:1.0	.	648	Q68CP4	HGNAT_HUMAN	A	648;620;337;352	ENSP00000389524:V648A;ENSP00000368965:V620A;ENSP00000429029:V337A;ENSP00000297798:V352A	ENSP00000297798:V352A	V	+	2	0	HGSNAT	43173820	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.525000	0.81892	1.988000	0.58038	0.460000	0.39030	GTG	.	.		0.507	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038	
PXDNL	137902	hgsc.bcm.edu	37	8	52359722	52359722	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:52359722C>A	ENST00000356297.4	-	12	1467	c.1367G>T	c.(1366-1368)gGa>gTa	p.G456V	PXDNL_ENST00000543296.1_Splice_Site_p.G456V	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	456	Ig-like C2-type 3.				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)				GAGCTGCCCTCCTGCAAAAAG	0.512																																					p.G456V		Atlas-SNP	.											PXDNL_ENST00000356297,NS,carcinoma,0,1	PXDNL	414	.	0			c.G1367T						.						88.0	87.0	87.0					8																	52359722		2012	4179	6191	SO:0001630	splice_region_variant	137902	exon12			TGCCCTCCTGCAA		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.1367-1G>T	chr8.hg19:g.52359722C>A		62.0	0.0		68.0	3.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.830139	0.50845	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.86694	-2.16;-2.16	3.84	3.84	0.44239	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94411	0.8202	M	0.93375	3.41	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.95047	0.8183	9	0.87932	D	0	.	11.2432	0.48980	0.0:1.0:0.0:0.0	.	456	A1KZ92	PXDNL_HUMAN	V	456	ENSP00000348645:G456V;ENSP00000444865:G456V	ENSP00000348645:G456V	G	-	2	0	PXDNL	52522275	1.000000	0.71417	0.731000	0.30826	0.436000	0.31835	5.882000	0.69714	1.677000	0.50941	0.467000	0.42956	GGA	.	.		0.512	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	Missense_Mutation
CHD7	55636	hgsc.bcm.edu	37	8	61757431	61757431	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:61757431G>T	ENST00000423902.2	+	22	5338	c.4859G>T	c.(4858-4860)cGg>cTg	p.R1620L	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1620					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AGTTGGGGACGGTGGACAGAC	0.468																																					p.R1620L		Atlas-SNP	.											.	CHD7	534	.	0			c.G4859T						.						65.0	61.0	63.0					8																	61757431		1951	4151	6102	SO:0001583	missense	55636	exon22			GGGGACGGTGGAC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.4859G>T	chr8.hg19:g.61757431G>T	ENSP00000392028:p.Arg1620Leu	70.0	0.0		110.0	5.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	35	5.421990	0.96111	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	T	0.74632	-0.86	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.88680	0.6502	M	0.88775	2.98	0.80722	D	1	D	0.60575	0.988	D	0.66979	0.948	D	0.89906	0.4048	10	0.87932	D	0	-18.7363	20.054	0.97641	0.0:0.0:1.0:0.0	.	1620	Q9P2D1	CHD7_HUMAN	L	1620	ENSP00000392028:R1620L	ENSP00000307304:R1620L	R	+	2	0	CHD7	61919985	1.000000	0.71417	0.936000	0.37596	0.991000	0.79684	9.869000	0.99810	2.808000	0.96608	0.655000	0.94253	CGG	.	.		0.468	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
CHD7	55636	hgsc.bcm.edu	37	8	61765453	61765453	+	Missense_Mutation	SNP	C	C	A	rs192260844		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:61765453C>A	ENST00000423902.2	+	31	6648	c.6169C>A	c.(6169-6171)Cgc>Agc	p.R2057S	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2057					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AACTCTGTACCGCATTGAGCT	0.562																																					p.R2057S		Atlas-SNP	.											.	CHD7	534	.	0			c.C6169A						.						116.0	119.0	118.0					8																	61765453		1944	4154	6098	SO:0001583	missense	55636	exon31			CTGTACCGCATTG	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6169C>A	chr8.hg19:g.61765453C>A	ENSP00000392028:p.Arg2057Ser	57.0	0.0		72.0	4.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	32	5.127115	0.94429	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.83163	-1.69	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.91452	0.7302	M	0.78916	2.43	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.92212	0.5777	10	0.87932	D	0	-12.4264	19.215	0.93772	0.0:1.0:0.0:0.0	.	2057	Q9P2D1	CHD7_HUMAN	S	2057	ENSP00000392028:R2057S	ENSP00000307304:R2057S	R	+	1	0	CHD7	61928007	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	6.062000	0.71155	2.539000	0.85634	0.655000	0.94253	CGC	.	C|1.000;T|0.000		0.562	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
ZFHX4	79776	hgsc.bcm.edu	37	8	77618142	77618142	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:77618142G>T	ENST00000521891.2	+	2	2267	c.1819G>T	c.(1819-1821)Ggc>Tgc	p.G607C	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Missense_Mutation_p.G607C|ZFHX4_ENST00000455469.2_Missense_Mutation_p.G607C|ZFHX4_ENST00000518282.1_Missense_Mutation_p.G607C	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	607					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)			TGGAGGAGACGGCTCACCGGG	0.572										HNSCC(33;0.089)																											p.G607C		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G1819T						.						72.0	79.0	76.0					8																	77618142		2098	4202	6300	SO:0001583	missense	79776	exon2			GGAGACGGCTCAC		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.1819G>T	chr8.hg19:g.77618142G>T	ENSP00000430497:p.Gly607Cys	51.0	0.0		78.0	4.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	18.87	3.715909	0.68844	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.55234	0.53;0.57;0.53;0.53	5.65	5.65	0.86999	.	0.000000	0.45361	U	0.000367	T	0.65026	0.2652	L	0.45581	1.43	0.80722	D	1	D;D;D;B	0.61697	0.983;0.99;0.99;0.262	P;P;P;B	0.61397	0.775;0.888;0.888;0.108	T	0.56884	-0.7905	10	0.30854	T	0.27	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	607;607;607;607	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	C	607	ENSP00000430497:G607C;ENSP00000399605:G607C;ENSP00000050961:G607C;ENSP00000430848:G607C	ENSP00000050961:G607C	G	+	1	0	ZFHX4	77780697	1.000000	0.71417	0.982000	0.44146	0.944000	0.59088	7.411000	0.80078	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.572	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
SLC7A13	157724	hgsc.bcm.edu	37	8	87226642	87226642	+	Silent	SNP	C	C	T	rs202114931|rs56993779	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:87226642C>T	ENST00000297524.3	-	4	1516	c.1413G>A	c.(1411-1413)taG>taA	p.*471*	CTD-3118D11.3_ENST00000523112.1_RNA|SLC7A13_ENST00000419776.2_3'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	0						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CTTCCGACATCTATTCCTCAG	0.303																																					p.X471X		Atlas-SNP	.											SLC7A13,NS,carcinoma,0,2	SLC7A13	97	.	0			c.G1413A						.						42.0	42.0	42.0					8																	87226642		2196	4256	6452	SO:0001819	synonymous_variant	157724	exon4			CGACATCTATTCC	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1413G>A	chr8.hg19:g.87226642C>T		5.0	1.0		20.0	3.0	NM_138817	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	hg19	CCDS34917.1																																																																																			.	.		0.303	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
WWP1	11059	hgsc.bcm.edu	37	8	87479044	87479044	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:87479044A>G	ENST00000517970.1	+	25	2998	c.2691A>G	c.(2689-2691)ccA>ccG	p.P897P	WWP1_ENST00000349423.2_Silent_p.P679P|WWP1_ENST00000341922.2_Silent_p.P767P|WWP1_ENST00000265428.4_Silent_p.P897P	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	897	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TGGATCTACCACCATATAAGA	0.308																																					p.P897P		Atlas-SNP	.											.	WWP1	97	.	0			c.A2691G						.						88.0	95.0	93.0					8																	87479044		2203	4300	6503	SO:0001819	synonymous_variant	11059	exon25			TCTACCACCATAT	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.2691A>G	chr8.hg19:g.87479044A>G		90.0	0.0		83.0	4.0	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	hg19	CCDS6242.1																																																																																			.	.		0.308	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
VPS13B	157680	hgsc.bcm.edu	37	8	100654256	100654256	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:100654256A>G	ENST00000358544.2	+	34	5624	c.5513A>G	c.(5512-5514)gAc>gGc	p.D1838G	VPS13B_ENST00000357162.2_Missense_Mutation_p.D1813G|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1838					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ATTCCCTTTGACATATTTATT	0.383																																					p.D1838G	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A5513G						.						74.0	75.0	74.0					8																	100654256		2203	4300	6503	SO:0001583	missense	157680	exon34			CCTTTGACATATT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.5513A>G	chr8.hg19:g.100654256A>G	ENSP00000351346:p.Asp1838Gly	51.0	0.0		64.0	4.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.737823	0.89573	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.74106	-0.81;-0.79	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.80904	0.4713	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.82991	-0.0182	10	0.87932	D	0	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	1813;1838	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	G	1813;1838	ENSP00000349685:D1813G;ENSP00000351346:D1838G	ENSP00000349685:D1813G	D	+	2	0	VPS13B	100723432	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.019000	0.93662	2.281000	0.76405	0.533000	0.62120	GAC	.	.		0.383	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
CSMD3	114788	hgsc.bcm.edu	37	8	113331157	113331157	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:113331157A>G	ENST00000297405.5	-	47	7513	c.7269T>C	c.(7267-7269)tgT>tgC	p.C2423C	CSMD3_ENST00000343508.3_Silent_p.C2383C|CSMD3_ENST00000455883.2_Silent_p.C2319C|CSMD3_ENST00000352409.3_Silent_p.C2353C	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2423	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATCCTGGAAGACACTGATACC	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.C2423C		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	.	0			c.T7269C						.						95.0	87.0	90.0					8																	113331157		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon47			TGGAAGACACTGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.7269T>C	chr8.hg19:g.113331157A>G		80.0	0.0		74.0	3.0	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
TAF2	6873	hgsc.bcm.edu	37	8	120793297	120793297	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:120793297T>C	ENST00000378164.2	-	17	2547	c.2249A>G	c.(2248-2250)cAg>cGg	p.Q750R		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	750					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CTGTACCTTCTGTAGAAAATA	0.323																																					p.Q750R		Atlas-SNP	.											.	TAF2	204	.	0			c.A2249G						.						59.0	66.0	63.0					8																	120793297		2203	4300	6503	SO:0001583	missense	6873	exon17			ACCTTCTGTAGAA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2249A>G	chr8.hg19:g.120793297T>C	ENSP00000367406:p.Gln750Arg	123.0	0.0		119.0	5.0	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	hg19	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.892076	0.72524	.	.	ENSG00000064313	ENST00000378164	T	0.47528	0.84	5.65	5.65	0.86999	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55178	0.1904	M	0.67953	2.075	0.80722	D	1	P	0.46621	0.881	P	0.46796	0.527	T	0.57929	-0.7726	10	0.48119	T	0.1	-25.2293	16.1864	0.81955	0.0:0.0:0.0:1.0	.	750	Q6P1X5	TAF2_HUMAN	R	750	ENSP00000367406:Q750R	ENSP00000367406:Q750R	Q	-	2	0	TAF2	120862478	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.099000	0.71466	2.281000	0.76405	0.528000	0.53228	CAG	.	.		0.323	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
DEPTOR	64798	hgsc.bcm.edu	37	8	120977517	120977517	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:120977517A>G	ENST00000286234.5	+	4	601	c.471A>G	c.(469-471)gaA>gaG	p.E157E	DEPTOR_ENST00000523492.1_Silent_p.E56E	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	157	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.				intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						GGGAGGAGGAAGGGGTCAAGT	0.517																																					p.E157E		Atlas-SNP	.											.	DEPTOR	41	.	0			c.A471G						.						106.0	94.0	98.0					8																	120977517		2203	4300	6503	SO:0001819	synonymous_variant	64798	exon4			GGAGGAAGGGGTC		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.471A>G	chr8.hg19:g.120977517A>G		72.0	0.0		86.0	4.0	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Silent	SNP	ENST00000286234.5	hg19	CCDS6331.1																																																																																			.	.		0.517	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
MTBP	27085	hgsc.bcm.edu	37	8	121528368	121528368	+	Missense_Mutation	SNP	G	G	T	rs574546258		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:121528368G>T	ENST00000305949.1	+	18	2228	c.2183G>T	c.(2182-2184)cGa>cTa	p.R728L		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	728	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)		p.R728Q(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			AATGAACTTCGAACTGAAGTA	0.398																																					p.R728L		Atlas-SNP	.											MTBP,caecum,carcinoma,0,1	MTBP	77	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2183T						.						65.0	63.0	64.0					8																	121528368		2203	4299	6502	SO:0001583	missense	27085	exon18			AACTTCGAACTGA		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.2183G>T	chr8.hg19:g.121528368G>T	ENSP00000303398:p.Arg728Leu	106.0	0.0		100.0	4.0	NM_022045	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	hg19	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.085033	0.55861	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.98	4.18	0.49190	.	0.140607	0.44688	D	0.000424	T	0.50274	0.1606	M	0.71581	2.175	0.09310	N	1	B	0.28439	0.212	B	0.36418	0.224	T	0.51834	-0.8655	9	0.72032	D	0.01	-3.0102	9.6219	0.39727	0.1027:0.2372:0.6601:0.0	.	728	Q96DY7	MTBP_HUMAN	L	728	.	ENSP00000303398:R728L	R	+	2	0	MTBP	121597549	0.002000	0.14202	0.007000	0.13788	0.010000	0.07245	1.024000	0.30077	0.848000	0.35191	-0.226000	0.12346	CGA	.	.		0.398	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	
ANXA13	312	hgsc.bcm.edu	37	8	124693533	124693533	+	Missense_Mutation	SNP	G	G	T	rs201212750		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:124693533G>T	ENST00000419625.1	-	11	970	c.898C>A	c.(898-900)Cgc>Agc	p.R300S	ANXA13_ENST00000262219.6_Missense_Mutation_p.R341S	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	300					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			GTATCTGAGCGAACCATGTCA	0.493																																					p.R341S		Atlas-SNP	.											.	ANXA13	38	.	0			c.C1021A						.						212.0	220.0	217.0					8																	124693533		2203	4300	6503	SO:0001583	missense	312	exon12			CTGAGCGAACCAT	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.898C>A	chr8.hg19:g.124693533G>T	ENSP00000390809:p.Arg300Ser	153.0	0.0		124.0	5.0	NM_001003954	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	hg19	CCDS47917.1	.	.	.	.	.	.	.	.	.	.	G	0.913	-0.718427	0.03182	.	.	ENSG00000104537	ENST00000262219;ENST00000419625	T;T	0.03152	4.03;4.03	5.71	3.83	0.44106	Annexin repeat, conserved site (1);	0.766484	0.13479	N	0.384821	T	0.01905	0.0060	N	0.10685	0.025	0.24403	N	0.994693	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.005	T	0.45760	-0.9239	10	0.02654	T	1	.	8.6176	0.33842	0.0:0.1495:0.5417:0.3088	.	300;341	P27216;P27216-2	ANX13_HUMAN;.	S	341;300	ENSP00000262219:R341S;ENSP00000390809:R300S	ENSP00000262219:R341S	R	-	1	0	ANXA13	124762714	0.627000	0.27129	0.983000	0.44433	0.595000	0.36748	0.298000	0.19120	0.677000	0.31305	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.493	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
FER1L6	654463	hgsc.bcm.edu	37	8	124989814	124989814	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:124989814T>C	ENST00000522917.1	+	10	1234	c.1028T>C	c.(1027-1029)cTg>cCg	p.L343P	FER1L6_ENST00000399018.1_Missense_Mutation_p.L343P	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	343	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TTCATTGACCTGAAGAAAATC	0.453																																					p.L343P		Atlas-SNP	.											.	FER1L6	268	.	0			c.T1028C						.						99.0	100.0	100.0					8																	124989814		1957	4153	6110	SO:0001583	missense	654463	exon10			TTGACCTGAAGAA	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.1028T>C	chr8.hg19:g.124989814T>C	ENSP00000428280:p.Leu343Pro	143.0	0.0		124.0	5.0	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440800	0.83993	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.15603	2.41;2.41	5.53	5.53	0.82687	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.52532	U	0.000062	T	0.48390	0.1497	M	0.88704	2.975	0.80722	D	1	D	0.76494	0.999	D	0.68621	0.959	T	0.58463	-0.7632	10	0.87932	D	0	.	15.6745	0.77303	0.0:0.0:0.0:1.0	.	343	Q2WGJ9	FR1L6_HUMAN	P	343	ENSP00000428280:L343P;ENSP00000381982:L343P	ENSP00000381982:L343P	L	+	2	0	FER1L6	125058995	1.000000	0.71417	0.985000	0.45067	0.985000	0.73830	7.997000	0.88414	2.109000	0.64355	0.459000	0.35465	CTG	.	.		0.453	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
KIAA0196	9897	hgsc.bcm.edu	37	8	126040930	126040930	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:126040930G>T	ENST00000318410.7	-	28	3704	c.3355C>A	c.(3355-3357)Cct>Act	p.P1119T	KIAA0196_ENST00000517845.1_Missense_Mutation_p.P971T	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	1119					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ACATCTGCAGGAATTTCAGGT	0.398																																					p.P1119T		Atlas-SNP	.											.	KIAA0196	90	.	0			c.C3355A						.						115.0	108.0	110.0					8																	126040930		2203	4300	6503	SO:0001583	missense	9897	exon28			CTGCAGGAATTTC		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.3355C>A	chr8.hg19:g.126040930G>T	ENSP00000318016:p.Pro1119Thr	61.0	0.0		99.0	4.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.45|13.45	2.239469|2.239469	0.39598|0.39598	.|.	.|.	ENSG00000164961|ENSG00000164961	ENST00000318410;ENST00000517845|ENST00000523273	D;D|.	0.86097|.	-2.07;-2.07|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72028|0.72028	0.3410|0.3410	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.76071|.	0.987|.	T|T	0.67848|0.67848	-0.5564|-0.5564	10|5	0.42905|.	T|.	0.14|.	-16.0633|-16.0633	19.7005|19.7005	0.96050|0.96050	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1119|.	Q12768|.	STRUM_HUMAN|.	T|Y	1119;971|684	ENSP00000318016:P1119T;ENSP00000429676:P971T|.	ENSP00000318016:P1119T|.	P|S	-|-	1|2	0|0	KIAA0196|KIAA0196	126110112|126110112	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	9.869000|9.869000	0.99810|0.99810	2.657000|2.657000	0.90304|0.90304	0.555000|0.555000	0.69702|0.69702	CCT|TCC	.	.		0.398	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141449296	141449296	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:141449296T>C	ENST00000438773.2	-	3	718	c.585A>G	c.(583-585)agA>agG	p.R195R	TRAPPC9_ENST00000389328.4_Splice_Site_p.R293R|TRAPPC9_ENST00000389327.3_Splice_Site_p.R195R	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	195					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						TCTTGTAATGTCTAGAAAATA	0.468																																					p.R293R		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.A879G						.						59.0	58.0	59.0					8																	141449296		2203	4300	6503	SO:0001630	splice_region_variant	83696	exon3			GTAATGTCTAGAA	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.585-1A>G	chr8.hg19:g.141449296T>C		57.0	0.0		93.0	4.0	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.963289	0.34659	.	.	ENSG00000167632	ENST00000520857	.	.	.	5.8	2.08	0.27032	.	.	.	.	.	T	0.58708	0.2141	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50955	-0.8766	4	.	.	.	.	9.8245	0.40903	0.0:0.3333:0.0:0.6667	.	.	.	.	A	48	.	.	T	-	1	0	TRAPPC9	141518478	1.000000	0.71417	0.978000	0.43139	0.726000	0.41606	0.762000	0.26503	0.117000	0.18138	0.528000	0.53228	ACA	.	.		0.468	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	Silent
AGO2	27161	hgsc.bcm.edu	37	8	141542567	141542567	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:141542567G>T	ENST00000220592.5	-	18	2531	c.2419C>A	c.(2419-2421)Cac>Aac	p.H807N	AGO2_ENST00000519980.1_Missense_Mutation_p.H773N|CASC7_ENST00000560295.1_lincRNA	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	807	Interaction with guide RNA.|Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				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)										GCCACCAGGTGAGCGTAGTAT	0.587																																					p.H807N		Atlas-SNP	.											.	.	.	.	0			c.C2419A						.						79.0	62.0	68.0					8																	141542567		2203	4300	6503	SO:0001583	missense	27161	exon18			CCAGGTGAGCGTA	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.2419C>A	chr8.hg19:g.141542567G>T	ENSP00000220592:p.His807Asn	72.0	0.0		95.0	4.0	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Missense_Mutation	SNP	ENST00000220592.5	hg19	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.503296	0.85176	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.31510	1.49;1.49	5.96	5.96	0.96718	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.70806	0.3266	H	0.95365	3.66	0.80722	D	1	P;P	0.48694	0.894;0.914	D;D	0.72075	0.945;0.976	T	0.77872	-0.2426	10	0.87932	D	0	1.7967	20.422	0.99049	0.0:0.0:1.0:0.0	.	773;807	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	N	807;773	ENSP00000220592:H807N;ENSP00000430176:H773N	ENSP00000220592:H807N	H	-	1	0	EIF2C2	141611749	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	7.877000	0.87225	2.832000	0.97577	0.655000	0.94253	CAC	.	.		0.587	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
SLC45A4	57210	hgsc.bcm.edu	37	8	142228278	142228278	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:142228278C>A	ENST00000024061.3	-	4	1615	c.1308G>T	c.(1306-1308)gaG>gaT	p.E436D	SLC45A4_ENST00000517878.1_Missense_Mutation_p.E487D|SLC45A4_ENST00000519067.1_Missense_Mutation_p.E436D|SLC45A4_ENST00000433583.2_Missense_Mutation_p.E429D	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			CGCCCTCCCCCTCCTCACTCT	0.672																																					p.E436D		Atlas-SNP	.											.	SLC45A4	71	.	0			c.G1308T						.						63.0	55.0	58.0					8																	142228278		2203	4300	6503	SO:0001583	missense	57210	exon4			CTCCCCCTCCTCA	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.1308G>T	chr8.hg19:g.142228278C>A	ENSP00000024061:p.Glu436Asp	71.0	0.0		85.0	33.0	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	hg19	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.575869	0.28092	.	.	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061	D;D;D;D	0.95482	-3.72;-3.72;-3.72;-3.72	5.07	4.18	0.49190	.	0.000000	0.85682	D	0.000000	D	0.90321	0.6972	N	0.25647	0.755	0.45194	D	0.998207	B;B;B	0.21452	0.034;0.056;0.056	B;B;B	0.21360	0.012;0.034;0.027	D	0.86630	0.1885	10	0.38643	T	0.18	-35.5141	10.8078	0.46529	0.0:0.8493:0.0:0.1507	.	487;436;436	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	D	436;487;429;436	ENSP00000429059:E436D;ENSP00000428137:E487D;ENSP00000400799:E429D;ENSP00000024061:E436D	ENSP00000024061:E436D	E	-	3	2	SLC45A4	142297460	0.986000	0.35501	1.000000	0.80357	0.169000	0.22640	0.211000	0.17474	2.535000	0.85469	0.561000	0.74099	GAG	.	.		0.672	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
GPIHBP1	338328	hgsc.bcm.edu	37	8	144296897	144296897	+	Missense_Mutation	SNP	G	G	T	rs578073937		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr8:144296897G>T	ENST00000330824.2	+	3	266	c.191G>T	c.(190-192)cGg>cTg	p.R64L		NM_178172.3	NP_835466.1	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	64	UPAR/Ly6.				cholesterol homeostasis (GO:0042632)|intracellular protein transport (GO:0006886)|positive regulation of chylomicron remnant clearance (GO:0090321)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein import (GO:0017038)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|protein transmembrane transport (GO:0071806)|response to heparin (GO:0071503)|transcytosis (GO:0045056)|triglyceride homeostasis (GO:0070328)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|external side of plasma membrane (GO:0009897)|high-density lipoprotein particle (GO:0034364)	chylomicron binding (GO:0035478)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|protein transmembrane transporter activity (GO:0008320)			lung(2)	2	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GTGCTGCTGCGGTGCTACACC	0.672																																					p.R64L		Atlas-SNP	.											.	GPIHBP1	12	.	0			c.G191T						.						42.0	31.0	35.0					8																	144296897		2183	4269	6452	SO:0001583	missense	338328	exon3			TGCTGCGGTGCTA	AF088057	CCDS34954.1	8q24.3	2014-07-14	2008-02-07						24945	protein-coding gene	gene with protein product	"""endothelial cell LPL transporter"""	612757	"""GPI anchored high density lipoprotein binding protein 1"""			12496272, 17883852, 17620854, 17403372	Standard	NM_178172		Approved	LOC338328, GPI-HBP1	uc003yxu.2	Q8IV16		ENST00000330824.2:c.191G>T	chr8.hg19:g.144296897G>T	ENSP00000329266:p.Arg64Leu	94.0	0.0		122.0	6.0	NM_178172	Q6P3T2|Q86W15	Missense_Mutation	SNP	ENST00000330824.2	hg19	CCDS34954.1	.	.	.	.	.	.	.	.	.	.	g	11.57	1.679548	0.29783	.	.	ENSG00000182851	ENST00000330824	T	0.77098	-1.07	3.95	-6.09	0.02145	Ly-6 antigen / uPA receptor -like (1);	1.872550	0.03244	N	0.180936	T	0.67173	0.2865	L	0.51422	1.61	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.51309	-0.8722	10	0.59425	D	0.04	-16.5311	3.1887	0.06609	0.5921:0.1332:0.141:0.1337	.	64	Q8IV16	HDBP1_HUMAN	L	64	ENSP00000329266:R64L	ENSP00000329266:R64L	R	+	2	0	GPIHBP1	144368272	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.697000	0.01910	-1.253000	0.02488	0.450000	0.29827	CGG	.	.		0.672	GPIHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381113.1	NM_178172	
DOCK8	81704	hgsc.bcm.edu	37	9	304685	304685	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:304685G>A	ENST00000453981.1	+	5	621	c.509G>A	c.(508-510)tGc>tAc	p.C170Y	DOCK8_ENST00000432829.2_Missense_Mutation_p.C102Y|DOCK8_ENST00000469391.1_Missense_Mutation_p.C102Y			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	170					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		ACCTTGGAGTGCAGTGAACCC	0.458																																					p.C170Y		Atlas-SNP	.											.	DOCK8	401	.	0			c.G509A						.						118.0	122.0	121.0					9																	304685		2203	4300	6503	SO:0001583	missense	81704	exon5			TGGAGTGCAGTGA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.509G>A	chr9.hg19:g.304685G>A	ENSP00000408464:p.Cys170Tyr	62.0	0.0		81.0	4.0	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	11.54	1.668349	0.29604	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000487230;ENST00000469391	T;T;T;T	0.30182	2.67;2.67;1.54;2.67	6.02	-1.91	0.07641	.	1.513220	0.03048	N	0.154177	T	0.22589	0.0545	L	0.34521	1.04	0.09310	N	1	B;B;B	0.12013	0.0;0.005;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.16748	-1.0392	10	0.27082	T	0.32	.	6.8557	0.24040	0.4355:0.3584:0.2061:0.0	.	102;170;170	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	Y	170;170;102;102;102	ENSP00000408464:C170Y;ENSP00000394888:C102Y;ENSP00000418318:C102Y;ENSP00000419438:C102Y	ENSP00000287364:C170Y	C	+	2	0	DOCK8	294685	0.000000	0.05858	0.000000	0.03702	0.963000	0.63663	-0.198000	0.09505	-0.390000	0.07774	0.655000	0.94253	TGC	.	.		0.458	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
KIAA0020	9933	hgsc.bcm.edu	37	9	2807906	2807906	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:2807906T>C	ENST00000397885.2	-	17	1930		c.e17-2			NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020							endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		CAAAACAACCTGTAAAATATA	0.353																																					.		Atlas-SNP	.											.	KIAA0020	56	.	0			c.1724-2A>G						.						74.0	70.0	71.0					9																	2807906		2203	4300	6503	SO:0001630	splice_region_variant	9933	exon18			ACAACCTGTAAAA	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1724-2A>G	chr9.hg19:g.2807906T>C		42.0	0.0		73.0	4.0	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Splice_Site	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	T	17.26	3.345515	0.61073	.	.	ENSG00000080608	ENST00000397885	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9	0.70672	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0020	2797906	1.000000	0.71417	0.994000	0.49952	0.835000	0.47333	6.124000	0.71620	2.258000	0.74832	0.529000	0.55759	.	.	.		0.353	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	Intron
DNAI1	27019	hgsc.bcm.edu	37	9	34506838	34506838	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:34506838C>T	ENST00000242317.4	+	13	1448	c.1277C>T	c.(1276-1278)gCc>gTc	p.A426V		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	426					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		TGCAGCTCAGCCAAGTCTGGC	0.627									Kartagener syndrome																												p.A426V		Atlas-SNP	.											.	DNAI1	72	.	0			c.C1277T						.						55.0	46.0	49.0					9																	34506838		2203	4300	6503	SO:0001583	missense	27019	exon13	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GCTCAGCCAAGTC	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"""Axonemal dyneins"", ""WD repeat domain containing"""	2954	protein-coding gene	gene with protein product		604366	"""dynein, axonemal, intermediate polypeptide 1"""			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1277C>T	chr9.hg19:g.34506838C>T	ENSP00000242317:p.Ala426Val	73.0	0.0		95.0	4.0	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	hg19	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	C	2.468	-0.322458	0.05350	.	.	ENSG00000122735	ENST00000242317	D	0.85861	-2.04	5.16	5.16	0.70880	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.336395	0.30320	N	0.009891	T	0.81211	0.4775	L	0.49455	1.56	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.75777	-0.3198	10	0.21540	T	0.41	.	15.8168	0.78608	0.0:1.0:0.0:0.0	.	426	Q9UI46	DNAI1_HUMAN	V	426	ENSP00000242317:A426V	ENSP00000242317:A426V	A	+	2	0	DNAI1	34496838	1.000000	0.71417	0.938000	0.37757	0.015000	0.08874	5.579000	0.67457	2.390000	0.81377	0.563000	0.77884	GCC	.	.		0.627	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1		
DNAJB5	25822	hgsc.bcm.edu	37	9	34990809	34990809	+	5'UTR	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:34990809G>T	ENST00000541010.1	+	0	591				DNAJB5_ENST00000545841.1_Intron|DNAJB5_ENST00000453597.3_Splice_Site_p.R103L|DNAJB5_ENST00000312316.5_Intron|DNAJB5_ENST00000335998.3_Splice_Site_p.R23L|DNAJB5_ENST00000454002.2_Splice_Site_p.R61L			O75953	DNJB5_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 5						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)			kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(32;0.00575)			GTAAAGTTTCGGTAAGTCCCT	0.527																																					p.R103L		Atlas-SNP	.											.	DNAJB5	69	.	0			c.G308T						.						42.0	40.0	40.0					9																	34990809		692	1591	2283	SO:0001623	5_prime_UTR_variant	25822	exon2			AGTTTCGGTAAGT	AF088982	CCDS35007.1, CCDS47959.1, CCDS47960.1, CCDS47960.2	9p	2011-09-02			ENSG00000137094	ENSG00000137094		"""Heat shock proteins / DNAJ (HSP40)"""	14887	protein-coding gene	gene with protein product		611328				10570961, 11147971	Standard	NM_001135004		Approved	Hsc40	uc003zvs.4	O75953	OTTHUMG00000019840	ENST00000541010.1:c.-2422G>T	chr9.hg19:g.34990809G>T		69.0	0.0		59.0	4.0	NM_001135004	B3KN14|B4DSA6|J3KQM9|J3KR08|Q5T656|Q8TDR7|Q96EM4	Missense_Mutation	SNP	ENST00000541010.1	hg19	CCDS35007.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039055	0.55003	.	.	ENSG00000137094	ENST00000453597;ENST00000335998;ENST00000454002	T;T;T	0.57107	0.42;0.53;0.46	4.59	4.59	0.56863	.	.	.	.	.	T	0.45915	0.1366	N	0.08118	0	0.80722	D	1	D	0.53745	0.962	P	0.53450	0.726	T	0.57283	-0.7838	9	0.87932	D	0	.	14.5683	0.68194	0.0:0.0:1.0:0.0	.	61	B4DSA6	.	L	103;23;61	ENSP00000404079:R103L;ENSP00000337626:R23L;ENSP00000413684:R61L	ENSP00000337626:R23L	R	+	2	0	DNAJB5	34980809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.954000	0.70298	2.102000	0.63906	0.561000	0.74099	CGA	.	.		0.527	DNAJB5-008	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401397.1		
CCIN	881	hgsc.bcm.edu	37	9	36170794	36170794	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:36170794G>T	ENST00000335119.2	+	1	1406	c.1295G>T	c.(1294-1296)cGg>cTg	p.R432L		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	432					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			GTCACTGGACGGTGCTTGGTG	0.552																																					p.R432L		Atlas-SNP	.											.	CCIN	56	.	0			c.G1295T						.						141.0	107.0	119.0					9																	36170794		2203	4300	6503	SO:0001583	missense	881	exon1			CTGGACGGTGCTT	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"""BTB/POZ domain containing"""	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.1295G>T	chr9.hg19:g.36170794G>T	ENSP00000334996:p.Arg432Leu	86.0	0.0		92.0	5.0	NM_005893	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	hg19	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291280	0.59976	.	.	ENSG00000185972	ENST00000335119	T	0.66099	-0.19	5.73	5.73	0.89815	Kelch-type beta propeller (1);	0.000000	0.51477	D	0.000095	T	0.65729	0.2719	L	0.27053	0.805	0.37591	D	0.920177	D	0.60160	0.987	D	0.67725	0.953	T	0.62586	-0.6823	10	0.18276	T	0.48	.	15.3816	0.74661	0.0:0.0:1.0:0.0	.	432	Q13939	CALI_HUMAN	L	432	ENSP00000334996:R432L	ENSP00000334996:R432L	R	+	2	0	CCIN	36160794	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	5.491000	0.66887	2.699000	0.92147	0.491000	0.48974	CGG	.	.		0.552	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893	
MAMDC2	256691	hgsc.bcm.edu	37	9	72659502	72659502	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:72659502C>T	ENST00000377182.4	+	2	654	c.37C>T	c.(37-39)Ctg>Ttg	p.L13L		NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	13					peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)	endoplasmic reticulum (GO:0005783)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	glycosaminoglycan binding (GO:0005539)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	14						GCCCGCAGCCCTGCAGCTCGC	0.622																																					p.L13L		Atlas-SNP	.											.	MAMDC2	55	.	0			c.C37T						.						40.0	36.0	37.0					9																	72659502		1976	3820	5796	SO:0001819	synonymous_variant	256691	exon2			GCAGCCCTGCAGC	BC040299	CCDS6631.1	9q21.2	2008-02-05			ENSG00000165072	ENSG00000165072			23673	protein-coding gene	gene with protein product		612879					Standard	NM_153267		Approved	MGC21981	uc004ahm.2	Q7Z304	OTTHUMG00000019990	ENST00000377182.4:c.37C>T	chr9.hg19:g.72659502C>T		86.0	0.0		99.0	4.0	NM_153267	Q5VW47|Q8WX43|Q96BM4	Silent	SNP	ENST00000377182.4	hg19	CCDS6631.1																																																																																			.	.		0.622	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267	
TRPM3	80036	hgsc.bcm.edu	37	9	73235023	73235023	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:73235023C>A	ENST00000377111.2	-	15	2305	c.2062G>T	c.(2062-2064)Gac>Tac	p.D688Y	TRPM3_ENST00000396292.4_Missense_Mutation_p.D560Y|TRPM3_ENST00000423814.3_Missense_Mutation_p.D715Y|TRPM3_ENST00000377105.1_Missense_Mutation_p.D547Y|TRPM3_ENST00000377110.3_Missense_Mutation_p.D688Y|TRPM3_ENST00000377106.1_Missense_Mutation_p.D560Y|TRPM3_ENST00000396280.5_Missense_Mutation_p.D537Y|TRPM3_ENST00000357533.2_Missense_Mutation_p.D692Y|TRPM3_ENST00000396285.1_Missense_Mutation_p.D535Y|TRPM3_ENST00000358082.3_Missense_Mutation_p.D550Y|TRPM3_ENST00000408909.2_Missense_Mutation_p.D547Y|TRPM3_ENST00000360823.2_Missense_Mutation_p.D550Y	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	713					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.D560N(1)|p.D692N(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TGGGAAATGTCGTCAACCATG	0.602																																					p.D688Y		Atlas-SNP	.											TRPM3_ENST00000423814,NS,carcinoma,0,2	TRPM3	700	.	2	Substitution - Missense(2)	lung(2)	c.G2062T						.						73.0	69.0	71.0					9																	73235023		2203	4300	6503	SO:0001583	missense	80036	exon15			AAATGTCGTCAAC	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.2062G>T	chr9.hg19:g.73235023C>A	ENSP00000366315:p.Asp688Tyr	73.0	0.0		82.0	4.0	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.3|25.3	4.620384|4.620384	0.87460|0.87460	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814|ENST00000396280	T;T;T;T;T;T;T;T;T;T;T|.	0.63580|.	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05|.	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82637|0.82637	0.5080|0.5080	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;0.998;1.0;0.995;1.0;1.0;0.999;0.999|.	D;D;D;D;D;D;D;D|.	0.97110|.	0.992;0.97;1.0;0.981;0.987;0.997;0.986;0.971|.	T|T	0.81455|0.81455	-0.0925|-0.0925	10|5	0.87932|.	D|.	0|.	-30.4518|-30.4518	20.6439|20.6439	0.99570|0.99570	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	688;688;678;692;550;547;660;535|.	Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.	.;.;.;.;.;.;.;.|.	Y|L	688;688;560;550;547;692;547;535;560;550;715|536	ENSP00000366315:D688Y;ENSP00000366314:D688Y;ENSP00000366310:D560Y;ENSP00000354066:D550Y;ENSP00000366309:D547Y;ENSP00000350140:D692Y;ENSP00000386127:D547Y;ENSP00000379581:D535Y;ENSP00000379587:D560Y;ENSP00000350791:D550Y;ENSP00000389542:D715Y|.	ENSP00000350140:D692Y|.	D|R	-|-	1|2	0|0	TRPM3|TRPM3	72424843|72424843	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.800000|0.800000	0.45204|0.45204	7.818000|7.818000	0.86416|0.86416	2.890000|2.890000	0.99128|0.99128	0.650000|0.650000	0.86243|0.86243	GAC|CGA	.	.		0.602	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500432	90500432	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:90500432C>T	ENST00000325643.5	+	4	1096	c.1030C>T	c.(1030-1032)Ccc>Tcc	p.P344S		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	344					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGGGGAGACCCCACACCCAA	0.597																																					p.P344S		Atlas-SNP	.											.	.	.	.	0			c.C1030T						.						58.0	59.0	59.0					9																	90500432		2203	4300	6503	SO:0001583	missense	286234	exon4			GGAGACCCCACAC	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.1030C>T	chr9.hg19:g.90500432C>T	ENSP00000322640:p.Pro344Ser	76.0	0.0		94.0	4.0	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	hg19	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	.	9.083	0.999705	0.19121	.	.	ENSG00000177992	ENST00000325643	T	0.03386	3.95	3.37	0.169	0.15017	.	.	.	.	.	T	0.02848	0.0085	L	0.35542	1.07	0.09310	N	1	B	0.33637	0.42	B	0.32928	0.155	T	0.46665	-0.9175	9	0.26408	T	0.33	.	4.9674	0.14098	0.0:0.4366:0.4329:0.1305	.	344	Q6ZUB1	CI079_HUMAN	S	344	ENSP00000322640:P344S	ENSP00000322640:P344S	P	+	1	0	C9orf79	89690252	0.000000	0.05858	0.001000	0.08648	0.110000	0.19582	-0.559000	0.05971	0.197000	0.20387	0.557000	0.71058	CCC	.	.		0.597	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
PHF2	5253	hgsc.bcm.edu	37	9	96428080	96428080	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:96428080G>T	ENST00000359246.4	+	15	2417	c.2050G>T	c.(2050-2052)Ggt>Tgt	p.G684C	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	684					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		GTCGGATGACGGTGAGCTCAA	0.597																																					p.G684C		Atlas-SNP	.											.	PHF2	113	.	0			c.G2050T						.						123.0	131.0	129.0					9																	96428080		2203	4300	6503	SO:0001583	missense	5253	exon15			GATGACGGTGAGC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2050G>T	chr9.hg19:g.96428080G>T	ENSP00000352185:p.Gly684Cys	98.0	0.0		106.0	5.0	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	hg19	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427605	0.62733	.	.	ENSG00000197724	ENST00000359246	T	0.20881	2.04	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.42404	0.1201	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.30966	-0.9960	10	0.72032	D	0.01	-30.6856	18.5484	0.91055	0.0:0.0:1.0:0.0	.	102;684	Q8N359;O75151	.;PHF2_HUMAN	C	684	ENSP00000352185:G684C	ENSP00000352185:G684C	G	+	1	0	PHF2	95467901	1.000000	0.71417	0.729000	0.30791	0.070000	0.16714	9.246000	0.95438	2.375000	0.81037	0.591000	0.81541	GGT	.	.		0.597	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
TMEFF1	8577	hgsc.bcm.edu	37	9	103312401	103312401	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:103312401G>A	ENST00000374879.4	+	7	1166	c.734G>A	c.(733-735)gGa>gAa	p.G245E	TMEFF1_ENST00000334943.6_Missense_Mutation_p.G206E|MSANTD3-TMEFF1_ENST00000502978.1_Silent_p.G208G	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	245					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				AGTTTGTTGGGAAAGAAAGAT	0.363																																					p.G319E		Atlas-SNP	.											.	.	.	.	0			c.G956A						.						127.0	119.0	122.0					9																	103312401		2203	4300	6503	SO:0001583	missense	100526694	exon7			TGTTGGGAAAGAA	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"""tomoregulin-1"", ""cancer/testis antigen family 120, member 1"""	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.734G>A	chr9.hg19:g.103312401G>A	ENSP00000364013:p.Gly245Glu	65.0	0.0		63.0	4.0	NM_001198812	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	hg19	CCDS6750.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099068	0.76983	.	.	ENSG00000241697	ENST00000334943;ENST00000374879	T;T	0.57273	0.44;0.41	5.74	5.74	0.90152	.	0.109197	0.64402	D	0.000006	T	0.53867	0.1823	N	0.14661	0.345	0.80722	D	1	P;D	0.76494	0.893;0.999	P;D	0.71656	0.706;0.974	T	0.45906	-0.9229	10	0.11182	T	0.66	-35.667	17.4089	0.87480	0.0:0.0:1.0:0.0	.	245;206	Q8IYR6;Q8IYR6-2	TEFF1_HUMAN;.	E	206;245	ENSP00000334447:G206E;ENSP00000364013:G245E	ENSP00000334447:G206E	G	+	2	0	TMEFF1	102352222	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.774000	0.75012	2.702000	0.92279	0.585000	0.79938	GGA	.	.		0.363	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692	
PLPPR1	54886	hgsc.bcm.edu	37	9	104079680	104079680	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:104079680C>T	ENST00000374874.3	+	7	1286	c.847C>T	c.(847-849)Caa>Taa	p.Q283*	LPPR1_ENST00000395056.2_Nonsense_Mutation_p.Q283*	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		283					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										TAAAGGAACGCAAGGATCTCC	0.512																																					p.Q283X		Atlas-SNP	.											.	.	.	.	0			c.C847T						.						159.0	163.0	161.0					9																	104079680		2203	4300	6503	SO:0001587	stop_gained	0	exon7			GGAACGCAAGGAT																												ENST00000374874.3:c.847C>T	chr9.hg19:g.104079680C>T	ENSP00000364008:p.Gln283*	97.0	0.0		68.0	4.0	NM_207299	Q5VX23|Q9NXE2	Nonsense_Mutation	SNP	ENST00000374874.3	hg19	CCDS6751.1	.	.	.	.	.	.	.	.	.	.	C	38	7.188050	0.98121	.	.	ENSG00000148123	ENST00000374874;ENST00000374871;ENST00000395056	.	.	.	5.79	5.79	0.91817	.	0.563221	0.18337	N	0.144320	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-6.635	12.34	0.55089	0.0:0.9238:0.0:0.0762	.	.	.	.	X	283	.	ENSP00000364005:Q283X	Q	+	1	0	RP11-35N6.1	103119501	1.000000	0.71417	0.987000	0.45799	0.997000	0.91878	4.587000	0.60991	2.746000	0.94184	0.655000	0.94253	CAA	.	.		0.512	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
BAAT	570	hgsc.bcm.edu	37	9	104130448	104130448	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:104130448A>G	ENST00000395051.3	-	2	693	c.623T>C	c.(622-624)tTg>tCg	p.L208S	BAAT_ENST00000259407.2_Missense_Mutation_p.L208S			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	208					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	AAAATATTCCAAATCTGTTAC	0.468																																					p.L208S		Atlas-SNP	.											.	BAAT	52	.	0			c.T623C						.						74.0	80.0	78.0					9																	104130448		2203	4300	6503	SO:0001583	missense	570	exon3			TATTCCAAATCTG	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"""glycine N-choloyltransferase"""	602938	"""bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)"", ""bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"""				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.623T>C	chr9.hg19:g.104130448A>G	ENSP00000378491:p.Leu208Ser	118.0	0.0		142.0	65.0	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	hg19	CCDS6752.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.583815	0.65992	.	.	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.38722	1.12;1.12	4.38	4.38	0.52667	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.155821	0.25575	N	0.029736	T	0.65176	0.2666	M	0.82517	2.595	0.26564	N	0.973674	D	0.89917	1.0	D	0.83275	0.996	T	0.60772	-0.7197	10	0.87932	D	0	-15.8757	11.6118	0.51064	1.0:0.0:0.0:0.0	.	208	Q14032	BAAT_HUMAN	S	208	ENSP00000259407:L208S;ENSP00000378491:L208S	ENSP00000259407:L208S	L	-	2	0	BAAT	103170269	1.000000	0.71417	0.268000	0.24571	0.880000	0.50808	8.507000	0.90522	1.850000	0.53721	0.459000	0.35465	TTG	.	.		0.468	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1		
ZNF462	58499	hgsc.bcm.edu	37	9	109689751	109689751	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:109689751T>C	ENST00000277225.5	+	3	3847	c.3558T>C	c.(3556-3558)ccT>ccC	p.P1186P	ZNF462_ENST00000441147.2_Silent_p.P31P|ZNF462_ENST00000457913.1_Silent_p.P1186P			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1186					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GAGATGGCCCTCCTGTGGAGA	0.557																																					p.P1186P		Atlas-SNP	.											.	ZNF462	322	.	0			c.T3558C						.						198.0	201.0	200.0					9																	109689751		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			TGGCCCTCCTGTG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.3558T>C	chr9.hg19:g.109689751T>C		55.0	0.0		85.0	4.0	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	hg19	CCDS35096.1																																																																																			.	.		0.557	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
AKAP2	11217	hgsc.bcm.edu	37	9	112900259	112900259	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:112900259C>A	ENST00000259318.7	+	2	1949	c.1742C>A	c.(1741-1743)gCc>gAc	p.A581D	AKAP2_ENST00000555236.1_Missense_Mutation_p.A812D|AKAP2_ENST00000510514.5_Missense_Mutation_p.A812D|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.A812D|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.A812D|AKAP2_ENST00000434623.2_Missense_Mutation_p.A670D|AKAP2_ENST00000374525.1_Missense_Mutation_p.A670D	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	581										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						ATTCAACAAGCCATAGCCGAG	0.562																																					p.A812D		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.C2435A						.						37.0	39.0	38.0					9																	112900259		2203	4300	6503	SO:0001583	missense	445815	exon8			AACAAGCCATAGC	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1742C>A	chr9.hg19:g.112900259C>A	ENSP00000259318:p.Ala581Asp	73.0	0.0		90.0	4.0	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	hg19	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.323456	0.81580	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.60040	1.55;1.58;1.55;1.58;0.79;0.24;0.22;0.87	6.06	6.06	0.98353	RII binding domain (1);	0.000000	0.85682	D	0.000000	T	0.76969	0.4062	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.997;0.999;0.999;0.999;1.0;0.999;0.999;0.999	T	0.76022	-0.3111	10	0.56958	D	0.05	-29.3009	19.6279	0.95687	0.0:1.0:0.0:0.0	.	581;670;664;670;671;812;812;630	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	D	812;812;812;812;670;670;630;581	ENSP00000363654:A812D;ENSP00000305861:A812D;ENSP00000451476:A812D;ENSP00000421522:A812D;ENSP00000404782:A670D;ENSP00000363649:A670D;ENSP00000419268:A630D;ENSP00000259318:A581D	ENSP00000259318:A581D	A	+	2	0	PALM2-AKAP2;AKAP2	111940080	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.076000	0.57591	2.880000	0.98712	0.650000	0.86243	GCC	.	.		0.562	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
SVEP1	79987	hgsc.bcm.edu	37	9	113169106	113169106	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:113169106C>T	ENST00000401783.2	-	38	9110	c.8774G>A	c.(8773-8775)gGt>gAt	p.G2925D	SVEP1_ENST00000297826.5_Missense_Mutation_p.G851D|SVEP1_ENST00000374469.1_Missense_Mutation_p.G2902D	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2925	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TTTTGGAGCACCGTGCAAGAT	0.537																																					p.G2925D		Atlas-SNP	.											.	SVEP1	326	.	0			c.G8774A						.						148.0	149.0	149.0					9																	113169106		2064	4209	6273	SO:0001583	missense	79987	exon38			GGAGCACCGTGCA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8774G>A	chr9.hg19:g.113169106C>T	ENSP00000384917:p.Gly2925Asp	70.0	0.0		81.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195395	0.58126	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.72725	-0.68;-0.68;-0.68	5.41	5.41	0.78517	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.89037	0.6601	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91255	0.5032	10	0.56958	D	0.05	.	19.1906	0.93664	0.0:1.0:0.0:0.0	.	2925	Q4LDE5	SVEP1_HUMAN	D	2925;2902;851	ENSP00000384917:G2925D;ENSP00000363593:G2902D;ENSP00000297826:G851D	ENSP00000297826:G851D	G	-	2	0	SVEP1	112208927	1.000000	0.71417	0.197000	0.23402	0.142000	0.21351	7.582000	0.82546	2.548000	0.85928	0.591000	0.81541	GGT	.	.		0.537	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TNC	3371	hgsc.bcm.edu	37	9	117853209	117853209	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:117853209C>A	ENST00000350763.4	-	2	500	c.89G>T	c.(88-90)cGg>cTg	p.R30L	TNC_ENST00000423613.2_Missense_Mutation_p.R30L|TNC_ENST00000345230.3_Missense_Mutation_p.R30L|TNC_ENST00000346706.3_Missense_Mutation_p.R30L|TNC_ENST00000537320.1_Missense_Mutation_p.R30L|TNC_ENST00000340094.3_Missense_Mutation_p.R30L|TNC_ENST00000542877.1_Missense_Mutation_p.R30L|TNC_ENST00000535648.1_Missense_Mutation_p.R30L|TNC_ENST00000341037.4_Missense_Mutation_p.R30L	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	30					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TCGCTTGTGCCGGATGACTTT	0.572																																					p.R30L		Atlas-SNP	.											.	TNC	282	.	0			c.G89T						.						72.0	71.0	71.0					9																	117853209		2203	4300	6503	SO:0001583	missense	3371	exon2			TTGTGCCGGATGA		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.89G>T	chr9.hg19:g.117853209C>A	ENSP00000265131:p.Arg30Leu	71.0	0.0		94.0	4.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	33	5.244959	0.95272	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877;ENST00000534839	T;T;T;T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.58	5.58	0.84498	.	0.056725	0.64402	D	0.000003	T	0.62889	0.2465	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.65717	-0.6100	10	0.87932	D	0	.	18.5353	0.91008	0.0:1.0:0.0:0.0	.	30;30	E9PC84;P24821	.;TENA_HUMAN	L	30	ENSP00000344400:R30L;ENSP00000438152:R30L;ENSP00000344555:R30L;ENSP00000345861:R30L;ENSP00000265131:R30L;ENSP00000339553:R30L;ENSP00000411406:R30L;ENSP00000443478:R30L;ENSP00000442242:R30L;ENSP00000443469:R30L	ENSP00000344400:R30L	R	-	2	0	TNC	116893030	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.640000	0.67875	2.609000	0.88269	0.462000	0.41574	CGG	.	.		0.572	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
OR1K1	392392	hgsc.bcm.edu	37	9	125562726	125562726	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:125562726G>T	ENST00000277309.2	+	1	357	c.325G>T	c.(325-327)Ggg>Tgg	p.G109W		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						CTTTGCCCTGGGGGTAACTGA	0.597																																					p.G109W		Atlas-SNP	.											.	OR1K1	34	.	0			c.G325T						.						107.0	91.0	96.0					9																	125562726		2203	4300	6503	SO:0001583	missense	392392	exon1			GCCCTGGGGGTAA	AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"""GPCR / Class A : Olfactory receptors"""	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.325G>T	chr9.hg19:g.125562726G>T	ENSP00000277309:p.Gly109Trp	51.0	0.0		64.0	4.0	NM_080859	B9EH41|Q4VXB7|Q96R23	Missense_Mutation	SNP	ENST00000277309.2	hg19	CCDS35132.1	.	.	.	.	.	.	.	.	.	.	G	8.813	0.935697	0.18206	.	.	ENSG00000165204	ENST00000277309	T	0.01369	4.97	4.37	0.299	0.15771	GPCR, rhodopsin-like superfamily (1);	0.456308	0.16047	U	0.232155	T	0.09379	0.0231	H	0.94582	3.555	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.07673	-1.0760	10	0.87932	D	0	.	4.7794	0.13195	0.2576:0.2983:0.444:0.0	.	109	Q8NGR3	OR1K1_HUMAN	W	109	ENSP00000277309:G109W	ENSP00000277309:G109W	G	+	1	0	OR1K1	124602547	0.010000	0.17322	0.006000	0.13384	0.073000	0.16967	1.649000	0.37281	-0.120000	0.11809	0.655000	0.94253	GGG	.	.		0.597	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1		
CRB2	286204	hgsc.bcm.edu	37	9	126133645	126133645	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:126133645G>T	ENST00000373631.3	+	8	2225	c.2224G>T	c.(2224-2226)Ggg>Tgg	p.G742W	CRB2_ENST00000359999.3_Missense_Mutation_p.G742W|CRB2_ENST00000373629.2_Missense_Mutation_p.G410W	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	742	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						GCAGGACCTGGGGCAGCACGT	0.692																																					p.G742W		Atlas-SNP	.											.	CRB2	86	.	0			c.G2224T						.						69.0	72.0	71.0					9																	126133645		2203	4299	6502	SO:0001583	missense	286204	exon8			GACCTGGGGCAGC	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.2224G>T	chr9.hg19:g.126133645G>T	ENSP00000362734:p.Gly742Trp	124.0	0.0		143.0	6.0	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	hg19	CCDS6852.2	.	.	.	.	.	.	.	.	.	.	.	18.97	3.735415	0.69189	.	.	ENSG00000148204	ENST00000359999;ENST00000373631;ENST00000373629	T;T;T	0.79940	-1.32;-1.32;-1.32	4.92	3.81	0.43845	Concanavalin A-like lectin/glucanase (1);Laminin G domain (1);	0.341780	0.21813	N	0.068728	D	0.90501	0.7024	M	0.89414	3.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.92209	0.5774	10	0.87932	D	0	.	14.1206	0.65184	0.0866:0.0:0.9134:0.0	.	742;742	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	W	742;742;410	ENSP00000353092:G742W;ENSP00000362734:G742W;ENSP00000362732:G410W	ENSP00000353092:G742W	G	+	1	0	CRB2	125173466	0.998000	0.40836	0.994000	0.49952	0.959000	0.62525	2.542000	0.45744	2.276000	0.75962	0.563000	0.77884	GGG	.	.		0.692	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
WDR38	401551	hgsc.bcm.edu	37	9	127619818	127619818	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:127619818C>A	ENST00000373574.1	+	9	910	c.854C>A	c.(853-855)cCa>cAa	p.P285Q		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	285					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GCCTTCACCCCAGATGGGAAA	0.552																																					p.P286Q		Atlas-SNP	.											.	WDR38	21	.	0			c.C857A						.						82.0	91.0	88.0					9																	127619818		1999	4170	6169	SO:0001583	missense	401551	exon9			TCACCCCAGATGG		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"""WD repeat domain containing"""	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.854C>A	chr9.hg19:g.127619818C>A	ENSP00000362677:p.Pro285Gln	125.0	0.0		108.0	5.0	NM_001276374	A0PK24	Missense_Mutation	SNP	ENST00000373574.1	hg19	CCDS43876.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.474754	0.43942	.	.	ENSG00000136918	ENST00000373574	D	0.84944	-1.92	5.01	2.12	0.27331	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.419228	0.21641	N	0.071336	D	0.89336	0.6686	M	0.81239	2.535	0.31405	N	0.676203	P;P;P;P	0.52577	0.954;0.906;0.906;0.954	P;P;P;P	0.57720	0.826;0.546;0.546;0.826	D	0.87407	0.2373	10	0.66056	D	0.02	.	8.6557	0.34062	0.0:0.6297:0.2894:0.0809	.	285;286;275;285	B9EK65;B7ZW23;B7ZW24;Q5JTN6	.;.;.;WDR38_HUMAN	Q	285	ENSP00000362677:P285Q	ENSP00000362677:P285Q	P	+	2	0	WDR38	126659639	0.082000	0.21442	0.468000	0.27192	0.506000	0.33950	1.737000	0.38197	0.377000	0.24735	-0.165000	0.13383	CCA	.	.		0.552	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476	
CIZ1	25792	hgsc.bcm.edu	37	9	130947925	130947925	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:130947925A>G	ENST00000393608.1	-	5	691	c.489T>C	c.(487-489)ccT>ccC	p.P163P	CIZ1_ENST00000541172.1_Silent_p.P62P|CIZ1_ENST00000372954.1_Silent_p.P139P|CIZ1_ENST00000325721.8_Silent_p.P139P|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000372948.3_Silent_p.P163P|CIZ1_ENST00000538431.1_Silent_p.P163P|CIZ1_ENST00000357558.5_Silent_p.P163P|CIZ1_ENST00000277465.4_Silent_p.P163P|CIZ1_ENST00000372938.5_Silent_p.P163P	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	163					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						CCCCAACAGGAGGAGGTCCCA	0.612																																					p.P193P		Atlas-SNP	.											.	CIZ1	75	.	0			c.T579C						.						65.0	65.0	65.0					9																	130947925		2203	4300	6503	SO:0001819	synonymous_variant	25792	exon5			AACAGGAGGAGGT	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.489T>C	chr9.hg19:g.130947925A>G		125.0	0.0		119.0	5.0	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	hg19	CCDS6894.1																																																																																			.	.		0.612	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
GLE1	2733	hgsc.bcm.edu	37	9	131277857	131277857	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:131277857G>T	ENST00000309971.4	+	3	477	c.371G>T	c.(370-372)cGg>cTg	p.R124L	GLE1_ENST00000539582.1_5'UTR|GLE1_ENST00000372770.4_Missense_Mutation_p.R124L	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	124					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						CAGTCCTCACGGGGGATCAAA	0.428																																					p.R124L		Atlas-SNP	.											.	GLE1	42	.	0			c.G371T						.						68.0	58.0	61.0					9																	131277857		2203	4300	6503	SO:0001583	missense	2733	exon3			CCTCACGGGGGAT	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"""GLE1 (yeast homolog)-like, RNA export mediator"", ""GLE1 RNA export mediator-like (yeast)"", ""GLE1 RNA export mediator (yeast)"", ""lethal congenital contracture syndrome 1"", ""GLE1 RNA export mediator homolog (yeast)"""	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.371G>T	chr9.hg19:g.131277857G>T	ENSP00000308622:p.Arg124Leu	93.0	0.0		51.0	4.0	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	hg19	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.524413	0.64747	.	.	ENSG00000119392	ENST00000309971;ENST00000372770	T;T	0.68903	-0.36;0.05	5.16	4.26	0.50523	.	0.178384	0.47455	D	0.000240	T	0.62853	0.2462	L	0.58101	1.795	0.58432	D	0.999999	P;P	0.44627	0.752;0.839	B;P	0.45276	0.283;0.475	T	0.59500	-0.7443	10	0.29301	T	0.29	-10.662	8.2898	0.31950	0.1817:0.0:0.8183:0.0	.	124;124	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	L	124	ENSP00000308622:R124L;ENSP00000361856:R124L	ENSP00000308622:R124L	R	+	2	0	GLE1	130317678	1.000000	0.71417	0.904000	0.35570	0.879000	0.50718	2.922000	0.48860	1.185000	0.42971	0.313000	0.20887	CGG	.	.		0.428	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722	
GPR107	57720	hgsc.bcm.edu	37	9	132897357	132897357	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:132897357A>G	ENST00000372406.1	+	20	2267	c.1760A>G	c.(1759-1761)aAc>aGc	p.N587S	GPR107_ENST00000372410.3_Missense_Mutation_p.N558S|GPR107_ENST00000347136.6_Missense_Mutation_p.N539S	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	587						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				AAGGTGACCAACGGCTCCGTG	0.493																																					p.N587S		Atlas-SNP	.											.	GPR107	30	.	0			c.A1760G						.						91.0	81.0	85.0					9																	132897357		2203	4300	6503	SO:0001583	missense	57720	exon20			TGACCAACGGCTC	AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358		"""GPCR / Unclassified : 7TM orphan receptors"""	17830	protein-coding gene	gene with protein product							Standard	NM_020960		Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000372406.1:c.1760A>G	chr9.hg19:g.132897357A>G	ENSP00000361483:p.Asn587Ser	46.0	0.0		71.0	5.0	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Missense_Mutation	SNP	ENST00000372406.1	hg19	CCDS48041.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.336884	0.60963	.	.	ENSG00000148358	ENST00000372406;ENST00000347136;ENST00000372410	T;T;T	0.29917	1.79;1.55;1.75	5.34	4.18	0.49190	.	0.062767	0.64402	D	0.000011	T	0.44705	0.1306	L	0.50333	1.59	0.46279	D	0.998964	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.83275	0.996;0.994;0.994	T	0.19353	-1.0308	10	0.27785	T	0.31	-31.4048	9.323	0.37975	0.84:0.0:0.0:0.16	.	558;587;539	G5E994;Q5VW38;Q5VW38-2	.;GP107_HUMAN;.	S	587;539;558	ENSP00000361483:N587S;ENSP00000336988:N539S;ENSP00000361487:N558S	ENSP00000336988:N539S	N	+	2	0	GPR107	131937178	1.000000	0.71417	0.845000	0.33349	0.985000	0.73830	6.669000	0.74462	0.832000	0.34804	0.379000	0.24179	AAC	.	.		0.493	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2		
TTF1	7270	hgsc.bcm.edu	37	9	135277238	135277238	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:135277238G>T	ENST00000334270.2	-	2	1010	c.971C>A	c.(970-972)cCa>cAa	p.P324Q		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	324					chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		AGCAGGTGCTGGTATTCCTGC	0.502																																					p.P324Q		Atlas-SNP	.											.	TTF1	82	.	0			c.C971A						.						102.0	101.0	101.0					9																	135277238		2203	4300	6503	SO:0001583	missense	7270	exon2			GGTGCTGGTATTC	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.971C>A	chr9.hg19:g.135277238G>T	ENSP00000333920:p.Pro324Gln	69.0	0.0		98.0	4.0	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	hg19	CCDS6948.1	.	.	.	.	.	.	.	.	.	.	G	8.526	0.869911	0.17322	.	.	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.09911	2.93	2.64	1.56	0.23342	.	.	.	.	.	T	0.07683	0.0193	L	0.36672	1.1	0.09310	N	1	P	0.48694	0.914	B	0.37731	0.257	T	0.29701	-1.0003	9	0.72032	D	0.01	.	5.9584	0.19286	0.0:0.0:0.6921:0.3079	.	324	Q15361	TTF1_HUMAN	Q	324	ENSP00000333920:P324Q	ENSP00000245588:P324Q	P	-	2	0	TTF1	134267059	0.000000	0.05858	0.005000	0.12908	0.010000	0.07245	0.192000	0.17096	1.158000	0.42547	0.467000	0.42956	CCA	.	.		0.502	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344	
SOHLH1	402381	hgsc.bcm.edu	37	9	138594134	138594134	+	5'Flank	SNP	G	G	T	rs139034501	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:138594134G>T	ENST00000298466.5	-	0	0				SOHLH1_ENST00000425225.1_5'Flank|KCNT1_ENST00000487664.1_Silent_p.P10P|KCNT1_ENST00000371757.2_Silent_p.P10P|KCNT1_ENST00000298480.5_Silent_p.P10P	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1						oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		cgcggaccccggggggcgtct	0.726																																					p.P10P		Atlas-SNP	.											.	KCNT1	139	.	0			c.G30T						.						11.0	15.0	14.0					9																	138594134		2150	4219	6369	SO:0001631	upstream_gene_variant	57582	exon1			GACCCCGGGGGGC	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"""Basic helix-loop-helix proteins"""	27845	protein-coding gene	gene with protein product	"""spermatogenesis associated 27"""	610224	"""chromosome 9 open reading frame 157"""	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915		chr9.hg19:g.138594134G>T	Exception_encountered	96.0	0.0		95.0	4.0	NM_001272003	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	hg19	CCDS35174.1																																																																																			.	G|0.996;A|0.004		0.726	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415	
FBXW5	54461	hgsc.bcm.edu	37	9	139836076	139836076	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:139836076C>A	ENST00000325285.3	-	7	1236	c.1157G>T	c.(1156-1158)cGg>cTg	p.R386L	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	386					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		ATCGGAGCCCCGGCCCTCACC	0.647																																					p.R386L		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1157T						.						66.0	54.0	58.0					9																	139836076		2187	4289	6476	SO:0001583	missense	54461	exon7			GAGCCCCGGCCCT	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.1157G>T	chr9.hg19:g.139836076C>A	ENSP00000313034:p.Arg386Leu	97.0	0.0		124.0	5.0	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	hg19	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898965	0.52227	.	.	ENSG00000159069	ENST00000325285;ENST00000433269	T;T	0.78707	-1.2;1.48	4.61	3.64	0.41730	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);	0.058160	0.64402	D	0.000003	T	0.78027	0.4219	L	0.60455	1.87	0.53688	D	0.999977	D;P	0.57899	0.981;0.945	P;P	0.54815	0.761;0.55	T	0.73968	-0.3815	10	0.25106	T	0.35	-5.1164	7.9241	0.29863	0.0:0.7183:0.1497:0.132	.	251;386	Q59ET5;Q969U6	.;FBXW5_HUMAN	L	386;221	ENSP00000313034:R386L;ENSP00000409102:R221L	ENSP00000313034:R386L	R	-	2	0	FBXW5	138955897	0.989000	0.36119	1.000000	0.80357	0.466000	0.32739	2.646000	0.46630	2.286000	0.76751	0.561000	0.74099	CGG	.	.		0.647	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
NDOR1	27158	hgsc.bcm.edu	37	9	140109380	140109380	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:140109380G>A	ENST00000344894.5	+	8	1058	c.975G>A	c.(973-975)ctG>ctA	p.L325L	NDOR1_ENST00000371521.4_Silent_p.L325L|NDOR1_ENST00000427047.2_Silent_p.L291L|NDOR1_ENST00000458322.2_Silent_p.L325L	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		TCCATGAGCTGGAGCGGGAGA	0.622																																					p.L325L		Atlas-SNP	.											.	NDOR1	71	.	0			c.G975A						.						44.0	48.0	47.0					9																	140109380		2203	4300	6503	SO:0001819	synonymous_variant	27158	exon8			TGAGCTGGAGCGG	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"""NADPH dependent FMN and FAD containing oxidoreductase"""	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.975G>A	chr9.hg19:g.140109380G>A		56.0	0.0		98.0	4.0	NM_001144026		Silent	SNP	ENST00000344894.5	hg19	CCDS7036.1																																																																																			.	.		0.622	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434	
TOR4A	54863	hgsc.bcm.edu	37	9	140173890	140173890	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:140173890T>C	ENST00000357503.2	+	2	945	c.749T>C	c.(748-750)gTg>gCg	p.V250A		NM_017723.2	NP_060193.2	Q9NXH8	TOR4A_HUMAN	torsin family 4, member A	250					chaperone mediated protein folding requiring cofactor (GO:0051085)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)										GTGGCCGACGTGGTGGCGCGG	0.726																																					p.V250A		Atlas-SNP	.											.	.	.	.	0			c.T749C						.						6.0	7.0	6.0					9																	140173890		1995	3865	5860	SO:0001583	missense	54863	exon2			CCGACGTGGTGGC	AK023361	CCDS7041.1	9q34.3	2012-04-03	2012-04-03	2012-04-03	ENSG00000198113	ENSG00000198113			25981	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 167"""	C9orf167			Standard	NM_017723		Approved	FLJ20245	uc004cmn.3	Q9NXH8	OTTHUMG00000131779	ENST00000357503.2:c.749T>C	chr9.hg19:g.140173890T>C	ENSP00000350102:p.Val250Ala	50.0	0.0		62.0	4.0	NM_017723	A2BFA4	Missense_Mutation	SNP	ENST00000357503.2	hg19	CCDS7041.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.254599	0.39896	.	.	ENSG00000198113	ENST00000357503	T	0.48201	0.82	4.95	4.95	0.65309	ATPase, AAA+ type, core (1);	0.139529	0.64402	D	0.000009	T	0.48804	0.1520	L	0.56769	1.78	0.36011	D	0.838041	P	0.48162	0.906	P	0.49085	0.6	T	0.53899	-0.8373	10	0.07990	T	0.79	-15.8208	13.4891	0.61384	0.0:0.0:0.0:1.0	.	250	Q9NXH8	CI167_HUMAN	A	250	ENSP00000350102:V250A	ENSP00000350102:V250A	V	+	2	0	C9orf167	139293711	0.983000	0.35010	0.884000	0.34674	0.005000	0.04900	2.128000	0.42045	1.841000	0.53522	0.529000	0.55759	GTG	.	.		0.726	TOR4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254711.1	NM_017723	
PITRM1	10531	hgsc.bcm.edu	37	10	3208566	3208566	+	Silent	SNP	C	C	T	rs33996077|rs114690446		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:3208566C>T	ENST00000224949.4	-	4	307	c.273G>A	c.(271-273)caG>caA	p.Q91Q	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Silent_p.Q91Q|PITRM1_ENST00000451104.2_Silent_p.Q59Q			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	91					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAGTACGGAACTGCACGCTAG	0.493																																					p.Q91Q		Atlas-SNP	.											PITRM1,colon,carcinoma,-1,3	PITRM1	109	.	0			c.G273A						.						104.0	104.0	104.0					10																	3208566		2070	4185	6255	SO:0001819	synonymous_variant	10531	exon4			ACGGAACTGCACG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.273G>A	chr10.hg19:g.3208566C>T		26.0	1.0		54.0	6.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	hg19	CCDS59208.1																																																																																			.	.		0.493	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
FAM188A	80013	hgsc.bcm.edu	37	10	15883432	15883432	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:15883432T>C	ENST00000277632.3	-	4	622	c.402A>G	c.(400-402)gaA>gaG	p.E134E	FAM188A_ENST00000477891.1_5'UTR	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	134					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						TACAAGAATGTTCCACTTGGC	0.318																																					p.E134E	Pancreas(159;946 1953 2111 4475 22008)	Atlas-SNP	.											.	FAM188A	44	.	0			c.A402G						.						68.0	66.0	67.0					10																	15883432		2203	4300	6503	SO:0001819	synonymous_variant	80013	exon4			AGAATGTTCCACT	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"""caspase recruitment domain containing pro-apoptotic protein"", ""CARD-containing protein"""	611649	"""chromosome 10 open reading frame 97"""	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.402A>G	chr10.hg19:g.15883432T>C		71.0	0.0		90.0	6.0	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Silent	SNP	ENST00000277632.3	hg19	CCDS7110.1																																																																																			.	.		0.318	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948	
CUBN	8029	hgsc.bcm.edu	37	10	17142090	17142090	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:17142090C>G	ENST00000377833.4	-	14	1744	c.1679G>C	c.(1678-1680)aGt>aCt	p.S560T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	560	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCATTGTCACTGCTGAGGAG	0.428																																					p.S560T		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	.	0			c.G1679C						.						115.0	115.0	115.0					10																	17142090		2203	4300	6503	SO:0001583	missense	8029	exon14			TTGTCACTGCTGA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1679G>C	chr10.hg19:g.17142090C>G	ENSP00000367064:p.Ser560Thr	205.0	0.0		264.0	116.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366420	0.61513	.	.	ENSG00000107611	ENST00000377833	T	0.60672	0.17	5.51	5.51	0.81932	CUB (5);	0.000000	0.50627	D	0.000111	T	0.57651	0.2068	L	0.41961	1.31	0.80722	D	1	P	0.38827	0.649	P	0.46940	0.532	T	0.50398	-0.8833	10	0.19590	T	0.45	.	14.894	0.70630	0.0:0.7463:0.2537:0.0	.	560	O60494	CUBN_HUMAN	T	560	ENSP00000367064:S560T	ENSP00000367064:S560T	S	-	2	0	CUBN	17182096	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	3.996000	0.57009	2.586000	0.87340	0.650000	0.86243	AGT	.	.		0.428	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
CAMK2G	818	hgsc.bcm.edu	37	10	75607747	75607747	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:75607747T>C	ENST00000351293.3	-	9	752	c.695A>G	c.(694-696)gAt>gGt	p.D232G	CAMK2G_ENST00000423381.1_Splice_Site_p.D232G|CAMK2G_ENST00000372765.1_Splice_Site_p.D232G|CAMK2G_ENST00000444854.2_Intron|CAMK2G_ENST00000394762.2_Splice_Site_p.D232G|RP11-574K11.8_ENST00000446730.2_RNA|CAMK2G_ENST00000322635.3_Splice_Site_p.D232G|CAMK2G_ENST00000322680.3_Splice_Site_p.D232G|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000305762.7_Splice_Site_p.D232G	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	232	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	GGTCCTTACATCATAGGCTCC	0.567																																					p.D232G		Atlas-SNP	.											.	CAMK2G	79	.	0			c.A695G						.						97.0	90.0	92.0					10																	75607747		2203	4300	6503	SO:0001630	splice_region_variant	818	exon9			CTTACATCATAGG	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"""	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.696+1A>G	chr10.hg19:g.75607747T>C		70.0	0.0		102.0	5.0	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Missense_Mutation	SNP	ENST00000351293.3	hg19	CCDS7336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.90|17.90	3.502198|3.502198	0.64298|0.64298	.|.	.|.	ENSG00000148660|ENSG00000148660	ENST00000351293;ENST00000322635;ENST00000423381;ENST00000394763;ENST00000322680;ENST00000394762;ENST00000433289;ENST00000305762;ENST00000372765|ENST00000441192	T;T;T;T;T;T;T;T|.	0.65916|.	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18|.	5.62|5.62	5.62|5.62	0.85841|0.85841	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.063315|.	0.64402|.	D|.	0.000009|.	T|.	0.54062|.	0.1835|.	N|N	0.25380|0.25380	0.74|0.74	0.80722|0.80722	D|D	1|1	B;B;B;B;B;B;B;B|.	0.32188|.	0.035;0.022;0.028;0.007;0.011;0.001;0.359;0.002|.	B;B;B;B;B;B;B;B|.	0.39258|.	0.203;0.105;0.129;0.01;0.071;0.013;0.295;0.043|.	T|.	0.50825|.	-0.8782|.	10|.	0.87932|.	D|.	0|.	.|.	15.8199|15.8199	0.78631|0.78631	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	224;232;232;232;232;232;232;232|.	B3KY86;Q13555-4;Q13555-6;Q13555-10;A8K6N9;Q13555;Q13555-5;Q13555-8|.	.;.;.;.;.;KCC2G_HUMAN;.;.|.	G|W	232;232;232;232;232;232;167;232;232|10	ENSP00000277853:D232G;ENSP00000315599:D232G;ENSP00000410298:D232G;ENSP00000319060:D232G;ENSP00000378243:D232G;ENSP00000393784:D167G;ENSP00000307082:D232G;ENSP00000361851:D232G|.	ENSP00000307082:D232G|.	D|X	-|-	2|3	0|0	CAMK2G|CAMK2G	75277753|75277753	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	2.133000|2.133000	0.65898|0.65898	0.533000|0.533000	0.62120|0.62120	GAT|TGA	.	.		0.567	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	Missense_Mutation
KAT6B	23522	hgsc.bcm.edu	37	10	76790465	76790465	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:76790465G>A	ENST00000287239.4	+	18	6372	c.5883G>A	c.(5881-5883)atG>atA	p.M1961I	KAT6B_ENST00000372714.1_Missense_Mutation_p.M1669I|KAT6B_ENST00000372724.1_Missense_Mutation_p.M1669I|KAT6B_ENST00000372711.1_Missense_Mutation_p.M1778I|KAT6B_ENST00000372725.1_Missense_Mutation_p.M1669I	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1961	Interaction with RUNX1 and RUNX2.|Met-rich.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CTTTAACGATGCAAAGAGGCA	0.527																																					p.M1961I		Atlas-SNP	.											.	.	.	.	0			c.G5883A						.						150.0	142.0	145.0					10																	76790465		2203	4300	6503	SO:0001583	missense	23522	exon18			AACGATGCAAAGA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.5883G>A	chr10.hg19:g.76790465G>A	ENSP00000287239:p.Met1961Ile	48.0	0.0		84.0	4.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.969524	0.34754	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.75938	-0.97;-0.97;-0.98;-0.97;-0.97	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000009	T	0.72326	0.3446	N	0.14661	0.345	0.48571	D	0.99967	P;P;B	0.44281	0.831;0.794;0.447	P;B;B	0.54664	0.758;0.406;0.212	T	0.75961	-0.3133	10	0.62326	D	0.03	-10.6573	15.3019	0.73958	0.0:0.1395:0.8605:0.0	.	1778;1669;1961	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	I	1669;1669;1961;1669;1778	ENSP00000361810:M1669I;ENSP00000361809:M1669I;ENSP00000287239:M1961I;ENSP00000361799:M1669I;ENSP00000361796:M1778I	ENSP00000287239:M1961I	M	+	3	0	KAT6B	76460471	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.328000	0.79160	2.682000	0.91365	0.563000	0.77884	ATG	.	.		0.527	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
COMTD1	118881	hgsc.bcm.edu	37	10	76995129	76995129	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:76995129A>G	ENST00000372538.3	-	3	306	c.224T>C	c.(223-225)cTg>cCg	p.L75P	COMTD1_ENST00000460899.1_5'UTR	NM_144589.2	NP_653190.2	Q86VU5	CMTD1_HUMAN	catechol-O-methyltransferase domain containing 1	75						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	O-methyltransferase activity (GO:0008171)			central_nervous_system(1)|large_intestine(1)|lung(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)					CTCCAGGGTCAGCTGCGTGAA	0.687																																					p.L75P	Colon(106;1192 2596 47278)	Atlas-SNP	.											.	COMTD1	6	.	0			c.T224C						.						7.0	9.0	8.0					10																	76995129		2130	4233	6363	SO:0001630	splice_region_variant	118881	exon3			AGGGTCAGCTGCG		CCDS7349.1	10q22.2	2013-09-20			ENSG00000165644	ENSG00000165644			26309	protein-coding gene	gene with protein product						12975309	Standard	NM_144589		Approved	FLJ23841	uc001jxb.3	Q86VU5	OTTHUMG00000018518	ENST00000372538.3:c.223-1T>C	chr10.hg19:g.76995129A>G		28.0	0.0		38.0	4.0	NM_144589	Q8TE79	Missense_Mutation	SNP	ENST00000372538.3	hg19	CCDS7349.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893335	0.72524	.	.	ENSG00000165644	ENST00000536650;ENST00000372538	T	0.23552	1.9	5.18	5.18	0.71444	.	0.081681	0.49305	D	0.000149	T	0.44787	0.1310	M	0.73962	2.25	0.80722	D	1	D	0.64830	0.994	P	0.60682	0.878	T	0.35822	-0.9773	10	0.33141	T	0.24	-16.9948	11.4178	0.49962	1.0:0.0:0.0:0.0	.	75	Q86VU5	CMTD1_HUMAN	P	75	ENSP00000361616:L75P	ENSP00000361616:L75P	L	-	2	0	COMTD1	76665135	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.145000	0.50623	1.942000	0.56320	0.379000	0.24179	CTG	.	.		0.687	COMTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048802.1	NM_144589	Missense_Mutation
DLG5	9231	hgsc.bcm.edu	37	10	79614037	79614037	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:79614037T>C	ENST00000372391.2	-	4	633	c.628A>G	c.(628-630)Acc>Gcc	p.T210A	DLG5_ENST00000372388.2_Missense_Mutation_p.T210A	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	210					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			AAGGCGTTGGTGTGCTGGTTC	0.602																																					p.T210A		Atlas-SNP	.											.	DLG5	154	.	0			c.A628G						.						106.0	78.0	88.0					10																	79614037		2203	4300	6503	SO:0001583	missense	9231	exon4			CGTTGGTGTGCTG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.628A>G	chr10.hg19:g.79614037T>C	ENSP00000361467:p.Thr210Ala	71.0	0.0		98.0	4.0	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	hg19	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	T	17.58	3.425876	0.62733	.	.	ENSG00000151208	ENST00000372391;ENST00000372388	T;T	0.44482	0.92;0.92	5.55	5.55	0.83447	.	0.000000	0.38164	N	0.001794	T	0.27489	0.0675	L	0.31294	0.92	0.32367	N	0.556406	P	0.34977	0.478	B	0.31390	0.129	T	0.35773	-0.9775	10	0.19590	T	0.45	.	10.105	0.42528	0.0:0.0747:0.0:0.9253	.	210	Q8TDM6	DLG5_HUMAN	A	210	ENSP00000361467:T210A;ENSP00000361464:T210A	ENSP00000361464:T210A	T	-	1	0	DLG5	79284043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.994000	0.56994	2.111000	0.64477	0.533000	0.62120	ACC	.	.		0.602	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
LIPA	3988	hgsc.bcm.edu	37	10	90974647	90974647	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:90974647C>A	ENST00000336233.5	-	10	1460	c.1138G>T	c.(1138-1140)Ggc>Tgc	p.G380C	LIPA_ENST00000371837.1_Missense_Mutation_p.G324C|LIPA_ENST00000456827.1_Missense_Mutation_p.G380C			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	380					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)			endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		GCATCCAGGCCCCAAATGAAG	0.428																																					p.G380C		Atlas-SNP	.											.	LIPA	29	.	0			c.G1138T						.						56.0	55.0	56.0					10																	90974647		2203	4300	6503	SO:0001583	missense	3988	exon10			CCAGGCCCCAAAT	M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"""Wolman disease"""	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.1138G>T	chr10.hg19:g.90974647C>A	ENSP00000337354:p.Gly380Cys	57.0	0.0		95.0	4.0	NM_000235	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Missense_Mutation	SNP	ENST00000336233.5	hg19	CCDS7401.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.323546	0.81580	.	.	ENSG00000107798	ENST00000336233;ENST00000371837;ENST00000371829;ENST00000541980;ENST00000354621;ENST00000456827;ENST00000425287	T;T;T	0.72615	-0.67;-0.67;-0.67	5.08	5.08	0.68730	Alpha/beta hydrolase fold-1 (1);	0.000000	0.85682	D	0.000000	D	0.90376	0.6988	H	0.97983	4.12	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.93551	0.6886	10	0.87932	D	0	-25.2992	18.018	0.89247	0.0:1.0:0.0:0.0	.	382;324;380	E7EUT7;P38571-2;P38571	.;.;LICH_HUMAN	C	380;324;380;380;338;380;382	ENSP00000337354:G380C;ENSP00000360903:G324C;ENSP00000413019:G380C	ENSP00000337354:G380C	G	-	1	0	LIPA	90964627	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	6.929000	0.75852	2.802000	0.96397	0.563000	0.77884	GGC	.	.		0.428	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235	
CEP55	55165	hgsc.bcm.edu	37	10	95275260	95275260	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:95275260G>T	ENST00000371485.3	+	5	931	c.627G>T	c.(625-627)acG>acT	p.T209T		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	209	Interaction with PDCD6IP.|Interaction with TSG101.				establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				AAAAGAAAACGGAAACAGCTG	0.428																																					p.T209T		Atlas-SNP	.											.	CEP55	35	.	0			c.G627T						.						90.0	97.0	95.0					10																	95275260		2203	4300	6503	SO:0001819	synonymous_variant	55165	exon5			GAAAACGGAAACA	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"""cancer/testis antigen 111"""	610000	"""chromosome 10 open reading frame 3"""	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.627G>T	chr10.hg19:g.95275260G>T		111.0	0.0		148.0	6.0	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Silent	SNP	ENST00000371485.3	hg19	CCDS7428.1	.	.	.	.	.	.	.	.	.	.	G	6.531	0.466146	0.12402	.	.	ENSG00000138180	ENST00000445435	.	.	.	5.15	-1.78	0.07957	.	.	.	.	.	T	0.58495	0.2126	.	.	.	0.42839	D	0.994042	.	.	.	.	.	.	T	0.57528	-0.7796	4	.	.	.	0.731	12.3702	0.55250	0.7186:0.0:0.2814:0.0	.	.	.	.	L	49	.	.	R	+	2	0	CEP55	95265250	0.001000	0.12720	0.816000	0.32577	0.858000	0.48976	-0.134000	0.10436	-0.200000	0.10300	0.655000	0.94253	CGG	.	.		0.428	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
C10orf12	26148	hgsc.bcm.edu	37	10	98741962	98741962	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:98741962T>C	ENST00000286067.2	+	1	922	c.815T>C	c.(814-816)gTt>gCt	p.V272A		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	272										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GGTGGAGACGTTTCACCTCGA	0.532																																					p.V272A		Atlas-SNP	.											.	C10orf12	94	.	0			c.T815C						.						85.0	87.0	86.0					10																	98741962		2203	4300	6503	SO:0001583	missense	26148	exon1			GAGACGTTTCACC	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.815T>C	chr10.hg19:g.98741962T>C	ENSP00000286067:p.Val272Ala	86.0	0.0		108.0	6.0	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.684454	0.00745	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.06142	3.34	6.05	2.0	0.26442	.	1.252050	0.05965	N	0.641308	T	0.02418	0.0074	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42413	-0.9453	10	0.02654	T	1	0.2746	1.7815	0.03032	0.1436:0.4815:0.1393:0.2357	.	106;272	A0PJI9;Q8N655	.;CJ012_HUMAN	A	272;106	ENSP00000286067:V272A	ENSP00000286067:V272A	V	+	2	0	C10orf12	98731952	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-0.470000	0.06639	0.102000	0.17638	0.533000	0.62120	GTT	.	.		0.532	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
RRP12	23223	hgsc.bcm.edu	37	10	99150246	99150246	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:99150246C>A	ENST00000370992.4	-	6	798	c.687G>T	c.(685-687)tgG>tgT	p.W229C	RRP12_ENST00000315563.6_Intron|RRP12_ENST00000414986.1_Missense_Mutation_p.W168C|RRP12_ENST00000536831.1_Missense_Mutation_p.W35C	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	229						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CGGGGTAGCCCCAGGCCTCCA	0.607																																					p.W229C		Atlas-SNP	.											.	RRP12	97	.	0			c.G687T						.						52.0	51.0	52.0					10																	99150246		2203	4300	6503	SO:0001583	missense	23223	exon6			GTAGCCCCAGGCC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.687G>T	chr10.hg19:g.99150246C>A	ENSP00000360031:p.Trp229Cys	52.0	0.0		57.0	4.0	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131751	0.77662	.	.	ENSG00000052749	ENST00000370992;ENST00000414986;ENST00000536831	T;T;T	0.69435	-0.15;-0.15;-0.4	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.054484	0.85682	D	0.000000	D	0.84588	0.5505	M	0.85197	2.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.86643	0.1893	10	0.87932	D	0	-13.0765	19.4752	0.94985	0.0:1.0:0.0:0.0	.	168;35;229	E9PCK7;F5H456;Q5JTH9	.;.;RRP12_HUMAN	C	229;168;35	ENSP00000360031:W229C;ENSP00000414863:W168C;ENSP00000446184:W35C	ENSP00000360031:W229C	W	-	3	0	RRP12	99140236	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	7.729000	0.84864	2.596000	0.87737	0.650000	0.86243	TGG	.	.		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
SCD	6319	hgsc.bcm.edu	37	10	102112216	102112216	+	Missense_Mutation	SNP	G	G	T	rs145182376		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:102112216G>T	ENST00000370355.2	+	3	785	c.404G>T	c.(403-405)cGg>cTg	p.R135L		NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	135					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		CTGCCCCTACGGCTCTTTCTG	0.512																																					p.R135L	Colon(67;260 1459 9574 11663)	Atlas-SNP	.											.	SCD	25	.	0			c.G404T						.						144.0	139.0	140.0					10																	102112216		2203	4300	6503	SO:0001583	missense	6319	exon3			CCCTACGGCTCTT	AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"""Fatty acid desaturases"""	10571	protein-coding gene	gene with protein product	"""acyl-CoA desaturase"", ""fatty acid desaturase"", ""delta-9-desaturase"""	604031	"""stearoyl-CoA desaturase opposite strand"""	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.404G>T	chr10.hg19:g.102112216G>T	ENSP00000359380:p.Arg135Leu	68.0	0.0		97.0	4.0	NM_005063	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	Missense_Mutation	SNP	ENST00000370355.2	hg19	CCDS7493.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099752	0.76983	.	.	ENSG00000099194	ENST00000423840;ENST00000370355	T	0.16743	2.32	5.24	5.24	0.73138	Fatty acid desaturase, type 1 (1);	0.000000	0.56097	D	0.000022	T	0.59662	0.2210	H	0.97365	3.99	0.58432	D	0.999993	D	0.65815	0.995	D	0.74023	0.982	T	0.76135	-0.3070	10	0.87932	D	0	-26.3907	18.8237	0.92108	0.0:0.0:1.0:0.0	.	135	O00767	ACOD_HUMAN	L	135	ENSP00000359380:R135L	ENSP00000359380:R135L	R	+	2	0	SCD	102102206	0.928000	0.31464	0.615000	0.29064	0.233000	0.25261	4.858000	0.62947	2.469000	0.83416	0.561000	0.74099	CGG	.	G|1.000;A|0.000		0.512	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049857.2	NM_005063	
BTRC	8945	hgsc.bcm.edu	37	10	103281409	103281409	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:103281409A>T	ENST00000370187.3	+	5	456	c.338A>T	c.(337-339)aAt>aTt	p.N113I	BTRC_ENST00000393441.4_Missense_Mutation_p.N72I|BTRC_ENST00000408038.2_Missense_Mutation_p.N77I	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	113					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		AAACTTGCCAATGGCACTTCC	0.378																																					p.N113I		Atlas-SNP	.											.	BTRC	64	.	0			c.A338T						.						72.0	68.0	69.0					10																	103281409		2203	4300	6503	SO:0001583	missense	8945	exon5			TTGCCAATGGCAC	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1144	protein-coding gene	gene with protein product		603482	"""beta-transducin repeat containing"""			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.338A>T	chr10.hg19:g.103281409A>T	ENSP00000359206:p.Asn113Ile	100.0	0.0		148.0	53.0	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.752726	0.49362	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038;ENST00000370183	T;T;T	0.60920	0.3;0.29;0.15	5.6	5.6	0.85130	.	0.137255	0.50627	D	0.000112	T	0.48660	0.1512	L	0.29908	0.895	0.38130	D	0.938118	B;B;B	0.16396	0.001;0.0;0.017	B;B;B	0.12156	0.005;0.003;0.007	T	0.50355	-0.8838	10	0.62326	D	0.03	-17.033	16.1249	0.81386	1.0:0.0:0.0:0.0	.	87;77;113	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	I	113;72;77;95	ENSP00000359206:N113I;ENSP00000377088:N72I;ENSP00000385339:N77I	ENSP00000359202:N95I	N	+	2	0	BTRC	103271399	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.547000	0.90665	2.262000	0.75019	0.529000	0.55759	AAT	.	.		0.378	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637	
CYP17A1	1586	hgsc.bcm.edu	37	10	104590471	104590471	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:104590471C>A	ENST00000369887.3	-	8	1686	c.1515G>T	c.(1513-1515)gaG>gaT	p.E505D	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'Flank	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	505					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	AGGTGCTACCCTCAGCCTGGG	0.562																																					p.E505D		Atlas-SNP	.											.	CYP17A1	48	.	0			c.G1515T						.						25.0	26.0	26.0					10																	104590471		2203	4300	6503	SO:0001583	missense	1586	exon8			GCTACCCTCAGCC	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"""Cytochrome P450s"""	2593	protein-coding gene	gene with protein product	"""Steroid 17-alpha-monooxygenase"""	609300	"""cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"""	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.1515G>T	chr10.hg19:g.104590471C>A	ENSP00000358903:p.Glu505Asp	73.0	0.0		92.0	4.0	NM_000102	Q5TZV7	Missense_Mutation	SNP	ENST00000369887.3	hg19	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.767519	0.49574	.	.	ENSG00000148795	ENST00000369887	T	0.69306	-0.39	5.31	2.36	0.29203	.	0.832824	0.11132	N	0.596157	T	0.42314	0.1197	N	0.08118	0	0.09310	N	1	B	0.30511	0.282	B	0.24394	0.053	T	0.28996	-1.0026	10	0.51188	T	0.08	.	7.1653	0.25687	0.0:0.5752:0.3354:0.0894	.	505	P05093	CP17A_HUMAN	D	505	ENSP00000358903:E505D	ENSP00000358903:E505D	E	-	3	2	CYP17A1	104580461	0.077000	0.21312	0.137000	0.22149	0.571000	0.35966	0.510000	0.22723	0.711000	0.32018	-0.225000	0.12378	GAG	.	.		0.562	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102	
GFRA1	2674	hgsc.bcm.edu	37	10	117853332	117853332	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:117853332G>T	ENST00000355422.6	-	8	1446	c.896C>A	c.(895-897)cCc>cAc	p.P299H	GFRA1_ENST00000369236.1_Missense_Mutation_p.P294H|GFRA1_ENST00000439649.3_Missense_Mutation_p.P294H|GFRA1_ENST00000544592.1_Missense_Mutation_p.P178H	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	299					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		TATGTAGTTGGGGGTCATGAC	0.423																																					p.P299H	Ovarian(128;329 1725 45498 46808 50759)	Atlas-SNP	.											.	GFRA1	107	.	0			c.C896A						.						80.0	77.0	78.0					10																	117853332		2203	4300	6503	SO:0001583	missense	2674	exon8			TAGTTGGGGGTCA	AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.896C>A	chr10.hg19:g.117853332G>T	ENSP00000347591:p.Pro299His	101.0	0.0		123.0	5.0	NM_005264	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	hg19	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.719313	0.89205	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T	0.65916	-0.18;-0.18	5.98	5.98	0.97165	GDNF/GAS1 (2);	0.000000	0.85682	D	0.000000	D	0.83344	0.5234	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84862	0.0820	10	0.87932	D	0	-27.5613	20.4366	0.99092	0.0:0.0:1.0:0.0	.	299;294	P56159;P56159-2	GFRA1_HUMAN;.	H	299;294;294;178;294	ENSP00000358239:P294H;ENSP00000442179:P178H	ENSP00000347591:P294H	P	-	2	0	GFRA1	117843322	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	9.033000	0.93741	2.837000	0.97791	0.591000	0.81541	CCC	.	.		0.423	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793	
MCMBP	79892	hgsc.bcm.edu	37	10	121608999	121608999	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:121608999A>G	ENST00000360003.3	-	7	833	c.664T>C	c.(664-666)Tct>Cct	p.S222P	MCMBP_ENST00000466047.1_5'UTR|MCMBP_ENST00000369077.3_Missense_Mutation_p.S222P	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	222					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						AAAGGAGAAGACAAGTTCAGA	0.423																																					p.S222P		Atlas-SNP	.											.	MCMBP	49	.	0			c.T664C						.						122.0	110.0	114.0					10																	121608999		2203	4300	6503	SO:0001583	missense	79892	exon7			GAGAAGACAAGTT	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.664T>C	chr10.hg19:g.121608999A>G	ENSP00000353098:p.Ser222Pro	51.0	0.0		94.0	4.0	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Missense_Mutation	SNP	ENST00000360003.3	hg19	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.707718	0.48412	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	T;T	0.53857	0.6;0.6	5.52	4.32	0.51571	.	0.135013	0.51477	D	0.000083	T	0.41880	0.1178	L	0.42245	1.32	0.47009	D	0.999282	P;P	0.46220	0.874;0.8	B;B	0.38616	0.277;0.143	T	0.33240	-0.9876	10	0.30854	T	0.27	-4.2227	12.3622	0.55209	0.8739:0.0:0.0:0.126	.	222;222	Q9BTE3-2;Q9BTE3	.;MCMBP_HUMAN	P	222	ENSP00000353098:S222P;ENSP00000358073:S222P	ENSP00000353098:S222P	S	-	1	0	MCMBP	121598989	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.001000	0.57046	2.228000	0.72767	0.533000	0.62120	TCT	.	.		0.423	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
TACC2	10579	hgsc.bcm.edu	37	10	123845759	123845759	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:123845759A>G	ENST00000369005.1	+	4	4084	c.3744A>G	c.(3742-3744)gcA>gcG	p.A1248A	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.A1248A|TACC2_ENST00000453444.2_Silent_p.A1248A|TACC2_ENST00000515273.1_Silent_p.A1248A|TACC2_ENST00000334433.3_Silent_p.A1248A|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1248					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AGAGAGGAGCAGAAGACAGTG	0.597																																					p.A1248A		Atlas-SNP	.											.	TACC2	271	.	0			c.A3744G						.						84.0	92.0	89.0					10																	123845759		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			AGGAGCAGAAGAC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3744A>G	chr10.hg19:g.123845759A>G		64.0	0.0		84.0	4.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.597	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
TACC2	10579	hgsc.bcm.edu	37	10	123848021	123848021	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:123848021T>C	ENST00000369005.1	+	5	5828	c.5488T>C	c.(5488-5490)Tta>Cta	p.L1830L	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.L1830L|TACC2_ENST00000453444.2_Silent_p.L1830L|TACC2_ENST00000515273.1_Silent_p.L1830L|TACC2_ENST00000334433.3_Silent_p.L1830L|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1830					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCCATCCATGTTACCTTCGGT	0.438																																					p.L1830L		Atlas-SNP	.											.	TACC2	271	.	0			c.T5488C						.						59.0	52.0	54.0					10																	123848021		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon5			TCCATGTTACCTT	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5488T>C	chr10.hg19:g.123848021T>C		100.0	0.0		143.0	6.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.438	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
TACC2	10579	hgsc.bcm.edu	37	10	123996925	123996925	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:123996925C>A	ENST00000369005.1	+	17	8483	c.8143C>A	c.(8143-8145)Cca>Aca	p.P2715T	TACC2_ENST00000369001.1_Missense_Mutation_p.P342T|TACC2_ENST00000358010.1_Missense_Mutation_p.P861T|TACC2_ENST00000260733.3_Missense_Mutation_p.P793T|TACC2_ENST00000515603.1_Missense_Mutation_p.P2593T|TACC2_ENST00000453444.2_Missense_Mutation_p.P2642T|TACC2_ENST00000515273.1_Missense_Mutation_p.P2642T|TACC2_ENST00000369000.1_Missense_Mutation_p.P338T|TACC2_ENST00000334433.3_Missense_Mutation_p.P2715T|TACC2_ENST00000513429.1_Missense_Mutation_p.P861T|TACC2_ENST00000369004.3_Missense_Mutation_p.P775T|TACC2_ENST00000368999.1_Missense_Mutation_p.P805T|TACC2_ENST00000360561.3_Missense_Mutation_p.P763T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2715					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GGCTGCTCACCCAACAGACGT	0.488																																					p.P2715T		Atlas-SNP	.											.	TACC2	271	.	0			c.C8143A						.						42.0	43.0	43.0					10																	123996925		2203	4300	6503	SO:0001583	missense	10579	exon17			GCTCACCCAACAG	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.8143C>A	chr10.hg19:g.123996925C>A	ENSP00000358001:p.Pro2715Thr	52.0	0.0		87.0	4.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.418832	0.62622	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000496913	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.22539	3.81;3.48;3.85;3.79;3.81;3.48;3.85;1.96;1.95;3.34;3.35;3.34;3.35;2.01	4.93	4.93	0.64822	.	0.000000	0.34777	N	0.003693	T	0.29158	0.0725	L	0.29908	0.895	0.40157	D	0.977016	D;P;D;D;P;P;P;P;D	0.56521	0.976;0.848;0.976;0.976;0.746;0.746;0.941;0.894;0.976	P;P;P;D;P;P;P;P;D	0.64506	0.877;0.521;0.877;0.926;0.487;0.557;0.761;0.688;0.909	T	0.01791	-1.1273	10	0.30078	T	0.28	-8.7553	11.2233	0.48869	0.0:0.9147:0.0:0.0853	.	2642;775;2593;2642;763;793;338;861;2715	E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	T	2715;861;2642;2593;2715;861;2642;2628;342;338;763;805;775;793;373	ENSP00000358001:P2715T;ENSP00000425062:P861T;ENSP00000424467:P2642T;ENSP00000427618:P2593T;ENSP00000334280:P2715T;ENSP00000350701:P861T;ENSP00000395048:P2642T;ENSP00000357997:P342T;ENSP00000357996:P338T;ENSP00000353763:P763T;ENSP00000357995:P805T;ENSP00000422815:P775T;ENSP00000260733:P793T;ENSP00000422725:P373T	ENSP00000260733:P793T	P	+	1	0	TACC2	123986915	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	1.815000	0.38981	2.431000	0.82371	0.655000	0.94253	CCA	.	.		0.488	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
KNDC1	85442	hgsc.bcm.edu	37	10	135025267	135025267	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr10:135025267G>T	ENST00000304613.3	+	23	4162	c.4141G>T	c.(4141-4143)Ggc>Tgc	p.G1381C	KNDC1_ENST00000368572.2_Missense_Mutation_p.G1383C			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1381					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.G1381C(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CAACCCTCGCGGCACAGACCT	0.662																																					p.G1381C		Atlas-SNP	.											KNDC1,NS,carcinoma,0,1	KNDC1	155	.	1	Substitution - Missense(1)	lung(1)	c.G4141T						.						39.0	39.0	39.0					10																	135025267		2202	4299	6501	SO:0001583	missense	85442	exon23			CCTCGCGGCACAG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.4141G>T	chr10.hg19:g.135025267G>T	ENSP00000304437:p.Gly1381Cys	44.0	0.0		89.0	4.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	0.834	-0.744189	0.03065	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.30981	1.51;1.51	3.34	-2.44	0.06502	Ras guanine nucleotide exchange factor, domain (1);	1.176820	0.06429	U	0.723675	T	0.19208	0.0461	N	0.14661	0.345	0.09310	N	1	B	0.25609	0.13	B	0.22386	0.039	T	0.25916	-1.0118	10	0.37606	T	0.19	-10.3462	12.5612	0.56281	0.1245:0.0:0.8755:0.0	.	1381	Q76NI1	VKIND_HUMAN	C	1381;1383	ENSP00000304437:G1381C;ENSP00000357561:G1383C	ENSP00000304437:G1381C	G	+	1	0	KNDC1	134875257	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.307000	0.08167	-1.014000	0.03379	-2.027000	0.00425	GGC	.	.		0.662	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
ATHL1	80162	hgsc.bcm.edu	37	11	292027	292027	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:292027G>A	ENST00000409548.2	+	5	1073	c.958G>A	c.(958-960)Gcc>Acc	p.A320T	ATHL1_ENST00000409479.1_Missense_Mutation_p.A320T|ATHL1_ENST00000409655.1_Missense_Mutation_p.A143T	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	320					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGCCGCCAGGGCCATCCTGGA	0.667																																					p.A320T		Atlas-SNP	.											.	ATHL1	88	.	0			c.G958A						.						56.0	46.0	49.0					11																	292027		2202	4297	6499	SO:0001583	missense	80162	exon5			GCCAGGGCCATCC	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.958G>A	chr11.hg19:g.292027G>A	ENSP00000387185:p.Ala320Thr	78.0	0.0		55.0	4.0	NM_025092	Q658X8|Q8TEG9|Q9H635	Missense_Mutation	SNP	ENST00000409548.2	hg19	CCDS31322.2	.	.	.	.	.	.	.	.	.	.	g	16.03	3.005962	0.54361	.	.	ENSG00000142102	ENST00000409548;ENST00000409655;ENST00000409479	.	.	.	4.45	3.29	0.37713	Glycoside hydrolase, family 65, central catalytic (1);Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.353127	0.28230	N	0.016106	T	0.47525	0.1450	L	0.45470	1.425	0.31428	N	0.673523	P;P;B	0.46064	0.774;0.872;0.232	P;P;B	0.52031	0.688;0.593;0.172	T	0.49899	-0.8890	9	0.30078	T	0.28	.	8.2845	0.31920	0.1031:0.1623:0.7346:0.0	.	320;320;143	Q32M88;E7EMA9;B8ZZ60	ATHL1_HUMAN;.;.	T	320;143;320	.	ENSP00000387099:A320T	A	+	1	0	ATHL1	282027	0.571000	0.26659	1.000000	0.80357	0.721000	0.41392	2.193000	0.42658	2.031000	0.59945	0.457000	0.33378	GCC	.	.		0.667	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
B4GALNT4	338707	hgsc.bcm.edu	37	11	377296	377296	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:377296T>C	ENST00000329962.6	+	14	2173	c.2173T>C	c.(2173-2175)Tac>Cac	p.Y725H		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	725					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GACCGCTCAGTACATGGAGCG	0.701																																					p.Y725H		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.T2173C						.						14.0	9.0	11.0					11																	377296		2045	4051	6096	SO:0001583	missense	338707	exon14			GCTCAGTACATGG	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2173T>C	chr11.hg19:g.377296T>C	ENSP00000328277:p.Tyr725His	79.0	0.0		91.0	4.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	t	16.11	3.031147	0.54790	.	.	ENSG00000182272	ENST00000329962	T	0.15139	2.45	3.28	3.28	0.37604	.	0.081321	0.51477	D	0.000094	T	0.37183	0.0994	M	0.68952	2.095	0.47659	D	0.99948	D	0.69078	0.997	D	0.79784	0.993	T	0.19844	-1.0293	10	0.59425	D	0.04	-27.5924	12.0889	0.53713	0.0:0.0:0.0:1.0	.	725	Q76KP1	B4GN4_HUMAN	H	725	ENSP00000328277:Y725H	ENSP00000328277:Y725H	Y	+	1	0	B4GALNT4	367296	1.000000	0.71417	1.000000	0.80357	0.083000	0.17756	7.329000	0.79170	1.508000	0.48769	0.172000	0.16884	TAC	.	.		0.701	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
SIGIRR	59307	hgsc.bcm.edu	37	11	407512	407512	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:407512A>G	ENST00000431843.2	-	6	844	c.538T>C	c.(538-540)Ttc>Ctc	p.F180L	SIGIRR_ENST00000397632.3_Missense_Mutation_p.F180L|SIGIRR_ENST00000531205.1_Missense_Mutation_p.F180L|SIGIRR_ENST00000382520.2_Missense_Mutation_p.F180L|SIGIRR_ENST00000529486.1_5'UTR|SIGIRR_ENST00000332725.3_Missense_Mutation_p.F180L	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	180	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGTTCACGAACTTGCGGTCC	0.677																																					p.F180L		Atlas-SNP	.											.	SIGIRR	22	.	0			c.T538C						.						26.0	26.0	26.0					11																	407512		2188	4289	6477	SO:0001583	missense	59307	exon6			TCACGAACTTGCG		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30575	protein-coding gene	gene with protein product	"""single immunoglobulin domain IL1R1 related"""	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.538T>C	chr11.hg19:g.407512A>G	ENSP00000403104:p.Phe180Leu	132.0	0.0		167.0	7.0	NM_001135053	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	hg19	CCDS31325.1	.	.	.	.	.	.	.	.	.	.	a	16.69	3.193513	0.58017	.	.	ENSG00000185187	ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520;ENST00000528209;ENST00000530494	T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92	2.75	2.75	0.32379	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.063235	0.64402	D	0.000004	T	0.28928	0.0718	M	0.78344	2.41	0.80722	D	1	P;B	0.42296	0.775;0.362	B;B	0.39660	0.306;0.166	T	0.15178	-1.0446	10	0.40728	T	0.16	.	10.2759	0.43510	1.0:0.0:0.0:0.0	.	180;180	C9JFX4;Q6IA17	.;SIGIR_HUMAN	L	180;180;180;180;180;76;124	ENSP00000403104:F180L;ENSP00000380756:F180L;ENSP00000333656:F180L;ENSP00000433022:F180L;ENSP00000371960:F180L;ENSP00000435135:F76L	ENSP00000333656:F180L	F	-	1	0	SIGIRR	397512	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	5.558000	0.67319	1.525000	0.49052	0.240000	0.17902	TTC	.	.		0.677	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805	
LRRC56	115399	hgsc.bcm.edu	37	11	540775	540775	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:540775C>T	ENST00000270115.7	+	4	591	c.91C>T	c.(91-93)Ccc>Tcc	p.P31S		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	31										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCTGCACAACCCCTGCCCACA	0.662																																					p.P31S		Atlas-SNP	.											.	LRRC56	23	.	0			c.C91T						.						50.0	46.0	47.0					11																	540775		2200	4299	6499	SO:0001583	missense	115399	exon4			CACAACCCCTGCC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.91C>T	chr11.hg19:g.540775C>T	ENSP00000270115:p.Pro31Ser	67.0	0.0		69.0	4.0	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	hg19	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	c	23.1	4.372993	0.82573	.	.	ENSG00000161328	ENST00000270115	T	0.41065	1.01	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	T	0.63768	0.2539	M	0.70275	2.135	0.38924	D	0.957805	D	0.89917	1.0	D	0.91635	0.999	T	0.69075	-0.5241	10	0.59425	D	0.04	-11.9051	15.5375	0.76016	0.0:1.0:0.0:0.0	.	31	Q8IYG6	LRC56_HUMAN	S	31	ENSP00000270115:P31S	ENSP00000270115:P31S	P	+	1	0	LRRC56	530775	0.697000	0.27767	1.000000	0.80357	0.940000	0.58332	1.652000	0.37313	2.287000	0.76781	0.556000	0.70494	CCC	.	.		0.662	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
TH	7054	hgsc.bcm.edu	37	11	2190970	2190970	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:2190970C>T	ENST00000381178.1	-	3	333	c.315G>A	c.(313-315)gaG>gaA	p.E105E	TH_ENST00000333684.5_Silent_p.E78E|TH_ENST00000352909.3_Silent_p.E74E|TH_ENST00000381175.1_Silent_p.E101E	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	105					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCTCCTTCTCCTCAAAGGCCA	0.687																																					p.E105E		Atlas-SNP	.											.	TH	43	.	0			c.G315A						.						41.0	42.0	42.0					11																	2190970		2202	4299	6501	SO:0001819	synonymous_variant	7054	exon3			CTTCTCCTCAAAG	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.315G>A	chr11.hg19:g.2190970C>T		197.0	0.0		155.0	86.0	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	hg19	CCDS7731.1																																																																																			.	.		0.687	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
ART1	417	hgsc.bcm.edu	37	11	3681383	3681383	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:3681383C>T	ENST00000250693.1	+	3	735	c.634C>T	c.(634-636)Cag>Tag	p.Q212*		NM_004314.2	NP_004305.2	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1	212					innate immune response (GO:0045087)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|skin(1)	8		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)		TGCAGCCCAGCAGTTTGGTGA	0.652																																					p.Q212X		Atlas-SNP	.											.	ART1	21	.	0			c.C634T						.						41.0	38.0	39.0					11																	3681383		2201	4298	6499	SO:0001587	stop_gained	417	exon3			GCCCAGCAGTTTG	S74683	CCDS7744.1	11p15	2006-02-23			ENSG00000129744	ENSG00000129744		"""CD molecules"""	723	protein-coding gene	gene with protein product		601625				8812442	Standard	NM_004314		Approved	ART2, CD296	uc001lye.1	P52961	OTTHUMG00000011845	ENST00000250693.1:c.634C>T	chr11.hg19:g.3681383C>T	ENSP00000250693:p.Gln212*	124.0	0.0		138.0	6.0	NM_004314	Q6NTD2|Q96KT9	Nonsense_Mutation	SNP	ENST00000250693.1	hg19	CCDS7744.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.261029	0.59431	.	.	ENSG00000129744	ENST00000250693	.	.	.	5.28	0.88	0.19161	.	1.067370	0.07168	N	0.851914	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.5498	0.27790	0.5685:0.3517:0.0:0.0798	.	.	.	.	X	212	.	.	Q	+	1	0	ART1	3637959	0.000000	0.05858	0.392000	0.26245	0.713000	0.41058	-1.075000	0.03423	-0.094000	0.12374	0.467000	0.42956	CAG	.	.		0.652	ART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032765.1	NM_004314	
NUP98	4928	hgsc.bcm.edu	37	11	3716712	3716712	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:3716712T>C	ENST00000324932.7	-	26	4554	c.4134A>G	c.(4132-4134)agA>agG	p.R1378R	NUP98_ENST00000355260.3_Silent_p.R1378R|NUP98_ENST00000488828.1_5'UTR|NUP98_ENST00000359171.4_Silent_p.R1378R	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1395					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		AGATGCGCAGTCTCTCATCCT	0.468			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.R1378R		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.A4134G						.						199.0	202.0	201.0					11																	3716712		2201	4298	6499	SO:0001819	synonymous_variant	4928	exon26			GCGCAGTCTCTCA	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4134A>G	chr11.hg19:g.3716712T>C		57.0	0.0		71.0	4.0	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	hg19	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	T	7.320	0.616757	0.14129	.	.	ENSG00000110713	ENST00000429801	.	.	.	5.05	2.63	0.31362	.	.	.	.	.	T	0.53367	0.1792	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42172	-0.9467	4	.	.	.	-8.7075	5.0929	0.14718	0.0:0.314:0.1488:0.5372	.	.	.	.	A	331	.	.	T	-	1	0	NUP98	3673288	0.833000	0.29383	0.992000	0.48379	0.590000	0.36582	-0.014000	0.12656	0.319000	0.23209	0.456000	0.33151	ACT	.	.		0.468	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
UBQLN3	50613	hgsc.bcm.edu	37	11	5530073	5530073	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:5530073C>G	ENST00000311659.4	-	2	863	c.716G>C	c.(715-717)cGg>cCg	p.R239P	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	239								p.R239L(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACTGAGCACCCGGTCCTGGCT	0.483																																					p.R239P	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											UBQLN3,right_lower_lobe,carcinoma,+1,1	UBQLN3	107	.	1	Substitution - Missense(1)	lung(1)	c.G716C						.						91.0	86.0	87.0					11																	5530073		2201	4297	6498	SO:0001583	missense	50613	exon2			AGCACCCGGTCCT	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.716G>C	chr11.hg19:g.5530073C>G	ENSP00000347997:p.Arg239Pro	122.0	1.0		98.0	4.0	NM_017481	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	hg19	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857233	0.71834	.	.	ENSG00000175520	ENST00000311659	T	0.46819	0.86	5.53	5.53	0.82687	.	0.000000	0.41294	D	0.000906	T	0.57917	0.2086	M	0.67517	2.055	0.45946	D	0.998773	P	0.38300	0.626	P	0.45681	0.49	T	0.61232	-0.7104	10	0.87932	D	0	-29.1404	17.3163	0.87225	0.0:1.0:0.0:0.0	.	239	Q9H347	UBQL3_HUMAN	P	239	ENSP00000347997:R239P	ENSP00000347997:R239P	R	-	2	0	UBQLN3	5486649	0.999000	0.42202	0.998000	0.56505	0.989000	0.77384	3.839000	0.55835	2.750000	0.94351	0.591000	0.81541	CGG	.	.		0.483	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481	
DNHD1	144132	hgsc.bcm.edu	37	11	6591490	6591490	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:6591490C>A	ENST00000527990.2	+	39	12969	c.12969C>A	c.(12967-12969)taC>taA	p.Y4323*	DNHD1_ENST00000254579.6_Nonsense_Mutation_p.Y4323*			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4323					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CAGTTTTCTACGGGGGTCCTC	0.562																																					p.Y4323X		Atlas-SNP	.											.	DNHD1	198	.	0			c.C12969A						.						26.0	29.0	28.0					11																	6591490		1884	4107	5991	SO:0001587	stop_gained	144132	exon41			TTTCTACGGGGGT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.12969C>A	chr11.hg19:g.6591490C>A	ENSP00000436180:p.Tyr4323*	96.0	0.0		97.0	4.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Nonsense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	56	25.934574	0.99967	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	.	.	.	5.43	0.343	0.16001	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3498	7.5916	0.28025	0.0:0.4312:0.0:0.5688	.	.	.	.	X	4323;4323;591	.	ENSP00000254579:Y4323X	Y	+	3	2	DNHD1	6548066	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	0.324000	0.19610	0.022000	0.15160	-0.302000	0.09304	TAC	.	.		0.562	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
PLEKHA7	144100	hgsc.bcm.edu	37	11	16838667	16838667	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:16838667G>T	ENST00000355661.3	-	11	1556	c.1546C>A	c.(1546-1548)Cgg>Agg	p.R516R	PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000448080.2_Silent_p.R516R|PLEKHA7_ENST00000531066.1_Silent_p.R516R			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	516					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						GTGCCATCCCGGTGCGCCCGG	0.662																																					p.R516R		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.C1546A						.						49.0	53.0	51.0					11																	16838667		2199	4294	6493	SO:0001819	synonymous_variant	144100	exon11			CATCCCGGTGCGC	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"""Pleckstrin homology (PH) domain containing"""	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.1546C>A	chr11.hg19:g.16838667G>T		77.0	0.0		100.0	4.0	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	hg19	CCDS31434.1																																																																																			.	.		0.662	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058	
ABCC8	6833	hgsc.bcm.edu	37	11	17428527	17428527	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:17428527T>C	ENST00000389817.3	-	25	3138	c.3070A>G	c.(3070-3072)Atg>Gtg	p.M1024V	ABCC8_ENST00000302539.4_Missense_Mutation_p.M1025V			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1024	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	ACCAGGACCATGTGCTTGAGC	0.637																																					p.M1024V		Atlas-SNP	.											.	ABCC8	170	.	0			c.A3070G						.						93.0	89.0	91.0					11																	17428527		2200	4293	6493	SO:0001583	missense	6833	exon25			GGACCATGTGCTT	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.3070A>G	chr11.hg19:g.17428527T>C	ENSP00000374467:p.Met1024Val	151.0	0.0		95.0	4.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Missense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	T	7.030	0.560413	0.13498	.	.	ENSG00000006071	ENST00000389817;ENST00000302539	D;D	0.87412	-2.25;-2.25	5.97	5.97	0.96955	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.096709	0.64402	D	0.000001	T	0.69726	0.3143	N	0.02345	-0.59	0.32596	N	0.526506	B	0.02656	0.0	B	0.01281	0.0	T	0.70193	-0.4939	10	0.33141	T	0.24	.	10.2347	0.43275	0.2549:0.0:0.0:0.7451	.	1024	Q09428	ABCC8_HUMAN	V	1024;1025	ENSP00000374467:M1024V;ENSP00000303960:M1025V	ENSP00000303960:M1025V	M	-	1	0	ABCC8	17385103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.932000	0.40143	2.275000	0.75901	0.533000	0.62120	ATG	.	.		0.637	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
FANCF	2188	hgsc.bcm.edu	37	11	22646564	22646564	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:22646564T>C	ENST00000327470.3	-	1	823	c.793A>G	c.(793-795)Agc>Ggc	p.S265G	AC103801.2_ENST00000428556.2_5'Flank	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	265					DNA repair (GO:0006281)|ovarian follicle development (GO:0001541)|spermatogenesis (GO:0007283)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						GGGTGGCGGCTAGTCACTAAA	0.547			"""N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S265G		Atlas-SNP	.	yes	Rec		Fanconi anaemia F	11	11p15	2188	"""Fanconi anemia, complementation group F"""		L	.	FANCF	24	.	0			c.A793G						.						51.0	61.0	57.0					11																	22646564		2203	4300	6503	SO:0001583	missense	2188	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGCGGCTAGTCAC		CCDS7857.1	11p15	2014-09-17				ENSG00000183161		"""Fanconi anemia, complementation groups"""	3587	protein-coding gene	gene with protein product		613897				9382107	Standard	NM_022725		Approved	FAF	uc001mql.1	Q9NPI8		ENST00000327470.3:c.793A>G	chr11.hg19:g.22646564T>C	ENSP00000330875:p.Ser265Gly	103.0	0.0	757	79.0	4.0	NM_022725	Q52LM0	Missense_Mutation	SNP	ENST00000327470.3	hg19	CCDS7857.1	.	.	.	.	.	.	.	.	.	.	T	2.373	-0.343870	0.05208	.	.	ENSG00000183161	ENST00000327470	T	0.31247	1.5	5.34	-0.254	0.12992	.	0.618762	0.16096	N	0.229836	T	0.05227	0.0139	N	0.00483	-1.445	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33879	-0.9851	10	0.02654	T	1	-2.4823	1.633	0.02736	0.131:0.4128:0.1282:0.328	.	265	Q9NPI8	FANCF_HUMAN	G	265	ENSP00000330875:S265G	ENSP00000330875:S265G	S	-	1	0	FANCF	22603140	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	0.260000	0.18424	0.034000	0.15491	0.459000	0.35465	AGC	.	.		0.547	FANCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387712.2	NM_022725	
LIN7C	55327	hgsc.bcm.edu	37	11	27523454	27523454	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:27523454T>C	ENST00000278193.2	-	2	71	c.51A>G	c.(49-51)gcA>gcG	p.A17A	LIN7C_ENST00000524596.1_Silent_p.A17A	NM_018362.3	NP_060832.1	Q9NUP9	LIN7C_HUMAN	lin-7 homolog C (C. elegans)	17	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				exocytosis (GO:0006887)|morphogenesis of an epithelial sheet (GO:0002011)|neurotransmitter secretion (GO:0007269)|protein transport (GO:0015031)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|MPP7-DLG1-LIN7 complex (GO:0097025)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|L27 domain binding (GO:0097016)|protein domain specific binding (GO:0019904)			endometrium(2)|lung(2)|upper_aerodigestive_tract(1)	5						ATAATTCAATTGCTCTACAAA	0.388																																					p.A17A		Atlas-SNP	.											LIN7C,NS,carcinoma,0,1	LIN7C	24	.	0			c.A51G						.						81.0	79.0	79.0					11																	27523454		2201	4298	6499	SO:0001819	synonymous_variant	55327	exon2			TTCAATTGCTCTA	AK002077	CCDS7864.1	11p14	2008-07-18				ENSG00000148943			17789	protein-coding gene	gene with protein product	"""LIN-7 protein 3"""	612332				10341223	Standard	NM_018362		Approved	MALS-3, Lin7c, LIN-7C, LIN-7-C, VELI3, FLJ11215	uc001mrl.3	Q9NUP9		ENST00000278193.2:c.51A>G	chr11.hg19:g.27523454T>C		94.0	0.0		87.0	28.0	NM_018362		Silent	SNP	ENST00000278193.2	hg19	CCDS7864.1																																																																																			.	.		0.388	LIN7C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388311.2	NM_018362	
DCDC1	341019	hgsc.bcm.edu	37	11	30938424	30938424	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:30938424T>C	ENST00000597505.1	-	24	3444	c.3445A>G	c.(3445-3447)Aaa>Gaa	p.K1149E	DCDC1_ENST00000339794.5_Missense_Mutation_p.K228E|DCDC1_ENST00000406071.2_5'UTR			P59894	DCDC1_HUMAN	doublecortin domain containing 1	0					intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					TACCTGTGTTTCTTCTGTGGT	0.403																																					p.K256E		Atlas-SNP	.											.	DCDC5	137	.	0			c.A766G						.						129.0	128.0	128.0					11																	30938424		2202	4299	6501	SO:0001583	missense	100506627	exon7			TGTGTTTCTTCTG	AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000597505.1:c.3445A>G	chr11.hg19:g.30938424T>C	ENSP00000472625:p.Lys1149Glu	152.0	0.0		146.0	6.0	NM_020869	A6PVL6|B7WNX6|Q6ZU04	Missense_Mutation	SNP	ENST00000597505.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.07	2.724805	0.48833	.	.	ENSG00000170959	ENST00000339794	.	.	.	5.65	0.485	0.16830	.	0.321787	0.26400	N	0.024598	T	0.24122	0.0584	N	0.20986	0.625	0.09310	N	1	B	0.20052	0.041	B	0.26202	0.067	T	0.12451	-1.0547	9	0.44086	T	0.13	-3.6689	4.0866	0.09950	0.1432:0.2426:0.0:0.6142	.	228	Q6ZRR9	DCDC5_HUMAN	E	228	.	ENSP00000341700:K228E	K	-	1	0	DCDC5	30895000	0.517000	0.26226	0.096000	0.21009	0.727000	0.41649	0.621000	0.24418	0.098000	0.17522	0.459000	0.35465	AAA	.	.		0.403	DCDC1-010	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000463167.1	NM_181807	
RCN1	5954	hgsc.bcm.edu	37	11	32125951	32125951	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:32125951A>G	ENST00000054950.3	+	6	1222	c.929A>G	c.(928-930)aAc>aGc	p.N310S	RP1-65P5.3_ENST00000533009.1_RNA|RCN1_ENST00000532942.1_Missense_Mutation_p.N259S	NM_002901.2	NP_002892.1	Q15293	RCN1_HUMAN	reticulocalbin 1, EF-hand calcium binding domain	310	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.				camera-type eye development (GO:0043010)|in utero embryonic development (GO:0001701)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)	17	Lung SC(675;0.225)					GAGAACTGGAACATGTTTGTC	0.403																																					p.N310S		Atlas-SNP	.											.	RCN1	37	.	0			c.A929G						.						97.0	82.0	87.0					11																	32125951		2202	4299	6501	SO:0001583	missense	5954	exon6			ACTGGAACATGTT	D42073	CCDS7876.1	11p13	2013-01-10			ENSG00000049449	ENSG00000049449		"""EF-hand domain containing"""	9934	protein-coding gene	gene with protein product	"""proliferation-inducing gene 20"""	602735		RCN		9192846, 8586628	Standard	NM_002901		Approved	Rcal, PIG20, FLJ37041	uc010reb.2	Q15293		ENST00000054950.3:c.929A>G	chr11.hg19:g.32125951A>G	ENSP00000054950:p.Asn310Ser	139.0	0.0		115.0	5.0	NM_002901	B7Z1M1|D3DR00	Missense_Mutation	SNP	ENST00000054950.3	hg19	CCDS7876.1	.	.	.	.	.	.	.	.	.	.	a	13.79	2.340836	0.41498	.	.	ENSG00000049449	ENST00000532942;ENST00000054950;ENST00000528630	T;T	0.53423	0.62;0.84	5.82	4.7	0.59300	EF-hand-like domain (1);	0.077381	0.85682	N	0.000000	T	0.46405	0.1391	M	0.62154	1.92	0.80722	D	1	B;B	0.23854	0.024;0.092	B;B	0.25884	0.036;0.064	T	0.42783	-0.9431	10	0.59425	D	0.04	-30.5925	11.5839	0.50908	0.9307:0.0:0.0693:0.0	.	310;259	Q15293;B7Z1M1	RCN1_HUMAN;.	S	259;310;7	ENSP00000436422:N259S;ENSP00000054950:N310S	ENSP00000054950:N310S	N	+	2	0	RCN1	32082527	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.312000	0.72840	1.045000	0.40225	0.533000	0.62120	AAC	.	.		0.403	RCN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388510.1	NM_002901	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33573676	33573676	+	Silent	SNP	G	G	T	rs372452571		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:33573676G>T	ENST00000321505.4	+	5	3033	c.2853G>T	c.(2851-2853)gcG>gcT	p.A951A	KIAA1549L_ENST00000389726.3_Silent_p.A957A|KIAA1549L_ENST00000265654.5_Silent_p.A957A			Q6ZVL6	K154L_HUMAN	KIAA1549-like	951						integral component of membrane (GO:0016021)											TGAGCCAAGCGGACAACATAC	0.453																																					p.A951A		Atlas-SNP	.											C11orf41_ENST00000321505,NS,carcinoma,0,2	.	.	.	0			c.G2853T						.						69.0	68.0	68.0					11																	33573676		1929	4140	6069	SO:0001819	synonymous_variant	25758	exon5			CCAAGCGGACAAC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.2853G>T	chr11.hg19:g.33573676G>T		103.0	0.0		75.0	4.0	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	hg19	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	G	5.776	0.327476	0.10956	.	.	ENSG00000110427	ENST00000526400	.	.	.	6.08	-12.2	0.00006	.	.	.	.	.	T	0.31295	0.0792	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.47586	-0.9106	4	.	.	.	-5.2645	1.6363	0.02743	0.1523:0.2863:0.297:0.2645	.	.	.	.	L	349	.	.	R	+	2	0	C11orf41	33530252	0.000000	0.05858	0.000000	0.03702	0.659000	0.38960	-4.800000	0.00184	-3.665000	0.00124	-2.047000	0.00414	CGG	.	.		0.453	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
LMO2	4005	hgsc.bcm.edu	37	11	33890910	33890910	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:33890910T>C	ENST00000395833.3	-	1	452	c.23A>G	c.(22-24)aAg>aGg	p.K8R	LMO2_ENST00000493667.1_5'Flank|LMO2_ENST00000257818.2_Missense_Mutation_p.K77R	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	8					cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|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 RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						GTCCAGGCTCTTCCTTTCGAT	0.771			T	TRD@	T-ALL																																p.K77R		Atlas-SNP	.		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	.	LMO2	21	.	0			c.A230G						.						6.0	5.0	5.0					11																	33890910		1480	2776	4256	SO:0001583	missense	4005	exon4			AGGCTCTTCCTTT	X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"""T-cell translocation gene 2"", ""rhombotin-like 1"""	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.23A>G	chr11.hg19:g.33890910T>C	ENSP00000379175:p.Lys8Arg	41.0	0.0		45.0	4.0	NM_005574	Q9HD58	Missense_Mutation	SNP	ENST00000395833.3	hg19	CCDS44567.1	.	.	.	.	.	.	.	.	.	.	T	15.47	2.844132	0.51164	.	.	ENSG00000135363	ENST00000395833;ENST00000257818	T;T	0.60672	0.17;0.56	4.38	4.38	0.52667	.	0.125963	0.49916	U	0.000126	T	0.44008	0.1273	L	0.46157	1.445	0.45580	D	0.998524	P;B	0.40144	0.704;0.011	B;B	0.29716	0.106;0.003	T	0.38499	-0.9658	10	0.20046	T	0.44	.	13.2524	0.60060	0.0:0.0:0.0:1.0	.	77;8	P25791-3;P25791	.;RBTN2_HUMAN	R	8;77	ENSP00000379175:K8R;ENSP00000257818:K77R	ENSP00000257818:K77R	K	-	2	0	LMO2	33847486	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.515000	0.67049	1.609000	0.50190	0.377000	0.23210	AAG	.	.		0.771	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574	
EHF	26298	hgsc.bcm.edu	37	11	34673334	34673334	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:34673334A>G	ENST00000533754.1	+	6	743	c.526A>G	c.(526-528)Acc>Gcc	p.T176A	EHF_ENST00000530286.1_Missense_Mutation_p.T176A|EHF_ENST00000531794.1_Missense_Mutation_p.T198A|EHF_ENST00000450654.2_Intron|EHF_ENST00000257831.3_Missense_Mutation_p.T176A					ets homologous factor										NFIA/EHF(2)	autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|lung(8)|upper_aerodigestive_tract(1)	17		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			CATGACAACCACCAGTCACCT	0.488																																					p.T198A		Atlas-SNP	.											.	EHF	38	.	0			c.A592G						.						124.0	114.0	117.0					11																	34673334		2202	4298	6500	SO:0001583	missense	26298	exon6			ACAACCACCAGTC	AF170583	CCDS7894.1, CCDS55752.1, CCDS55753.1	11p12	2008-07-18				ENSG00000135373			3246	protein-coding gene	gene with protein product	"""epithelium-specific ets factor 3"", ""ESE3 transcription factor"""	605439				10527851	Standard	NM_012153		Approved	ESE3, ESEJ	uc021qfu.1	Q9NZC4		ENST00000533754.1:c.526A>G	chr11.hg19:g.34673334A>G	ENSP00000435837:p.Thr176Ala	85.0	0.0		57.0	4.0	NM_001206616		Missense_Mutation	SNP	ENST00000533754.1	hg19	CCDS7894.1	.	.	.	.	.	.	.	.	.	.	A	5.794	0.330767	0.10956	.	.	ENSG00000135373	ENST00000257831;ENST00000530286;ENST00000533754;ENST00000531794	T;T;T;T	0.06687	3.29;3.29;3.29;3.27	6.17	-0.36	0.12568	.	0.378824	0.22635	N	0.057538	T	0.02304	0.0071	N	0.03608	-0.345	0.24015	N	0.996169	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40136	-0.9579	10	0.17369	T	0.5	.	0.6405	0.00810	0.3025:0.1157:0.263:0.3188	.	198;176	E9PSB2;Q9NZC4	.;EHF_HUMAN	A	176;176;176;198	ENSP00000257831:T176A;ENSP00000433508:T176A;ENSP00000435837:T176A;ENSP00000435835:T198A	ENSP00000257831:T176A	T	+	1	0	EHF	34629910	0.006000	0.16342	0.270000	0.24601	0.969000	0.65631	0.044000	0.13992	-0.052000	0.13311	0.533000	0.62120	ACC	.	.		0.488	EHF-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389855.1	NM_012153	
PHF21A	51317	hgsc.bcm.edu	37	11	46098351	46098351	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:46098351T>C	ENST00000418153.2	-	5	306	c.107A>G	c.(106-108)cAg>cGg	p.Q36R	PHF21A_ENST00000257821.4_Missense_Mutation_p.Q36R|PHF21A_ENST00000323180.6_Missense_Mutation_p.Q36R			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	36	Gln-rich.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						TTCATGAAGCTGTTTCTTTAA	0.373																																					p.Q36R		Atlas-SNP	.											.	PHF21A	107	.	0			c.A107G						.						132.0	123.0	126.0					11																	46098351		2202	4299	6501	SO:0001583	missense	51317	exon5			TGAAGCTGTTTCT	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.107A>G	chr11.hg19:g.46098351T>C	ENSP00000398824:p.Gln36Arg	105.0	0.0		89.0	4.0	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Missense_Mutation	SNP	ENST00000418153.2	hg19	CCDS44578.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.949696	0.73787	.	.	ENSG00000135365	ENST00000257821;ENST00000323180;ENST00000418153;ENST00000524497;ENST00000531959;ENST00000529734;ENST00000529782;ENST00000533757	T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.55273	0.1910	N	0.24115	0.695	0.46317	D	0.998986	D;D	0.60160	0.987;0.981	D;D	0.70487	0.953;0.969	T	0.56257	-0.8009	10	0.44086	T	0.13	-4.1686	16.3786	0.83431	0.0:0.0:0.0:1.0	.	36;36	Q96BD5;Q96BD5-2	PF21A_HUMAN;.	R	36;36;36;43;43;36;13;36	ENSP00000257821:Q36R;ENSP00000323152:Q36R;ENSP00000398824:Q36R;ENSP00000431273:Q43R;ENSP00000432916:Q43R;ENSP00000436157:Q36R;ENSP00000435121:Q13R;ENSP00000432406:Q36R	ENSP00000257821:Q36R	Q	-	2	0	PHF21A	46054927	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.676000	0.74498	2.323000	0.78572	0.528000	0.53228	CAG	.	.		0.373	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735603	55735603	+	Missense_Mutation	SNP	G	G	T	rs150679428		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:55735603G>T	ENST00000312345.2	-	1	387	c.337C>A	c.(337-339)Cgc>Agc	p.R113S		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R113C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					GCCACGTAGCGGTCATAGGCC	0.428																																					p.R113S		Atlas-SNP	.											OR10AG1,NS,carcinoma,+1,2	OR10AG1	100	.	1	Substitution - Missense(1)	large_intestine(1)	c.C337A						.						88.0	86.0	86.0					11																	55735603		2201	4296	6497	SO:0001583	missense	282770	exon1			CGTAGCGGTCATA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.337C>A	chr11.hg19:g.55735603G>T	ENSP00000311477:p.Arg113Ser	92.0	1.0		88.0	4.0	NM_001005491	B2RNH4|Q6IEU3	Missense_Mutation	SNP	ENST00000312345.2	hg19	CCDS31514.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184166	0.38609	.	.	ENSG00000174970	ENST00000312345	T	0.77620	-1.11	5.47	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000159	D	0.90532	0.7033	H	0.97540	4.025	0.29222	N	0.873839	D	0.67145	0.996	D	0.69824	0.966	D	0.86697	0.1927	10	0.87932	D	0	.	7.4436	0.27198	0.0851:0.0:0.7504:0.1645	.	113	Q8NH19	O10AG_HUMAN	S	113	ENSP00000311477:R113S	ENSP00000311477:R113S	R	-	1	0	OR10AG1	55492179	0.972000	0.33761	0.961000	0.40146	0.030000	0.12068	1.405000	0.34635	1.357000	0.45904	0.477000	0.44152	CGC	.	G|1.000;A|0.000		0.428	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
OR9G4	283189	hgsc.bcm.edu	37	11	56511197	56511197	+	Missense_Mutation	SNP	C	C	A	rs367701319		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:56511197C>A	ENST00000302957.3	-	1	90	c.91G>T	c.(91-93)Ggt>Tgt	p.G31C		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G31S(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						GCTGAGAAACCCAACAAGATG	0.428																																					p.G31C		Atlas-SNP	.											OR9G4,NS,carcinoma,0,1	OR9G4	73	.	1	Substitution - Missense(1)	prostate(1)	c.G91T						.	C	CYS/GLY	1,4401	2.1+/-5.4	0,1,2200	84.0	77.0	79.0		91	4.9	1.0	11		79	0,8592		0,0,4296	no	missense	OR9G4	NM_001005284.1	159	0,1,6496	AA,AC,CC		0.0,0.0227,0.0077	probably-damaging	31/328	56511197	1,12993	2201	4296	6497	SO:0001583	missense	283189	exon1			AGAAACCCAACAA	BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"""GPCR / Class A : Olfactory receptors"""	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.91G>T	chr11.hg19:g.56511197C>A	ENSP00000307515:p.Gly31Cys	138.0	0.0		95.0	4.0	NM_001005284	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	hg19	CCDS31537.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729180	0.48833	2.27E-4	0.0	ENSG00000172457	ENST00000302957	T	0.00662	5.93	4.9	4.9	0.64082	.	0.000000	0.40385	N	0.001118	T	0.03136	0.0092	H	0.94734	3.575	0.48830	D	0.999713	B	0.23735	0.09	B	0.25506	0.061	T	0.06144	-1.0843	10	0.87932	D	0	-13.0418	16.802	0.85617	0.0:1.0:0.0:0.0	.	31	Q8NGQ1	OR9G4_HUMAN	C	31	ENSP00000307515:G31C	ENSP00000307515:G31C	G	-	1	0	OR9G4	56267773	0.985000	0.35326	0.984000	0.44739	0.716000	0.41182	3.940000	0.56599	2.546000	0.85860	0.549000	0.68633	GGT	.	.		0.428	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284	
YPEL4	219539	hgsc.bcm.edu	37	11	57413467	57413467	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:57413467T>C	ENST00000524669.1	-	5	3093	c.371A>G	c.(370-372)aAc>aGc	p.N124S	AP000662.4_ENST00000530595.1_RNA|YPEL4_ENST00000544993.1_Missense_Mutation_p.N124S|YPEL4_ENST00000534711.1_Missense_Mutation_p.N124S|YPEL4_ENST00000531442.1_5'Flank|YPEL4_ENST00000300022.3_Missense_Mutation_p.N124S			Q96NS1	YPEL4_HUMAN	yippee-like 4 (Drosophila)	124						nucleus (GO:0005634)				lung(2)|skin(1)	3						GTCCCAGCCGTTGTCCTTCAC	0.552																																					p.N124S		Atlas-SNP	.											.	YPEL4	5	.	0			c.A371G						.						173.0	130.0	145.0					11																	57413467		2201	4296	6497	SO:0001583	missense	219539	exon5			CAGCCGTTGTCCT	AK054775	CCDS7963.1	11q12	2008-02-05				ENSG00000166793			18328	protein-coding gene	gene with protein product		609725					Standard	NM_145008		Approved	FLJ30213	uc001nkv.4	Q96NS1		ENST00000524669.1:c.371A>G	chr11.hg19:g.57413467T>C	ENSP00000432648:p.Asn124Ser	64.0	0.0		75.0	4.0	NM_145008	B3KW92|Q2M3U7|Q65Z98	Missense_Mutation	SNP	ENST00000524669.1	hg19	CCDS7963.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.309891	0.81247	.	.	ENSG00000166793	ENST00000524669;ENST00000300022;ENST00000544993;ENST00000534711	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	T	0.51415	0.1673	L	0.45285	1.41	0.80722	D	1	P	0.37612	0.602	B	0.38803	0.282	T	0.48127	-0.9062	9	0.24483	T	0.36	-7.3639	15.1263	0.72486	0.0:0.0:0.0:1.0	.	124	Q96NS1	YPEL4_HUMAN	S	124	.	ENSP00000300022:N124S	N	-	2	0	YPEL4	57170043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.775000	0.85489	2.057000	0.61298	0.459000	0.35465	AAC	.	.		0.552	YPEL4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393370.1	NM_145008	
FAM111B	374393	hgsc.bcm.edu	37	11	58877115	58877115	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:58877115C>A	ENST00000343597.3	+	3	208	c.17C>A	c.(16-18)aCt>aAt	p.T6N	FAM111B_ENST00000529618.1_Intron|FAM111B_ENST00000411426.1_Intron	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	6							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						TCCATGAAGACTGAAGAAAAC	0.368																																					p.T6N		Atlas-SNP	.											.	FAM111B	84	.	0			c.C17A						.						97.0	88.0	91.0					11																	58877115		2201	4295	6496	SO:0001583	missense	374393	exon3			TGAAGACTGAAGA	BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.17C>A	chr11.hg19:g.58877115C>A	ENSP00000341565:p.Thr6Asn	61.0	0.0		64.0	4.0	NM_198947	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	hg19	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	C	0.627	-0.818934	0.02776	.	.	ENSG00000189057	ENST00000343597	T	0.31769	1.48	1.65	-0.869	0.10649	.	.	.	.	.	T	0.14917	0.0360	N	0.22421	0.69	0.09310	N	1	B	0.27594	0.182	B	0.15870	0.014	T	0.18209	-1.0344	9	0.37606	T	0.19	.	2.8272	0.05488	0.0:0.4:0.3498:0.2503	.	6	Q6SJ93	F111B_HUMAN	N	6	ENSP00000341565:T6N	ENSP00000341565:T6N	T	+	2	0	FAM111B	58633691	0.039000	0.19947	0.011000	0.14972	0.005000	0.04900	-0.073000	0.11468	-0.208000	0.10171	-0.378000	0.06908	ACT	.	.		0.368	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947	
PATL1	219988	hgsc.bcm.edu	37	11	59406813	59406813	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:59406813T>C	ENST00000300146.9	-	17	2177	c.2093A>G	c.(2092-2094)gAc>gGc	p.D698G	AP000442.1_ENST00000531311.1_RNA|AP000442.1_ENST00000531108.1_RNA	NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	698	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						ACTCTGTAGGTCTTCACCACG	0.438																																					p.D698G		Atlas-SNP	.											.	PATL1	92	.	0			c.A2093G						.																																			SO:0001583	missense	219988	exon17			TGTAGGTCTTCAC	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.2093A>G	chr11.hg19:g.59406813T>C	ENSP00000300146:p.Asp698Gly	109.0	0.0		91.0	4.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Missense_Mutation	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	T	17.03	3.284592	0.59867	.	.	ENSG00000166889	ENST00000300146	T	0.42513	0.97	5.67	5.67	0.87782	.	0.195541	0.53938	D	0.000056	T	0.26810	0.0656	N	0.11427	0.14	0.44042	D	0.996777	B	0.27316	0.175	B	0.29267	0.1	T	0.11060	-1.0603	10	0.20046	T	0.44	-15.7101	15.5908	0.76526	0.0:0.0:0.0:1.0	.	698	Q86TB9	PATL1_HUMAN	G	698	ENSP00000300146:D698G	ENSP00000300146:D698G	D	-	2	0	PATL1	59163389	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.072000	0.57563	2.170000	0.68504	0.533000	0.62120	GAC	.	.		0.438	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716	
EML3	256364	hgsc.bcm.edu	37	11	62370651	62370651	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:62370651A>G	ENST00000394773.2	-	20	2633	c.2326T>C	c.(2326-2328)Tac>Cac	p.Y776H	RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000494176.2_Missense_Mutation_p.Y748H|EML3_ENST00000278845.4_Missense_Mutation_p.Y777H|EML3_ENST00000531557.1_Missense_Mutation_p.Y559H|EML3_ENST00000438258.1_5'Flank|MTA2_ENST00000527204.1_5'Flank|MTA2_ENST00000278823.2_5'Flank|EML3_ENST00000529309.1_Missense_Mutation_p.Y776H	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	776						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ACACAGGTGTAGGTAGCCCAT	0.632																																					p.Y776H		Atlas-SNP	.											.	EML3	61	.	0			c.T2326C						.						120.0	114.0	116.0					11																	62370651		2202	4299	6501	SO:0001583	missense	256364	exon20			AGGTGTAGGTAGC	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.2326T>C	chr11.hg19:g.62370651A>G	ENSP00000378254:p.Tyr776His	51.0	0.0		62.0	4.0	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	hg19	CCDS8023.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.72|17.72	3.458939|3.458939	0.63401|0.63401	.|.	.|.	ENSG00000149499|ENSG00000149499	ENST00000394776|ENST00000439994;ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	.|T;T;T;T;T	.|0.29917	.|1.71;1.67;1.55;1.69;1.62	4.78|4.78	4.78|4.78	0.61160|0.61160	.|WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	.|0.071188	.|0.64402	.|D	.|0.000020	T|T	0.44993|0.44993	0.1320|0.1320	L|L	0.43152|0.43152	1.355|1.355	0.47276|0.47276	D|D	0.999371|0.999371	.|D;D;B;D;D	.|0.89917	.|1.0;0.999;0.02;0.999;1.0	.|D;D;B;D;D	.|0.91635	.|0.999;0.979;0.039;0.994;0.974	T|T	0.23726|0.23726	-1.0180|-1.0180	5|10	.|0.32370	.|T	.|0.25	-28.4302|-28.4302	12.2654|12.2654	0.54674|0.54674	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|776;776;559;777;748	.|Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0	.|.;EMAL3_HUMAN;.;.;.	P|H	770|27;776;777;559;748;776	.|ENSP00000378254:Y776H;ENSP00000278845:Y777H;ENSP00000433417:Y559H;ENSP00000435064:Y748H;ENSP00000434513:Y776H	.|ENSP00000278845:Y777H	L|Y	-|-	2|1	0|0	EML3|EML3	62127227|62127227	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.696000|5.696000	0.68287|0.68287	1.787000|1.787000	0.52448|0.52448	0.459000|0.459000	0.35465|0.35465	CTA|TAC	.	.		0.632	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
EML3	256364	hgsc.bcm.edu	37	11	62375157	62375157	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:62375157C>A	ENST00000394773.2	-	11	1650	c.1343G>T	c.(1342-1344)cGg>cTg	p.R448L	RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000494176.2_Missense_Mutation_p.R420L|EML3_ENST00000278845.4_Missense_Mutation_p.R449L|EML3_ENST00000531557.1_Missense_Mutation_p.R231L|EML3_ENST00000438258.1_Intron|EML3_ENST00000529309.1_Missense_Mutation_p.R448L	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	448						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ACCCTGTTTCCGGGTAAGGGT	0.567																																					p.R448L		Atlas-SNP	.											.	EML3	61	.	0			c.G1343T						.						110.0	101.0	104.0					11																	62375157		2202	4299	6501	SO:0001583	missense	256364	exon11			TGTTTCCGGGTAA	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.1343G>T	chr11.hg19:g.62375157C>A	ENSP00000378254:p.Arg448Leu	102.0	0.0		90.0	4.0	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572935	0.65765	.	.	ENSG00000149499	ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	T;T;T;T;T	0.41065	1.01;1.01;1.57;1.57;1.57	5.2	5.2	0.72013	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.140261	0.47093	D	0.000260	T	0.52058	0.1711	L	0.54323	1.7	0.37064	D	0.898224	P;P;B;B;D	0.61697	0.768;0.658;0.035;0.36;0.99	P;B;B;B;P	0.58454	0.573;0.369;0.042;0.044;0.839	T	0.61282	-0.7094	10	0.87932	D	0	-2.1889	9.855	0.41079	0.0:0.9067:0.0:0.0933	.	448;448;231;449;420	Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0	.;EMAL3_HUMAN;.;.;.	L	448;449;231;420;448	ENSP00000378254:R448L;ENSP00000278845:R449L;ENSP00000433417:R231L;ENSP00000435064:R420L;ENSP00000434513:R448L	ENSP00000278845:R449L	R	-	2	0	EML3	62131733	1.000000	0.71417	0.977000	0.42913	0.919000	0.55068	2.977000	0.49297	2.446000	0.82766	0.460000	0.39030	CGG	.	.		0.567	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
MARK2	2011	hgsc.bcm.edu	37	11	63666539	63666539	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:63666539C>T	ENST00000509502.2	+	7	854	c.391C>T	c.(391-393)Cag>Tag	p.Q131*	MARK2_ENST00000502399.3_Nonsense_Mutation_p.Q164*|MARK2_ENST00000402010.2_Nonsense_Mutation_p.Q164*|MARK2_ENST00000377809.4_Nonsense_Mutation_p.Q164*|MARK2_ENST00000350490.7_Nonsense_Mutation_p.Q164*|MARK2_ENST00000425897.2_Nonsense_Mutation_p.Q131*|MARK2_ENST00000513765.2_Nonsense_Mutation_p.Q131*|MARK2_ENST00000508192.1_Nonsense_Mutation_p.Q164*|MARK2_ENST00000413835.2_Nonsense_Mutation_p.Q164*|MARK2_ENST00000361128.5_Nonsense_Mutation_p.Q164*|MARK2_ENST00000408948.3_Nonsense_Mutation_p.Q131*|MARK2_ENST00000315032.8_Nonsense_Mutation_p.Q164*|MARK2_ENST00000377810.3_Nonsense_Mutation_p.Q131*	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2											autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						GTCTGCTGTGCAGTACTGTCA	0.517																																					p.Q164X		Atlas-SNP	.											.	MARK2	91	.	0			c.C490T						.						209.0	198.0	202.0					11																	63666539		2201	4297	6498	SO:0001587	stop_gained	2011	exon7			GCTGTGCAGTACT	BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"""ELKL motif kinase 1"", ""serine/threonine kinase"", ""protein-serine/threonine kinase"", ""Ser/Thr protein kinase PAR-1B"""	600526	"""ELKL motif kinase"""	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.391C>T	chr11.hg19:g.63666539C>T	ENSP00000423974:p.Gln131*	93.0	0.0		103.0	5.0	NM_001163296		Nonsense_Mutation	SNP	ENST00000509502.2	hg19	CCDS41665.1	.	.	.	.	.	.	.	.	.	.	c	40	8.234273	0.98719	.	.	ENSG00000072518	ENST00000402010;ENST00000315032;ENST00000377809;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000361128;ENST00000350490;ENST00000502399;ENST00000543220;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897	.	.	.	4.98	4.98	0.66077	.	0.124939	0.56097	D	0.000035	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.1794	0.86851	0.0:1.0:0.0:0.0	.	.	.	.	X	164;164;164;164;131;164;164;164;164;131;131;131;131;131	.	ENSP00000326632:Q164X	Q	+	1	0	MARK2	63423115	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.648000	0.83479	2.583000	0.87209	0.558000	0.71614	CAG	.	.		0.517	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490	
SNX15	29907	hgsc.bcm.edu	37	11	64802421	64802421	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:64802421A>G	ENST00000377244.3	+	4	489	c.359A>G	c.(358-360)aAg>aGg	p.K120R	SNX15_ENST00000352068.5_Missense_Mutation_p.K120R|RP11-399J13.3_ENST00000301886.3_3'UTR	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	120	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						CCCCAGCTCAAGGAGTTCTTC	0.572																																					p.K120R	Esophageal Squamous(56;269 1304 3324 8253)	Atlas-SNP	.											.	SNX15	35	.	0			c.A359G						.						64.0	58.0	60.0					11																	64802421		2201	4297	6498	SO:0001583	missense	29907	exon4			AGCTCAAGGAGTT	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"""Sorting nexins"""	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.359A>G	chr11.hg19:g.64802421A>G	ENSP00000366452:p.Lys120Arg	89.0	0.0		105.0	5.0	NM_147777	E5KQS6|Q9NRS5	Missense_Mutation	SNP	ENST00000377244.3	hg19	CCDS8089.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.245899	0.80024	.	.	ENSG00000110025	ENST00000377244;ENST00000534637;ENST00000524831;ENST00000352068	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.38	5.38	0.77491	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.46870	0.1415	N	0.25245	0.725	0.80722	D	1	D;P;D	0.89917	1.0;0.92;1.0	D;P;D	0.87578	0.998;0.491;0.998	T	0.31806	-0.9930	10	0.13470	T	0.59	-6.2292	13.33	0.60480	1.0:0.0:0.0:0.0	.	120;120;120	E5KQS5;E5KQS6;Q9NRS6	.;.;SNX15_HUMAN	R	120;116;108;120	ENSP00000366452:K120R;ENSP00000437277:K116R;ENSP00000431690:K108R;ENSP00000316410:K120R	ENSP00000316410:K120R	K	+	2	0	SNX15	64558997	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	8.529000	0.90602	2.046000	0.60703	0.455000	0.32223	AAG	.	.		0.572	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3		
SCYL1	57410	hgsc.bcm.edu	37	11	65299085	65299085	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:65299085G>T	ENST00000270176.5	+	8	1124	c.1047G>T	c.(1045-1047)aaG>aaT	p.K349N	SCYL1_ENST00000527009.1_Missense_Mutation_p.K206N|SCYL1_ENST00000420247.2_Missense_Mutation_p.K349N|SCYL1_ENST00000533862.1_Missense_Mutation_p.K349N|SCYL1_ENST00000279270.6_Missense_Mutation_p.K349N|SCYL1_ENST00000525364.1_Missense_Mutation_p.K349N|SCYL1_ENST00000524944.1_Missense_Mutation_p.K349N	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	349					peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						ATCAGCAGAAGATCATCCCTG	0.567																																					p.K349N		Atlas-SNP	.											.	SCYL1	76	.	0			c.G1047T						.						90.0	92.0	91.0					11																	65299085		2141	4246	6387	SO:0001583	missense	57410	exon8			GCAGAAGATCATC	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.1047G>T	chr11.hg19:g.65299085G>T	ENSP00000270176:p.Lys349Asn	69.0	0.0		89.0	4.0	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	hg19	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830629	0.50845	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009	T;T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.17	4.24	0.50183	Armadillo-like helical (1);Armadillo-type fold (1);	0.220459	0.45867	D	0.000338	T	0.36386	0.0965	M	0.67953	2.075	0.48830	D	0.999717	B;B;B;B	0.29716	0.004;0.109;0.018;0.255	B;B;B;B	0.32624	0.027;0.149;0.047;0.07	T	0.37820	-0.9689	10	0.72032	D	0.01	-32.2004	8.5896	0.33679	0.1756:0.0:0.8244:0.0	.	349;349;349;349	E9PS17;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;NTKL_HUMAN	N	349;349;349;349;349;349;349;349;206	ENSP00000270176:K349N;ENSP00000431635:K349N;ENSP00000408192:K349N;ENSP00000437254:K349N;ENSP00000433450:K349N;ENSP00000279270:K349N;ENSP00000432175:K349N;ENSP00000436993:K206N	ENSP00000270176:K349N	K	+	3	2	SCYL1	65055661	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.452000	0.35156	2.609000	0.88269	0.650000	0.86243	AAG	.	.		0.567	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680	
TMEM151A	256472	hgsc.bcm.edu	37	11	66062755	66062755	+	Silent	SNP	C	C	A	rs377003155		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66062755C>A	ENST00000327259.4	+	2	1182	c.1038C>A	c.(1036-1038)ctC>ctA	p.L346L		NM_153266.3	NP_694998.1	Q8N4L1	T151A_HUMAN	transmembrane protein 151A	346						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(4)|lung(6)	11						TCACTGAGCTCGAGTGGCACA	0.716																																					p.L346L		Atlas-SNP	.											.	TMEM151A	39	.	0			c.C1038A						.						8.0	8.0	8.0					11																	66062755		2151	4199	6350	SO:0001819	synonymous_variant	256472	exon2			TGAGCTCGAGTGG	BC033898	CCDS8133.1	11q13.2	2007-10-25	2007-10-25	2007-10-25	ENSG00000179292	ENSG00000179292			28497	protein-coding gene	gene with protein product			"""transmembrane protein 151"""	TMEM151		12477932	Standard	NM_153266		Approved	MGC33486	uc001ohl.3	Q8N4L1	OTTHUMG00000166920	ENST00000327259.4:c.1038C>A	chr11.hg19:g.66062755C>A		76.0	0.0		65.0	4.0	NM_153266	Q8ND14	Silent	SNP	ENST00000327259.4	hg19	CCDS8133.1																																																																																			.	.		0.716	TMEM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391897.1	NM_153266	
SPTBN2	6712	hgsc.bcm.edu	37	11	66468660	66468660	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66468660G>T	ENST00000533211.1	-	17	3241	c.2910C>A	c.(2908-2910)acC>acA	p.T970T	SPTBN2_ENST00000529997.1_Silent_p.T970T|SPTBN2_ENST00000309996.2_Silent_p.T970T			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	970					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						TCCAGGCCTGGGTCTCCGTGC	0.617																																					p.T970T		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C2910A						.						51.0	48.0	49.0					11																	66468660		2199	4295	6494	SO:0001819	synonymous_variant	6712	exon16			GGCCTGGGTCTCC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.2910C>A	chr11.hg19:g.66468660G>T		112.0	0.0		119.0	6.0	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	hg19	CCDS8150.1																																																																																			.	.		0.617	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
PC	5091	hgsc.bcm.edu	37	11	66639169	66639169	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66639169T>C	ENST00000393958.2	-	4	403	c.310A>G	c.(310-312)Aag>Gag	p.K104E	PC_ENST00000393960.1_Missense_Mutation_p.K104E|PC_ENST00000355677.3_Missense_Mutation_p.K104E|PC_ENST00000393955.2_Missense_Mutation_p.K104E|PC_ENST00000524491.1_Missense_Mutation_p.K64E	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	104	Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	TTGGCCACCTTGATGATGTCT	0.657																																					p.K104E		Atlas-SNP	.											.	PC	116	.	0			c.A310G						.						21.0	21.0	21.0					11																	66639169		2175	4281	6456	SO:0001583	missense	5091	exon4			CCACCTTGATGAT	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.310A>G	chr11.hg19:g.66639169T>C	ENSP00000377530:p.Lys104Glu	86.0	0.0		88.0	4.0	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	T	10.02	1.236804	0.22711	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.97328	-4.34;-4.34;-4.34;-4.34;-4.34	4.45	4.45	0.53987	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Biotin carboxylation domain (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.062464	0.64402	D	0.000010	D	0.88247	0.6385	N	0.01515	-0.825	0.46849	D	0.999229	B	0.10296	0.003	B	0.19666	0.026	D	0.84399	0.0559	10	0.10902	T	0.67	-30.511	11.7276	0.51718	0.0:0.0:0.0:1.0	.	104	P11498	PYC_HUMAN	E	104;104;104;64;104	ENSP00000377527:K104E;ENSP00000377530:K104E;ENSP00000377532:K104E;ENSP00000434192:K64E;ENSP00000347900:K104E	ENSP00000347900:K104E	K	-	1	0	PC	66395745	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.069000	0.50026	1.874000	0.54306	0.533000	0.62120	AAG	.	.		0.657	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	
PC	5091	hgsc.bcm.edu	37	11	66639568	66639568	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:66639568G>T	ENST00000393958.2	-	3	156	c.63C>A	c.(61-63)acC>acA	p.T21T	PC_ENST00000393960.1_Silent_p.T21T|PC_ENST00000355677.3_Silent_p.T21T|PC_ENST00000393955.2_Silent_p.T21T|PC_ENST00000524491.1_5'UTR	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	21					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CAGCGGGGGCGGTGGAGGTTC	0.622																																					p.T21T		Atlas-SNP	.											.	PC	116	.	0			c.C63A						.						23.0	19.0	21.0					11																	66639568		2186	4277	6463	SO:0001819	synonymous_variant	5091	exon3			GGGGGCGGTGGAG	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.63C>A	chr11.hg19:g.66639568G>T		89.0	0.0		89.0	4.0	NM_000920	B4DN00|Q16705	Silent	SNP	ENST00000393958.2	hg19	CCDS8152.1																																																																																			.	.		0.622	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	
CORO1B	57175	hgsc.bcm.edu	37	11	67210003	67210003	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:67210003G>T	ENST00000341356.5	-	2	207	c.97C>A	c.(97-99)Cgt>Agt	p.R33S	CORO1B_ENST00000393893.1_Missense_Mutation_p.R33S|CORO1B_ENST00000539724.1_5'Flank|CORO1B_ENST00000453768.2_Missense_Mutation_p.R33S|CORO1B_ENST00000545016.1_Missense_Mutation_p.R33S	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	33					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)	p.R33C(1)		cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CAGGTAACACGGGACACGCGA	0.597																																					p.R33S		Atlas-SNP	.											CORO1B,NS,carcinoma,0,1	CORO1B	30	.	1	Substitution - Missense(1)	ovary(1)	c.C97A						.						129.0	94.0	106.0					11																	67210003		2199	4295	6494	SO:0001583	missense	57175	exon2			TAACACGGGACAC	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"""Coronins"", ""WD repeat domain containing"""	2253	protein-coding gene	gene with protein product		609849	"""coronin, actin-binding protein, 1B"""			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.97C>A	chr11.hg19:g.67210003G>T	ENSP00000340211:p.Arg33Ser	123.0	1.0		149.0	6.0	NM_020441	B2RD45	Missense_Mutation	SNP	ENST00000341356.5	hg19	CCDS8164.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.932938	0.92458	.	.	ENSG00000172725	ENST00000393893;ENST00000341356;ENST00000393886;ENST00000453768;ENST00000545016	T;T;T;T	0.76316	0.15;0.15;1.84;-1.01	4.31	3.39	0.38822	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);Domain of unknown function DUF1899 (1);	0.000000	0.44285	D	0.000474	T	0.81936	0.4928	M	0.71581	2.175	0.58432	D	0.999991	B;P;P	0.51057	0.064;0.535;0.941	B;B;P	0.53593	0.111;0.325;0.73	T	0.81703	-0.0812	10	0.41790	T	0.15	-13.6447	12.3892	0.55348	0.0839:0.0:0.9161:0.0	.	33;33;33	E7EW44;F5H0D2;Q9BR76	.;.;COR1B_HUMAN	S	33;33;60;33;33	ENSP00000377471:R33S;ENSP00000340211:R33S;ENSP00000416006:R33S;ENSP00000438056:R33S	ENSP00000340211:R33S	R	-	1	0	CORO1B	66966579	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.577000	0.46042	1.145000	0.42336	0.563000	0.77884	CGT	.	.		0.597	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441	
SHANK2	22941	hgsc.bcm.edu	37	11	70336441	70336441	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:70336441T>C	ENST00000423696.2	-	13	1390	c.1354A>G	c.(1354-1356)Agc>Ggc	p.S452G	SHANK2_ENST00000449116.2_Missense_Mutation_p.S233G|SHANK2_ENST00000409161.1_Missense_Mutation_p.S235G|SHANK2_ENST00000409530.1_Missense_Mutation_p.S242G|SHANK2_ENST00000338508.4_Missense_Mutation_p.S832G|SHANK2_ENST00000357171.3_Missense_Mutation_p.S243G|SHANK2_ENST00000449833.2_Missense_Mutation_p.S236G			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	452					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			GCTTTTGGGCTCCCAGGAACA	0.597																																					p.S243G		Atlas-SNP	.											.	SHANK2	340	.	0			c.A727G						.						121.0	114.0	116.0					11																	70336441		2200	4294	6494	SO:0001583	missense	22941	exon8			TTGGGCTCCCAGG	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.1354A>G	chr11.hg19:g.70336441T>C	ENSP00000394536:p.Ser452Gly	99.0	0.0		102.0	5.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.65|13.65	2.300054|2.300054	0.40694|0.40694	.|.	.|.	ENSG00000162105|ENSG00000162105	ENST00000412252|ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018;ENST00000409530;ENST00000449116;ENST00000357171	.|T;T;T;T;T;T;T;T;T	.|0.57752	.|2.25;2.25;3.02;0.98;2.4;2.39;0.78;0.38;0.79	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	.|0.068309	.|0.53938	.|D	.|0.000056	T|T	0.55847|0.55847	0.1946|0.1946	M|M	0.74881|0.74881	2.28|2.28	0.47476|0.47476	D|D	0.999434|0.999434	.|B;B;B;B	.|0.30179	.|0.002;0.271;0.198;0.132	.|B;B;B;B	.|0.35727	.|0.004;0.066;0.157;0.209	T|T	0.55153|0.55153	-0.8185|-0.8185	5|10	.|0.27785	.|T	.|0.31	.|.	14.06|14.06	0.64793|0.64793	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|233;452;831;236	.|B7ZKU9;Q9UPX8;Q9UPX8-3;Q9UPX8-4	.|.;SHAN2_HUMAN;.;.	G|G	241|236;235;110;832;452;470;455;242;233;243	.|ENSP00000399423:S236G;ENSP00000386491:S235G;ENSP00000402944:S110G;ENSP00000345193:S832G;ENSP00000394536:S452G;ENSP00000294018:S455G;ENSP00000387324:S242G;ENSP00000394939:S233G;ENSP00000349694:S243G	.|ENSP00000294018:S455G	E|S	-|-	2|1	0|0	SHANK2|SHANK2	70014089|70014089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	4.315000|4.315000	0.59172|0.59172	1.715000|1.715000	0.51383|0.51383	0.379000|0.379000	0.24179|0.24179	GAG|AGC	.	.		0.597	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
PDE2A	5138	hgsc.bcm.edu	37	11	72292016	72292016	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:72292016C>T	ENST00000334456.5	-	24	2292	c.2047G>A	c.(2047-2049)Gac>Aac	p.D683N	PDE2A_ENST00000418754.2_Splice_Site_p.D568N|PDE2A_ENST00000540345.1_Splice_Site_p.D674N|PDE2A_ENST00000376450.3_Splice_Site_p.D427N|PDE2A_ENST00000544570.1_Splice_Site_p.D676N|PDE2A_ENST00000444035.2_Splice_Site_p.D674N	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	683	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	ATCTCGATGTCCCTGGTTGAG	0.522																																					p.D683N		Atlas-SNP	.											.	PDE2A	156	.	0			c.G2047A						.						109.0	92.0	98.0					11																	72292016		2200	4293	6493	SO:0001630	splice_region_variant	5138	exon24			CGATGTCCCTGGT	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.2046-1G>A	chr11.hg19:g.72292016C>T		89.0	0.0		71.0	4.0	NM_002599	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Missense_Mutation	SNP	ENST00000334456.5	hg19	CCDS8216.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831249	0.91036	.	.	ENSG00000186642	ENST00000334456;ENST00000376450;ENST00000444035;ENST00000429363;ENST00000544570;ENST00000418754;ENST00000540345;ENST00000420501;ENST00000441209;ENST00000542223	D;D;D;D;D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77	5.36	5.36	0.76844	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.133385	0.48767	D	0.000161	D	0.88477	0.6447	M	0.74258	2.255	0.49798	D	0.999824	D;P;D;P;P;P	0.59767	0.986;0.867;0.958;0.903;0.926;0.851	P;P;P;P;P;P	0.58780	0.476;0.714;0.805;0.667;0.845;0.644	D	0.89579	0.3819	10	0.87932	D	0	.	12.7673	0.57399	0.1639:0.8361:0.0:0.0	.	568;683;674;676;683;427	E9PEF1;O00408;E9PGI1;F6W5Z0;B2R646;Q6ZMR1	.;PDE2A_HUMAN;.;.;.;.	N	683;427;674;752;676;568;674;62;224;114	ENSP00000334910:D683N;ENSP00000365633:D427N;ENSP00000411657:D674N;ENSP00000442256:D676N;ENSP00000410310:D568N;ENSP00000446399:D674N;ENSP00000388997:D62N;ENSP00000392457:D224N;ENSP00000440834:D114N	ENSP00000334910:D683N	D	-	1	0	PDE2A	71969664	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.308000	0.65768	2.523000	0.85059	0.655000	0.94253	GAC	.	.		0.522	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	Missense_Mutation
TENM4	26011	hgsc.bcm.edu	37	11	78437179	78437179	+	Silent	SNP	C	C	A	rs369844183		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:78437179C>A	ENST00000278550.7	-	23	3957	c.3495G>T	c.(3493-3495)gcG>gcT	p.A1165A		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1165					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)										CAAGCTTGGACGCGTCAATTT	0.458																																					p.A1165A		Atlas-SNP	.											ODZ4_ENST00000278550,NS,carcinoma,0,2	.	.	.	0			c.G3495T						.						320.0	310.0	313.0					11																	78437179		1943	4136	6079	SO:0001819	synonymous_variant	26011	exon23			CTTGGACGCGTCA	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.3495G>T	chr11.hg19:g.78437179C>A		432.0	0.0		372.0	138.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.458	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
FAT3	120114	hgsc.bcm.edu	37	11	92087868	92087868	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:92087868G>T	ENST00000298047.6	+	1	2607	c.2590G>T	c.(2590-2592)Ggt>Tgt	p.G864C	FAT3_ENST00000409404.2_Missense_Mutation_p.G864C|FAT3_ENST00000525166.1_Missense_Mutation_p.G714C|FAT3_ENST00000541502.1_Missense_Mutation_p.G864C			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	864	Cadherin 8. {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)				AGGTTCTAATGGTGAAGTGAC	0.408										TCGA Ovarian(4;0.039)																											p.G864C		Atlas-SNP	.											.	FAT3	1822	.	0			c.G2590T						.						94.0	91.0	92.0					11																	92087868		1948	4145	6093	SO:0001583	missense	120114	exon1			TCTAATGGTGAAG	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.2590G>T	chr11.hg19:g.92087868G>T	ENSP00000298047:p.Gly864Cys	73.0	0.0		98.0	4.0	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	17.59	3.426755	0.62733	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.54675	4.62;4.62;0.56;4.62	5.71	5.71	0.89125	.	.	.	.	.	D	0.82825	0.5121	H	0.96805	3.885	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.88238	0.2908	9	0.87932	D	0	.	18.8459	0.92205	0.0:0.0:1.0:0.0	.	864	Q8TDW7-3	.	C	864;864;864;714	ENSP00000298047:G864C;ENSP00000387040:G864C;ENSP00000443786:G864C;ENSP00000432586:G714C	ENSP00000298047:G864C	G	+	1	0	FAT3	91727516	1.000000	0.71417	0.843000	0.33291	0.978000	0.69477	9.787000	0.99055	2.700000	0.92200	0.467000	0.42956	GGT	.	.		0.408	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
CNTN5	53942	hgsc.bcm.edu	37	11	100061877	100061877	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:100061877G>T	ENST00000524871.1	+	14	1890	c.1600G>T	c.(1600-1602)Ggg>Tgg	p.G534W	CNTN5_ENST00000528682.1_Missense_Mutation_p.G534W|CNTN5_ENST00000279463.3_Missense_Mutation_p.G534W|CNTN5_ENST00000418526.2_Missense_Mutation_p.G460W|CNTN5_ENST00000527185.1_Missense_Mutation_p.G534W	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	534	Ig-like C2-type 5.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.G534W(2)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TCTTCCAGACGGGAGTCTACG	0.368																																					p.G534W		Atlas-SNP	.											CNTN5_ENST00000524871,right_upper_lobe,carcinoma,0,2	CNTN5	324	.	2	Substitution - Missense(2)	lung(2)	c.G1600T						.						61.0	60.0	60.0					11																	100061877		1816	4070	5886	SO:0001583	missense	53942	exon13			CCAGACGGGAGTC	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.1600G>T	chr11.hg19:g.100061877G>T	ENSP00000435637:p.Gly534Trp	39.0	0.0		47.0	3.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118768	0.56505	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	5.52	4.59	0.56863	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.142130	0.64402	D	0.000003	T	0.71048	0.3294	H	0.95780	3.72	0.46654	D	0.999149	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.76575	0.988;0.957;0.975	T	0.81867	-0.0735	10	0.87932	D	0	.	15.7452	0.77936	0.0:0.1369:0.8631:0.0	.	534;460;534	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	W	534;534;534;460;534	ENSP00000433575:G534W;ENSP00000436185:G534W;ENSP00000435637:G534W;ENSP00000393229:G460W;ENSP00000279463:G534W	ENSP00000279463:G534W	G	+	1	0	CNTN5	99567087	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.309000	0.59135	1.439000	0.47511	0.650000	0.86243	GGG	.	.		0.368	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
BIRC3	330	hgsc.bcm.edu	37	11	102206786	102206786	+	Nonsense_Mutation	SNP	G	G	T	rs145025961		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:102206786G>T	ENST00000263464.3	+	7	4164	c.1414G>T	c.(1414-1416)Gga>Tga	p.G472*	BIRC3_ENST00000532808.1_Nonsense_Mutation_p.G472*	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	472	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G472R(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		ACTAACTGCCGGAATTATTAA	0.303			T	MALT1	MALT																																p.G472X		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	BIRC3,colon,carcinoma,0,1	BIRC3	56	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1414T						.						92.0	96.0	94.0					11																	102206786		2203	4298	6501	SO:0001587	stop_gained	330	exon7			ACTGCCGGAATTA	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	591	protein-coding gene	gene with protein product	"""apoptosis inhibitor 2"", ""TNFR2-TRAF signaling complex protein"", ""mammalian IAP homolog C"", ""inhibitor of apoptosis protein 1"""	601721	"""baculoviral IAP repeat-containing 3"""	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.1414G>T	chr11.hg19:g.102206786G>T	ENSP00000263464:p.Gly472*	115.0	0.0		127.0	7.0	NM_001165	Q16628|Q9HC27|Q9UP46	Nonsense_Mutation	SNP	ENST00000263464.3	hg19	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748137	0.69533	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609	.	.	.	5.28	0.32	0.15878	.	0.466068	0.27631	N	0.018503	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	9.1626	0.37032	0.7035:0.0:0.2965:0.0	.	.	.	.	X	472;472;240	.	ENSP00000263464:G472X	G	+	1	0	BIRC3	101711996	0.005000	0.15991	0.001000	0.08648	0.074000	0.17049	0.374000	0.20501	-0.101000	0.12219	-0.294000	0.09567	GGA	.	G|1.000;A|0.000		0.303	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152947	103152947	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:103152947T>C	ENST00000375735.2	+	72	10945	c.10801T>C	c.(10801-10803)Tta>Cta	p.L3601L	DYNC2H1_ENST00000398093.3_Silent_p.L3608L|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3601					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGGAGACATGTTACGGAAAGC	0.299																																					p.L3608L		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10822C						.						90.0	89.0	89.0					11																	103152947		1800	4054	5854	SO:0001819	synonymous_variant	79659	exon73			GACATGTTACGGA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10801T>C	chr11.hg19:g.103152947T>C		106.0	0.0		76.0	4.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.299	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035709	110035709	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:110035709C>T	ENST00000278590.3	+	6	1950	c.1899C>T	c.(1897-1899)agC>agT	p.S633S	ZC3H12C_ENST00000453089.2_Silent_p.S602S|ZC3H12C_ENST00000528673.1_Silent_p.S634S	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	633							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GGAGCATGAGCTGTGGGAGCA	0.522																																					p.S633S		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.C1899T						.						57.0	60.0	59.0					11																	110035709		2053	4209	6262	SO:0001819	synonymous_variant	85463	exon6			CATGAGCTGTGGG		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1899C>T	chr11.hg19:g.110035709C>T		74.0	0.0		55.0	4.0	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	hg19	CCDS44727.1																																																																																			.	.		0.522	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
ARHGAP20	57569	hgsc.bcm.edu	37	11	110479748	110479748	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:110479748C>A	ENST00000260283.4	-	9	1019	c.735G>T	c.(733-735)tgG>tgT	p.W245C	ARHGAP20_ENST00000528829.1_Missense_Mutation_p.W209C|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.W222C|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.W219C|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.W219C|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.W209C	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	245	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CAGAATTGACCCACAACTGGT	0.333																																					p.W245C		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.G735T						.						118.0	129.0	125.0					11																	110479748		2201	4298	6499	SO:0001583	missense	57569	exon9			ATTGACCCACAAC	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.735G>T	chr11.hg19:g.110479748C>A	ENSP00000260283:p.Trp245Cys	124.0	0.0		102.0	5.0	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	hg19	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.489791	0.44249	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32;2.32	5.76	5.76	0.90799	Ras-association (2);	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	M	0.79011	2.435	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.40683	-0.9550	10	0.87932	D	0	.	19.9345	0.97131	0.0:1.0:0.0:0.0	.	245;222	Q9P2F6;Q9P2F6-3	RHG20_HUMAN;.	C	245;219;222;209;219;209	ENSP00000260283:W245C;ENSP00000349660:W219C;ENSP00000432076:W222C;ENSP00000436319:W209C;ENSP00000436522:W219C;ENSP00000431399:W209C	ENSP00000260283:W245C	W	-	3	0	ARHGAP20	109984958	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	6.588000	0.74076	2.882000	0.98803	0.655000	0.94253	TGG	.	.		0.333	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
SIK2	23235	hgsc.bcm.edu	37	11	111594228	111594228	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:111594228A>G	ENST00000304987.3	+	15	2329	c.2156A>G	c.(2155-2157)cAg>cGg	p.Q719R		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	719					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						AGGCTCCAGCAGAAGCGACTC	0.423																																					p.Q719R		Atlas-SNP	.											.	SIK2	89	.	0			c.A2156G						.						49.0	57.0	54.0					11																	111594228		2201	4297	6498	SO:0001583	missense	23235	exon15			TCCAGCAGAAGCG	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"""SNF1-like kinase 2"""	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.2156A>G	chr11.hg19:g.111594228A>G	ENSP00000305976:p.Gln719Arg	87.0	0.0		88.0	4.0	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Missense_Mutation	SNP	ENST00000304987.3	hg19	CCDS8347.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.180288	0.78677	.	.	ENSG00000170145	ENST00000304987	D	0.83914	-1.78	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.89536	0.6743	M	0.61703	1.905	0.58432	D	0.999999	D	0.63880	0.993	D	0.70227	0.968	D	0.90303	0.4331	10	0.66056	D	0.02	.	15.7606	0.78076	1.0:0.0:0.0:0.0	.	719	Q9H0K1	SIK2_HUMAN	R	719	ENSP00000305976:Q719R	ENSP00000305976:Q719R	Q	+	2	0	SIK2	111099438	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.783000	0.91813	2.202000	0.70862	0.533000	0.62120	CAG	.	.		0.423	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191	
PTS	5805	hgsc.bcm.edu	37	11	112097190	112097190	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:112097190T>C	ENST00000280362.3	+	1	103	c.24T>C	c.(22-24)cgT>cgC	p.R8R	PTS_ENST00000525803.1_Silent_p.R8R|PTS_ENST00000524931.1_5'Flank	NM_000317.2	NP_000308.1	Q03393	PTPS_HUMAN	6-pyruvoyltetrahydropterin synthase	8					cellular amino acid metabolic process (GO:0006520)|central nervous system development (GO:0007417)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	6-pyruvoyltetrahydropterin synthase activity (GO:0003874)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|large_intestine(1)	2		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)		GTGGTGGCCGTCGCTGCCAGG	0.721																																					p.R8R		Atlas-SNP	.											.	PTS	7	.	0			c.T24C						.						24.0	20.0	21.0					11																	112097190		2168	4246	6414	SO:0001819	synonymous_variant	5805	exon1			TGGCCGTCGCTGC	U63382	CCDS8359.1	11q22.3	2014-04-01				ENSG00000150787	4.2.3.12		9689	protein-coding gene	gene with protein product		612719				8188266	Standard	NM_000317		Approved	PTPS	uc001pnj.4	Q03393		ENST00000280362.3:c.24T>C	chr11.hg19:g.112097190T>C		77.0	0.0		76.0	4.0	NM_000317	B0YJ87|Q8WVG8	Silent	SNP	ENST00000280362.3	hg19	CCDS8359.1																																																																																			.	.		0.721	PTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393541.1	NM_000317	
ANKK1	255239	hgsc.bcm.edu	37	11	113266922	113266922	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:113266922C>A	ENST00000303941.3	+	5	910	c.816C>A	c.(814-816)ccC>ccA	p.P272P		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		ACCAGGACCCCAAGAAGAGGC	0.642																																					p.P272P		Atlas-SNP	.											.	ANKK1	83	.	0			c.C816A						.						90.0	95.0	93.0					11																	113266922		1967	4134	6101	SO:0001819	synonymous_variant	255239	exon5			GGACCCCAAGAAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.816C>A	chr11.hg19:g.113266922C>A		121.0	0.0		104.0	5.0	NM_178510		Silent	SNP	ENST00000303941.3	hg19	CCDS44734.1																																																																																			.	.		0.642	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
FXYD6	53826	hgsc.bcm.edu	37	11	117712509	117712509	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:117712509G>T	ENST00000526014.1	-	4	764	c.169C>A	c.(169-171)Cta>Ata	p.L57I	FXYD6_ENST00000527717.1_Missense_Mutation_p.L57I|FXYD6_ENST00000524656.1_Missense_Mutation_p.L57I|FXYD6_ENST00000530956.1_Missense_Mutation_p.L57I|FXYD6_ENST00000540359.1_Missense_Mutation_p.L57I|FXYD6_ENST00000527429.1_Missense_Mutation_p.L57I|FXYD6-FXYD2_ENST00000532984.1_Missense_Mutation_p.L57I|FXYD6_ENST00000260282.4_Missense_Mutation_p.L57I|FXYD6_ENST00000584394.1_Missense_Mutation_p.L57I|FXYD6_ENST00000539526.1_Missense_Mutation_p.L57I|RP11-728F11.4_ENST00000581173.2_RNA|FXYD6_ENST00000583233.1_5'UTR|FXYD6_ENST00000529335.2_Missense_Mutation_p.L56I|FXYD6_ENST00000584230.1_Missense_Mutation_p.L57I	NM_022003.3	NP_071286.1	Q9H0Q3	FXYD6_HUMAN	FXYD domain containing ion transport regulator 6	57					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)			central_nervous_system(1)|large_intestine(5)|lung(1)|skin(1)	8	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.89e-05)|Epithelial(105;0.00122)		AACTTACTTAGGATAAGGAGG	0.527																																					p.L57I		Atlas-SNP	.											.	.	.	.	0			c.C169A						.						106.0	100.0	102.0					11																	117712509		2201	4296	6497	SO:0001583	missense	100533181	exon4			TACTTAGGATAAG	BC093040	CCDS8387.1	11q23.3	2010-04-14	2002-01-14		ENSG00000137726	ENSG00000137726			4030	protein-coding gene	gene with protein product	"""phosphohippolin"""	606683	"""FXYD domain-containing ion transport regulator 6"""			10950925	Standard	NM_022003		Approved			Q9H0Q3		ENST00000526014.1:c.169C>A	chr11.hg19:g.117712509G>T	ENSP00000433312:p.Leu57Ile	112.0	0.0		87.0	5.0	NM_001243598	A8K0R4|J3QLD2|Q6FIG9|Q6UW52	Missense_Mutation	SNP	ENST00000526014.1	hg19	CCDS8387.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253512	0.59212	.	.	ENSG00000137726	ENST00000540359;ENST00000539526;ENST00000260282;ENST00000527717;ENST00000526014;ENST00000524656;ENST00000529335	T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62	5.42	4.51	0.55191	.	.	.	.	.	D	0.82360	0.5020	.	.	.	0.51767	D	0.999933	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.83361	0.0002	8	0.62326	D	0.03	.	10.4055	0.44254	0.0904:0.0:0.9096:0.0	.	57;57	E9PJ02;Q9H0Q3	.;FXYD6_HUMAN	I	57;57;57;57;57;57;56	ENSP00000444243:L57I;ENSP00000442756:L57I;ENSP00000260282:L57I;ENSP00000431446:L57I;ENSP00000433312:L57I;ENSP00000431427:L57I;ENSP00000436629:L56I	ENSP00000260282:L57I	L	-	1	2	FXYD6	117217719	1.000000	0.71417	0.933000	0.37362	0.483000	0.33249	4.120000	0.57897	1.282000	0.44496	-0.126000	0.14955	CTA	.	.		0.527	FXYD6-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392307.1	NM_022003	
OR8D2	283160	hgsc.bcm.edu	37	11	124189725	124189725	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:124189725A>G	ENST00000357438.2	-	1	459	c.369T>C	c.(367-369)taT>taC	p.Y123Y		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		AGATAGCAACATAACGGTCAT	0.418																																					p.Y123Y		Atlas-SNP	.											OR8D2,right_upper_lobe,carcinoma,0,1	OR8D2	65	.	0			c.T369C						.						94.0	89.0	91.0					11																	124189725		2201	4299	6500	SO:0001819	synonymous_variant	283160	exon1			AGCAACATAACGG	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"""GPCR / Class A : Olfactory receptors"""	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.369T>C	chr11.hg19:g.124189725A>G		56.0	0.0		50.0	2.0	NM_001002918	B9EH49|Q6IFR0	Silent	SNP	ENST00000357438.2	hg19	CCDS31707.1																																																																																			.	.		0.418	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918	
OR8A1	390275	hgsc.bcm.edu	37	11	124440852	124440852	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:124440852G>T	ENST00000284287.3	+	1	960	c.888G>T	c.(886-888)acG>acT	p.T296T		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	296					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TCTACACCACGGTAATCCCCA	0.468																																					p.T296T		Atlas-SNP	.											.	OR8A1	61	.	0			c.G888T						.						79.0	70.0	73.0					11																	124440852		2201	4299	6500	SO:0001819	synonymous_variant	390275	exon1			CACCACGGTAATC	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"""GPCR / Class A : Olfactory receptors"""	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.888G>T	chr11.hg19:g.124440852G>T		180.0	0.0		154.0	8.0	NM_001005194	Q6IEW7|Q96RC6	Silent	SNP	ENST00000284287.3	hg19	CCDS31712.1																																																																																			.	.		0.468	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194	
SPATA19	219938	hgsc.bcm.edu	37	11	133714476	133714476	+	Missense_Mutation	SNP	C	C	G	rs138068697		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr11:133714476C>G	ENST00000299140.3	-	3	249	c.195G>C	c.(193-195)caG>caC	p.Q65H	SPATA19_ENST00000532889.1_Missense_Mutation_p.Q65H	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	65					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		CCCTTACACCCTGGGAAGGGT	0.512																																					p.Q65H		Atlas-SNP	.											.	SPATA19	36	.	0			c.G195C						.						136.0	131.0	132.0					11																	133714476		2201	4297	6498	SO:0001583	missense	219938	exon3			TACACCCTGGGAA	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"""spergen 1"", ""cancer/testis antigen 132"""	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.195G>C	chr11.hg19:g.133714476C>G	ENSP00000299140:p.Gln65His	225.0	0.0		178.0	110.0	NM_174927	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	hg19	CCDS8493.1	.	.	.	.	.	.	.	.	.	.	C	8.443	0.851238	0.17034	.	.	ENSG00000166118	ENST00000299140;ENST00000532889	T;T	0.46451	0.87;0.87	1.33	1.33	0.21861	.	.	.	.	.	T	0.36193	0.0958	N	0.08118	0	0.09310	N	1	D	0.54397	0.966	P	0.61592	0.891	T	0.16070	-1.0415	9	0.87932	D	0	.	6.4121	0.21696	0.0:1.0:0.0:0.0	.	65	Q7Z5L4	SPT19_HUMAN	H	65	ENSP00000299140:Q65H;ENSP00000435248:Q65H	ENSP00000299140:Q65H	Q	-	3	2	SPATA19	133219686	0.038000	0.19896	0.010000	0.14722	0.010000	0.07245	0.441000	0.21611	0.585000	0.29608	0.591000	0.81541	CAG	.	C|1.000;T|0.000		0.512	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927	
PLEKHG6	55200	hgsc.bcm.edu	37	12	6436814	6436814	+	Silent	SNP	C	C	A	rs149885168		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:6436814C>A	ENST00000396988.3	+	15	2295	c.2065C>A	c.(2065-2067)Cgg>Agg	p.R689R	PLEKHG6_ENST00000449001.2_Silent_p.R657R|PLEKHG6_ENST00000304581.8_Silent_p.R219R|PLEKHG6_ENST00000011684.7_Silent_p.R689R	NM_001144856.1	NP_001138328.1	Q3KR16	PKHG6_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	689						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(4)	23						CCACAGGGCCCGGCTTCGGGG	0.637																																					p.R689R		Atlas-SNP	.											PLEKHG6,NS,carcinoma,0,1	PLEKHG6	62	.	0			c.C2065A						.						12.0	15.0	14.0					12																	6436814		2189	4277	6466	SO:0001819	synonymous_variant	55200	exon15			AGGGCCCGGCTTC	AK001527	CCDS8541.1, CCDS44808.1	12p13.31	2013-01-11			ENSG00000008323	ENSG00000008323		"""Pleckstrin homology (PH) domain containing"""	25562	protein-coding gene	gene with protein product		611743					Standard	NM_018173		Approved	FLJ10665	uc001qnr.3	Q3KR16	OTTHUMG00000168266	ENST00000396988.3:c.2065C>A	chr12.hg19:g.6436814C>A		43.0	0.0		48.0	2.0	NM_001144856	Q3SWR1|Q8N1P1|Q8WYY1|Q9H8F4|Q9NVK9	Silent	SNP	ENST00000396988.3	hg19	CCDS8541.1																																																																																			.	C|1.000;G|0.000		0.637	PLEKHG6-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399031.1	NM_018173	
CLEC1A	51267	hgsc.bcm.edu	37	12	10224077	10224077	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:10224077C>T	ENST00000315330.4	-	6	760	c.698G>A	c.(697-699)aGc>aAc	p.S233N	CLEC1A_ENST00000420265.2_Missense_Mutation_p.S141N|CLEC1A_ENST00000457018.2_Missense_Mutation_p.S200N	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	233	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.S233N(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						ACAGTCTCTGCTTCTTGGGCT	0.383																																					p.S233N		Atlas-SNP	.											CLEC1A,NS,carcinoma,0,1	CLEC1A	48	.	1	Substitution - Missense(1)	lung(1)	c.G698A						.						169.0	157.0	161.0					12																	10224077		2203	4300	6503	SO:0001583	missense	51267	exon6			TCTCTGCTTCTTG	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"""C-type lectin domain containing"""	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.698G>A	chr12.hg19:g.10224077C>T	ENSP00000326407:p.Ser233Asn	72.0	0.0		63.0	3.0	NM_016511	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	hg19	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	C	0.146	-1.096261	0.01843	.	.	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265	T;T;T	0.16597	2.33;2.33;2.33	5.42	-0.634	0.11516	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.724899	0.13080	N	0.415351	T	0.09730	0.0239	L	0.28344	0.845	0.21020	N	0.999804	B;B;B	0.20164	0.042;0.018;0.001	B;B;B	0.22601	0.04;0.028;0.012	T	0.43196	-0.9406	10	0.08381	T	0.77	.	9.157	0.36998	0.0:0.5607:0.0:0.4393	.	141;200;233	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	N	233;200;141	ENSP00000326407:S233N;ENSP00000415048:S200N;ENSP00000417010:S141N	ENSP00000326407:S233N	S	-	2	0	CLEC1A	10115344	0.157000	0.22836	0.034000	0.17996	0.578000	0.36192	-0.765000	0.04730	-0.459000	0.07013	-0.253000	0.11424	AGC	.	.		0.383	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511	
TAS2R42	353164	hgsc.bcm.edu	37	12	11338858	11338858	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:11338858T>C	ENST00000334266.1	-	1	685	c.686A>G	c.(685-687)cAt>cGt	p.H229R		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	229					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			GGCCCTCCTATGGGCCTCTGT	0.413																																					p.H229R	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.A686G						.						74.0	77.0	76.0					12																	11338858		2203	4300	6503	SO:0001583	missense	353164	exon1			CTCCTATGGGCCT	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.686A>G	chr12.hg19:g.11338858T>C	ENSP00000334050:p.His229Arg	81.0	0.0		87.0	4.0	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	hg19	CCDS31747.1	.	.	.	.	.	.	.	.	.	.	T	9.369	1.070082	0.20147	.	.	ENSG00000186136	ENST00000334266	T	0.00958	5.5	3.6	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.076157	0.52532	D	0.000072	T	0.07279	0.0184	H	0.94886	3.595	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05289	-1.0894	10	0.87932	D	0	.	8.7846	0.34811	0.0:0.0:0.0:1.0	.	229	Q7RTR8	T2R42_HUMAN	R	229	ENSP00000334050:H229R	ENSP00000334050:H229R	H	-	2	0	TAS2R42	11230125	0.807000	0.29009	0.144000	0.22314	0.003000	0.03518	2.142000	0.42177	1.669000	0.50854	0.533000	0.62120	CAT	.	.		0.413	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
SYT10	341359	hgsc.bcm.edu	37	12	33579155	33579155	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:33579155C>T	ENST00000228567.3	-	2	723	c.427G>A	c.(427-429)Gaa>Aaa	p.E143K	SYT10_ENST00000567656.1_5'Flank|SYT10_ENST00000535526.1_5'UTR	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	143					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					GTTTGGACTTCTGCTGGGATG	0.383																																					p.E143K		Atlas-SNP	.											.	SYT10	109	.	0			c.G427A						.						186.0	193.0	191.0					12																	33579155		2203	4300	6503	SO:0001583	missense	341359	exon2			GGACTTCTGCTGG	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"""Synaptotagmins"""	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.427G>A	chr12.hg19:g.33579155C>T	ENSP00000228567:p.Glu143Lys	675.0	2.0		621.0	235.0	NM_198992	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	hg19	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782972	0.90282	.	.	ENSG00000110975	ENST00000228567	T	0.56103	0.48	3.78	3.78	0.43462	.	0.000000	0.41938	U	0.000791	T	0.53449	0.1797	M	0.71036	2.16	0.80722	D	1	P	0.38711	0.643	B	0.38327	0.271	T	0.60352	-0.7280	10	0.40728	T	0.16	.	15.8987	0.79356	0.0:1.0:0.0:0.0	.	143	Q6XYQ8	SYT10_HUMAN	K	143	ENSP00000228567:E143K	ENSP00000228567:E143K	E	-	1	0	SYT10	33470422	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.798000	0.75155	2.390000	0.81377	0.655000	0.94253	GAA	.	.		0.383	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
PDZRN4	29951	hgsc.bcm.edu	37	12	41946515	41946515	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:41946515C>A	ENST00000402685.2	+	6	1269	c.1261C>A	c.(1261-1263)Cga>Aga	p.R421R	PDZRN4_ENST00000298919.7_Silent_p.R161R|PDZRN4_ENST00000539469.2_Silent_p.R163R	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	421	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R163R(1)|p.R421R(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AGTCTGTTACCGAACAGATGA	0.473																																					p.R421R		Atlas-SNP	.											.	PDZRN4	346	.	2	Substitution - coding silent(2)	lung(2)	c.C1261A						.						149.0	132.0	138.0					12																	41946515		2203	4300	6503	SO:0001819	synonymous_variant	29951	exon6			TGTTACCGAACAG	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1261C>A	chr12.hg19:g.41946515C>A		122.0	0.0		96.0	4.0	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	hg19	CCDS53777.1																																																																																			.	.		0.473	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
PRPH	5630	hgsc.bcm.edu	37	12	49690226	49690226	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:49690226T>C	ENST00000257860.4	+	3	2117	c.618T>C	c.(616-618)gaT>gaC	p.D206D	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						ACGTGGACGATGCCACTCTGT	0.577																																					p.D206D		Atlas-SNP	.											.	PRPH	26	.	0			c.T618C						.						84.0	76.0	78.0					12																	49690226		2203	4300	6503	SO:0001819	synonymous_variant	5630	exon3			GGACGATGCCACT		CCDS8783.1	12q12-q13	2013-01-16						"""Intermediate filaments type III"""	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.618T>C	chr12.hg19:g.49690226T>C		74.0	0.0		77.0	4.0	NM_006262	Q5TFH5|Q6DK65	Silent	SNP	ENST00000257860.4	hg19	CCDS8783.1																																																																																			.	.		0.577	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262	
TROAP	10024	hgsc.bcm.edu	37	12	49725141	49725141	+	Missense_Mutation	SNP	G	G	T	rs200487146	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:49725141G>T	ENST00000257909.3	+	14	2319	c.2243G>T	c.(2242-2244)cGg>cTg	p.R748L	TROAP_ENST00000551245.1_Missense_Mutation_p.R838L|TROAP_ENST00000547923.1_Missense_Mutation_p.R427L	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	748					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						GGCCCCACCCGGGTCTGCACC	0.602											OREG0021792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R748L		Atlas-SNP	.											.	TROAP	80	.	0			c.G2243T						.						52.0	50.0	51.0					12																	49725141		2203	4300	6503	SO:0001583	missense	10024	exon14			CCACCCGGGTCTG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.2243G>T	chr12.hg19:g.49725141G>T	ENSP00000257909:p.Arg748Leu	97.0	0.0	964	123.0	5.0	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	hg19	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.612630	0.87258	.	.	ENSG00000135451	ENST00000551245;ENST00000257909;ENST00000547923	.	.	.	5.93	5.93	0.95920	.	0.000000	0.53938	D	0.000058	T	0.70806	0.3266	L	0.47190	1.495	0.34673	D	0.72388	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.78033	-0.2362	9	0.87932	D	0	-20.8276	15.8438	0.78871	0.0:0.0:1.0:0.0	.	838;427;748	F8W130;F8W1U0;Q12815	.;.;TROAP_HUMAN	L	838;748;427	.	ENSP00000257909:R748L	R	+	2	0	TROAP	48011408	0.985000	0.35326	0.892000	0.35008	0.967000	0.64934	3.669000	0.54561	2.815000	0.96918	0.561000	0.74099	CGG	.	G|0.999;A|0.001		0.602	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
KRT2	3849	hgsc.bcm.edu	37	12	53040547	53040547	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53040547T>C	ENST00000309680.3	-	7	1467	c.1446A>G	c.(1444-1446)aaA>aaG	p.K482K		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	482	Coil 2.|Rod.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		CCTCCAGCAGTTTGCGGTAGG	0.627																																					p.K482K		Atlas-SNP	.											.	KRT2	94	.	0			c.A1446G						.						96.0	86.0	89.0					12																	53040547		2203	4300	6503	SO:0001819	synonymous_variant	3849	exon7			CAGCAGTTTGCGG		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1446A>G	chr12.hg19:g.53040547T>C		66.0	0.0		67.0	4.0	NM_000423	Q4VAQ2	Silent	SNP	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.627	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
KRT1	3848	hgsc.bcm.edu	37	12	53069530	53069530	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53069530T>C	ENST00000252244.3	-	8	1534		c.e8-2			NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1						complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CCAGACATCCTGTAGGAGAAA	0.517																																					.		Atlas-SNP	.											.	KRT1	110	.	0			c.1476-2A>G						.						87.0	81.0	83.0					12																	53069530		2203	4300	6503	SO:0001630	splice_region_variant	3848	exon9			ACATCCTGTAGGA	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1476-2A>G	chr12.hg19:g.53069530T>C		153.0	0.0		139.0	6.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Splice_Site	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.540002	0.27563	.	.	ENSG00000167768	ENST00000252244	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.244	0.37513	0.0:0.0951:0.0:0.9049	.	.	.	.	.	-1	.	.	.	-	.	.	KRT1	51355797	0.997000	0.39634	0.953000	0.39169	0.419000	0.31324	2.849000	0.48286	1.812000	0.52913	0.379000	0.24179	.	.	.		0.517	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	Intron
KRT77	374454	hgsc.bcm.edu	37	12	53086273	53086273	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53086273C>T	ENST00000341809.3	-	7	1387	c.1359G>A	c.(1357-1359)ctG>ctA	p.L453L	KRT77_ENST00000537195.1_Silent_p.L220L|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	453	Coil 2.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						GCTTGACCCCCAGCATGGCCT	0.657																																					p.L453L		Atlas-SNP	.											.	KRT77	58	.	0			c.G1359A						.						54.0	49.0	51.0					12																	53086273		2203	4300	6503	SO:0001819	synonymous_variant	374454	exon7			GACCCCCAGCATG	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1359G>A	chr12.hg19:g.53086273C>T		102.0	0.0		100.0	5.0	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	hg19	CCDS8837.1																																																																																			.	.		0.657	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
NPFF	8620	hgsc.bcm.edu	37	12	53899518	53899518	+	IGR	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:53899518T>C	ENST00000267017.3	-	0	592				TARBP2_ENST00000456234.2_Missense_Mutation_p.I255T|TARBP2_ENST00000552857.1_Silent_p.D142D|TARBP2_ENST00000394357.2_Missense_Mutation_p.I255T|TARBP2_ENST00000266987.2_Missense_Mutation_p.I276T	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						GGAGAGAAGATCCTGTCCCTC	0.617																																					p.I276T		Atlas-SNP	.											.	TARBP2	35	.	0			c.T827C						.						104.0	107.0	106.0					12																	53899518		2203	4300	6503	SO:0001628	intergenic_variant	6895	exon8			AGAAGATCCTGTC	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"""Endogenous ligands"""	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		chr12.hg19:g.53899518T>C		46.0	0.0		61.0	4.0	NM_134323	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	hg19	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.701358	0.88924	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000394357	T;T;T	0.65364	-0.15;-0.14;-0.14	4.98	4.98	0.66077	.	0.050187	0.85682	D	0.000000	T	0.59569	0.2203	L	0.59436	1.845	0.80722	D	1	P	0.34522	0.455	B	0.34991	0.193	T	0.63888	-0.6535	10	0.54805	T	0.06	-8.0569	14.0884	0.64973	0.0:0.0:0.0:1.0	.	276	Q15633	TRBP2_HUMAN	T	276;255;255	ENSP00000266987:I276T;ENSP00000416077:I255T;ENSP00000377885:I255T	ENSP00000266987:I276T	I	+	2	0	TARBP2	52185785	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.690000	0.61731	2.227000	0.72691	0.459000	0.35465	ATC	.	.		0.617	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717	
GTSF1	121355	hgsc.bcm.edu	37	12	54858950	54858950	+	Splice_Site	SNP	G	G	T	rs146835334		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:54858950G>T	ENST00000552397.1	-	3	914	c.18C>A	c.(16-18)acC>acA	p.T6T	GTSF1_ENST00000305879.5_Splice_Site_p.T6T|RP11-753H16.3_ENST00000550474.1_RNA|GTSF1_ENST00000552395.1_Intron|RP11-753H16.5_ENST00000552785.1_RNA			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1	6						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				CCAGGGAGTCGGCTGAAAGAC	0.428																																					p.T6T		Atlas-SNP	.											.	GTSF1	15	.	0			c.C18A						.						103.0	97.0	99.0					12																	54858950		2203	4300	6503	SO:0001630	splice_region_variant	121355	exon3			GGAGTCGGCTGAA	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"""family with sequence similarity 112, member B"""	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.17-1C>A	chr12.hg19:g.54858950G>T		82.0	0.0		87.0	4.0	NM_144594	B3KQ60|Q0VGM4|Q8N778	Silent	SNP	ENST00000552397.1	hg19	CCDS8881.1																																																																																			.	G|1.000;A|0.000		0.428	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594	Silent
MMP19	4327	hgsc.bcm.edu	37	12	56234938	56234938	+	Missense_Mutation	SNP	C	C	A	rs202159629		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56234938C>A	ENST00000322569.4	-	3	347	c.256G>T	c.(256-258)Ggc>Tgc	p.G86C	MMP19_ENST00000394182.1_5'Flank|MMP19_ENST00000409200.3_Missense_Mutation_p.G86C|MMP19_ENST00000547487.1_5'UTR|MMP19_ENST00000548629.1_Missense_Mutation_p.G86C	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	86					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	TCCTCTAGGCCACAACGAGGC	0.547																																					p.G86C		Atlas-SNP	.											.	MMP19	61	.	0			c.G256T						.						96.0	98.0	97.0					12																	56234938		2203	4300	6503	SO:0001583	missense	4327	exon3			CTAGGCCACAACG	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.256G>T	chr12.hg19:g.56234938C>A	ENSP00000313437:p.Gly86Cys	35.0	0.0		45.0	4.0	NM_001272101	B4E030|O15278|O95606|Q99580	Missense_Mutation	SNP	ENST00000322569.4	hg19	CCDS8895.1	.	.	.	.	.	.	.	.	.	.	C	32	5.106959	0.94292	.	.	ENSG00000123342	ENST00000322569;ENST00000548629;ENST00000409200	T;T;T	0.67171	-0.25;-0.25;-0.25	5.8	5.8	0.92144	Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87116	0.6097	M	0.93939	3.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89741	0.3933	10	0.87932	D	0	.	18.8323	0.92145	0.0:1.0:0.0:0.0	.	86;86	B4E030;Q99542	.;MMP19_HUMAN	C	86	ENSP00000313437:G86C;ENSP00000446979:G86C;ENSP00000386625:G86C	ENSP00000313437:G86C	G	-	1	0	MMP19	54521205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.860000	0.75473	2.755000	0.94549	0.655000	0.94253	GGC	.	C|0.999;T|0.001		0.547	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	
ESYT1	23344	hgsc.bcm.edu	37	12	56530663	56530663	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56530663A>G	ENST00000394048.5	+	16	2032	c.1768A>G	c.(1768-1770)Aaa>Gaa	p.K590E	ESYT1_ENST00000541590.1_Missense_Mutation_p.K600E|ESYT1_ENST00000267113.4_Missense_Mutation_p.K600E	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	590					lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						ACTCTATATGAAACTAGTCAT	0.527																																					p.K600E		Atlas-SNP	.											.	ESYT1	84	.	0			c.A1798G						.						69.0	70.0	69.0					12																	56530663		2203	4300	6503	SO:0001583	missense	23344	exon16			TATATGAAACTAG	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"""Synaptotagmins"""	29534	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member A"""	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.1768A>G	chr12.hg19:g.56530663A>G	ENSP00000377612:p.Lys590Glu	88.0	0.0		77.0	4.0	NM_001184796	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Missense_Mutation	SNP	ENST00000394048.5	hg19	CCDS8904.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.587028	0.66105	.	.	ENSG00000139641	ENST00000394048;ENST00000402331;ENST00000267113;ENST00000541590	T;T;T	0.69685	-0.42;-0.42;-0.42	4.95	4.95	0.65309	C2 calcium/lipid-binding domain, CaLB (1);	0.094256	0.64402	D	0.000001	T	0.71567	0.3355	M	0.78456	2.415	0.51767	D	0.999936	P;B	0.38129	0.619;0.307	P;B	0.44359	0.447;0.138	T	0.70306	-0.4908	10	0.25751	T	0.34	-12.5496	13.8923	0.63747	1.0:0.0:0.0:0.0	.	600;590	Q9BSJ8-2;Q9BSJ8	.;ESYT1_HUMAN	E	590;544;600;600	ENSP00000377612:K590E;ENSP00000267113:K600E;ENSP00000445952:K600E	ENSP00000267113:K600E	K	+	1	0	ESYT1	54816930	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	8.098000	0.89540	1.991000	0.58162	0.533000	0.62120	AAA	.	.		0.527	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292	
SMARCC2	6601	hgsc.bcm.edu	37	12	56580987	56580987	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56580987G>T	ENST00000267064.4	-	2	301	c.215C>A	c.(214-216)cCg>cAg	p.P72Q	SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000394023.3_Missense_Mutation_p.P72Q|SMARCC2_ENST00000347471.4_Missense_Mutation_p.P72Q|SMARCC2_ENST00000550164.1_Missense_Mutation_p.P72Q|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	72					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.P72L(2)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			TTTAGTGAGCGGTGCATTGCT	0.463																																					p.P72Q		Atlas-SNP	.											SMARCC2_ENST00000267064,NS,carcinoma,0,2	SMARCC2	212	.	2	Substitution - Missense(2)	lung(2)	c.C215A						.						95.0	95.0	95.0					12																	56580987		2203	4300	6503	SO:0001583	missense	6601	exon2			GTGAGCGGTGCAT	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.215C>A	chr12.hg19:g.56580987G>T	ENSP00000267064:p.Pro72Gln	89.0	0.0		71.0	4.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841509	0.71488	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T	0.49139	0.79;0.81;0.79	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.66436	0.2789	M	0.71036	2.16	0.58432	D	0.999997	D;D;D;D	0.71674	0.993;0.988;0.998;0.993	D;P;P;D	0.63877	0.919;0.832;0.881;0.919	T	0.65742	-0.6094	10	0.46703	T	0.11	-12.5461	17.8735	0.88818	0.0:0.0:1.0:0.0	.	72;77;72;72	F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;SMRC2_HUMAN;.	Q	72	ENSP00000449396:P72Q;ENSP00000302919:P72Q;ENSP00000267064:P72Q	ENSP00000267064:P72Q	P	-	2	0	SMARCC2	54867254	1.000000	0.71417	0.993000	0.49108	0.974000	0.67602	9.196000	0.94978	2.836000	0.97738	0.655000	0.94253	CCG	.	.		0.463	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
RBMS2	5939	hgsc.bcm.edu	37	12	56982115	56982115	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56982115T>C	ENST00000262031.5	+	12	1195	c.1100T>C	c.(1099-1101)aTc>aCc	p.I367T	RNU6-343P_ENST00000364709.1_RNA|RBMS2_ENST00000542360.1_Missense_Mutation_p.I222T|RBMS2_ENST00000550726.1_Missense_Mutation_p.I242T|RBMS2_ENST00000552247.2_Missense_Mutation_p.I304T	NM_002898.3	NP_002889.1	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting protein 2	367					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.I367T(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(3)|skin(2)|urinary_tract(1)	18						GGAGCTTACATCTCCCAGTAC	0.453																																					p.I367T		Atlas-SNP	.											RBMS2,NS,carcinoma,0,1	RBMS2	29	.	1	Substitution - Missense(1)	endometrium(1)	c.T1100C						.						158.0	139.0	146.0					12																	56982115		2203	4300	6503	SO:0001583	missense	5939	exon12			CTTACATCTCCCA	D28483	CCDS8923.1	12q13.13	2013-02-12			ENSG00000076067	ENSG00000076067		"""RNA binding motif (RRM) containing"""	9909	protein-coding gene	gene with protein product		602387				8041632	Standard	NM_002898		Approved	SCR3	uc001sln.2	Q15434	OTTHUMG00000170488	ENST00000262031.5:c.1100T>C	chr12.hg19:g.56982115T>C	ENSP00000262031:p.Ile367Thr	102.0	1.0		122.0	5.0	NM_002898		Missense_Mutation	SNP	ENST00000262031.5	hg19	CCDS8923.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.152326	0.78001	.	.	ENSG00000076067	ENST00000262031;ENST00000552247;ENST00000550726;ENST00000542360	T;T;T	0.27256	2.53;2.49;1.68	4.8	4.8	0.61643	.	0.156720	0.53938	D	0.000048	T	0.41949	0.1181	M	0.61703	1.905	0.80722	D	1	P;D	0.62365	0.95;0.991	P;P	0.61477	0.635;0.889	T	0.15636	-1.0430	10	0.20046	T	0.44	.	13.7659	0.62995	0.0:0.0:0.0:1.0	.	222;367	F5H5C8;Q15434	.;RBMS2_HUMAN	T	367;304;242;222	ENSP00000262031:I367T;ENSP00000447426:I304T;ENSP00000449678:I242T	ENSP00000262031:I367T	I	+	2	0	RBMS2	55268382	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.234000	0.78134	2.155000	0.67459	0.482000	0.46254	ATC	.	.		0.453	RBMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409366.2	NM_002898	
BAZ2A	11176	hgsc.bcm.edu	37	12	56992704	56992704	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:56992704T>C	ENST00000551812.1	-	28	5693	c.5500A>G	c.(5500-5502)Atc>Gtc	p.I1834V	BAZ2A_ENST00000379441.3_Missense_Mutation_p.I1804V|BAZ2A_ENST00000179765.5_Missense_Mutation_p.I1802V|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000549884.1_Missense_Mutation_p.I1832V	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1834	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GGATTTTTGATGATGCGCCGG	0.532																																					p.I1834V		Atlas-SNP	.											.	BAZ2A	263	.	0			c.A5500G						.						28.0	29.0	29.0					12																	56992704		1889	4119	6008	SO:0001583	missense	11176	exon28			TTTTGATGATGCG	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.5500A>G	chr12.hg19:g.56992704T>C	ENSP00000446880:p.Ile1834Val	64.0	0.0		65.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.140015	0.56936	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	5.81	4.66	0.58398	Bromodomain (6);Bromodomain, conserved site (1);	0.127834	0.51477	D	0.000096	T	0.52484	0.1737	M	0.73598	2.24	0.47698	D	0.999492	B;P;P;B	0.36378	0.094;0.495;0.55;0.0	B;P;P;B	0.56042	0.387;0.686;0.79;0.007	T	0.53078	-0.8489	10	0.59425	D	0.04	-11.7719	11.3801	0.49752	0.0:0.0721:0.0:0.9279	.	1832;1830;1834;1807	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	V	1804;1802;1834;766;1832	ENSP00000368754:I1804V;ENSP00000179765:I1802V;ENSP00000446880:I1834V;ENSP00000448760:I766V;ENSP00000447941:I1832V	ENSP00000179765:I1802V	I	-	1	0	BAZ2A	55278971	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.886000	0.48578	1.141000	0.42275	0.529000	0.55759	ATC	.	.		0.532	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
TMEM194A	23306	hgsc.bcm.edu	37	12	57472459	57472459	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57472459C>T	ENST00000300128.4	-	1	93	c.70G>A	c.(70-72)Ggc>Agc	p.G24S	TMEM194A_ENST00000553654.1_Intron|TMEM194A_ENST00000379391.3_Missense_Mutation_p.G24S	NM_001130963.1	NP_001124435.1	O14524	T194A_HUMAN	transmembrane protein 194A	24						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(3)|lung(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GTCCCACCGCCCCCGACTCCC	0.692																																					p.G24S		Atlas-SNP	.											.	TMEM194A	64	.	0			c.G70A						.						46.0	60.0	55.0					12																	57472459		2200	4296	6496	SO:0001583	missense	23306	exon1			CACCGCCCCCGAC	AB006624	CCDS31841.1, CCDS44927.1	12q13.3	2008-06-10	2008-06-10	2008-06-10		ENSG00000166881			29001	protein-coding gene	gene with protein product			"""transmembrane protein 194"""	TMEM194			Standard	NM_015257		Approved	KIAA0286	uc001smy.3	O14524		ENST00000300128.4:c.70G>A	chr12.hg19:g.57472459C>T	ENSP00000300128:p.Gly24Ser	124.0	0.0		104.0	5.0	NM_015257	Q17R72|Q68DH0|Q6IQ25	Missense_Mutation	SNP	ENST00000300128.4	hg19	CCDS44927.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010282	0.35511	.	.	ENSG00000166881	ENST00000379391;ENST00000300128	T;T	0.53206	0.63;0.85	3.82	3.82	0.43975	.	0.531789	0.17932	N	0.157122	T	0.42787	0.1218	L	0.51422	1.61	0.19575	N	0.999969	P;P	0.37330	0.455;0.59	B;B	0.37888	0.133;0.26	T	0.41805	-0.9488	10	0.52906	T	0.07	-0.1012	11.5069	0.50472	0.0:1.0:0.0:0.0	.	24;24	O14524;O14524-2	T194A_HUMAN;.	S	24	ENSP00000368701:G24S;ENSP00000300128:G24S	ENSP00000300128:G24S	G	-	1	0	TMEM194A	55758726	0.037000	0.19845	0.288000	0.24862	0.047000	0.14425	2.059000	0.41384	2.415000	0.81967	0.655000	0.94253	GGC	.	.		0.692	TMEM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411272.1	NM_015257	
LRP1	4035	hgsc.bcm.edu	37	12	57539101	57539101	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57539101A>G	ENST00000243077.3	+	6	1135	c.669A>G	c.(667-669)acA>acG	p.T223T	LRP1_ENST00000338962.4_Silent_p.T223T|LRP1_ENST00000554174.1_Silent_p.T223T|RP11-545N8.3_ENST00000554476.1_RNA|LRP1_ENST00000553277.1_Silent_p.T223T|RP11-545N8.3_ENST00000555461.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	223					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CTACCATCACACCTACGAGCA	0.592																																					p.T223T		Atlas-SNP	.											.	LRP1	428	.	0			c.A669G						.						106.0	64.0	78.0					12																	57539101		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon6			CATCACACCTACG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.669A>G	chr12.hg19:g.57539101A>G		84.0	0.0		87.0	4.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
LRP1	4035	hgsc.bcm.edu	37	12	57599189	57599189	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57599189C>A	ENST00000243077.3	+	74	11857	c.11391C>A	c.(11389-11391)cgC>cgA	p.R3797R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3797	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ACGAGGCACGCTGCGTGCGCA	0.677																																					p.R3797R		Atlas-SNP	.											.	LRP1	428	.	0			c.C11391A						.						35.0	36.0	36.0					12																	57599189		2200	4299	6499	SO:0001819	synonymous_variant	4035	exon74			GGCACGCTGCGTG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.11391C>A	chr12.hg19:g.57599189C>A		66.0	0.0		93.0	4.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.677	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
GLI1	2735	hgsc.bcm.edu	37	12	57864991	57864991	+	Missense_Mutation	SNP	G	G	T	rs149553839	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57864991G>T	ENST00000228682.2	+	12	2559	c.2468G>T	c.(2467-2469)gGg>gTg	p.G823V	GLI1_ENST00000546141.1_Missense_Mutation_p.G782V|GLI1_ENST00000543426.1_Missense_Mutation_p.G695V	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	823					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TGCCCAGTGGGGTCTGACTCC	0.597																																					p.G823V	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G2468T						.						69.0	75.0	73.0					12																	57864991		2203	4300	6503	SO:0001583	missense	2735	exon12			CAGTGGGGTCTGA		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.2468G>T	chr12.hg19:g.57864991G>T	ENSP00000228682:p.Gly823Val	69.0	0.0		84.0	4.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.194657	0.58017	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467	T;T;T;T	0.13196	2.72;2.61;2.69;2.69	4.62	3.72	0.42706	.	0.000000	0.43110	D	0.000603	T	0.18257	0.0438	N	0.22421	0.69	0.80722	D	1	D	0.71674	0.998	P	0.58721	0.844	T	0.01056	-1.1466	10	0.59425	D	0.04	.	12.4531	0.55688	0.0884:0.0:0.9116:0.0	.	823	P08151	GLI1_HUMAN	V	695;823;782;782	ENSP00000437607:G695V;ENSP00000228682:G823V;ENSP00000441006:G782V;ENSP00000434408:G782V	ENSP00000228682:G823V	G	+	2	0	GLI1	56151258	0.998000	0.40836	1.000000	0.80357	0.888000	0.51559	4.325000	0.59234	2.566000	0.86566	0.484000	0.47621	GGG	.	G|0.999;A|0.001		0.597	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
MARS	4141	hgsc.bcm.edu	37	12	57910119	57910119	+	Splice_Site	SNP	A	A	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:57910119A>C	ENST00000262027.5	+	20	2689	c.2555A>C	c.(2554-2556)cAa>cCa	p.Q852P	MIR616_ENST00000385293.1_RNA|RN7SL312P_ENST00000582079.1_RNA	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	852	WHEP-TRS.				gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GTGACAAAACAAGTATGAAGC	0.483																																					p.Q852P		Atlas-SNP	.											.	MARS	84	.	0			c.A2555C						.						75.0	65.0	69.0					12																	57910119		2203	4300	6503	SO:0001630	splice_region_variant	4141	exon20			CAAAACAAGTATG	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"""Aminoacyl tRNA synthetases / Class I"""	6898	protein-coding gene	gene with protein product	"""methionine tRNA ligase 1, cytoplasmic"""	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.2556+1A>C	chr12.hg19:g.57910119A>C		163.0	0.0		156.0	69.0	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	hg19	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.230007	0.79688	.	.	ENSG00000166986	ENST00000262027;ENST00000552914	T;T	0.67865	-0.29;-0.29	5.47	5.47	0.80525	WHEP-TRS (3);S15/NS1, RNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.85159	0.5633	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87925	0.2706	10	0.54805	T	0.06	-16.7991	13.806	0.63233	1.0:0.0:0.0:0.0	.	852	P56192	SYMC_HUMAN	P	852;171	ENSP00000262027:Q852P;ENSP00000449787:Q171P	ENSP00000262027:Q852P	Q	+	2	0	MARS	56196386	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.696000	0.68287	2.216000	0.71823	0.459000	0.35465	CAA	.	.		0.483	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990	Missense_Mutation
CAND1	55832	hgsc.bcm.edu	37	12	67699020	67699020	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:67699020G>T	ENST00000545606.1	+	10	2009	c.1572G>T	c.(1570-1572)gtG>gtT	p.V524V		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	524					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TTCCTCCAGTGGTGGCTTGTG	0.423																																					p.V524V		Atlas-SNP	.											.	CAND1	100	.	0			c.G1572T						.						202.0	176.0	185.0					12																	67699020		2203	4300	6503	SO:0001819	synonymous_variant	55832	exon10			TCCAGTGGTGGCT		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"""TBP interacting protein"""	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.1572G>T	chr12.hg19:g.67699020G>T		163.0	0.0		173.0	7.0	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	hg19	CCDS8977.1																																																																																			.	.		0.423	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448	
IFNG	3458	hgsc.bcm.edu	37	12	68551870	68551870	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:68551870A>T	ENST00000229135.3	-	3	320	c.189T>A	c.(187-189)agT>agA	p.S63R	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	63					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	TTTTTCTGTCACTCTCCTTGG	0.373																																					p.S63R		Atlas-SNP	.											.	IFNG	38	.	0			c.T189A						.						87.0	87.0	87.0					12																	68551870		2203	4300	6503	SO:0001583	missense	3458	exon3			TCTGTCACTCTCC		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"""Interferons"""	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.189T>A	chr12.hg19:g.68551870A>T	ENSP00000229135:p.Ser63Arg	93.0	0.0		112.0	37.0	NM_000619	B5BU88|Q53ZV4	Missense_Mutation	SNP	ENST00000229135.3	hg19	CCDS8980.1	.	.	.	.	.	.	.	.	.	.	A	15.10	2.733736	0.48939	.	.	ENSG00000111537	ENST00000229135	T	0.53423	0.62	5.38	3.05	0.35203	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.570944	0.19887	N	0.103839	T	0.57975	0.2090	M	0.71581	2.175	0.29060	N	0.883959	P	0.51240	0.943	P	0.57846	0.828	T	0.54180	-0.8332	9	.	.	.	-1.2533	6.9182	0.24371	0.8183:0.0:0.1817:0.0	.	63	P01579	IFNG_HUMAN	R	63	ENSP00000229135:S63R	.	S	-	3	2	IFNG	66838137	0.985000	0.35326	0.986000	0.45419	0.551000	0.35334	1.381000	0.34362	0.458000	0.26988	-0.250000	0.11733	AGT	.	.		0.373	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1		
CSRP2	1466	hgsc.bcm.edu	37	12	77253334	77253334	+	Silent	SNP	A	A	G	rs202057442	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:77253334A>G	ENST00000311083.5	-	5	621	c.498T>C	c.(496-498)taT>taC	p.Y166Y	CSRP2_ENST00000547435.1_Silent_p.Y166Y|CSRP2_ENST00000552330.1_Silent_p.Y216Y|CSRP2_ENST00000546966.1_Silent_p.Y166Y	NM_001321.1	NP_001312.1	Q16527	CSRP2_HUMAN	cysteine and glycine-rich protein 2	166	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)	8						TACCTTTACAATAGATTTCAC	0.353													A|||	4	0.000798722	0.0	0.0	5008	,	,		20252	0.0		0.0	False		,,,				2504	0.0041				p.Y166Y		Atlas-SNP	.											.	CSRP2	22	.	0			c.T498C						.						76.0	70.0	72.0					12																	77253334		2203	4300	6503	SO:0001819	synonymous_variant	1466	exon5			TTTACAATAGATT	BC000992	CCDS9015.1	12q21.1	2005-10-30				ENSG00000175183			2470	protein-coding gene	gene with protein product		601871				7499425, 9286703	Standard	XM_006719258		Approved	SmLIM, CRP2, LMO5	uc001syl.1	Q16527		ENST00000311083.5:c.498T>C	chr12.hg19:g.77253334A>G		333.0	1.0		332.0	161.0	NM_001321	Q93030	Silent	SNP	ENST00000311083.5	hg19	CCDS9015.1																																																																																			.	A|0.999;G|0.001		0.353	CSRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406572.1	NM_001321	
RASSF9	9182	hgsc.bcm.edu	37	12	86198974	86198974	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:86198974G>A	ENST00000361228.3	-	2	1182	c.814C>T	c.(814-816)Cga>Tga	p.R272*		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	272					endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)	p.R272*(2)		endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TATTTCAGTCGTTCTTCCAGC	0.398																																					p.R272X		Atlas-SNP	.											RASSF9_ENST00000361228,rectum,carcinoma,0,2	RASSF9	100	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C814T						.						113.0	108.0	110.0					12																	86198974		1886	4108	5994	SO:0001587	stop_gained	9182	exon2			TCAGTCGTTCTTC		CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"""peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"""	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.814C>T	chr12.hg19:g.86198974G>A	ENSP00000354884:p.Arg272*	141.0	0.0		109.0	35.0	NM_005447	B3KMQ4|Q8N5U8	Nonsense_Mutation	SNP	ENST00000361228.3	hg19	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.685307	0.68157	.	.	ENSG00000198774	ENST00000361228	.	.	.	4.9	1.88	0.25563	.	0.581472	0.16373	U	0.217227	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-15.3805	10.6117	0.45425	0.0:0.1108:0.2861:0.6031	.	.	.	.	X	272	.	ENSP00000354884:R272X	R	-	1	2	RASSF9	84723105	0.009000	0.17119	0.003000	0.11579	0.198000	0.23893	0.492000	0.22435	0.148000	0.19059	-0.188000	0.12872	CGA	.	.		0.398	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1		
C12orf50	160419	hgsc.bcm.edu	37	12	88376940	88376940	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:88376940C>T	ENST00000298699.2	-	12	1339	c.1159G>A	c.(1159-1161)Gcc>Acc	p.A387T	C12orf50_ENST00000550553.1_Missense_Mutation_p.A348T	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	387										NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						TTTCGCCAGGCTGAATCATTA	0.279																																					p.A387T		Atlas-SNP	.											.	C12orf50	70	.	0			c.G1159A						.						83.0	88.0	86.0					12																	88376940		2202	4291	6493	SO:0001583	missense	160419	exon12			GCCAGGCTGAATC	AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.1159G>A	chr12.hg19:g.88376940C>T	ENSP00000298699:p.Ala387Thr	94.0	0.0		82.0	4.0	NM_152589	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	hg19	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	c	10.18	1.279964	0.23392	.	.	ENSG00000165805	ENST00000298699;ENST00000550553	T;T	0.31510	1.5;1.49	5.67	1.84	0.25277	.	0.490245	0.20530	N	0.090524	T	0.19685	0.0473	L	0.35288	1.05	0.80722	D	1	B	0.12630	0.006	B	0.16289	0.015	T	0.06232	-1.0838	10	0.20519	T	0.43	.	8.2739	0.31860	0.0:0.6665:0.0:0.3335	.	387	Q8NA57	CL050_HUMAN	T	387;348	ENSP00000298699:A387T;ENSP00000448344:A348T	ENSP00000298699:A387T	A	-	1	0	C12orf50	86901071	0.991000	0.36638	1.000000	0.80357	0.883000	0.51084	0.671000	0.25172	0.450000	0.26774	-0.726000	0.03593	GCC	.	.		0.279	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589	
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100441351	100441351	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:100441351A>G	ENST00000279907.7	-	19	4250	c.4038T>C	c.(4036-4038)caT>caC	p.H1346H	UHRF1BP1L_ENST00000545232.2_Silent_p.H996H	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	1346										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						CTACCACAAGATGATCAATAT	0.368																																					p.H1346H		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.T4038C						.						134.0	131.0	132.0					12																	100441351		2203	4300	6503	SO:0001819	synonymous_variant	23074	exon19			CACAAGATGATCA		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.4038T>C	chr12.hg19:g.100441351A>G		87.0	0.0		87.0	4.0	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Silent	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	A	9.313	1.056189	0.19907	.	.	ENSG00000111647	ENST00000548712	.	.	.	5.53	0.757	0.18427	.	.	.	.	.	T	0.51160	0.1658	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40001	-0.9586	4	.	.	.	-2.7127	4.9898	0.14209	0.5483:0.0:0.2921:0.1596	.	.	.	.	T	107	.	.	I	-	2	0	UHRF1BP1L	98965482	0.955000	0.32602	0.998000	0.56505	0.980000	0.70556	0.035000	0.13797	0.409000	0.25649	0.379000	0.24179	ATC	.	.		0.368	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947	
UTP20	27340	hgsc.bcm.edu	37	12	101736358	101736358	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:101736358G>T	ENST00000261637.4	+	33	4410	c.4236G>T	c.(4234-4236)acG>acT	p.T1412T		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1412					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TGCTTTGTACGGTTTTTGAGG	0.343																																					p.T1412T		Atlas-SNP	.											.	UTP20	222	.	0			c.G4236T						.						54.0	55.0	54.0					12																	101736358		2202	4299	6501	SO:0001819	synonymous_variant	27340	exon33			TTGTACGGTTTTT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.4236G>T	chr12.hg19:g.101736358G>T		97.0	0.0		92.0	4.0	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.343	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
HCFC2	29915	hgsc.bcm.edu	37	12	104495757	104495757	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:104495757A>G	ENST00000229330.4	+	14	1994	c.1890A>G	c.(1888-1890)gcA>gcG	p.A630A	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	630	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TAGGAAATGCAGATGTACCTG	0.318																																					p.A630A	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-SNP	.											.	HCFC2	94	.	0			c.A1890G						.						109.0	98.0	102.0					12																	104495757		2203	4300	6503	SO:0001819	synonymous_variant	29915	exon14			AAATGCAGATGTA	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1890A>G	chr12.hg19:g.104495757A>G		91.0	0.0		95.0	4.0	NM_013320	B2R8Q5|C0H5X3	Silent	SNP	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.318	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320	
TCP11L2	255394	hgsc.bcm.edu	37	12	106740125	106740125	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:106740125G>A	ENST00000299045.3	+	10	1551	c.1377G>A	c.(1375-1377)atG>atA	p.M459I		NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	459										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						AAAAATGCATGCCTCCTATGC	0.413																																					p.M459I		Atlas-SNP	.											.	TCP11L2	59	.	0			c.G1377A						.						64.0	58.0	60.0					12																	106740125		2203	4300	6503	SO:0001583	missense	255394	exon10			ATGCATGCCTCCT	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 2"", ""t-complex 11 (mouse)-like 2"""				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.1377G>A	chr12.hg19:g.106740125G>A	ENSP00000299045:p.Met459Ile	127.0	0.0		108.0	42.0	NM_152772	B2RA65|G3V1Y9	Missense_Mutation	SNP	ENST00000299045.3	hg19	CCDS9104.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.625977	0.46840	.	.	ENSG00000166046	ENST00000299045	T	0.10960	2.82	5.69	5.69	0.88448	.	0.588706	0.19966	N	0.102109	T	0.08980	0.0222	N	0.21142	0.635	0.80722	D	1	B	0.11235	0.004	B	0.16722	0.016	T	0.21895	-1.0232	10	0.34782	T	0.22	-3.3243	13.0662	0.59034	0.0733:0.0:0.9267:0.0	.	459	Q8N4U5	T11L2_HUMAN	I	459	ENSP00000299045:M459I	ENSP00000299045:M459I	M	+	3	0	TCP11L2	105264255	1.000000	0.71417	0.988000	0.46212	0.984000	0.73092	3.394000	0.52551	2.685000	0.91497	0.655000	0.94253	ATG	.	.		0.413	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772	
POLR3B	55703	hgsc.bcm.edu	37	12	106824192	106824192	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:106824192C>T	ENST00000228347.4	+	14	1627	c.1405C>T	c.(1405-1407)Cgc>Tgc	p.R469C	POLR3B_ENST00000539066.1_Missense_Mutation_p.R411C	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	469					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GAGTGGTCCTCGCTCCCTCCA	0.493																																					p.R469C		Atlas-SNP	.											.	POLR3B	123	.	0			c.C1405T						.						114.0	105.0	108.0					12																	106824192		2203	4300	6503	SO:0001583	missense	55703	exon14			GGTCCTCGCTCCC	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1405C>T	chr12.hg19:g.106824192C>T	ENSP00000228347:p.Arg469Cys	115.0	0.0		91.0	4.0	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	hg19	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737375	0.89482	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	D;D	0.97553	-4.43;-4.43	5.56	4.66	0.58398	RNA polymerase Rpb2, domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.99124	0.9698	H	0.98559	4.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98855	1.0760	10	0.87932	D	0	-12.6298	15.7308	0.77804	0.1378:0.8622:0.0:0.0	.	469	Q9NW08	RPC2_HUMAN	C	469;469;411	ENSP00000228347:R469C;ENSP00000445721:R411C	ENSP00000228347:R469C	R	+	1	0	POLR3B	105348322	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	7.452000	0.80683	1.301000	0.44836	0.655000	0.94253	CGC	.	.		0.493	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082	
GIT2	9815	hgsc.bcm.edu	37	12	110390999	110390999	+	Silent	SNP	G	G	A	rs369471977		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:110390999G>A	ENST00000355312.3	-	13	1139	c.1140C>T	c.(1138-1140)caC>caT	p.H380H	GIT2_ENST00000547815.1_Silent_p.H380H|GIT2_ENST00000553118.1_Silent_p.H380H|GIT2_ENST00000457474.2_Silent_p.H382H|GIT2_ENST00000338373.5_Silent_p.H380H|GIT2_ENST00000356259.4_Silent_p.H380H|GIT2_ENST00000360185.4_Silent_p.H380H|GIT2_ENST00000551209.1_Silent_p.H379H|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000361006.5_Silent_p.H380H|GIT2_ENST00000343646.5_Intron|GIT2_ENST00000320063.9_Silent_p.H380H|GIT2_ENST00000354574.4_Silent_p.H382H	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	380					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						TCTCAACGCTGTGCTGGTTAT	0.418																																					p.H382H		Atlas-SNP	.											.	GIT2	81	.	0			c.C1146T						.	G	,,,,,	0,4406		0,0,2203	244.0	207.0	220.0		1146,1140,1140,1140,1140,1140	5.2	1.0	12		220	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GIT2	NM_001135213.1,NM_001135214.1,NM_014776.3,NM_057169.3,NM_057170.3,NM_139201.2	,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,	382/682,380/730,380/680,380/760,380/632,380/472	110390999	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9815	exon14			AACGCTGTGCTGG	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4273	protein-coding gene	gene with protein product		608564	"""G protein-coupled receptor kinase interactor 2"""			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1140C>T	chr12.hg19:g.110390999G>A		448.0	0.0		467.0	195.0	NM_001135213	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Silent	SNP	ENST00000355312.3	hg19	CCDS9138.1																																																																																			.	.		0.418	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169	
ATP2A2	488	hgsc.bcm.edu	37	12	110729905	110729905	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:110729905C>A	ENST00000539276.2	+	4	409	c.300C>A	c.(298-300)gcC>gcA	p.A100A	ATP2A2_ENST00000552636.1_5'UTR|ATP2A2_ENST00000395494.2_Silent_p.A100A|ATP2A2_ENST00000308664.6_Silent_p.A100A			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	100					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						TATTAGTAGCCAATGCAATTG	0.348																																					p.A100A		Atlas-SNP	.											.	ATP2A2	78	.	0			c.C300A						.						114.0	111.0	112.0					12																	110729905		2203	4300	6503	SO:0001819	synonymous_variant	488	exon4			AGTAGCCAATGCA		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"""ATPases / P-type"""	812	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 2"", ""calcium pump 2"""	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.300C>A	chr12.hg19:g.110729905C>A		217.0	0.0		199.0	8.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	hg19	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.292457	0.23564	.	.	ENSG00000174437	ENST00000548169	.	.	.	5.33	4.44	0.53790	.	.	.	.	.	T	0.68952	0.3057	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67726	-0.5596	4	.	.	.	.	13.1455	0.59459	0.2912:0.7088:0.0:0.0	.	.	.	.	K	18	.	.	Q	+	1	0	ATP2A2	109214288	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.750000	0.26334	1.228000	0.43614	0.563000	0.77884	CAA	.	.		0.348	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681	
ALDH2	217	hgsc.bcm.edu	37	12	112204899	112204899	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:112204899A>G	ENST00000261733.2	+	1	174	c.113A>G	c.(112-114)cAg>cGg	p.Q38R	ALDH2_ENST00000416293.3_Splice_Site_p.Q38R|RP11-162P23.2_ENST00000546840.2_Intron	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	38					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	TTCTGCAACCAGGTGAGCCCA	0.741			T	HMGA2	leiomyoma																																p.Q38R		Atlas-SNP	.		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	.	ALDH2	91	.	0			c.A113G						.						3.0	4.0	3.0					12																	112204899		1828	3711	5539	SO:0001630	splice_region_variant	217	exon1			GCAACCAGGTGAG	M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"""Aldehyde dehydrogenases"""	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.114+1A>G	chr12.hg19:g.112204899A>G		5.0	0.0		14.0	5.0	NM_001204889	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	hg19	CCDS9155.1	.	.	.	.	.	.	.	.	.	.	a	13.52	2.260407	0.39995	.	.	ENSG00000111275	ENST00000416293;ENST00000261733;ENST00000553044	T;T	0.15834	2.39;2.39	4.62	4.62	0.57501	Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.305652	0.35739	N	0.003008	T	0.10895	0.0266	N	0.14661	0.345	0.80722	D	1	B;B;B	0.17667	0.001;0.023;0.005	B;B;B	0.18561	0.005;0.022;0.004	T	0.10337	-1.0634	10	0.40728	T	0.16	.	11.8849	0.52596	1.0:0.0:0.0:0.0	.	38;38;38	E7EUE5;F8VXI5;P05091	.;.;ALDH2_HUMAN	R	38	ENSP00000403349:Q38R;ENSP00000261733:Q38R	ENSP00000261733:Q38R	Q	+	2	0	ALDH2	110689282	1.000000	0.71417	0.987000	0.45799	0.004000	0.04260	2.620000	0.46410	1.846000	0.53633	0.529000	0.55759	CAG	.	.		0.741	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690	Missense_Mutation
HECTD4	283450	hgsc.bcm.edu	37	12	112622466	112622466	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:112622466G>A	ENST00000430131.2	-	60	10183	c.9038C>T	c.(9037-9039)cCg>cTg	p.P3013L	HECTD4_ENST00000550722.1_Missense_Mutation_p.P3289L|HECTD4_ENST00000377560.5_Missense_Mutation_p.P3263L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3013					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.P3263Q(1)|p.P3013Q(1)									TTCCTGCAGCGGGATGTAGAT	0.632																																					p.P3301L		Atlas-SNP	.											.	.	.	.	2	Substitution - Missense(2)	kidney(2)	c.C9902T						.						102.0	123.0	116.0					12																	112622466		2119	4237	6356	SO:0001583	missense	283450	exon61			TGCAGCGGGATGT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.9038C>T	chr12.hg19:g.112622466G>A	ENSP00000404379:p.Pro3013Leu	94.0	0.0		88.0	4.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.56	2.868299	0.51588	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.69040	-0.36;-0.33;-0.37	5.52	4.63	0.57726	.	.	.	.	.	T	0.55800	0.1943	L	0.29908	0.895	0.80722	D	1	B	0.18310	0.027	B	0.08055	0.003	T	0.55108	-0.8192	9	0.87932	D	0	.	14.0839	0.64942	0.0724:0.0:0.9276:0.0	.	3013	Q9Y4D8	K0614_HUMAN	L	3263;3013;3289	ENSP00000366783:P3263L;ENSP00000404379:P3013L;ENSP00000449784:P3289L	ENSP00000366783:P3263L	P	-	2	0	C12orf51	111106849	1.000000	0.71417	0.984000	0.44739	0.046000	0.14306	8.972000	0.93424	1.338000	0.45544	0.591000	0.81541	CCG	.	.		0.632	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
OAS2	4939	hgsc.bcm.edu	37	12	113444238	113444238	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:113444238A>G	ENST00000342315.4	+	8	1703	c.1489A>G	c.(1489-1491)Aca>Gca	p.T497A	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.T497A	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	497	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TTCTGGCTCCACACCCAGCCC	0.463																																					p.T497A	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.A1489G						.						66.0	65.0	65.0					12																	113444238		2203	4300	6503	SO:0001583	missense	4939	exon8			GGCTCCACACCCA	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1489A>G	chr12.hg19:g.113444238A>G	ENSP00000342278:p.Thr497Ala	131.0	0.0		98.0	4.0	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	hg19	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249420	0.22880	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.08546	3.08;3.08	4.51	-4.63	0.03359	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	1.183370	0.06544	N	0.743700	T	0.04003	0.0112	N	0.13043	0.29	0.09310	N	1	B;B	0.14805	0.011;0.005	B;B	0.18561	0.022;0.022	T	0.42275	-0.9461	10	0.44086	T	0.13	-18.8292	1.0937	0.01668	0.3049:0.2906:0.2632:0.1412	.	497;497	P29728;P29728-2	OAS2_HUMAN;.	A	497	ENSP00000342278:T497A;ENSP00000376362:T497A	ENSP00000342278:T497A	T	+	1	0	OAS2	111928621	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.022000	0.13511	-1.146000	0.02854	-0.290000	0.09829	ACA	.	.		0.463	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
TBX3	6926	hgsc.bcm.edu	37	12	115114249	115114249	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:115114249C>A	ENST00000257566.3	-	6	1357	c.968G>T	c.(967-969)aGg>aTg	p.R323M	TBX3_ENST00000349155.2_Missense_Mutation_p.R303M	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	323					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		ATCAAACACCCTCATGGACTG	0.493																																					p.R323M		Atlas-SNP	.											.	TBX3	106	.	0			c.G968T						.						132.0	120.0	124.0					12																	115114249		2203	4300	6503	SO:0001583	missense	6926	exon6			AACACCCTCATGG	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.968G>T	chr12.hg19:g.115114249C>A	ENSP00000257566:p.Arg323Met	126.0	0.0		108.0	5.0	NM_016569	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	hg19	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804866	0.90623	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.89270	-2.49;-2.47	5.11	5.11	0.69529	Transcription factor, T-box, region of unknown function (1);	0.114431	0.31612	N	0.007357	D	0.93213	0.7838	L	0.59436	1.845	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.87578	0.987;0.998	D	0.93164	0.6560	10	0.49607	T	0.09	.	17.516	0.87773	0.0:1.0:0.0:0.0	.	303;323	O15119-2;O15119	.;TBX3_HUMAN	M	303;323;323	ENSP00000257567:R303M;ENSP00000257566:R323M	ENSP00000257566:R323M	R	-	2	0	TBX3	113598632	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	7.260000	0.78391	2.363000	0.80096	0.655000	0.94253	AGG	.	.		0.493	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
NOS1	4842	hgsc.bcm.edu	37	12	117653120	117653120	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:117653120G>T	ENST00000338101.4	-	29	4405	c.4401C>A	c.(4399-4401)agC>agA	p.S1467R	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.S1433R			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCAGTTAGGAGCTGAAAACCC	0.582																																					p.S1467R	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C4401A						.						70.0	76.0	74.0					12																	117653120		1888	4104	5992	SO:0001583	missense	4842	exon30			TTAGGAGCTGAAA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4401C>A	chr12.hg19:g.117653120G>T	ENSP00000337459:p.Ser1467Arg	92.0	0.0		86.0	4.0	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.829256	0.50845	.	.	ENSG00000089250	ENST00000317775;ENST00000338101	T;T	0.01347	4.99;5.01	4.95	2.94	0.34122	.	0.164696	0.53938	D	0.000043	T	0.00815	0.0027	N	0.02011	-0.69	0.80722	D	1	B	0.27498	0.18	B	0.27076	0.076	T	0.66180	-0.5988	10	0.62326	D	0.03	-27.6639	10.5436	0.45047	0.0:0.1445:0.7059:0.1497	.	1433	P29475	NOS1_HUMAN	R	1433;1467	ENSP00000320758:S1433R;ENSP00000337459:S1467R	ENSP00000320758:S1433R	S	-	3	2	NOS1	116137503	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.337000	0.52120	1.185000	0.42971	0.655000	0.94253	AGC	.	.		0.582	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
KNTC1	9735	hgsc.bcm.edu	37	12	123055607	123055607	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:123055607G>C	ENST00000333479.7	+	24	2130	c.1953G>C	c.(1951-1953)gaG>gaC	p.E651D	KNTC1_ENST00000450485.2_Missense_Mutation_p.E614D	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	651					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.E651D(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AATTGGCAGAGATATTTTTTA	0.363																																					p.E651D		Atlas-SNP	.											KNTC1,NS,carcinoma,0,2	KNTC1	182	.	1	Substitution - Missense(1)	endometrium(1)	c.G1953C						.						91.0	88.0	89.0					12																	123055607		1815	4076	5891	SO:0001583	missense	9735	exon24			GGCAGAGATATTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.1953G>C	chr12.hg19:g.123055607G>C	ENSP00000328236:p.Glu651Asp	254.0	0.0		232.0	15.0	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692717	0.30052	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.24350	1.86;2.4	5.49	2.17	0.27698	.	0.157403	0.44483	D	0.000453	T	0.18718	0.0449	L	0.51422	1.61	0.80722	D	1	P;B	0.36282	0.546;0.361	B;B	0.29353	0.101;0.075	T	0.04454	-1.0950	10	0.51188	T	0.08	-16.2422	8.0109	0.30353	0.4138:0.0:0.5862:0.0	.	614;651	E7ES84;P50748	.;KNTC1_HUMAN	D	614;651	ENSP00000397992:E614D;ENSP00000328236:E651D	ENSP00000328236:E651D	E	+	3	2	KNTC1	121621560	0.998000	0.40836	0.936000	0.37596	0.798000	0.45092	1.472000	0.35376	0.800000	0.34041	0.643000	0.83706	GAG	.	.		0.363	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
SBNO1	55206	hgsc.bcm.edu	37	12	123798234	123798234	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:123798234T>C	ENST00000602398.1	-	24	3280	c.3153A>G	c.(3151-3153)aaA>aaG	p.K1051K	SBNO1_ENST00000267176.4_Silent_p.K1050K|SBNO1_ENST00000602750.1_Silent_p.K1050K|SBNO1_ENST00000420886.2_Silent_p.K1051K			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1051					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TTACAATGGATTTCATGACAA	0.333																																					p.K1051K		Atlas-SNP	.											.	SBNO1	138	.	0			c.A3153G						.						73.0	74.0	73.0					12																	123798234		2203	4300	6503	SO:0001819	synonymous_variant	55206	exon23			AATGGATTTCATG	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3153A>G	chr12.hg19:g.123798234T>C		66.0	0.0		68.0	4.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	hg19	CCDS53844.1																																																																																			.	.		0.333	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
TCTN2	79867	hgsc.bcm.edu	37	12	124189191	124189191	+	Silent	SNP	G	G	T	rs145483549		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:124189191G>T	ENST00000303372.5	+	15	1853	c.1725G>T	c.(1723-1725)gcG>gcT	p.A575A	RP11-338K17.8_ENST00000538837.1_lincRNA|TCTN2_ENST00000426174.2_Silent_p.A574A	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	575					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)		p.A575A(1)		breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		ATGCTGGCGCGGTGGAAGGGA	0.532																																					p.A575A		Atlas-SNP	.											TCTN2,NS,carcinoma,0,2	TCTN2	50	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1725T						.						92.0	74.0	80.0					12																	124189191		2203	4300	6503	SO:0001819	synonymous_variant	79867	exon15			TGGCGCGGTGGAA	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.1725G>T	chr12.hg19:g.124189191G>T		95.0	0.0		65.0	3.0	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	hg19	CCDS9253.1																																																																																			.	G|1.000;A|0.000		0.532	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
NCOR2	9612	hgsc.bcm.edu	37	12	124824721	124824721	+	Missense_Mutation	SNP	C	C	T	rs61519723|rs112797765|rs143952466	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:124824721C>T	ENST00000405201.1	-	37	5518	c.5518G>A	c.(5518-5520)Ggg>Agg	p.G1840R	NCOR2_ENST00000356219.3_Missense_Mutation_p.G1847R|NCOR2_ENST00000404121.2_Missense_Mutation_p.G1401R|NCOR2_ENST00000397355.1_Missense_Mutation_p.G1831R|NCOR2_ENST00000404621.1_Missense_Mutation_p.G1830R|NCOR2_ENST00000429285.2_Missense_Mutation_p.G1830R			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1851					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		cccccacccccgccgctgctg	0.711																																					p.G1840R		Atlas-SNP	.											.,32	NCOR2	475	.	0			c.G5518A						.						14.0	20.0	18.0					12																	124824721		1941	4120	6061	SO:0001583	missense	9612	exon39			CACCCCCGCCGCT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5518G>A	chr12.hg19:g.124824721C>T	ENSP00000384018:p.Gly1840Arg	68.0	1.0		79.0	5.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.12|12.12	1.844110|1.844110	0.32606|0.32606	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285|ENST00000440187;ENST00000453428	T;T;T;T;T;T|.	0.21191|.	2.03;2.29;2.02;2.29;2.04;2.29|.	2.64|2.64	2.64|2.64	0.31445|0.31445	.|.	0.074331|.	0.53938|.	U|.	0.000049|.	T|T	0.32704|0.32704	0.0838|0.0838	L|L	0.29908|0.29908	0.895|0.895	0.23855|0.23855	N|N	0.996651|0.996651	D;P|.	0.71674|.	0.998;0.929|.	P;B|.	0.51297|.	0.665;0.088|.	T|T	0.18650|0.18650	-1.0330|-1.0330	10|5	0.13470|.	T|.	0.59|.	.|.	8.4775|8.4775	0.33023|0.33023	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1831;1840|.	C9J239;C9JFD3|.	.;.|.	R|Q	1840;1830;1847;1831;1839;1401;1830|74;169	ENSP00000384018:G1840R;ENSP00000384202:G1830R;ENSP00000348551:G1847R;ENSP00000380513:G1831R;ENSP00000385618:G1401R;ENSP00000400281:G1830R|.	ENSP00000348551:G1847R|.	G|R	-|-	1|2	0|0	NCOR2|NCOR2	123390674|123390674	0.931000|0.931000	0.31567|0.31567	0.959000|0.959000	0.39883|0.39883	0.993000|0.993000	0.82548|0.82548	-0.026000|-0.026000	0.12392|0.12392	1.307000|1.307000	0.44944|0.44944	0.491000|0.491000	0.48974|0.48974	GGG|CGG	.	.		0.711	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
DDX51	317781	hgsc.bcm.edu	37	12	132626881	132626881	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:132626881A>G	ENST00000397333.3	-	4	795	c.757T>C	c.(757-759)Tgt>Cgt	p.C253R	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	253	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		GCAGAAACACAGAGGTCGCTA	0.607																																					p.C253R		Atlas-SNP	.											.	DDX51	33	.	0			c.T757C						.						63.0	74.0	70.0					12																	132626881		2071	4202	6273	SO:0001583	missense	317781	exon4			AAACACAGAGGTC	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.757T>C	chr12.hg19:g.132626881A>G	ENSP00000380495:p.Cys253Arg	33.0	0.0		49.0	4.0	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	hg19	CCDS41865.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.051028	0.75960	.	.	ENSG00000185163	ENST00000397333	T	0.15139	2.45	4.71	4.71	0.59529	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.34395	0.0896	L	0.51914	1.62	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.07028	-1.0794	10	0.87932	D	0	-8.5514	12.1532	0.54062	1.0:0.0:0.0:0.0	.	253	Q8N8A6	DDX51_HUMAN	R	253	ENSP00000380495:C253R	ENSP00000380495:C253R	C	-	1	0	DDX51	131192834	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	8.427000	0.90275	1.756000	0.51951	0.402000	0.26972	TGT	.	.		0.607	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
ANKLE2	23141	hgsc.bcm.edu	37	12	133313525	133313525	+	Missense_Mutation	SNP	G	G	T	rs201586661		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:133313525G>T	ENST00000357997.5	-	8	1636	c.1547C>A	c.(1546-1548)cCg>cAg	p.P516Q	ANKLE2_ENST00000337516.5_Missense_Mutation_p.P516Q|ANKLE2_ENST00000542374.1_5'Flank|ANKLE2_ENST00000539605.1_Missense_Mutation_p.P454Q	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	516					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GGTCAGTACCGGGTCTCTGGG	0.622																																					p.P516Q		Atlas-SNP	.											ANKLE2,NS,carcinoma,0,1	ANKLE2	76	.	0			c.C1547A						.						65.0	78.0	74.0					12																	133313525		1982	4154	6136	SO:0001583	missense	23141	exon8			AGTACCGGGTCTC	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1547C>A	chr12.hg19:g.133313525G>T	ENSP00000350686:p.Pro516Gln	64.0	0.0		76.0	4.0	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	hg19	CCDS41869.1	.	.	.	.	.	.	.	.	.	.	g	21.1	4.102404	0.76983	.	.	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516;ENST00000535036	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.75287	0.3829	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77161	-0.2689	10	0.87932	D	0	-19.8516	19.9201	0.97084	0.0:0.0:1.0:0.0	.	516;516	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	Q	454;516;516;79	ENSP00000446268:P454Q;ENSP00000350686:P516Q;ENSP00000337651:P516Q;ENSP00000437585:P79Q	ENSP00000337651:P516Q	P	-	2	0	ANKLE2	131823598	1.000000	0.71417	0.913000	0.36048	0.294000	0.27393	9.005000	0.93587	2.785000	0.95823	0.650000	0.86243	CCG	.	.		0.622	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
ZNF10	7556	hgsc.bcm.edu	37	12	133727625	133727625	+	Silent	SNP	C	C	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr12:133727625C>G	ENST00000248211.6	+	3	267	c.45C>G	c.(43-45)acC>acG	p.T15T	ZNF10_ENST00000540927.1_Intron|ZNF10_ENST00000402932.2_Silent_p.T15T|ZNF268_ENST00000416488.1_Silent_p.T15T|CTD-2140B24.4_ENST00000540096.2_Silent_p.T15T|ZNF10_ENST00000426665.2_Silent_p.T15T	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CACTGGTGACCTTCAAGGATG	0.453																																					p.T15T		Atlas-SNP	.											.	ZNF10	58	.	0			c.C45G						.						279.0	245.0	257.0					12																	133727625		2203	4300	6503	SO:0001819	synonymous_variant	7556	exon3			GGTGACCTTCAAG	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"""Zinc fingers, C2H2-type"", ""-"""	12879	protein-coding gene	gene with protein product		194538	"""zinc finger protein 10 (KOX 1)"""			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.45C>G	chr12.hg19:g.133727625C>G		206.0	0.0		208.0	84.0	NM_015394	B2RBS1|Q8TC91	Silent	SNP	ENST00000248211.6	hg19	CCDS9283.1																																																																																			.	.		0.453	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394	
ZMYM2	7750	hgsc.bcm.edu	37	13	20659971	20659971	+	Silent	SNP	T	T	C	rs374447547		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:20659971T>C	ENST00000382874.2	+	26	4141	c.3951T>C	c.(3949-3951)aaT>aaC	p.N1317N	ZMYM2_ENST00000382869.3_Silent_p.N1317N|ZMYM2_ENST00000382871.2_Silent_p.N1317N	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		GTCCACAGAATCTTAATCAGA	0.378																																					p.N1317N		Atlas-SNP	.											.	ZMYM2	191	.	0			c.T3951C						.	T	,,,	0,3638		0,0,1819	70.0	64.0	66.0		3951,3951,3951,3951	0.0	1.0	13		66	1,8149		0,1,4074	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZMYM2	NM_001190964.1,NM_001190965.1,NM_003453.3,NM_197968.2	,,,	0,1,5893	CC,CT,TT		0.0123,0.0,0.0085	,,,	1317/1378,1317/1378,1317/1378,1317/1378	20659971	1,11787	1819	4075	5894	SO:0001819	synonymous_variant	7750	exon26			ACAGAATCTTAAT	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"""Zinc fingers, MYM type"""	12989	protein-coding gene	gene with protein product		602221	"""zinc finger protein 198"""	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3951T>C	chr13.hg19:g.20659971T>C		108.0	0.0		85.0	4.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	hg19	CCDS45016.1																																																																																			.	.		0.378	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453	
LATS2	26524	hgsc.bcm.edu	37	13	21555762	21555762	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:21555762C>A	ENST00000382592.4	-	6	2913	c.2508G>T	c.(2506-2508)atG>atT	p.M836I	LATS2_ENST00000542899.1_Missense_Mutation_p.M836I	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CGCTGGGCTCCATGCTGTCCT	0.512																																					p.M836I		Atlas-SNP	.											.	LATS2	176	.	0			c.G2508T						.						53.0	49.0	50.0					13																	21555762		2203	4300	6503	SO:0001583	missense	26524	exon6			GGGCTCCATGCTG	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.2508G>T	chr13.hg19:g.21555762C>A	ENSP00000372035:p.Met836Ile	64.0	0.0		90.0	4.0	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	hg19	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789402	0.70337	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.60171	0.21;0.21	5.69	5.69	0.88448	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.49695	0.1572	N	0.21324	0.655	0.80722	D	1	B	0.28998	0.23	B	0.30646	0.118	T	0.49312	-0.8953	10	0.59425	D	0.04	.	19.8632	0.96793	0.0:1.0:0.0:0.0	.	836	Q9NRM7	LATS2_HUMAN	I	836	ENSP00000372035:M836I;ENSP00000441817:M836I	ENSP00000372035:M836I	M	-	3	0	LATS2	20453762	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	7.770000	0.85390	2.713000	0.92767	0.644000	0.83932	ATG	.	.		0.512	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
ATP12A	479	hgsc.bcm.edu	37	13	25276160	25276160	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:25276160G>T	ENST00000381946.3	+	14	2136	c.1969G>T	c.(1969-1971)Gaa>Taa	p.E657*	ATP12A_ENST00000218548.6_Nonsense_Mutation_p.E663*|RNY1P7_ENST00000384743.1_RNA			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	657					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TGAAACAGTGGAAGACATTGC	0.458																																					p.E663X	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.G1987T						.						227.0	185.0	199.0					13																	25276160		2203	4300	6503	SO:0001587	stop_gained	479	exon14			ACAGTGGAAGACA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1969G>T	chr13.hg19:g.25276160G>T	ENSP00000371372:p.Glu657*	112.0	0.0		107.0	5.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Nonsense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	41	9.131705	0.99077	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	.	.	.	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.0213	0.86434	0.0:0.0:1.0:0.0	.	.	.	.	X	663;657	.	ENSP00000218548:E663X	E	+	1	0	ATP12A	24174160	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	9.695000	0.98691	2.692000	0.91855	0.467000	0.42956	GAA	.	.		0.458	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
ATP8A2	51761	hgsc.bcm.edu	37	13	26273474	26273474	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:26273474T>C	ENST00000381655.2	+	25	2517	c.2375T>C	c.(2374-2376)aTa>aCa	p.I792T	ATP8A2_ENST00000255283.8_Missense_Mutation_p.I752T|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	752					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|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(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		AAAGCGGTCATATGCTGCAGG	0.532																																					p.I792T		Atlas-SNP	.											.	ATP8A2	181	.	0			c.T2375C						.						63.0	62.0	63.0					13																	26273474		1946	4136	6082	SO:0001583	missense	51761	exon25			CGGTCATATGCTG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2375T>C	chr13.hg19:g.26273474T>C	ENSP00000371070:p.Ile792Thr	91.0	0.0		90.0	48.0	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	hg19	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.741347	0.69304	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	D;D	0.82803	-1.65;-1.65	5.88	5.88	0.94601	HAD-like domain (2);	0.049064	0.85682	D	0.000000	D	0.94627	0.8268	H	0.98111	4.15	0.80722	D	1	D;D;D	0.62365	0.991;0.989;0.991	D;D;D	0.72625	0.978;0.962;0.967	D	0.96526	0.9389	10	0.87932	D	0	.	16.2824	0.82697	0.0:0.0:0.0:1.0	.	752;572;752	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	T	792;752;572	ENSP00000371070:I792T;ENSP00000255283:I752T	ENSP00000255283:I752T	I	+	2	0	ATP8A2	25171474	1.000000	0.71417	0.498000	0.27564	0.450000	0.32258	8.035000	0.88872	2.250000	0.74265	0.533000	0.62120	ATA	.	.		0.532	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
SLC46A3	283537	hgsc.bcm.edu	37	13	29287117	29287117	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:29287117C>A	ENST00000266943.6	-	3	1129	c.760G>T	c.(760-762)Ggt>Tgt	p.G254C	SLC46A3_ENST00000380814.4_Missense_Mutation_p.G254C	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	254					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		CGTCTCTTACCAGAAGCATTC	0.333																																					p.G254C		Atlas-SNP	.											.	SLC46A3	86	.	0			c.G760T						.						45.0	45.0	45.0					13																	29287117		2203	4299	6502	SO:0001583	missense	283537	exon3			TCTTACCAGAAGC		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"""Solute carriers"""	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.760G>T	chr13.hg19:g.29287117C>A	ENSP00000266943:p.Gly254Cys	89.0	0.0		95.0	4.0	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	hg19	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	C	0.612	-0.824657	0.02755	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.51817	0.69;0.69	5.63	-6.26	0.02033	Major facilitator superfamily domain, general substrate transporter (1);	0.966988	0.08658	N	0.912940	T	0.24547	0.0595	N	0.21448	0.665	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.10450	0.003;0.003;0.005	T	0.15838	-1.0423	10	0.33141	T	0.24	-1.1839	2.8164	0.05457	0.2368:0.2601:0.0692:0.434	.	179;254;254	B5MEH0;Q7Z3Q1-2;Q7Z3Q1	.;.;S46A3_HUMAN	C	254	ENSP00000266943:G254C;ENSP00000370192:G254C	ENSP00000266943:G254C	G	-	1	0	SLC46A3	28185117	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.202000	0.09451	-1.350000	0.02199	-0.797000	0.03246	GGT	.	.		0.333	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785	
FRY	10129	hgsc.bcm.edu	37	13	32776658	32776658	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:32776658T>C	ENST00000380250.3	+	31	4508	c.4012T>C	c.(4012-4014)Ttc>Ctc	p.F1338L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1338						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ACTCCCCCTCTTCTCAGGTAC	0.463																																					p.F1338L		Atlas-SNP	.											.	FRY	312	.	0			c.T4012C						.						67.0	65.0	66.0					13																	32776658		1957	4151	6108	SO:0001583	missense	10129	exon31			CCCCTCTTCTCAG	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.4012T>C	chr13.hg19:g.32776658T>C	ENSP00000369600:p.Phe1338Leu	72.0	0.0		84.0	5.0	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.893649	0.91889	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.34667	1.35	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.58906	0.2155	M	0.73962	2.25	0.80722	D	1	D	0.55605	0.972	D	0.68621	0.959	T	0.57969	-0.7719	10	0.33940	T	0.23	.	15.405	0.74871	0.0:0.0:0.0:1.0	.	1338	Q5TBA9	FRY_HUMAN	L	1338;177	ENSP00000369600:F1338L	ENSP00000369600:F1338L	F	+	1	0	FRY	31674658	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	7.640000	0.83355	2.060000	0.61445	0.374000	0.22700	TTC	.	.		0.463	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
BRCA2	675	hgsc.bcm.edu	37	13	32950834	32950834	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:32950834C>T	ENST00000380152.3	+	21	8893	c.8660C>T	c.(8659-8661)tCa>tTa	p.S2887L	BRCA2_ENST00000544455.1_Missense_Mutation_p.S2887L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2887					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TATTTACCATCACGTGCACTA	0.373			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.S2887L	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.C8660T						.						96.0	89.0	92.0					13																	32950834		2203	4300	6503	SO:0001583	missense	675	exon21	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TACCATCACGTGC	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8660C>T	chr13.hg19:g.32950834C>T	ENSP00000369497:p.Ser2887Leu	89.0	0.0		89.0	4.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266028	0.80358	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.59224	0.28;0.28	5.32	5.32	0.75619	Nucleic acid-binding, OB-fold-like (1);	0.262114	0.32488	N	0.006038	T	0.65322	0.2680	L	0.55834	1.745	0.09310	N	1	D	0.59767	0.986	P	0.53266	0.722	T	0.60905	-0.7170	10	0.45353	T	0.12	.	17.1817	0.86857	0.0:1.0:0.0:0.0	.	2887	P51587	BRCA2_HUMAN	L	2887	ENSP00000369497:S2887L;ENSP00000439902:S2887L	ENSP00000369497:S2887L	S	+	2	0	BRCA2	31848834	0.144000	0.22641	0.009000	0.14445	0.551000	0.35334	3.051000	0.49885	2.469000	0.83416	0.655000	0.94253	TCA	.	.		0.373	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
KL	9365	hgsc.bcm.edu	37	13	33635814	33635814	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:33635814C>T	ENST00000380099.3	+	4	2606	c.2598C>T	c.(2596-2598)ctC>ctT	p.L866L	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	866	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		ACGGAGACCTCCCCATGTACA	0.522																																					p.L866L		Atlas-SNP	.											.	KL	106	.	0			c.C2598T						.						116.0	114.0	115.0					13																	33635814		2203	4300	6503	SO:0001819	synonymous_variant	9365	exon4			AGACCTCCCCATG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2598C>T	chr13.hg19:g.33635814C>T		88.0	0.0		83.0	4.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.		0.522	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
NBEA	26960	hgsc.bcm.edu	37	13	35517180	35517180	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:35517180G>T	ENST00000400445.3	+	1	757	c.223G>T	c.(223-225)Gca>Tca	p.A75S	NBEA_ENST00000379939.2_Missense_Mutation_p.A75S|NBEA_ENST00000310336.4_Missense_Mutation_p.A75S|NBEA_ENST00000540320.1_Missense_Mutation_p.A75S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	75					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GATGAAATTCGCAGTGTTGAT	0.587																																					p.A75S		Atlas-SNP	.											.	NBEA	340	.	0			c.G223T						.						118.0	130.0	126.0					13																	35517180		2088	4211	6299	SO:0001583	missense	26960	exon1			AAATTCGCAGTGT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.223G>T	chr13.hg19:g.35517180G>T	ENSP00000383295:p.Ala75Ser	165.0	0.0		116.0	5.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592953	0.86953	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	4.49	4.49	0.54785	.	0.186397	0.31542	N	0.007462	T	0.66607	0.2806	M	0.64567	1.98	0.80722	D	1	D	0.69078	0.997	D	0.74023	0.982	T	0.62676	-0.6804	10	0.13853	T	0.58	.	16.1514	0.81624	0.0:0.0:1.0:0.0	.	75	Q5T321	.	S	75	ENSP00000440951:A75S;ENSP00000383295:A75S;ENSP00000369271:A75S;ENSP00000308534:A75S	ENSP00000308534:A75S	A	+	1	0	NBEA	34415180	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.950000	0.93019	2.068000	0.61886	0.561000	0.74099	GCA	.	.		0.587	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
NHLRC3	387921	hgsc.bcm.edu	37	13	39613731	39613731	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:39613731T>C	ENST00000379600.3	+	3	590	c.268T>C	c.(268-270)Ttc>Ctc	p.F90L	PROSER1_ENST00000350125.3_5'Flank|PROSER1_ENST00000352251.3_5'Flank|NHLRC3_ENST00000379599.2_Missense_Mutation_p.F90L|NHLRC3_ENST00000470258.1_5'UTR	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	90						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		GATATTAGTGTTCACAGAGGA	0.388																																					p.F90L		Atlas-SNP	.											.	NHLRC3	35	.	0			c.T268C						.						69.0	68.0	69.0					13																	39613731		2203	4300	6503	SO:0001583	missense	387921	exon3			TTAGTGTTCACAG		CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.268T>C	chr13.hg19:g.39613731T>C	ENSP00000368920:p.Phe90Leu	81.0	0.0		85.0	4.0	NM_001012754	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	hg19	CCDS31961.1	.	.	.	.	.	.	.	.	.	.	T	33	5.206169	0.95033	.	.	ENSG00000188811	ENST00000379600;ENST00000379599;ENST00000537150	D;D	0.89939	-2.54;-2.59	5.39	5.39	0.77823	Six-bladed beta-propeller, TolB-like (1);	0.046859	0.85682	N	0.000000	D	0.90283	0.6961	L	0.54908	1.71	0.51767	D	0.999937	D;D;B;B	0.59767	0.982;0.986;0.058;0.197	P;P;B;B	0.53649	0.661;0.731;0.028;0.083	D	0.89720	0.3918	9	.	.	.	-14.8357	14.8927	0.70620	0.0:0.0:0.0:1.0	.	90;90;90;90	B4DTL0;Q5JS37;B4DRC8;F5GZB5	.;NHLC3_HUMAN;.;.	L	90	ENSP00000368920:F90L;ENSP00000368919:F90L	.	F	+	1	0	NHLRC3	38511731	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.899000	0.87370	2.162000	0.67917	0.460000	0.39030	TTC	.	.		0.388	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754	
NAA16	79612	hgsc.bcm.edu	37	13	41892974	41892974	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:41892974T>C	ENST00000379406.3	+	3	496	c.172T>C	c.(172-174)Tgt>Cgt	p.C58R	NAA16_ENST00000379367.3_Missense_Mutation_p.C58R|NAA16_ENST00000403412.3_Missense_Mutation_p.C58R	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	58					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AACACTGAACTGTTTAGGAAA	0.294																																					p.C58R		Atlas-SNP	.											.	NAA16	74	.	0			c.T172C						.						88.0	89.0	89.0					13																	41892974		2202	4294	6496	SO:0001583	missense	79612	exon3			CTGAACTGTTTAG	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"""N(alpha)-acetyltransferase subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	26164	protein-coding gene	gene with protein product			"""NMDA receptor regulated 1-like"""	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.172T>C	chr13.hg19:g.41892974T>C	ENSP00000368716:p.Cys58Arg	84.0	0.0		82.0	4.0	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.916345	0.73098	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.72394	0.74;0.74;-0.65	4.23	4.23	0.50019	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000002	D	0.84437	0.5472	M	0.88570	2.965	0.80722	D	1	D;D;P	0.89917	0.97;1.0;0.906	P;D;P	0.97110	0.665;1.0;0.57	D	0.84033	0.0360	10	0.21014	T	0.42	-10.8295	13.7888	0.63126	0.0:0.0:0.0:1.0	.	58;58;58	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	R	58	ENSP00000368674:C58R;ENSP00000368716:C58R;ENSP00000386103:C58R	ENSP00000368674:C58R	C	+	1	0	NAA16	40790974	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.355000	0.79434	1.897000	0.54924	0.533000	0.62120	TGT	.	.		0.294	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527	
NAA16	79612	hgsc.bcm.edu	37	13	41897285	41897285	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:41897285A>G	ENST00000379406.3	+	5	820	c.496A>G	c.(496-498)Atg>Gtg	p.M166V	NAA16_ENST00000379367.3_Missense_Mutation_p.M166V|NAA16_ENST00000403412.3_Missense_Mutation_p.M166V	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	166					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AGATTATGATATGGCCCTAAA	0.383																																					p.M166V		Atlas-SNP	.											.	NAA16	74	.	0			c.A496G						.						152.0	149.0	150.0					13																	41897285		2203	4300	6503	SO:0001583	missense	79612	exon5			TATGATATGGCCC	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"""N(alpha)-acetyltransferase subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	26164	protein-coding gene	gene with protein product			"""NMDA receptor regulated 1-like"""	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.496A>G	chr13.hg19:g.41897285A>G	ENSP00000368716:p.Met166Val	97.0	0.0		94.0	4.0	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.726646	0.48833	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.73575	0.67;0.67;-0.76	5.74	5.74	0.90152	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.059999	0.64402	D	0.000002	T	0.74465	0.3720	L	0.56769	1.78	0.50813	D	0.99989	B;B;B	0.18610	0.005;0.029;0.004	B;B;B	0.31946	0.017;0.138;0.021	T	0.69789	-0.5050	10	0.33141	T	0.24	-6.42	16.0153	0.80434	1.0:0.0:0.0:0.0	.	166;166;166	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	V	166	ENSP00000368674:M166V;ENSP00000368716:M166V;ENSP00000386103:M166V	ENSP00000368674:M166V	M	+	1	0	NAA16	40795285	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.637000	0.91014	2.187000	0.69744	0.528000	0.53228	ATG	.	.		0.383	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527	
NUDT15	55270	hgsc.bcm.edu	37	13	48611895	48611895	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:48611895G>A	ENST00000258662.2	+	1	193	c.13G>A	c.(13-15)Gca>Aca	p.A5T	SUCLA2_ENST00000543413.1_5'UTR	NM_018283.1	NP_060753.1	Q9NV35	NUD15_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 15	5					dGTP catabolic process (GO:0006203)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	7		all_cancers(8;3.75e-25)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|all_hematologic(8;0.000219)|Lung NSC(96;0.000226)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;4.83e-07)		GACGGCCAGCGCACAGCCGCG	0.716											OREG0022405	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A5T		Atlas-SNP	.											.	NUDT15	12	.	0			c.G13A						.																																			SO:0001583	missense	55270	exon1			GCCAGCGCACAGC		CCDS9407.1	13q14.12	2006-04-12			ENSG00000136159	ENSG00000136159		"""Nudix motif containing"""	23063	protein-coding gene	gene with protein product		615792				12767940	Standard	NM_018283		Approved	MTH2, FLJ10956	uc001vbw.1	Q9NV35	OTTHUMG00000016890	ENST00000258662.2:c.13G>A	chr13.hg19:g.48611895G>A	ENSP00000258662:p.Ala5Thr	74.0	0.0	955	61.0	4.0	NM_018283	A2RUR6|Q32Q27|Q6P2C9	Missense_Mutation	SNP	ENST00000258662.2	hg19	CCDS9407.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846455	0.32606	.	.	ENSG00000136159	ENST00000258662	T	0.34859	1.34	4.72	2.97	0.34412	NUDIX hydrolase domain-like (1);	0.727696	0.13528	N	0.381185	T	0.26304	0.0642	L	0.40543	1.245	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.19321	-1.0309	10	0.26408	T	0.33	-5.0166	6.6964	0.23201	0.0964:0.1793:0.7243:0.0	.	5	Q9NV35	NUD15_HUMAN	T	5	ENSP00000258662:A5T	ENSP00000258662:A5T	A	+	1	0	NUDT15	47509896	0.009000	0.17119	0.001000	0.08648	0.000000	0.00434	1.572000	0.36461	0.718000	0.32166	-0.140000	0.14226	GCA	.	.		0.716	NUDT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044862.3	NM_018283	
FNDC3A	22862	hgsc.bcm.edu	37	13	49781309	49781309	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:49781309A>G	ENST00000492622.2	+	26	3680	c.3375A>G	c.(3373-3375)caA>caG	p.Q1125Q	FNDC3A_ENST00000541916.1_Silent_p.Q1125Q|FNDC3A_ENST00000398316.3_Silent_p.Q1069Q	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1125	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		GCCAGTGCCAAGACTCTCTGG	0.527																																					p.Q1125Q		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3375G						.						116.0	103.0	107.0					13																	49781309		2203	4300	6503	SO:0001819	synonymous_variant	22862	exon26			GTGCCAAGACTCT	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3375A>G	chr13.hg19:g.49781309A>G		77.0	0.0		85.0	4.0	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Silent	SNP	ENST00000492622.2	hg19	CCDS41886.1																																																																																			.	.		0.527	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
COMMD6	170622	hgsc.bcm.edu	37	13	76104273	76104273	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:76104273C>T	ENST00000377615.3	-	4	348	c.184G>A	c.(184-186)Gaa>Aaa	p.E62K	COMMD6_ENST00000460675.1_5'UTR|COMMD6_ENST00000377619.5_Missense_Mutation_p.E77K|COMMD6_ENST00000355801.4_Missense_Mutation_p.E62K|COMMD6_ENST00000406936.3_Missense_Mutation_p.E62K			Q7Z4G1	COMD6_HUMAN	COMM domain containing 6	62	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			breast(1)|lung(1)|urinary_tract(1)	3		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		ATCGTCATTTCAAAGCACTTG	0.383																																					p.E62K		Atlas-SNP	.											.	COMMD6	4	.	0			c.G184A						.						148.0	132.0	138.0					13																	76104273		2203	4300	6503	SO:0001583	missense	170622	exon3			TCATTTCAAAGCA	AY542161	CCDS9451.1, CCDS9452.1	13q22	2004-02-18			ENSG00000188243	ENSG00000188243			24015	protein-coding gene	gene with protein product		612377				15799966	Standard	NM_203497		Approved	Acrg	uc001vjn.1	Q7Z4G1	OTTHUMG00000017089	ENST00000377615.3:c.184G>A	chr13.hg19:g.76104273C>T	ENSP00000366841:p.Glu62Lys	81.0	0.0		79.0	5.0	NM_203495	A6NF28|B7ZLN0|Q5TBK4	Missense_Mutation	SNP	ENST00000377615.3	hg19	CCDS9451.1	.	.	.	.	.	.	.	.	.	.	C	36	5.637347	0.96693	.	.	ENSG00000188243	ENST00000406936;ENST00000377615;ENST00000377619;ENST00000355801	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	5.23	5.23	0.72850	COMM domain (1);	0.000000	0.85682	D	0.000000	T	0.46092	0.1375	.	.	.	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.994	T	0.46219	-0.9207	9	0.72032	D	0.01	.	18.7681	0.91881	0.0:1.0:0.0:0.0	.	62;62	Q7Z4G1;Q7Z4G1-2	COMD6_HUMAN;.	K	62;62;77;62	ENSP00000385660:E62K;ENSP00000366841:E62K;ENSP00000366845:E77K;ENSP00000348054:E62K	ENSP00000348054:E62K	E	-	1	0	COMMD6	75002274	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.313000	0.78978	2.613000	0.88420	0.655000	0.94253	GAA	.	.		0.383	COMMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045288.4	XM_085023	
SCEL	8796	hgsc.bcm.edu	37	13	78130761	78130761	+	Missense_Mutation	SNP	G	G	T	rs200836262		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:78130761G>T	ENST00000349847.3	+	3	158	c.74G>T	c.(73-75)cGg>cTg	p.R25L	SCEL_ENST00000535157.1_Missense_Mutation_p.R25L|SCEL_ENST00000377246.3_Missense_Mutation_p.R25L	NM_144777.2	NP_659001.2	O95171	SCEL_HUMAN	sciellin	25					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)	p.R25L(1)		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)		GGAACCACACGGAAGCAGCAG	0.433																																					p.R25L		Atlas-SNP	.											.	SCEL	85	.	1	Substitution - Missense(1)	lung(1)	c.G74T						.						182.0	187.0	186.0					13																	78130761		2203	4300	6503	SO:0001583	missense	8796	exon3			CCACACGGAAGCA	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.74G>T	chr13.hg19:g.78130761G>T	ENSP00000302579:p.Arg25Leu	84.0	0.0		92.0	4.0	NM_003843	B7Z797|F5H651|Q53H61|Q5W0S8|Q5W0S9|Q86X00	Missense_Mutation	SNP	ENST00000349847.3	hg19	CCDS9459.1	.	.	.	.	.	.	.	.	.	.	g	0.005	-2.196575	0.00299	.	.	ENSG00000136155	ENST00000348770;ENST00000535157;ENST00000377246;ENST00000349847	T;T;T	0.21734	1.99;1.99;1.99	5.16	-2.02	0.07388	.	0.552403	0.15231	N	0.273429	T	0.04048	0.0113	N	0.00583	-1.355	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.31475	-0.9942	10	0.30854	T	0.27	1.2565	2.1981	0.03916	0.3887:0.0711:0.2974:0.2428	.	25;25;25	F5H651;O95171-2;O95171	.;.;SCEL_HUMAN	L	25	ENSP00000437895:R25L;ENSP00000366454:R25L;ENSP00000302579:R25L	ENSP00000315127:R25L	R	+	2	0	SCEL	77028762	0.020000	0.18652	0.001000	0.08648	0.000000	0.00434	-0.378000	0.07446	-0.882000	0.03987	-3.487000	0.00034	CGG	.	.		0.433	SCEL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045339.2	NM_144777	
DZIP1	22873	hgsc.bcm.edu	37	13	96293971	96293971	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:96293971G>A	ENST00000376829.2	-	5	1026	c.175C>T	c.(175-177)Cag>Tag	p.Q59*	DZIP1_ENST00000361396.2_Nonsense_Mutation_p.Q59*|DZIP1_ENST00000347108.3_Nonsense_Mutation_p.Q59*|DZIP1_ENST00000466027.1_5'UTR|DZIP1_ENST00000361156.3_Nonsense_Mutation_p.Q59*	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	59					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GGCCTGAACTGGAAGAAGGGC	0.741																																					p.Q59X		Atlas-SNP	.											.	DZIP1	195	.	0			c.C175T						.						31.0	35.0	34.0					13																	96293971		2188	4258	6446	SO:0001587	stop_gained	22873	exon5			TGAACTGGAAGAA	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.175C>T	chr13.hg19:g.96293971G>A	ENSP00000366025:p.Gln59*	13.0	0.0		18.0	5.0	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Nonsense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959865	0.74016	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	.	.	.	4.78	4.78	0.61160	.	0.109676	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.9704	12.888	0.58055	0.0:0.0:0.8374:0.1626	.	.	.	.	X	59	.	ENSP00000257312:Q59X	Q	-	1	0	DZIP1	95091972	1.000000	0.71417	1.000000	0.80357	0.252000	0.25951	2.342000	0.43992	2.212000	0.71576	0.551000	0.68910	CAG	.	.		0.741	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
SLC10A2	6555	hgsc.bcm.edu	37	13	103703608	103703608	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:103703608T>C	ENST00000245312.3	-	4	1356	c.760A>G	c.(760-762)Agg>Ggg	p.R254G		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	254					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	ATGCCATACCTGTACCAGGGT	0.428																																					p.R254G		Atlas-SNP	.											.	SLC10A2	67	.	0			c.A760G						.						68.0	70.0	70.0					13																	103703608		2203	4300	6503	SO:0001630	splice_region_variant	6555	exon4			CATACCTGTACCA	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"""Solute carriers"""	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.761+1A>G	chr13.hg19:g.103703608T>C		46.0	0.0		54.0	4.0	NM_000452	A1L4F4|Q13839	Missense_Mutation	SNP	ENST00000245312.3	hg19	CCDS9506.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.270568	0.59540	.	.	ENSG00000125255	ENST00000245312	T	0.78707	-1.2	5.46	5.46	0.80206	.	0.042424	0.85682	D	0.000000	T	0.77974	0.4211	M	0.76433	2.335	0.53688	D	0.99997	B	0.24920	0.114	B	0.21917	0.037	T	0.76061	-0.3097	10	0.48119	T	0.1	-14.0415	15.5257	0.75901	0.0:0.0:0.0:1.0	.	254	Q12908	NTCP2_HUMAN	G	254	ENSP00000245312:R254G	ENSP00000245312:R254G	R	-	1	2	SLC10A2	102501609	1.000000	0.71417	1.000000	0.80357	0.091000	0.18340	7.818000	0.86416	2.082000	0.62665	0.377000	0.23210	AGG	.	.		0.428	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1		Missense_Mutation
MYO16	23026	hgsc.bcm.edu	37	13	109318307	109318307	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr13:109318307C>A	ENST00000357550.2	+	1	77	c.36C>A	c.(34-36)ccC>ccA	p.P12P	MYO16_ENST00000356711.2_Silent_p.P12P|MYO16_ENST00000251041.5_Silent_p.P12P	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AGTCCCTTCCCCTTGGCCAAC	0.517																																					p.P34P		Atlas-SNP	.											.	MYO16	285	.	0			c.C102A						.						84.0	75.0	78.0					13																	109318307		2203	4300	6503	SO:0001819	synonymous_variant	23026	exon2			CCTTCCCCTTGGC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.36C>A	chr13.hg19:g.109318307C>A		50.0	0.0		63.0	4.0	NM_001198950		Silent	SNP	ENST00000357550.2	hg19	CCDS32008.1																																																																																			.	.		0.517	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
RNASE4	6038	hgsc.bcm.edu	37	14	21167714	21167714	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:21167714A>G	ENST00000555835.1	+	2	860	c.184A>G	c.(184-186)Atg>Gtg	p.M62V	AL163636.6_ENST00000553909.1_3'UTR|RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000397995.2_Missense_Mutation_p.M62V|RNASE4_ENST00000555597.1_Missense_Mutation_p.M62V|RNASE4_ENST00000304704.4_Missense_Mutation_p.M62V	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	62					cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		AAGACGGAAGATGACTTTGTA	0.498																																					p.M62V	Esophageal Squamous(59;1059 1362 26290 51151)	Atlas-SNP	.											.	RNASE4	18	.	0			c.A184G						.						154.0	125.0	135.0					14																	21167714		2203	4300	6503	SO:0001583	missense	6038	exon2			CGGAAGATGACTT	U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"""Ribonucleases, RNase A"""	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.184A>G	chr14.hg19:g.21167714A>G	ENSP00000452245:p.Met62Val	89.0	0.0		55.0	4.0	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	hg19	CCDS9555.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.659341	0.67586	.	.	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02	5.81	5.81	0.92471	Ribonuclease A, domain (4);	0.112323	0.64402	D	0.000004	T	0.67608	0.2911	M	0.89715	3.055	0.35604	D	0.808104	D	0.67145	0.996	D	0.63283	0.913	T	0.80627	-0.1298	10	0.72032	D	0.01	-32.3892	12.8374	0.57782	1.0:0.0:0.0:0.0	.	62	P34096	RNAS4_HUMAN	V	62	ENSP00000452245:M62V;ENSP00000381081:M62V;ENSP00000451624:M62V;ENSP00000381087:M62V;ENSP00000307096:M62V;ENSP00000381085:M62V	ENSP00000307096:M62V	M	+	1	0	AL163636.2;RNASE4	20237554	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	3.185000	0.50934	2.343000	0.79666	0.533000	0.62120	ATG	.	.		0.498	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3		
PABPN1	8106	hgsc.bcm.edu	37	14	23794468	23794468	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:23794468A>G	ENST00000216727.4	+	7	1075	c.894A>G	c.(892-894)agA>agG	p.R298R	BCL2L2-PABPN1_ENST00000553781.1_Silent_p.R325R|PABPN1_ENST00000397276.2_3'UTR|AL049829.1_ENST00000594872.1_5'Flank|PABPN1_ENST00000556821.1_Silent_p.R170R|BCL2L2-PABPN1_ENST00000557008.1_Silent_p.R325R	NM_004643.3	NP_004634.1	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	298	Interacts with PAPOLA. {ECO:0000250}.|Necessary for homooligomerization.				gene expression (GO:0010467)|modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|muscle contraction (GO:0006936)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			large_intestine(1)|lung(1)|ovary(2)	4	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GCCGGGCTAGAGCGACATCAT	0.428																																					p.R325R		Atlas-SNP	.											.	.	.	.	0			c.A975G						.						109.0	108.0	108.0					14																	23794468		2203	4300	6503	SO:0001819	synonymous_variant	100529063	exon9			GGCTAGAGCGACA	AF026029	CCDS9592.1	14q11.2	2013-02-12	2001-11-28		ENSG00000100836	ENSG00000100836		"""RNA binding motif (RRM) containing"""	8565	protein-coding gene	gene with protein product		602279	"""poly(A)-binding protein, nuclear 1"""	OPMD, PABP2		7795598	Standard	NM_004643		Approved	PAB2		Q86U42	OTTHUMG00000028739	ENST00000216727.4:c.894A>G	chr14.hg19:g.23794468A>G		201.0	0.0		109.0	5.0	NM_001199864	D3DS49|O43484	Silent	SNP	ENST00000216727.4	hg19	CCDS9592.1																																																																																			.	.		0.428	PABPN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071767.4	NM_004643	
LRRC16B	90668	hgsc.bcm.edu	37	14	24523712	24523712	+	Silent	SNP	T	T	C	rs561201986		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:24523712T>C	ENST00000342740.5	+	5	508	c.354T>C	c.(352-354)ccT>ccC	p.P118P	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	118						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		AGGTCTGCCCTGGCCCTGGGT	0.582																																					p.P118P		Atlas-SNP	.											.	LRRC16B	120	.	0			c.T354C						.						71.0	62.0	65.0					14																	24523712		2203	4300	6503	SO:0001819	synonymous_variant	90668	exon5			CTGCCCTGGCCCT	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.354T>C	chr14.hg19:g.24523712T>C		79.0	0.0		71.0	4.0	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	hg19	CCDS32054.1																																																																																			.	.		0.582	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
RNF31	55072	hgsc.bcm.edu	37	14	24621043	24621043	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:24621043C>A	ENST00000324103.6	+	11	2292	c.1972C>A	c.(1972-1974)Cgg>Agg	p.R658R	RP11-468E2.4_ENST00000558468.1_Silent_p.R133R|RNF31_ENST00000382687.3_Silent_p.R507R|RNF31_ENST00000559275.1_Silent_p.R507R	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	658					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		CAGCTGGGGCCGGGCAGAGCT	0.617																																					p.R658R		Atlas-SNP	.											RNF31,NS,carcinoma,0,1	RNF31	95	.	0			c.C1972A						.						63.0	70.0	68.0					14																	24621043		1971	4157	6128	SO:0001819	synonymous_variant	55072	exon11			TGGGGCCGGGCAG	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"""RING-type (C3HC4) zinc fingers"""	16031	protein-coding gene	gene with protein product	"""HOIL-1-interacting protein"""	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1972C>A	chr14.hg19:g.24621043C>A		50.0	0.0		28.0	2.0	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Silent	SNP	ENST00000324103.6	hg19	CCDS41931.1																																																																																			.	.		0.617	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999	
C14orf166	51637	hgsc.bcm.edu	37	14	52471128	52471128	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:52471128A>G	ENST00000261700.3	+	8	794	c.629A>G	c.(628-630)gAg>gGg	p.E210G	C14orf166_ENST00000556760.1_3'UTR	NM_016039.2	NP_057123.1	Q9Y224	CN166_HUMAN	chromosome 14 open reading frame 166	210					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA transport (GO:0050658)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core binding (GO:0000993)			endometrium(1)|large_intestine(3)|lung(2)	6	Breast(41;0.0639)|all_epithelial(31;0.101)					CTGCACATAGAGGAGCTCAGA	0.393																																					p.E210G		Atlas-SNP	.											.	C14orf166	23	.	0			c.A629G						.						66.0	69.0	68.0					14																	52471128		2203	4300	6503	SO:0001583	missense	51637	exon8			ACATAGAGGAGCT	AF151857	CCDS9705.1	14q22.1	2014-05-29			ENSG00000087302	ENSG00000087302			23169	protein-coding gene	gene with protein product	"""RLL motif containing 1"""	610858				10810093, 24608264	Standard	NM_016039		Approved	CGI-99, RLLM1, CLE, CLE7, LCRP369	uc010aod.3	Q9Y224	OTTHUMG00000152332	ENST00000261700.3:c.629A>G	chr14.hg19:g.52471128A>G	ENSP00000261700:p.Glu210Gly	144.0	0.0		96.0	5.0	NM_016039		Missense_Mutation	SNP	ENST00000261700.3	hg19	CCDS9705.1	.	.	.	.	.	.	.	.	.	.	A	17.42	3.385530	0.61956	.	.	ENSG00000087302	ENST00000261700	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.65883	0.2734	M	0.64404	1.975	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.60255	-0.7299	9	0.33141	T	0.24	-13.0206	16.8222	0.85835	1.0:0.0:0.0:0.0	.	210;210	Q9Y224;Q549M8	CN166_HUMAN;.	G	210	.	ENSP00000261700:E210G	E	+	2	0	C14orf166	51540878	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.105000	0.94246	2.371000	0.80710	0.533000	0.62120	GAG	.	.		0.393	C14orf166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276887.1	NM_016039	
PTGER2	5732	hgsc.bcm.edu	37	14	52781586	52781586	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:52781586G>T	ENST00000245457.5	+	1	474	c.320G>T	c.(319-321)cGc>cTc	p.R107L	PTGER2_ENST00000557436.1_Intron	NM_000956.3	NP_000947.2	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	107					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to prostaglandin E stimulus (GO:0071380)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Dinoprostone(DB00917)|Misoprostol(DB00929)	CCCGAGAGCCGCGCGTGCACC	0.647																																					p.R107L		Atlas-SNP	.											.	PTGER2	27	.	0			c.G320T						.						43.0	39.0	41.0					14																	52781586		2191	4277	6468	SO:0001583	missense	5732	exon1			AGAGCCGCGCGTG		CCDS9708.1	14q22	2012-08-08	2002-08-29		ENSG00000125384	ENSG00000125384		"""GPCR / Class A : Prostanoid receptors"""	9594	protein-coding gene	gene with protein product		176804	"""prostaglandin E receptor 2 (subtype EP2), 53kD"""			8250933, 7759114	Standard	NM_000956		Approved	EP2	uc001wzr.3	P43116	OTTHUMG00000140300	ENST00000245457.5:c.320G>T	chr14.hg19:g.52781586G>T	ENSP00000245457:p.Arg107Leu	128.0	0.0		91.0	4.0	NM_000956	D3DSC0|Q52LG8	Missense_Mutation	SNP	ENST00000245457.5	hg19	CCDS9708.1	.	.	.	.	.	.	.	.	.	.	G	9.490	1.100330	0.20552	.	.	ENSG00000125384	ENST00000245457	T	0.70045	-0.45	5.09	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.662303	0.15967	N	0.235991	T	0.48003	0.1476	L	0.32530	0.975	0.09310	N	1	B	0.14438	0.01	B	0.18871	0.023	T	0.29579	-1.0007	10	0.10377	T	0.69	-7.4094	5.3613	0.16089	0.1739:0.0:0.6661:0.1599	.	107	P43116	PE2R2_HUMAN	L	107	ENSP00000245457:R107L	ENSP00000245457:R107L	R	+	2	0	PTGER2	51851336	0.000000	0.05858	0.674000	0.29902	0.967000	0.64934	0.187000	0.16998	0.631000	0.30412	0.563000	0.77884	CGC	.	.		0.647	PTGER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276890.1		
OTX2	5015	hgsc.bcm.edu	37	14	57271044	57271044	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:57271044T>C	ENST00000555006.1	-	3	519	c.111A>G	c.(109-111)aaA>aaG	p.K37K	OTX2_ENST00000554788.1_Intron|OTX2_ENST00000554559.1_Intron|OTX2_ENST00000339475.5_Silent_p.K45K|OTX2_ENST00000408990.3_Silent_p.K37K			P32243	OTX2_HUMAN	orthodenticle homeobox 2	37					axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|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)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					CCCGGCGCTGTTTCCGGGGGG	0.632																																					p.K45K		Atlas-SNP	.											.	OTX2	47	.	0			c.A135G						.						40.0	39.0	40.0					14																	57271044		2203	4300	6503	SO:0001819	synonymous_variant	5015	exon2			GCGCTGTTTCCGG	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"""Homeoboxes / PRD class"""	8522	protein-coding gene	gene with protein product		600037	"""orthodenticle homolog 2 (Drosophila)"""			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.111A>G	chr14.hg19:g.57271044T>C		127.0	0.0		89.0	4.0	NM_001270525	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Silent	SNP	ENST00000555006.1	hg19	CCDS41960.1																																																																																			.	.		0.632	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.	
DACT1	51339	hgsc.bcm.edu	37	14	59112097	59112097	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:59112097C>A	ENST00000335867.4	+	4	780	c.756C>A	c.(754-756)ccC>ccA	p.P252P	DACT1_ENST00000541264.2_5'UTR|DACT1_ENST00000395153.3_Silent_p.P215P|DACT1_ENST00000555845.1_3'UTR|DACT1_ENST00000556859.1_5'UTR			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	252					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						ATGTGAATCCCAAGTACCAGT	0.478																																					p.P252P		Atlas-SNP	.											.	DACT1	119	.	0			c.C756A						.						164.0	151.0	155.0					14																	59112097		2203	4300	6503	SO:0001819	synonymous_variant	51339	exon4			GAATCCCAAGTAC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.756C>A	chr14.hg19:g.59112097C>A		151.0	0.0		106.0	5.0	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	hg19	CCDS9736.1																																																																																			.	.		0.478	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
SYNE2	23224	hgsc.bcm.edu	37	14	64492096	64492096	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:64492096C>A	ENST00000344113.4	+	41	6421	c.6209C>A	c.(6208-6210)tCc>tAc	p.S2070Y	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.S2070Y|SYNE2_ENST00000358025.3_Missense_Mutation_p.S2070Y	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2070					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TTGAATTCATCCGAAGGCAAA	0.348																																					p.S2070Y		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	.	0			c.C6209A						.						65.0	61.0	62.0					14																	64492096		1815	4081	5896	SO:0001583	missense	23224	exon41			ATTCATCCGAAGG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6209C>A	chr14.hg19:g.64492096C>A	ENSP00000341781:p.Ser2070Tyr	110.0	0.0		56.0	3.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.376495	0.42105	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57107	0.78;0.78;0.42	5.9	5.9	0.94986	.	0.464601	0.20763	N	0.086123	T	0.52008	0.1708	N	0.24115	0.695	0.80722	D	1	D;D	0.59767	0.976;0.986	P;P	0.56700	0.642;0.804	T	0.43814	-0.9368	10	0.33141	T	0.24	.	13.0004	0.58672	0.2011:0.7989:0.0:0.0	.	2070;2070	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	Y	2070	ENSP00000350719:S2070Y;ENSP00000341781:S2070Y;ENSP00000452570:S2070Y	ENSP00000261678:S2070Y	S	+	2	0	SYNE2	63561849	0.894000	0.30519	0.999000	0.59377	0.961000	0.63080	1.321000	0.33678	2.800000	0.96347	0.455000	0.32223	TCC	.	.		0.348	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
PPP1R36	145376	hgsc.bcm.edu	37	14	65054066	65054066	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:65054066A>G	ENST00000298705.1	+	10	962	c.866A>G	c.(865-867)aAa>aGa	p.K289R	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	289					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGGGAAAAGAAACGCATGACT	0.408																																					p.K289R		Atlas-SNP	.											.	.	.	.	0			c.A866G						.						108.0	110.0	109.0					14																	65054066		2203	4300	6503	SO:0001583	missense	145376	exon10			AAAAGAAACGCAT		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.866A>G	chr14.hg19:g.65054066A>G	ENSP00000298705:p.Lys289Arg	92.0	0.0		78.0	4.0	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	hg19	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	A	10.42	1.346610	0.24426	.	.	ENSG00000165807	ENST00000298705	T	0.31769	1.48	5.55	3.23	0.37069	.	0.260360	0.33290	N	0.005062	T	0.20618	0.0496	L	0.41710	1.295	0.30347	N	0.785176	B	0.20671	0.047	B	0.18263	0.021	T	0.10337	-1.0634	10	0.31617	T	0.26	-21.223	4.8722	0.13639	0.7216:0.0:0.2784:0.0	.	289	Q96LQ0	PPR36_HUMAN	R	289	ENSP00000298705:K289R	ENSP00000298705:K289R	K	+	2	0	C14orf50	64123819	0.989000	0.36119	0.995000	0.50966	0.994000	0.84299	1.872000	0.39549	0.940000	0.37473	0.533000	0.62120	AAA	.	.		0.408	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
SPTB	6710	hgsc.bcm.edu	37	14	65252316	65252316	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:65252316T>C	ENST00000389721.5	-	17	3826	c.3794A>G	c.(3793-3795)gAg>gGg	p.E1265G	SPTB_ENST00000542895.1_Missense_Mutation_p.E1265G|SPTB_ENST00000389720.3_Missense_Mutation_p.E1265G|SPTB_ENST00000556626.1_Missense_Mutation_p.E1265G|SPTB_ENST00000389722.3_Missense_Mutation_p.E1265G	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1265					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GACAGAGGCCTCCTGGGCCTT	0.557																																					p.E1265G		Atlas-SNP	.											.	SPTB	378	.	0			c.A3794G						.						71.0	62.0	65.0					14																	65252316		2203	4300	6503	SO:0001583	missense	6710	exon17			GAGGCCTCCTGGG		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.3794A>G	chr14.hg19:g.65252316T>C	ENSP00000374371:p.Glu1265Gly	56.0	0.0		62.0	4.0	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.487581	0.44249	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	5.18	5.18	0.71444	.	0.054164	0.64402	D	0.000001	T	0.50990	0.1648	M	0.78637	2.42	0.80722	D	1	B;P	0.43314	0.085;0.803	B;P	0.48795	0.126;0.59	T	0.57219	-0.7849	10	0.66056	D	0.02	.	14.2976	0.66325	0.0:0.0:0.0:1.0	.	1265;1269	P11277;Q59FP5	SPTB1_HUMAN;.	G	1269;1265;49;1265;1265;1265;1265	ENSP00000374372:E1265G;ENSP00000451752:E1265G;ENSP00000374371:E1265G;ENSP00000443882:E1265G;ENSP00000374370:E1265G	ENSP00000334218:E49G	E	-	2	0	SPTB	64322069	1.000000	0.71417	0.999000	0.59377	0.104000	0.19210	7.981000	0.88123	2.080000	0.62538	0.443000	0.29094	GAG	.	.		0.557	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
SLC39A9	55334	hgsc.bcm.edu	37	14	69922540	69922540	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:69922540C>T	ENST00000336643.5	+	6	1328	c.650C>T	c.(649-651)gCa>gTa	p.A217V	SLC39A9_ENST00000555245.1_3'UTR|SLC39A9_ENST00000031146.4_Missense_Mutation_p.A151V|SLC39A9_ENST00000556605.1_Missense_Mutation_p.A217V|SLC39A9_ENST00000557046.1_Missense_Mutation_p.A194V	NM_018375.4	NP_060845.2	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	217					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		TTTGCATTGGCAGCACCAGTT	0.438																																					p.A217V		Atlas-SNP	.											.	SLC39A9	27	.	0			c.C650T						.						141.0	128.0	132.0					14																	69922540		2203	4300	6503	SO:0001583	missense	55334	exon6			CATTGGCAGCACC		CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364		"""Solute carriers"""	20182	protein-coding gene	gene with protein product							Standard	NM_018375		Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000336643.5:c.650C>T	chr14.hg19:g.69922540C>T	ENSP00000336887:p.Ala217Val	179.0	0.0		92.0	4.0	NM_001252150	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	Missense_Mutation	SNP	ENST00000336643.5	hg19	CCDS9795.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062484	0.76187	.	.	ENSG00000029364	ENST00000556605;ENST00000336643;ENST00000557046	T;T;T	0.47869	0.83;0.83;0.83	5.19	5.19	0.71726	.	0.094168	0.64402	D	0.000001	T	0.67401	0.2889	M	0.65320	2	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.993	D;D;D	0.74674	0.984;0.951;0.934	T	0.69331	-0.5173	10	0.72032	D	0.01	-12.7867	18.8944	0.92417	0.0:1.0:0.0:0.0	.	194;217;217	Q9NUM3-2;G3V5J8;Q9NUM3	.;.;S39A9_HUMAN	V	217;217;194	ENSP00000452385:A217V;ENSP00000336887:A217V;ENSP00000451833:A194V	ENSP00000031146:A217V	A	+	2	0	SLC39A9	68992293	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	7.649000	0.83500	2.696000	0.92011	0.467000	0.42956	GCA	.	.		0.438	SLC39A9-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412446.1	NM_018375	
ADAM20	8748	hgsc.bcm.edu	37	14	70989894	70989894	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:70989894A>G	ENST00000256389.3	-	2	1975	c.1731T>C	c.(1729-1731)tcT>tcC	p.S577S	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	527	Cys-rich.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		AGCAACTCTGAGATGCACTCC	0.408																																					p.S577S		Atlas-SNP	.											.	ADAM20	59	.	0			c.T1731C						.						197.0	142.0	161.0					14																	70989894		2203	4300	6503	SO:0001819	synonymous_variant	8748	exon2			ACTCTGAGATGCA	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1731T>C	chr14.hg19:g.70989894A>G		125.0	0.0		85.0	5.0	NM_003814	Q6GTZ1|Q9UKJ9	Silent	SNP	ENST00000256389.3	hg19	CCDS32111.1																																																																																			.	.		0.408	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
PCNX	22990	hgsc.bcm.edu	37	14	71517418	71517418	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:71517418C>T	ENST00000304743.2	+	23	4834	c.4388C>T	c.(4387-4389)cCa>cTa	p.P1463L	PCNX_ENST00000439984.3_Missense_Mutation_p.P1352L|PCNX_ENST00000238570.5_Missense_Mutation_p.P1463L	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1463						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TATATTGCCCCATGGCAGATC	0.378																																					p.P1463L		Atlas-SNP	.											.	PCNX	198	.	0			c.C4388T						.						147.0	149.0	148.0					14																	71517418		2203	4300	6503	SO:0001583	missense	22990	exon23			TTGCCCCATGGCA	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4388C>T	chr14.hg19:g.71517418C>T	ENSP00000304192:p.Pro1463Leu	152.0	0.0		97.0	4.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.2|21.2	4.110140|4.110140	0.77210|0.77210	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000554691|ENST00000304743;ENST00000238570;ENST00000439984	.|T;T;T	.|0.14391	.|2.84;2.53;2.51	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.47488|0.47488	0.1448|0.1448	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.997	T|T	0.54788|0.54788	-0.8241|-0.8241	5|10	.|0.87932	.|D	.|0	.|.	19.6512|19.6512	0.95812|0.95812	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1463;1352;1463	.|Q96RV3-3;B2RTR6;Q96RV3	.|.;.;PCX1_HUMAN	Y|L	522|1463;1463;1352	.|ENSP00000304192:P1463L;ENSP00000238570:P1463L;ENSP00000396617:P1352L	.|ENSP00000238570:P1463L	H|P	+|+	1|2	0|0	PCNX|PCNX	70587171|70587171	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.744000|0.744000	0.42396|0.42396	7.776000|7.776000	0.85560|0.85560	2.646000|2.646000	0.89796|0.89796	0.563000|0.563000	0.77884|0.77884	CAT|CCA	.	.		0.378	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
PAPLN	89932	hgsc.bcm.edu	37	14	73719406	73719406	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:73719406C>A	ENST00000554301.1	+	10	1180	c.1017C>A	c.(1015-1017)ccC>ccA	p.P339P	PAPLN_ENST00000381166.3_Silent_p.P339P|PAPLN_ENST00000427855.1_Silent_p.P339P|PAPLN_ENST00000340738.5_Silent_p.P312P|PAPLN_ENST00000555445.1_Silent_p.P339P			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	339	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		AGGCCTACCCCGACCACATGT	0.647																																					p.P312P		Atlas-SNP	.											.	PAPLN	180	.	0			c.C936A						.						75.0	75.0	75.0					14																	73719406		2203	4299	6502	SO:0001819	synonymous_variant	89932	exon10			CTACCCCGACCAC	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1017C>A	chr14.hg19:g.73719406C>A		117.0	0.0		60.0	4.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	hg19																																																																																				.	.		0.647	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
PTGR2	145482	hgsc.bcm.edu	37	14	74350824	74350824	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:74350824A>G	ENST00000555661.1	+	10	1145	c.1000A>G	c.(1000-1002)Aca>Gca	p.T334A	ZNF410_ENST00000324593.6_5'Flank|ZNF410_ENST00000555044.1_5'Flank|PTGR2_ENST00000267568.4_Missense_Mutation_p.T334A|ZNF410_ENST00000540593.1_5'Flank|ZNF410_ENST00000442160.3_5'Flank|RP5-1021I20.4_ENST00000556551.2_Missense_Mutation_p.T264A|PTGR2_ENST00000553813.1_Missense_Mutation_p.T200A|PTGR2_ENST00000555228.1_Missense_Mutation_p.T334A			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	334					prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)			NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	GTCCATGATGACAGGAGGTAA	0.333																																					p.T334A	Esophageal Squamous(98;1155 1417 16452 47043 47872)	Atlas-SNP	.											.	PTGR2	21	.	0			c.A1000G						.						122.0	106.0	111.0					14																	74350824		2203	4298	6501	SO:0001583	missense	145482	exon10			ATGATGACAGGAG	AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043			20149	protein-coding gene	gene with protein product		608642	"""zinc binding alcohol dehydrogenase domain containing 1"""	ZADH1		17449869	Standard	NM_152444		Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.1000A>G	chr14.hg19:g.74350824A>G	ENSP00000452280:p.Thr334Ala	106.0	0.0		91.0	4.0	NM_152444	Q3L8A4|Q6MZH8	Missense_Mutation	SNP	ENST00000555661.1	hg19	CCDS9820.1	.	.	.	.	.	.	.	.	.	.	A	15.73	2.919849	0.52653	.	.	ENSG00000140043;ENSG00000140043;ENSG00000140043;ENSG00000258653	ENST00000555228;ENST00000555661;ENST00000267568;ENST00000553813	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.7	5.7	0.88788	GroES-like (1);	0.249108	0.45606	D	0.000359	T	0.58075	0.2097	L	0.28054	0.825	0.39287	D	0.964665	B	0.06786	0.001	B	0.06405	0.002	T	0.56492	-0.7970	10	0.32370	T	0.25	-14.5219	6.2839	0.21023	0.7847:0.0:0.0735:0.1418	.	334	Q8N8N7	PTGR2_HUMAN	A	334;334;334;200	ENSP00000450975:T334A;ENSP00000452280:T334A;ENSP00000267568:T334A;ENSP00000450824:T200A	ENSP00000267568:T334A	T	+	1	0	RP5-1021I20.4;PTGR2	73420577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.175000	0.68902	0.533000	0.62120	ACA	.	.		0.333	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412575.1		
IRF2BPL	64207	hgsc.bcm.edu	37	14	77491917	77491917	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:77491917A>G	ENST00000238647.3	-	1	3117	c.2219T>C	c.(2218-2220)tTc>tCc	p.F740S		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	740					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						AGAGCAAGGGAAGCAAAATTT	0.577																																					p.F740S		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.T2219C						.						62.0	57.0	59.0					14																	77491917		2203	4300	6503	SO:0001583	missense	64207	exon1			CAAGGGAAGCAAA	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.2219T>C	chr14.hg19:g.77491917A>G	ENSP00000238647:p.Phe740Ser	115.0	0.0		79.0	4.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	hg19	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.823779	0.71143	.	.	ENSG00000119669	ENST00000238647	T	0.77877	-1.13	4.64	4.64	0.57946	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	U	0.000000	D	0.86653	0.5984	M	0.84326	2.69	0.80722	D	1	D	0.60160	0.987	P	0.60682	0.878	D	0.88885	0.3342	10	0.87932	D	0	.	13.3656	0.60682	1.0:0.0:0.0:0.0	.	740	Q9H1B7	I2BPL_HUMAN	S	740	ENSP00000238647:F740S	ENSP00000238647:F740S	F	-	2	0	IRF2BPL	76561670	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.097000	0.94193	1.948000	0.56530	0.379000	0.24179	TTC	.	.		0.577	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496	
SPATA7	55812	hgsc.bcm.edu	37	14	88892683	88892683	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:88892683T>C	ENST00000393545.4	+	6	769	c.480T>C	c.(478-480)agT>agC	p.S160S	SPATA7_ENST00000356583.5_Silent_p.S128S|SPATA7_ENST00000556553.1_Silent_p.S128S|SPATA7_ENST00000045347.7_Silent_p.S160S	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	160					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						TACACCTAAGTCTACATAAAT	0.458																																					p.S160S		Atlas-SNP	.											.	SPATA7	58	.	0			c.T480C						.						80.0	71.0	74.0					14																	88892683		2203	4300	6503	SO:0001819	synonymous_variant	55812	exon6			CCTAAGTCTACAT	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"""Leber congenital amaurosis 3"""	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.480T>C	chr14.hg19:g.88892683T>C		92.0	0.0		76.0	4.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Silent	SNP	ENST00000393545.4	hg19	CCDS9883.1																																																																																			.	.		0.458	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1		
TTC8	123016	hgsc.bcm.edu	37	14	89338781	89338781	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:89338781G>T	ENST00000345383.5	+	12	1386	c.1302G>T	c.(1300-1302)aaG>aaT	p.K434N	TTC8_ENST00000354441.6_Missense_Mutation_p.K179N|TTC8_ENST00000346301.4_Missense_Mutation_p.K404N|TTC8_ENST00000338104.6_Missense_Mutation_p.K460N|TTC8_ENST00000536576.1_Missense_Mutation_p.K205N|TTC8_ENST00000380656.2_Missense_Mutation_p.K444N|TTC8_ENST00000358622.5_Missense_Mutation_p.K246N	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	470					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						AGATGCGGAAGGGCCACGTTG	0.527																																					p.K444N		Atlas-SNP	.											TTC8,colon,carcinoma,0,1	TTC8	42	.	0			c.G1332T						.						135.0	113.0	120.0					14																	89338781		2203	4300	6503	SO:0001583	missense	123016	exon13			GCGGAAGGGCCAC	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"""Tetratricopeptide (TTC) repeat domain containing"""	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1302G>T	chr14.hg19:g.89338781G>T	ENSP00000339486:p.Lys434Asn	89.0	0.0		48.0	3.0	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	hg19	CCDS9885.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	15.20|15.20|15.20	2.764018|2.764018|2.764018	0.49574|0.49574|0.49574	.|.|.	.|.|.	ENSG00000165533|ENSG00000165533|ENSG00000165533	ENST00000557580|ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686	.|T;T;T;T;T;T;T|.	.|0.59638|.	.|0.25;0.25;0.25;0.25;0.25;0.25;0.25|.	5.59|5.59|5.59	5.59|5.59|5.59	0.84812|0.84812|0.84812	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	.|0.091515|.	.|0.64402|.	.|D|.	.|0.000001|.	T|T|T	0.67382|0.67382|0.67382	0.2887|0.2887|0.2887	M|M|M	0.77820|0.77820|0.77820	2.39|2.39|2.39	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	.|B;B;B;B;B|.	.|0.32467|.	.|0.372;0.007;0.22;0.002;0.005|.	.|B;B;B;B;B|.	.|0.30716|.	.|0.065;0.031;0.119;0.012;0.018|.	T|T|T	0.68655|0.68655|0.68655	-0.5351|-0.5351|-0.5351	5|10|5	.|0.23302|.	.|T|.	.|0.38|.	-13.9832|-13.9832|-13.9832	7.6284|7.6284|7.6284	0.28226|0.28226|0.28226	0.1954:0.0:0.8046:0.0|0.1954:0.0:0.8046:0.0|0.1954:0.0:0.8046:0.0	.|.|.	.|179;205;470;414;444|.	.|Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.	.|.;.;TTC8_HUMAN;.;.|.	W|N|M	233|434;205;404;460;179;444;246|394	.|ENSP00000339486:K434N;ENSP00000445067:K205N;ENSP00000298324:K404N;ENSP00000337653:K460N;ENSP00000346427:K179N;ENSP00000370031:K444N;ENSP00000351439:K246N|.	.|ENSP00000337653:K460N|.	G|K|R	+|+|+	1|3|2	0|2|0	TTC8|TTC8|TTC8	88408534|88408534|88408534	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.993000|0.993000|0.993000	0.82548|0.82548|0.82548	2.383000|2.383000|2.383000	0.44354|0.44354|0.44354	2.793000|2.793000|2.793000	0.96121|0.96121|0.96121	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GGG|AAG|AGG	.	.		0.527	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596	
TTC7B	145567	hgsc.bcm.edu	37	14	91142948	91142948	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91142948G>T	ENST00000328459.6	-	9	1192	c.1071C>A	c.(1069-1071)atC>atA	p.I357I	RP11-661G16.1_ENST00000554967.1_RNA|TTC7B_ENST00000357056.2_Silent_p.I357I	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	357										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				TCTGCAGACTGATGAGGCGGT	0.507																																					p.I357I		Atlas-SNP	.											.	TTC7B	93	.	0			c.C1071A						.						178.0	138.0	151.0					14																	91142948		2203	4300	6503	SO:0001819	synonymous_variant	145567	exon9			CAGACTGATGAGG	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"""Tetratricopeptide (TTC) repeat domain containing"""	19858	protein-coding gene	gene with protein product			"""tetratricopeptide repeat domain 7 like 1"""	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.1071C>A	chr14.hg19:g.91142948G>T		129.0	0.0		75.0	4.0	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	hg19	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	G	7.902	0.734532	0.15574	.	.	ENSG00000165914	ENST00000554462	.	.	.	5.15	4.25	0.50352	.	.	.	.	.	T	0.55986	0.1955	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52771	-0.8531	4	.	.	.	-18.8632	6.6615	0.23016	0.1513:0.1511:0.6975:0.0	.	.	.	.	K	27	.	.	Q	-	1	0	TTC7B	90212701	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	3.417000	0.52714	1.153000	0.42468	0.563000	0.77884	CAG	.	.		0.507	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
C14orf159	80017	hgsc.bcm.edu	37	14	91655256	91655256	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91655256A>G	ENST00000523771.1	+	9	1525	c.922A>G	c.(922-924)Aac>Gac	p.N308D	C14orf159_ENST00000428926.2_Missense_Mutation_p.N308D|C14orf159_ENST00000521077.2_Missense_Mutation_p.N313D|C14orf159_ENST00000523816.1_Missense_Mutation_p.N308D|C14orf159_ENST00000520328.1_Missense_Mutation_p.N296D|C14orf159_ENST00000412671.2_Missense_Mutation_p.N313D|C14orf159_ENST00000518868.1_Missense_Mutation_p.N313D|C14orf159_ENST00000256324.10_Missense_Mutation_p.N313D|C14orf159_ENST00000525393.2_Missense_Mutation_p.N184D|C14orf159_ENST00000522322.1_Missense_Mutation_p.N308D			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	308						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CATTTCAGGGAACCGGGGGAT	0.418																																					p.N313D		Atlas-SNP	.											.	C14orf159	57	.	0			c.A937G						.						34.0	31.0	32.0					14																	91655256		2203	4300	6503	SO:0001583	missense	80017	exon9			TCAGGGAACCGGG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.922A>G	chr14.hg19:g.91655256A>G	ENSP00000429655:p.Asn308Asp	68.0	0.0		45.0	4.0	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	hg19	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	A	9.641	1.139046	0.21205	.	.	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000517518;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	4.45	3.29	0.37713	.	0.397550	0.27991	N	0.017036	T	0.28267	0.0698	M	0.77103	2.36	0.09310	N	1	P;P;P;P;P;P	0.47484	0.77;0.58;0.896;0.728;0.728;0.728	B;B;P;B;B;B	0.46510	0.422;0.272;0.519;0.297;0.297;0.297	T	0.12268	-1.0554	10	0.39692	T	0.17	.	7.1423	0.25562	0.7619:0.1566:0.0815:0.0	.	308;184;313;296;313;313	Q7Z3D6;Q8NB88;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.;.	D	296;313;313;313;308;313;184;308;308;308;313	ENSP00000429453:N296D;ENSP00000256324:N313D;ENSP00000430137:N313D;ENSP00000428263:N313D;ENSP00000428974:N308D;ENSP00000428652:N313D;ENSP00000435459:N184D;ENSP00000404343:N308D;ENSP00000427953:N308D;ENSP00000429655:N308D;ENSP00000404196:N313D	ENSP00000256324:N313D	N	+	1	0	C14orf159	90725009	0.002000	0.14202	0.004000	0.12327	0.022000	0.10575	0.554000	0.23407	0.562000	0.29204	0.533000	0.62120	AAC	.	.		0.418	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
GPR68	8111	hgsc.bcm.edu	37	14	91700731	91700731	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91700731G>A	ENST00000531499.2	-	2	1003	c.664C>T	c.(664-666)Cgc>Tgc	p.R222C	GPR68_ENST00000535815.1_Missense_Mutation_p.R222C|GPR68_ENST00000238699.3_Missense_Mutation_p.R232C|GPR68_ENST00000529300.1_5'Flank			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	222					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		TGGTCCTTGCGGCTCTTCTGG	0.672																																					p.R222C		Atlas-SNP	.											GPR68,colon,carcinoma,0,1	GPR68	32	.	0			c.C664T						.						33.0	19.0	24.0					14																	91700731		2194	4286	6480	SO:0001583	missense	8111	exon2			CCTTGCGGCTCTT	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"""GPCR / Class A : Orphans"""	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.664C>T	chr14.hg19:g.91700731G>A	ENSP00000434045:p.Arg222Cys	55.0	0.0		27.0	2.0	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	hg19	CCDS9894.2	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966791	0.74131	.	.	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815;ENST00000529102	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.22	4.25	0.50352	GPCR, rhodopsin-like superfamily (1);	0.138533	0.46442	D	0.000295	T	0.77498	0.4139	L	0.38175	1.15	0.48236	D	0.999615	D;D	0.89917	1.0;1.0	D;D	0.66847	0.947;0.947	T	0.78753	-0.2081	10	0.72032	D	0.01	.	10.6504	0.45645	0.0:0.0:0.5656:0.4344	.	222;222	Q6NWR5;Q15743	.;OGR1_HUMAN	C	222;232;222;222	ENSP00000434045:R222C;ENSP00000238699:R232C;ENSP00000440797:R222C;ENSP00000432740:R222C	ENSP00000238699:R232C	R	-	1	0	GPR68	90770484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.819000	0.62664	2.453000	0.82957	0.549000	0.68633	CGC	.	.		0.672	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2		
SMEK1	55671	hgsc.bcm.edu	37	14	91937188	91937188	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:91937188C>A	ENST00000554943.1	-	10	1768	c.1653G>T	c.(1651-1653)ttG>ttT	p.L551F	SMEK1_ENST00000554684.1_Missense_Mutation_p.L538F|SMEK1_ENST00000555462.1_Missense_Mutation_p.L312F|SMEK1_ENST00000337238.4_Missense_Mutation_p.L538F|SMEK1_ENST00000428424.2_Missense_Mutation_p.L312F			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	551					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		TACATAATGCCAAGAAAGCAT	0.353																																					p.L538F		Atlas-SNP	.											.	SMEK1	94	.	0			c.G1614T						.						110.0	112.0	111.0					14																	91937188		2203	4300	6503	SO:0001583	missense	55671	exon11			TAATGCCAAGAAA	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"""KIAA2010"""	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.1653G>T	chr14.hg19:g.91937188C>A	ENSP00000450883:p.Leu551Phe	142.0	0.0		93.0	4.0	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.44	3.389892	0.61956	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390	T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34	5.8	3.92	0.45320	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72342	0.3448	M	0.89601	3.045	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.87578	0.986;0.99;0.998	T	0.71948	-0.4438	10	0.72032	D	0.01	-9.0136	4.8908	0.13726	0.1475:0.6134:0.0:0.2391	.	312;551;538	Q6IN85-4;Q6IN85;Q6IN85-2	.;P4R3A_HUMAN;.	F	538;538;312;551;312;538	ENSP00000450864:L538F;ENSP00000337125:L538F;ENSP00000392704:L312F;ENSP00000450883:L551F;ENSP00000450891:L312F;ENSP00000452596:L538F	ENSP00000337125:L538F	L	-	3	2	SMEK1	91006941	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	0.843000	0.27640	0.729000	0.32403	0.650000	0.86243	TTG	.	.		0.353	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560	
TC2N	123036	hgsc.bcm.edu	37	14	92258866	92258866	+	Nonsense_Mutation	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:92258866T>A	ENST00000435962.2	-	9	1215	c.892A>T	c.(892-894)Aaa>Taa	p.K298*	TC2N_ENST00000340892.5_Nonsense_Mutation_p.K298*|TC2N_ENST00000360594.5_Nonsense_Mutation_p.K298*|TC2N_ENST00000556018.1_Intron	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	298					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		TTTTGAAGTTTAATAGCAAAT	0.294																																					p.K298X		Atlas-SNP	.											.	TC2N	49	.	0			c.A892T						.						87.0	86.0	86.0					14																	92258866		2203	4300	6503	SO:0001587	stop_gained	123036	exon9			GAAGTTTAATAGC	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"""C2 calcium-dependent domain containing 1"""		"""chromosome 14 open reading frame 47"", ""membrane targeting (tandem) C2 domain containing 1"""	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.892A>T	chr14.hg19:g.92258866T>A	ENSP00000387882:p.Lys298*	108.0	0.0		81.0	4.0	NM_001128596		Nonsense_Mutation	SNP	ENST00000435962.2	hg19	CCDS9897.1	.	.	.	.	.	.	.	.	.	.	T	34	5.397552	0.96009	.	.	ENSG00000165929	ENST00000435962;ENST00000340892;ENST00000360594;ENST00000556590	.	.	.	5.65	5.65	0.86999	.	0.194116	0.53938	D	0.000054	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.4697	15.87	0.79108	0.0:0.0:0.0:1.0	.	.	.	.	X	298;298;298;50	.	ENSP00000343199:K298X	K	-	1	0	TC2N	91328619	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.360000	0.73064	2.137000	0.66172	0.455000	0.32223	AAA	.	.		0.294	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332	
UNC79	57578	hgsc.bcm.edu	37	14	94088153	94088153	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:94088153G>T	ENST00000393151.2	+	30	4574	c.4574G>T	c.(4573-4575)cGg>cTg	p.R1525L	UNC79_ENST00000555664.1_Missense_Mutation_p.R1525L|UNC79_ENST00000256339.4_Missense_Mutation_p.R1348L|UNC79_ENST00000553484.1_Missense_Mutation_p.R1547L			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1525					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TGCATAGATCGGTGTGACATA	0.453																																					p.R1348L		Atlas-SNP	.											UNC79,NS,carcinoma,+1,2	UNC79	366	.	0			c.G4043T						.						95.0	89.0	91.0					14																	94088153		2203	4300	6503	SO:0001583	missense	57578	exon30			TAGATCGGTGTGA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4574G>T	chr14.hg19:g.94088153G>T	ENSP00000376858:p.Arg1525Leu	139.0	0.0		75.0	3.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.70	2.912066	0.52439	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.24538	1.88;1.85;1.88;1.88	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.22205	0.0535	L	0.32530	0.975	0.49915	D	0.999838	P	0.40302	0.712	B	0.37731	0.257	T	0.01290	-1.1394	10	0.54805	T	0.06	-20.337	14.5913	0.68368	0.0694:0.0:0.9306:0.0	.	1547	C9JQL1	.	L	1348;1525;1547;1525;1547	ENSP00000256339:R1348L;ENSP00000450868:R1525L;ENSP00000451360:R1547L;ENSP00000376858:R1525L	ENSP00000256339:R1348L	R	+	2	0	KIAA1409	93157906	1.000000	0.71417	0.991000	0.47740	0.849000	0.48306	6.424000	0.73366	2.847000	0.97988	0.591000	0.81541	CGG	.	.		0.453	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
IFI27L1	122509	hgsc.bcm.edu	37	14	94568841	94568841	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:94568841T>C	ENST00000555523.1	+	5	461	c.242T>C	c.(241-243)gTg>gCg	p.V81A	IFI27L1_ENST00000554562.1_3'UTR|IFI27L1_ENST00000556381.1_3'UTR|IFI27L1_ENST00000557218.1_Missense_Mutation_p.V27A|IFI27L1_ENST00000557066.1_Missense_Mutation_p.V27A|IFI27L1_ENST00000554544.1_Missense_Mutation_p.V16A|IFI27L1_ENST00000393115.3_Missense_Mutation_p.V81A|IFI27L1_ENST00000553664.1_Silent_p.C103C|IFI27L1_ENST00000553350.1_Intron	NM_206949.2	NP_996832.1	Q96BM0	I27L1_HUMAN	interferon, alpha-inducible protein 27-like 1	81						integral component of membrane (GO:0016021)				lung(2)	2						GGACTCTCTGTGACATCTAAA	0.612																																					p.V81A		Atlas-SNP	.											.	IFI27L1	11	.	0			c.T242C						.						62.0	58.0	60.0					14																	94568841		2203	4300	6503	SO:0001583	missense	122509	exon5			TCTCTGTGACATC	BC015423	CCDS9919.1	14q32.13	2008-10-08	2008-10-08	2008-10-08		ENSG00000165948			19754	protein-coding gene	gene with protein product		611320	"""family with sequence similarity 14, member B"""	FAM14B			Standard	NM_145249		Approved		uc001yck.3	Q96BM0		ENST00000555523.1:c.242T>C	chr14.hg19:g.94568841T>C	ENSP00000451851:p.Val81Ala	136.0	0.0		83.0	4.0	NM_145249		Missense_Mutation	SNP	ENST00000555523.1	hg19	CCDS9919.1	.	.	.	.	.	.	.	.	.	.	t	8.223	0.802934	0.16397	.	.	ENSG00000165948	ENST00000555523;ENST00000393115;ENST00000554166;ENST00000555341;ENST00000557218;ENST00000554544;ENST00000557066	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	3.27	-3.93	0.04143	.	1.300780	0.06118	U	0.668363	T	0.18341	0.0440	N	0.17474	0.49	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.29336	-1.0015	10	0.32370	T	0.25	.	10.7815	0.46379	0.0:0.6969:0.0:0.3031	.	81	Q96BM0	I27L1_HUMAN	A	81;81;80;80;27;16;27	ENSP00000451851:V81A;ENSP00000376824:V81A;ENSP00000452226:V80A;ENSP00000451608:V80A	ENSP00000376824:V81A	V	+	2	0	IFI27L1	93638594	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.504000	0.00449	-0.877000	0.04012	-0.332000	0.08345	GTG	.	.		0.612	IFI27L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412868.1	NM_206949	
ATG2B	55102	hgsc.bcm.edu	37	14	96781572	96781572	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:96781572C>A	ENST00000359933.4	-	23	4455		c.e23-1			NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B						autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TGAGAAATTCCTATACAGAAC	0.368																																					.		Atlas-SNP	.											.	ATG2B	169	.	0			c.3562-1G>T						.						32.0	31.0	31.0					14																	96781572		2203	4300	6503	SO:0001630	splice_region_variant	55102	exon24			AAATTCCTATACA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.3562-1G>T	chr14.hg19:g.96781572C>A		205.0	0.0		98.0	4.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Splice_Site	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.127594	0.77549	.	.	ENSG00000066739	ENST00000359933	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6732	0.95918	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATG2B	95851325	1.000000	0.71417	0.997000	0.53966	0.773000	0.43773	6.915000	0.75770	2.730000	0.93505	0.591000	0.81541	.	.	.		0.368	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	Intron
SETD3	84193	hgsc.bcm.edu	37	14	99927679	99927679	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:99927679T>C	ENST00000331768.5	-	4	356		c.e4-2		SETD3_ENST00000329331.3_Splice_Site|SETD3_ENST00000453938.1_Intron|SETD3_ENST00000436070.2_Splice_Site	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3						histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				CGGACAGACCTATATTAATCC	0.373																																					.		Atlas-SNP	.											.	SETD3	56	.	0			c.197-2A>G						.						77.0	78.0	78.0					14																	99927679		2203	4299	6502	SO:0001630	splice_region_variant	84193	exon5			CAGACCTATATTA	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"""chromosome 14 open reading frame 154"""	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.197-2A>G	chr14.hg19:g.99927679T>C		73.0	0.0		49.0	4.0	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Splice_Site	SNP	ENST00000331768.5	hg19	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	T	17.69	3.451830	0.63290	.	.	ENSG00000183576	ENST00000331768;ENST00000329331;ENST00000436070	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8249	0.78690	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD3	98997432	1.000000	0.71417	0.945000	0.38365	0.664000	0.39144	7.965000	0.87945	2.194000	0.70268	0.533000	0.62120	.	.	.		0.373	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233	Intron
RTL1	388015	hgsc.bcm.edu	37	14	101351053	101351053	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr14:101351053A>G	ENST00000534062.1	-	1	131	c.73T>C	c.(73-75)Tcc>Ccc	p.S25P	MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	25					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CCCTCGGAGGACTCCATTTGT	0.552																																					p.S25P		Atlas-SNP	.											.	RTL1	120	.	0			c.T73C						.						35.0	34.0	34.0					14																	101351053		1568	3582	5150	SO:0001583	missense	388015	exon1			CGGAGGACTCCAT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.73T>C	chr14.hg19:g.101351053A>G	ENSP00000435342:p.Ser25Pro	76.0	0.0		68.0	4.0	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	hg19	CCDS53910.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.947356	0.73672	.	.	ENSG00000254656	ENST00000534062	T	0.34072	1.38	3.48	3.48	0.39840	.	.	.	.	.	T	0.42630	0.1211	N	0.24115	0.695	0.27226	N	0.959524	D	0.71674	0.998	D	0.77557	0.99	T	0.15896	-1.0421	9	0.66056	D	0.02	.	8.659	0.34081	1.0:0.0:0.0:0.0	.	25	E9PKS8	.	P	25	ENSP00000435342:S25P	ENSP00000435342:S25P	S	-	1	0	RTL1	100420806	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.308000	0.43690	1.819000	0.53055	0.459000	0.35465	TCC	.	.		0.552	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
TUBGCP5	114791	hgsc.bcm.edu	37	15	22846911	22846911	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:22846911G>T	ENST00000283645.4	+	8	916	c.786G>T	c.(784-786)agG>agT	p.R262S	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.R262S	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	262					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.R262S(1)		breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CAGATGACAGGGTTTTGGTTA	0.353																																					p.R262S		Atlas-SNP	.											TUBGCP5,NS,carcinoma,0,1	TUBGCP5	82	.	1	Substitution - Missense(1)	kidney(1)	c.G786T						.						145.0	125.0	132.0					15																	22846911		2203	4300	6503	SO:0001583	missense	114791	exon8			TGACAGGGTTTTG	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"""gamma-tubulin complex component GCP5"""	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.786G>T	chr15.hg19:g.22846911G>T	ENSP00000283645:p.Arg262Ser	127.0	0.0		99.0	4.0	NM_052903	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	hg19	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	.	11.95	1.791713	0.31685	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.23754	1.89;1.89	4.93	-6.3	0.02007	.	0.108809	0.64402	N	0.000009	T	0.09992	0.0245	L	0.27053	0.805	0.23391	N	0.99777	B;B	0.33583	0.418;0.418	B;B	0.21151	0.033;0.033	T	0.32508	-0.9904	10	0.14656	T	0.56	-14.6251	10.5009	0.44804	0.5496:0.087:0.3634:0.0	.	262;262	Q96RT8;E9PB12	GCP5_HUMAN;.	S	262	ENSP00000283645:R262S;ENSP00000409217:R262S	ENSP00000283645:R262S	R	+	3	2	TUBGCP5	20398352	0.994000	0.37717	0.052000	0.19188	0.967000	0.64934	0.506000	0.22658	-1.218000	0.02601	-0.880000	0.02959	AGG	.	.		0.353	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903	
RYR3	6263	hgsc.bcm.edu	37	15	33855061	33855061	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:33855061C>A	ENST00000389232.4	+	11	1066	c.996C>A	c.(994-996)tcC>tcA	p.S332S	RYR3_ENST00000415757.3_Silent_p.S332S	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	332	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				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)		AATTAGACTCCAGTCACAAGC	0.403																																					p.S332S		Atlas-SNP	.											.	RYR3	760	.	0			c.C996A						.						69.0	68.0	68.0					15																	33855061		1867	4108	5975	SO:0001819	synonymous_variant	6263	exon11			AGACTCCAGTCAC		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.996C>A	chr15.hg19:g.33855061C>A		127.0	0.0		100.0	4.0	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.403	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
SLC12A6	9990	hgsc.bcm.edu	37	15	34547524	34547524	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:34547524A>G	ENST00000354181.3	-	8	1307	c.815T>C	c.(814-816)tTt>tCt	p.F272S	SLC12A6_ENST00000560164.1_Missense_Mutation_p.F84S|SLC12A6_ENST00000558589.1_Missense_Mutation_p.F263S|SLC12A6_ENST00000558667.1_Missense_Mutation_p.F272S|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000290209.5_Missense_Mutation_p.F221S|SLC12A6_ENST00000397702.2_Missense_Mutation_p.F213S|SLC12A6_ENST00000560611.1_Missense_Mutation_p.F272S|SLC12A6_ENST00000458406.2_Missense_Mutation_p.F213S|SLC12A6_ENST00000451844.2_Missense_Mutation_p.F84S|SLC12A6_ENST00000397707.2_Missense_Mutation_p.F257S			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	272					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	ACCAAGATAAAAGCAGAGGCC	0.438																																					p.F272S		Atlas-SNP	.											.	SLC12A6	205	.	0			c.T815C						.						90.0	93.0	92.0					15																	34547524		2201	4298	6499	SO:0001583	missense	9990	exon7			AGATAAAAGCAGA	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.815T>C	chr15.hg19:g.34547524A>G	ENSP00000346112:p.Phe272Ser	91.0	0.0		69.0	5.0	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	hg19	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.822965	0.90873	.	.	ENSG00000140199	ENST00000290209;ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406;ENST00000451844	D;D;D;D;D	0.88975	-2.42;-2.45;-2.44;-2.44;-1.98	5.43	5.43	0.79202	Amino acid permease domain (1);	0.114524	0.64402	D	0.000015	D	0.96750	0.8939	H	0.98333	4.205	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;1.0;1.0	D;D;D;D	0.87578	0.928;0.998;0.973;0.995	D	0.98152	1.0442	10	0.87932	D	0	.	14.5986	0.68424	1.0:0.0:0.0:0.0	.	257;272;221;84	Q9UHW9-3;Q9UHW9;A0AV76;B3KXX3	.;S12A6_HUMAN;.;.	S	221;257;263;213;213;84	ENSP00000290209:F221S;ENSP00000380819:F257S;ENSP00000380814:F213S;ENSP00000387725:F213S;ENSP00000390199:F84S	ENSP00000290209:F221S	F	-	2	0	SLC12A6	32334816	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.139000	0.94554	2.279000	0.76181	0.533000	0.62120	TTT	.	.		0.438	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
THBS1	7057	hgsc.bcm.edu	37	15	39886569	39886569	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:39886569G>T	ENST00000260356.5	+	21	3598	c.3433G>T	c.(3433-3435)Ggt>Tgt	p.G1145C	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1145	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AACCTATGCTGGTGGTAGACT	0.403																																					p.G1145C		Atlas-SNP	.											.	THBS1	106	.	0			c.G3433T						.						154.0	145.0	148.0					15																	39886569		2200	4297	6497	SO:0001583	missense	7057	exon21			TATGCTGGTGGTA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3433G>T	chr15.hg19:g.39886569G>T	ENSP00000260356:p.Gly1145Cys	106.0	0.0		98.0	4.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.986764	0.93106	.	.	ENSG00000137801	ENST00000260356	D	0.98060	-4.69	5.44	5.44	0.79542	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.35320	N	0.003294	D	0.98953	0.9644	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99659	1.0993	10	0.87932	D	0	-23.7926	19.6125	0.95613	0.0:0.0:1.0:0.0	.	1060;1145	B4E3J7;P07996	.;TSP1_HUMAN	C	1145	ENSP00000260356:G1145C	ENSP00000260356:G1145C	G	+	1	0	THBS1	37673861	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	9.813000	0.99286	2.698000	0.92095	0.591000	0.81541	GGT	.	.		0.403	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
PLCB2	5330	hgsc.bcm.edu	37	15	40588496	40588496	+	Splice_Site	SNP	C	C	T	rs377366618		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:40588496C>T	ENST00000260402.3	-	16	1946		c.e16+1		PLCB2_ENST00000456256.2_Splice_Site|PLCB2_ENST00000557821.1_Splice_Site	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2						activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.?(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		TGCTAACTTACGGGCAGAGAA	0.537																																					.		Atlas-SNP	.											PLCB2_ENST00000260402,NS,carcinoma,0,2	PLCB2	177	.	2	Unknown(2)	lung(2)	c.1696+1G>A						.	C		0,3848		0,0,1924	49.0	49.0	49.0			4.2	1.0	15		49	1,8259		0,1,4129	no	splice-5	PLCB2	NM_004573.2		0,1,6053	TT,TC,CC		0.0121,0.0,0.0083			40588496	1,12107	1924	4130	6054	SO:0001630	splice_region_variant	5330	exon17			AACTTACGGGCAG		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1696+1G>A	chr15.hg19:g.40588496C>T		69.0	0.0		41.0	2.0	NM_004573	A8K6J2|B9EGH5	Splice_Site	SNP	ENST00000260402.3	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.087138	0.55968	0.0	1.21E-4	ENSG00000137841	ENST00000260402;ENST00000456256	.	.	.	4.25	4.25	0.50352	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8043	0.46507	0.0:0.9123:0.0:0.0877	.	.	.	.	.	-1	.	.	.	-	.	.	PLCB2	38375788	1.000000	0.71417	0.997000	0.53966	0.769000	0.43574	6.525000	0.73795	2.379000	0.81126	0.561000	0.74099	.	.	.		0.537	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		Intron
NDUFAF1	51103	hgsc.bcm.edu	37	15	41689120	41689120	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:41689120A>G	ENST00000260361.4	-	2	519	c.138T>C	c.(136-138)ccT>ccC	p.P46P		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	46					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		AGGCTTTGCCAGGAGAAGCCA	0.443																																					p.P46P		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.T138C						.						60.0	63.0	62.0					15																	41689120		2203	4300	6503	SO:0001819	synonymous_variant	51103	exon2			TTTGCCAGGAGAA	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"""Mitochondrial respiratory chain complex assembly factors"""	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.138T>C	chr15.hg19:g.41689120A>G		188.0	0.0		100.0	4.0	NM_016013	Q9BVZ5	Silent	SNP	ENST00000260361.4	hg19	CCDS10075.1																																																																																			.	.		0.443	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42364008	42364008	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:42364008T>C	ENST00000290472.3	-	15	1631	c.1537A>G	c.(1537-1539)Agg>Ggg	p.R513G		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	513	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.R513G(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GGGATCCTCCTCATCAGCCGT	0.617																																					p.R513G		Atlas-SNP	.											PLA2G4D,caecum,carcinoma,0,1	PLA2G4D	72	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1537G						.						49.0	53.0	52.0					15																	42364008		2203	4299	6502	SO:0001583	missense	283748	exon15			TCCTCCTCATCAG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1537A>G	chr15.hg19:g.42364008T>C	ENSP00000290472:p.Arg513Gly	117.0	1.0		88.0	4.0	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	hg19	CCDS32203.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252913	0.59212	.	.	ENSG00000159337	ENST00000290472	T	0.04194	3.68	4.79	4.79	0.61399	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.374808	0.23768	N	0.044741	T	0.07188	0.0182	L	0.34521	1.04	0.36349	D	0.859993	P	0.47484	0.896	P	0.46172	0.506	T	0.31641	-0.9936	10	0.59425	D	0.04	-7.4413	14.0078	0.64475	0.0:0.0:0.0:1.0	.	513	Q86XP0	PA24D_HUMAN	G	513	ENSP00000290472:R513G	ENSP00000290472:R513G	R	-	1	2	PLA2G4D	40151300	1.000000	0.71417	0.950000	0.38849	0.231000	0.25187	2.538000	0.45710	1.798000	0.52647	0.459000	0.35465	AGG	.	.		0.617	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
TRIM69	140691	hgsc.bcm.edu	37	15	45051022	45051022	+	Silent	SNP	G	G	T	rs148920822		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:45051022G>T	ENST00000559390.1	+	5	1711	c.783G>T	c.(781-783)acG>acT	p.T261T	TRIM69_ENST00000560442.1_Silent_p.T57T|TRIM69_ENST00000338264.4_Silent_p.T102T|TRIM69_ENST00000558173.1_Silent_p.T57T|TRIM69_ENST00000558329.1_Intron|TRIM69_ENST00000561043.1_Intron|TRIM69_ENST00000329464.4_Silent_p.T261T			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	261					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T261T(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		AGGCAAAGACGGAACAACAGA	0.463																																					p.T261T	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											TRIM69,NS,carcinoma,0,1	TRIM69	47	.	1	Substitution - coding silent(1)	endometrium(1)	c.G783T						.						71.0	60.0	63.0					15																	45051022		2198	4298	6496	SO:0001819	synonymous_variant	140691	exon4			AAAGACGGAACAA	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	17857	protein-coding gene	gene with protein product			"""ring finger protein 36"", ""tripartite motif-containing 69"""	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.783G>T	chr15.hg19:g.45051022G>T		118.0	0.0		86.0	4.0	NM_182985	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Silent	SNP	ENST00000559390.1	hg19	CCDS32220.1																																																																																			.	G|0.999;A|0.001		0.463	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		
SHF	90525	hgsc.bcm.edu	37	15	45490991	45490991	+	Silent	SNP	C	C	T	rs545098594		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:45490991C>T	ENST00000290894.8	-	2	776	c.282G>A	c.(280-282)agG>agA	p.R94R	CTD-2651B20.6_ENST00000563103.1_RNA|RP11-519G16.2_ENST00000560034.1_RNA|CTD-2651B20.7_ENST00000568314.1_RNA|SHF_ENST00000318390.6_Silent_p.R151R	NM_138356.2	NP_612365			Src homology 2 domain containing F									p.R94R(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		CCAGCCTGTCCCTGAGTCTGA	0.532											OREG0023105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R94R		Atlas-SNP	.											SHF,NS,carcinoma,0,1	SHF	27	.	1	Substitution - coding silent(1)	endometrium(1)	c.G282A						.						155.0	157.0	157.0					15																	45490991		1978	4151	6129	SO:0001819	synonymous_variant	90525	exon2			CCTGTCCCTGAGT	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"""SH2 domain containing"""	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.282G>A	chr15.hg19:g.45490991C>T		47.0	0.0	932	51.0	3.0	NM_138356		Silent	SNP	ENST00000290894.8	hg19	CCDS10120.2																																																																																			.	.		0.532	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356	
SLC12A1	6557	hgsc.bcm.edu	37	15	48593518	48593518	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:48593518C>A	ENST00000558405.1	+	25	3117	c.3103C>A	c.(3103-3105)Cgc>Agc	p.R1035S	SLC12A1_ENST00000396577.3_Missense_Mutation_p.R1035S|SLC12A1_ENST00000380993.3_Missense_Mutation_p.R1035S			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	1035					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	ACAGAGTTACCGCCAAGTTCG	0.363																																					p.R1035S		Atlas-SNP	.											SLC12A1_ENST00000396577,NS,carcinoma,-1,2	SLC12A1	243	.	0			c.C3103A						.						83.0	67.0	72.0					15																	48593518		2198	4297	6495	SO:0001583	missense	6557	exon26			AGTTACCGCCAAG		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.3103C>A	chr15.hg19:g.48593518C>A	ENSP00000453409:p.Arg1035Ser	104.0	1.0		72.0	3.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	c	25.7	4.662565	0.88251	.	.	ENSG00000074803	ENST00000380993;ENST00000396577	D;D	0.85702	-2.02;-2.02	5.14	5.14	0.70334	.	0.066635	0.64402	D	0.000007	D	0.91449	0.7301	M	0.78801	2.425	0.80722	D	1	D;D	0.67145	0.996;0.979	P;P	0.59487	0.724;0.858	D	0.92638	0.6122	10	0.87932	D	0	.	18.588	0.91197	0.0:1.0:0.0:0.0	.	1035;1035	E9PDW4;Q13621	.;S12A1_HUMAN	S	1035	ENSP00000370381:R1035S;ENSP00000379822:R1035S	ENSP00000370381:R1035S	R	+	1	0	SLC12A1	46380810	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.574000	0.82434	2.385000	0.81259	0.650000	0.86243	CGC	.	.		0.363	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
CYP19A1	1588	hgsc.bcm.edu	37	15	51504537	51504537	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:51504537G>T	ENST00000396402.1	-	9	1396	c.1243C>A	c.(1243-1245)Ctt>Att	p.L415I	CYP19A1_ENST00000396404.4_Missense_Mutation_p.L415I|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000559878.1_Missense_Mutation_p.L415I|CYP19A1_ENST00000260433.2_Missense_Mutation_p.L415I	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	415					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|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)|oxygen binding (GO:0019825)			endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	AAATTTTCAAGAGTAAATTCA	0.393																																					p.L415I	Melanoma(142;1016 1807 39614 48966 51721)	Atlas-SNP	.											.	CYP19A1	75	.	0			c.C1243A						.						88.0	91.0	90.0					15																	51504537		2196	4293	6489	SO:0001583	missense	1588	exon10			TTTCAAGAGTAAA	D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"""Cytochrome P450s"""	2594	protein-coding gene	gene with protein product		107910	"""cytochrome P450, subfamily XIX (aromatization of androgens)"""	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.1243C>A	chr15.hg19:g.51504537G>T	ENSP00000379683:p.Leu415Ile	195.0	0.0		107.0	6.0	NM_031226	Q16731|Q3B764|Q58FA0|Q8IYJ7	Missense_Mutation	SNP	ENST00000396402.1	hg19	CCDS10139.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.256347	0.80246	.	.	ENSG00000137869	ENST00000396402;ENST00000260433;ENST00000396404	T;T;T	0.68025	-0.3;-0.3;-0.3	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.82756	0.5106	M	0.86740	2.835	0.80722	D	1	P	0.48162	0.906	D	0.66602	0.945	D	0.83981	0.0332	10	0.54805	T	0.06	-21.5947	13.3083	0.60365	0.0718:0.0:0.9282:0.0	.	415	P11511	CP19A_HUMAN	I	415	ENSP00000379683:L415I;ENSP00000260433:L415I;ENSP00000379685:L415I	ENSP00000260433:L415I	L	-	1	0	CYP19A1	49291829	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.606000	0.82863	2.767000	0.95098	0.655000	0.94253	CTT	.	.		0.393	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1		
MYO5C	55930	hgsc.bcm.edu	37	15	52532010	52532010	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:52532010A>G	ENST00000261839.7	-	21	2784	c.2623T>C	c.(2623-2625)Ttc>Ctc	p.F875L	MYO5C_ENST00000443683.2_Intron	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	875	IQ 5. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ATACTCTGGAATCTGCGTCTG	0.453																																					p.F875L		Atlas-SNP	.											.	MYO5C	162	.	0			c.T2623C						.						69.0	69.0	69.0					15																	52532010		1977	4161	6138	SO:0001583	missense	55930	exon21			TCTGGAATCTGCG	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2623T>C	chr15.hg19:g.52532010A>G	ENSP00000261839:p.Phe875Leu	130.0	0.0		100.0	4.0	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	hg19	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.957245	0.92726	.	.	ENSG00000128833	ENST00000261839	T	0.28454	1.61	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.48822	0.1521	L	0.59967	1.855	0.80722	D	1	D	0.55800	0.973	P	0.60789	0.879	T	0.46133	-0.9213	10	0.51188	T	0.08	.	15.1608	0.72782	1.0:0.0:0.0:0.0	.	875	Q9NQX4	MYO5C_HUMAN	L	875	ENSP00000261839:F875L	ENSP00000261839:F875L	F	-	1	0	MYO5C	50319302	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	7.168000	0.77570	2.058000	0.61347	0.528000	0.53228	TTC	.	.		0.453	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
RAB27A	5873	hgsc.bcm.edu	37	15	55520885	55520885	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:55520885A>G	ENST00000396307.2	-	4	516	c.265T>C	c.(265-267)Ttc>Ctc	p.F89L	RAB27A_ENST00000336787.1_Missense_Mutation_p.F89L|RAB27A_ENST00000569493.1_Missense_Mutation_p.F89L|RAB27A_ENST00000564609.1_Missense_Mutation_p.F89L	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	89					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		GCATCTCTGAAGAACGCTGTC	0.398																																					p.F89L		Atlas-SNP	.											.	RAB27A	18	.	0			c.T265C						.						110.0	103.0	106.0					15																	55520885		2193	4292	6485	SO:0001583	missense	5873	exon5			CTCTGAAGAACGC	U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"""RAB, member RAS oncogene"""	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.265T>C	chr15.hg19:g.55520885A>G	ENSP00000379601:p.Phe89Leu	127.0	0.0		94.0	4.0	NM_183235	O00195|Q6FI40|Q9UIR9|Q9Y5U3	Missense_Mutation	SNP	ENST00000396307.2	hg19	CCDS10153.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.570844	0.86542	.	.	ENSG00000069974	ENST00000396307;ENST00000396304;ENST00000336787	T;T	0.75704	-0.96;-0.96	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.64227	0.2579	N	0.16098	0.37	0.80722	D	1	P	0.41159	0.74	B	0.42138	0.377	T	0.70842	-0.4762	10	0.87932	D	0	-13.5705	15.5447	0.76090	1.0:0.0:0.0:0.0	.	89	P51159	RB27A_HUMAN	L	89	ENSP00000379601:F89L;ENSP00000337761:F89L	ENSP00000337761:F89L	F	-	1	0	RAB27A	53308177	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.228000	0.95250	2.267000	0.75376	0.528000	0.53228	TTC	.	.		0.398	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236	
HERC1	8925	hgsc.bcm.edu	37	15	63916007	63916007	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:63916007G>T	ENST00000443617.2	-	73	13615	c.13528C>A	c.(13528-13530)Cga>Aga	p.R4510R		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4510	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TTCCACGCTCGGGAAGGCAGG	0.483																																					p.R4510R		Atlas-SNP	.											.	HERC1	624	.	0			c.C13528A						.						95.0	96.0	96.0					15																	63916007		2024	4174	6198	SO:0001819	synonymous_variant	8925	exon73			ACGCTCGGGAAGG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13528C>A	chr15.hg19:g.63916007G>T		75.0	0.0		50.0	4.0	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.483	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
HERC1	8925	hgsc.bcm.edu	37	15	63918224	63918224	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:63918224T>A	ENST00000443617.2	-	71	13322	c.13235A>T	c.(13234-13236)tAc>tTc	p.Y4412F		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4412					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCAGGATGAGTACATGAGGTC	0.592																																					p.Y4412F		Atlas-SNP	.											.	HERC1	624	.	0			c.A13235T						.						68.0	70.0	69.0					15																	63918224		2061	4206	6267	SO:0001583	missense	8925	exon71			GATGAGTACATGA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13235A>T	chr15.hg19:g.63918224T>A	ENSP00000390158:p.Tyr4412Phe	97.0	0.0		60.0	4.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.504984	0.44558	.	.	ENSG00000103657	ENST00000443617	T	0.25912	1.77	5.51	5.51	0.81932	.	0.078149	0.52532	D	0.000065	T	0.24198	0.0586	L	0.38531	1.155	0.58432	D	0.999999	P	0.41232	0.743	B	0.39617	0.305	T	0.01966	-1.1238	10	0.46703	T	0.11	.	15.924	0.79597	0.0:0.0:0.0:1.0	.	4412	Q15751	HERC1_HUMAN	F	4412	ENSP00000390158:Y4412F	ENSP00000390158:Y4412F	Y	-	2	0	HERC1	61705277	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	7.997000	0.88414	2.217000	0.71921	0.533000	0.62120	TAC	.	.		0.592	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
SPG21	51324	hgsc.bcm.edu	37	15	65261628	65261628	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:65261628A>G	ENST00000204566.2	-	7	928	c.633T>C	c.(631-633)ccT>ccC	p.P211P	SPG21_ENST00000416889.2_Silent_p.P184P|SPG21_ENST00000559199.1_Silent_p.P57P|SPG21_ENST00000433215.2_Silent_p.P211P	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	211					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						GAATTTTATGAGGTTCCACAT	0.348																																					p.P211P		Atlas-SNP	.											.	SPG21	29	.	0			c.T633C						.						105.0	109.0	108.0					15																	65261628		2202	4299	6501	SO:0001819	synonymous_variant	51324	exon7			TTTATGAGGTTCC	AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"""maspardin"""	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.633T>C	chr15.hg19:g.65261628A>G		85.0	0.0		71.0	4.0	NM_001127889	B4DW44|Q6ZMB6	Silent	SNP	ENST00000204566.2	hg19	CCDS10198.1																																																																																			.	.		0.348	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630	
KBTBD13	390594	hgsc.bcm.edu	37	15	65370197	65370197	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:65370197C>A	ENST00000432196.2	+	1	1044	c.1044C>A	c.(1042-1044)gcC>gcA	p.A348A	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	348					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						GCATGGTGGCCCACCGCGACA	0.687																																					p.A348A		Atlas-SNP	.											.	KBTBD13	9	.	0			c.C1044A						.						16.0	17.0	17.0					15																	65370197		1774	3679	5453	SO:0001819	synonymous_variant	390594	exon1			GGTGGCCCACCGC		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"""BTB/POZ domain containing"""	37227	protein-coding gene	gene with protein product	"""nemaline myopathy type 6"""	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.1044C>A	chr15.hg19:g.65370197C>A		103.0	0.0		85.0	4.0	NM_001101362		Silent	SNP	ENST00000432196.2	hg19	CCDS45281.1																																																																																			.	.		0.687	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362	
ITGA11	22801	hgsc.bcm.edu	37	15	68631922	68631922	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:68631922T>C	ENST00000315757.7	-	11	1278	c.1192A>G	c.(1192-1194)Acg>Gcg	p.T398A	ITGA11_ENST00000423218.2_Missense_Mutation_p.T398A	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	398					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CCGGCACTCGTCTCCTTTAGC	0.582																																					p.T398A		Atlas-SNP	.											.	ITGA11	110	.	0			c.A1192G						.						70.0	76.0	74.0					15																	68631922		2022	4175	6197	SO:0001583	missense	22801	exon11			CACTCGTCTCCTT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1192A>G	chr15.hg19:g.68631922T>C	ENSP00000327290:p.Thr398Ala	85.0	0.0		58.0	5.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.810639	0.32053	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491;ENST00000537153	T;T	0.71817	-0.6;-0.6	5.09	5.09	0.68999	.	0.094573	0.64402	D	0.000001	T	0.65821	0.2728	L	0.55481	1.735	0.43039	D	0.994626	B;P	0.38767	0.068;0.646	B;B	0.40825	0.097;0.341	T	0.62987	-0.6737	10	0.10377	T	0.69	.	14.1169	0.65159	0.0:0.0:0.0:1.0	.	398;398	A8K8T0;Q9UKX5	.;ITA11_HUMAN	A	398;398;33;398	ENSP00000327290:T398A;ENSP00000403392:T398A	ENSP00000327290:T398A	T	-	1	0	ITGA11	66418976	1.000000	0.71417	0.743000	0.31040	0.163000	0.22366	6.289000	0.72696	1.938000	0.56188	0.454000	0.30748	ACG	.	.		0.582	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
SPESP1	246777	hgsc.bcm.edu	37	15	69238897	69238897	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:69238897A>G	ENST00000310673.3	+	2	1178	c.1024A>G	c.(1024-1026)Aga>Gga	p.R342G	NOX5_ENST00000448182.3_Intron|NOX5_ENST00000455873.3_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000260364.5_Intron	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	342					acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						TAGATCAAGGAGAGTCACAGC	0.264																																					p.R342G		Atlas-SNP	.											.	SPESP1	39	.	0			c.A1024G						.						31.0	33.0	32.0					15																	69238897		1940	4083	6023	SO:0001583	missense	246777	exon2			TCAAGGAGAGTCA	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.1024A>G	chr15.hg19:g.69238897A>G	ENSP00000312284:p.Arg342Gly	41.0	0.0		38.0	4.0	NM_145658	Q8NG22|Q8WVH8	Missense_Mutation	SNP	ENST00000310673.3	hg19	CCDS10230.1	.	.	.	.	.	.	.	.	.	.	A	3.487	-0.104586	0.06967	.	.	ENSG00000258484	ENST00000310673	T	0.27720	1.65	5.19	1.62	0.23740	.	0.617328	0.14594	N	0.310099	T	0.14442	0.0349	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31668	-0.9935	10	0.13853	T	0.58	-0.7094	6.5665	0.22515	0.716:0.0:0.284:0.0	.	342	Q6UW49	SPESP_HUMAN	G	342	ENSP00000312284:R342G	ENSP00000312284:R342G	R	+	1	2	SPESP1	67025951	0.004000	0.15560	0.023000	0.16930	0.022000	0.10575	-0.118000	0.10692	0.386000	0.24997	-0.274000	0.10170	AGA	.	.		0.264	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658	
MYO9A	4649	hgsc.bcm.edu	37	15	72196317	72196317	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:72196317T>C	ENST00000356056.5	-	21	3302	c.2830A>G	c.(2830-2832)Aca>Gca	p.T944A	MYO9A_ENST00000424560.1_Missense_Mutation_p.T944A|MYO9A_ENST00000566885.1_Missense_Mutation_p.T564A|MYO9A_ENST00000444904.1_Missense_Mutation_p.T925A|MYO9A_ENST00000564571.1_Missense_Mutation_p.T944A|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	944	Myosin motor.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						ATTCGAACTGTTTCCAGCATC	0.378																																					p.T944A		Atlas-SNP	.											.	MYO9A	203	.	0			c.A2830G						.						94.0	86.0	88.0					15																	72196317		2199	4297	6496	SO:0001583	missense	4649	exon21			GAACTGTTTCCAG	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.2830A>G	chr15.hg19:g.72196317T>C	ENSP00000348349:p.Thr944Ala	125.0	0.0		91.0	4.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.013916	0.93404	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	D;D;D	0.87491	-2.26;-2.26;-2.26	5.24	5.24	0.73138	Myosin head, motor domain (2);	.	.	.	.	D	0.90978	0.7163	L	0.50333	1.59	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.87578	0.998;0.978;0.992	D	0.89742	0.3934	9	0.33141	T	0.24	.	15.3061	0.73992	0.0:0.0:0.0:1.0	.	925;925;944	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	A	944;944;925;925	ENSP00000348349:T944A;ENSP00000399162:T944A;ENSP00000398250:T925A	ENSP00000261864:T925A	T	-	1	0	MYO9A	69983371	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.499000	0.81566	2.203000	0.70933	0.533000	0.62120	ACA	.	.		0.378	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
PARP6	56965	hgsc.bcm.edu	37	15	72552968	72552968	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:72552968G>T	ENST00000569795.1	-	10	1294	c.607C>A	c.(607-609)Ctt>Att	p.L203I	PARP6_ENST00000287196.9_Missense_Mutation_p.L203I|PARP6_ENST00000260376.7_Missense_Mutation_p.L203I|PARP6_ENST00000413097.2_5'UTR			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	203							NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						CCAACCCGAAGCTCTGGTACA	0.532																																					p.L203I		Atlas-SNP	.											.	PARP6	44	.	0			c.C607A						.						371.0	360.0	363.0					15																	72552968		1894	4124	6018	SO:0001583	missense	56965	exon9			CCCGAAGCTCTGG	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"""Poly (ADP-ribose) polymerases"""	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.607C>A	chr15.hg19:g.72552968G>T	ENSP00000456348:p.Leu203Ile	109.0	0.0		67.0	4.0	NM_020214	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	hg19	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169618	0.38315	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000413097;ENST00000544520;ENST00000336471	.	.	.	4.93	4.93	0.64822	.	0.073354	0.56097	D	0.000033	T	0.47544	0.1451	L	0.50333	1.59	0.32288	N	0.566733	B;B;B	0.17038	0.002;0.004;0.02	B;B;B	0.13407	0.007;0.005;0.009	T	0.54768	-0.8244	9	0.35671	T	0.21	-8.8612	14.4766	0.67551	0.0:0.1474:0.8526:0.0	.	203;203;155	Q0VDG0;Q2NL67;A0PJ50	.;PARP6_HUMAN;.	I	203;203;203;68;68;203	.	ENSP00000260376:L203I	L	-	1	0	PARP6	70340022	1.000000	0.71417	1.000000	0.80357	0.331000	0.28603	5.178000	0.65037	2.277000	0.76020	0.585000	0.79938	CTT	.	.		0.532	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214	
MPI	4351	hgsc.bcm.edu	37	15	75182887	75182887	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75182887G>T	ENST00000352410.4	+	2	103	c.36G>T	c.(34-36)gcG>gcT	p.A12A	MPI_ENST00000563786.1_5'UTR|MPI_ENST00000535694.1_Intron|MPI_ENST00000566377.1_Silent_p.A12A|MPI_ENST00000564003.1_Intron|MPI_ENST00000563422.1_Silent_p.A12A|MPI_ENST00000565576.1_Silent_p.A12A|MPI_ENST00000562606.1_Intron|MPI_ENST00000323744.6_Silent_p.A12A			P34949	MPI_HUMAN	mannose phosphate isomerase	12					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						TTTCCTGTGCGGTGCAGCAGT	0.617																																					p.A12A		Atlas-SNP	.											.	MPI	32	.	0			c.G36T						.						82.0	69.0	74.0					15																	75182887		2197	4295	6492	SO:0001819	synonymous_variant	4351	exon2			CTGTGCGGTGCAG		CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"""mannose-6-phosphate isomerase"""	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.36G>T	chr15.hg19:g.75182887G>T		108.0	0.0		66.0	4.0	NM_002435	A8K8K9|Q96AB0	Silent	SNP	ENST00000352410.4	hg19	CCDS10272.1																																																																																			.	.		0.617	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286418.4		
COX5A	9377	hgsc.bcm.edu	37	15	75221502	75221502	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75221502T>C	ENST00000322347.6	-	2	325	c.172A>G	c.(172-174)Aca>Gca	p.T58A	COX5A_ENST00000568517.1_5'UTR|COX5A_ENST00000568783.1_Missense_Mutation_p.T58A|COX5A_ENST00000562233.1_Missense_Mutation_p.T58A|COX5A_ENST00000564811.1_Missense_Mutation_p.T58A|COX5A_ENST00000567270.1_Intron	NM_004255.3	NP_004246.2	P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	58					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|pancreas(1)	3						TTGAAGTATGTTACCCAGCGA	0.398																																					p.T58A		Atlas-SNP	.											.	COX5A	9	.	0			c.A172G						.						155.0	141.0	146.0					15																	75221502		2197	4295	6492	SO:0001583	missense	9377	exon2			AGTATGTTACCCA	M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2267	protein-coding gene	gene with protein product		603773				10072584, 2853101	Standard	NM_004255		Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000322347.6:c.172A>G	chr15.hg19:g.75221502T>C	ENSP00000317780:p.Thr58Ala	183.0	0.0		121.0	39.0	NM_004255	P30045|Q8TB65	Missense_Mutation	SNP	ENST00000322347.6	hg19	CCDS10273.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628961	0.67015	.	.	ENSG00000178741	ENST00000322347	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.35393	0.0930	N	0.05467	-0.045	0.58432	D	0.999997	B	0.09022	0.002	B	0.19666	0.026	T	0.26849	-1.0091	9	0.06625	T	0.88	-10.27	14.6722	0.68953	0.0:0.0:0.0:1.0	.	58	P20674	COX5A_HUMAN	A	58	.	ENSP00000317780:T58A	T	-	1	0	COX5A	73008555	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.454000	0.80714	2.150000	0.67090	0.528000	0.53228	ACA	.	.		0.398	COX5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286417.1	NM_004255	
MAN2C1	4123	hgsc.bcm.edu	37	15	75649212	75649212	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75649212T>C	ENST00000267978.5	-	22	2625	c.2579A>G	c.(2578-2580)gAa>gGa	p.E860G	RP11-817O13.6_ENST00000563660.1_lincRNA|MAN2C1_ENST00000569482.1_Missense_Mutation_p.E860G|MAN2C1_ENST00000565683.1_Missense_Mutation_p.E877G|MAN2C1_ENST00000563622.1_Missense_Mutation_p.E761G	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	860					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						AAAGCCGTGTTCTGACAGATC	0.622																																					p.E877G		Atlas-SNP	.											.	MAN2C1	76	.	0			c.A2630G						.						84.0	70.0	75.0					15																	75649212		2197	4294	6491	SO:0001583	missense	4123	exon22			CCGTGTTCTGACA	AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.2579A>G	chr15.hg19:g.75649212T>C	ENSP00000267978:p.Glu860Gly	115.0	0.0		86.0	4.0	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	hg19	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.826047	0.90955	.	.	ENSG00000140400	ENST00000267978	T	0.20598	2.06	5.09	5.09	0.68999	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	D	0.000000	T	0.53351	0.1791	M	0.90759	3.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.993	T	0.64198	-0.6464	10	0.87932	D	0	-30.0163	14.0368	0.64649	0.0:0.0:0.0:1.0	.	860;860	Q68EM8;Q9NTJ4	.;MA2C1_HUMAN	G	860	ENSP00000267978:E860G	ENSP00000267978:E860G	E	-	2	0	MAN2C1	73436265	1.000000	0.71417	0.900000	0.35374	0.920000	0.55202	5.946000	0.70234	1.932000	0.55993	0.459000	0.35465	GAA	.	.		0.622	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1		
PTPN9	5780	hgsc.bcm.edu	37	15	75761250	75761250	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75761250A>G	ENST00000306726.2	-	13	2154	c.1642T>C	c.(1642-1644)Tca>Cca	p.S548P		NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	548	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTCATGCGTGACACCGTCTGG	0.542																																					p.S548P		Atlas-SNP	.											.	PTPN9	53	.	0			c.T1642C						.						98.0	80.0	86.0					15																	75761250		2197	4294	6491	SO:0001583	missense	5780	exon13			TGCGTGACACCGT		CCDS10280.1	15q23	2011-06-09			ENSG00000169410	ENSG00000169410		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9661	protein-coding gene	gene with protein product		600768				1557404	Standard	NM_002833		Approved	MEG2	uc002bal.3	P43378	OTTHUMG00000142838	ENST00000306726.2:c.1642T>C	chr15.hg19:g.75761250A>G	ENSP00000303554:p.Ser548Pro	100.0	0.0		67.0	4.0	NM_002833	Q53XR9	Missense_Mutation	SNP	ENST00000306726.2	hg19	CCDS10280.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492680	0.64074	.	.	ENSG00000169410	ENST00000306726;ENST00000544966	D	0.84070	-1.8	6.17	4.99	0.66335	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.326738	0.32987	N	0.005418	T	0.75693	0.3884	M	0.66439	2.03	0.40294	D	0.978539	P	0.45240	0.854	B	0.36534	0.227	T	0.77680	-0.2497	10	0.51188	T	0.08	.	4.2373	0.10632	0.6653:0.1864:0.1483:0.0	.	548	P43378	PTN9_HUMAN	P	548;538	ENSP00000303554:S548P	ENSP00000303554:S548P	S	-	1	0	PTPN9	73548303	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.971000	0.49248	2.371000	0.80710	0.533000	0.62120	TCA	.	.		0.542	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75982391	75982391	+	Missense_Mutation	SNP	G	G	T	rs200187536		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:75982391G>T	ENST00000308508.5	-	3	1107	c.1015C>A	c.(1015-1017)Cgc>Agc	p.R339S		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	339	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGGCCCAGGCGGTGTTCCTGG	0.642																																					p.R339S		Atlas-SNP	.											.	CSPG4	175	.	0			c.C1015A						.						17.0	15.0	16.0					15																	75982391		2192	4283	6475	SO:0001583	missense	1464	exon3			CCAGGCGGTGTTC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1015C>A	chr15.hg19:g.75982391G>T	ENSP00000312506:p.Arg339Ser	63.0	0.0		62.0	4.0	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	14.64	2.596974	0.46318	.	.	ENSG00000173546	ENST00000308508	T	0.18502	2.21	5.26	4.26	0.50523	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.181054	0.36815	N	0.002398	T	0.19167	0.0460	L	0.29908	0.895	0.32592	N	0.527029	P	0.52170	0.951	P	0.50934	0.654	T	0.05146	-1.0903	10	0.19590	T	0.45	.	15.6861	0.77411	0.0:0.0:0.8538:0.1462	.	339	Q6UVK1	CSPG4_HUMAN	S	339	ENSP00000312506:R339S	ENSP00000312506:R339S	R	-	1	0	CSPG4	73769446	0.996000	0.38824	1.000000	0.80357	0.667000	0.39255	2.026000	0.41069	2.463000	0.83235	0.555000	0.69702	CGC	.	G|0.999;A|0.001		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
RASGRF1	5923	hgsc.bcm.edu	37	15	79254552	79254552	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:79254552A>G	ENST00000419573.3	-	28	4030	c.3756T>C	c.(3754-3756)tcT>tcC	p.S1252S	RASGRF1_ENST00000394745.3_Silent_p.S468S|RASGRF1_ENST00000558480.2_Silent_p.S1236S	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1252	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CCATTACAAAAGATTGGTCCA	0.478																																					p.S1252S		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T3756C						.						67.0	65.0	66.0					15																	79254552		2196	4292	6488	SO:0001819	synonymous_variant	5923	exon28			TACAAAAGATTGG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3756T>C	chr15.hg19:g.79254552A>G		92.0	0.0		54.0	4.0	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	hg19	CCDS10309.1																																																																																			.	.		0.478	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
IL16	3603	hgsc.bcm.edu	37	15	81592606	81592606	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:81592606T>C	ENST00000302987.4	+	13	2939	c.2939T>C	c.(2938-2940)cTt>cCt	p.L980P	IL16_ENST00000394652.2_Missense_Mutation_p.L279P|IL16_ENST00000394660.2_Missense_Mutation_p.L980P|RP11-761I4.4_ENST00000607019.1_RNA			Q14005	IL16_HUMAN	interleukin 16	980					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						ACGAAGCTACTTGACGAAAAG	0.537																																					p.L980P		Atlas-SNP	.											.	IL16	254	.	0			c.T2939C						.						99.0	85.0	89.0					15																	81592606		2203	4300	6503	SO:0001583	missense	3603	exon14			AGCTACTTGACGA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.2939T>C	chr15.hg19:g.81592606T>C	ENSP00000302935:p.Leu980Pro	133.0	0.0		98.0	4.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	T	9.145	1.014763	0.19355	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.12147	2.72;2.71;3.32	4.91	-0.636	0.11508	.	1.216530	0.06243	N	0.690824	T	0.20251	0.0487	L	0.56769	1.78	0.09310	N	0.999998	P;D;D;P;P;P	0.62365	0.875;0.991;0.971;0.93;0.898;0.938	P;P;P;P;B;P	0.53861	0.549;0.736;0.691;0.564;0.352;0.555	T	0.19192	-1.0313	10	0.36615	T	0.2	.	2.7427	0.05258	0.1132:0.3187:0.1154:0.4526	.	812;473;517;370;980;980	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	P	980;812;980;517;370;279;279	ENSP00000378155:L980P;ENSP00000302935:L980P;ENSP00000378147:L279P	ENSP00000302935:L980P	L	+	2	0	IL16	79379661	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-0.668000	0.05268	-0.031000	0.13781	0.482000	0.46254	CTT	.	.		0.537	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
MEX3B	84206	hgsc.bcm.edu	37	15	82335547	82335547	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:82335547G>T	ENST00000329713.4	-	2	2099	c.1664C>A	c.(1663-1665)cCg>cAg	p.P555Q	AC026956.1_ENST00000410589.1_RNA|MEX3B_ENST00000558133.1_3'UTR	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	555					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P555L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						GTGGCAGACCGGGCACTCGGG	0.637																																					p.P555Q		Atlas-SNP	.											MEX3B,caecum,carcinoma,+1,1	MEX3B	50	.	1	Substitution - Missense(1)	breast(1)	c.C1664A						.						47.0	47.0	47.0					15																	82335547		2203	4300	6503	SO:0001583	missense	84206	exon2			CAGACCGGGCACT	AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	25297	protein-coding gene	gene with protein product		611008	"""ring finger and KH domain containing 3"", ""mex-3 homolog B (C. elegans)"""	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.1664C>A	chr15.hg19:g.82335547G>T	ENSP00000329918:p.Pro555Gln	89.0	0.0		59.0	3.0	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Missense_Mutation	SNP	ENST00000329713.4	hg19	CCDS10319.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.016541	0.75161	.	.	ENSG00000183496	ENST00000329713	D	0.94613	-3.47	4.3	4.3	0.51218	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.142695	0.47093	D	0.000260	D	0.98460	0.9487	H	0.98388	4.22	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99761	1.1021	10	0.87932	D	0	-26.3696	17.2971	0.87173	0.0:0.0:1.0:0.0	.	555	Q6ZN04	MEX3B_HUMAN	Q	555	ENSP00000329918:P555Q	ENSP00000329918:P555Q	P	-	2	0	MEX3B	80122602	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	9.191000	0.94940	2.381000	0.81170	0.561000	0.74099	CCG	.	.		0.637	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645	
ZNF592	9640	hgsc.bcm.edu	37	15	85327163	85327163	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:85327163C>A	ENST00000560079.2	+	4	1545	c.1257C>A	c.(1255-1257)agC>agA	p.S419R	ZNF592_ENST00000299927.3_Missense_Mutation_p.S419R	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	419					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGGCCCCCAGCGAGATGCCAG	0.582																																					p.S419R		Atlas-SNP	.											.	ZNF592	95	.	0			c.C1257A						.						49.0	55.0	53.0					15																	85327163		2203	4299	6502	SO:0001583	missense	9640	exon4			CCCCAGCGAGATG	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.1257C>A	chr15.hg19:g.85327163C>A	ENSP00000452877:p.Ser419Arg	80.0	0.0		100.0	4.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	1.893	-0.455094	0.04540	.	.	ENSG00000166716	ENST00000299927	T	0.00620	6.17	5.65	-7.46	0.01369	.	0.491158	0.25425	N	0.030768	T	0.00384	0.0012	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.15052	0.012	T	0.47661	-0.9100	10	0.45353	T	0.12	-1.8687	10.4445	0.44486	0.0:0.2587:0.1042:0.6372	.	419	Q92610	ZN592_HUMAN	R	419	ENSP00000299927:S419R	ENSP00000299927:S419R	S	+	3	2	ZNF592	83128167	0.000000	0.05858	0.007000	0.13788	0.015000	0.08874	-1.787000	0.01764	-1.212000	0.02620	-0.812000	0.03155	AGC	.	.		0.582	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
AKAP13	11214	hgsc.bcm.edu	37	15	86286858	86286858	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:86286858A>G	ENST00000394518.2	+	36	8289	c.8194A>G	c.(8194-8196)Aac>Gac	p.N2732D	RP11-158M2.3_ENST00000558375.1_RNA|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000394510.2_Missense_Mutation_p.N977D|AKAP13_ENST00000361243.2_Missense_Mutation_p.N2736D	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2732	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CCCAAAAAGGAACAGCATCTC	0.532																																					p.N2736D	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A8206G						.						159.0	162.0	161.0					15																	86286858		2202	4299	6501	SO:0001583	missense	11214	exon36			AAAAGGAACAGCA	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.8194A>G	chr15.hg19:g.86286858A>G	ENSP00000378026:p.Asn2732Asp	129.0	0.0		78.0	4.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.183948	0.38609	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.49139	0.79;0.79;0.79	5.72	4.6	0.57074	.	.	.	.	.	T	0.41236	0.1150	M	0.63843	1.955	0.38449	D	0.94691	P;P	0.41524	0.639;0.753	B;B	0.37091	0.122;0.241	T	0.38845	-0.9642	9	0.35671	T	0.21	.	8.371	0.32415	0.8496:0.0:0.1504:0.0	.	2732;2736	Q12802;Q12802-2	AKP13_HUMAN;.	D	2736;2732;2735;2711;977	ENSP00000354718:N2736D;ENSP00000378026:N2732D;ENSP00000378018:N977D	ENSP00000354718:N2736D	N	+	1	0	AKAP13	84087862	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	4.156000	0.58138	1.001000	0.39076	-0.297000	0.09499	AAC	.	.		0.532	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
ACAN	176	hgsc.bcm.edu	37	15	89398363	89398363	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:89398363C>T	ENST00000561243.1	+	11	2547	c.2547C>T	c.(2545-2547)ccC>ccT	p.P849P	ACAN_ENST00000352105.7_Silent_p.P849P|ACAN_ENST00000439576.2_Silent_p.P849P|ACAN_ENST00000559004.1_Silent_p.P849P			P16112	PGCA_HUMAN	aggrecan	848					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CCCCCGTGCCCAGCTGGACTG	0.597																																					p.P849P		Atlas-SNP	.											.	ACAN	220	.	0			c.C2547T						.						37.0	42.0	40.0					15																	89398363		1970	4150	6120	SO:0001819	synonymous_variant	176	exon12			CGTGCCCAGCTGG	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2547C>T	chr15.hg19:g.89398363C>T		142.0	0.0		110.0	5.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
RLBP1	6017	hgsc.bcm.edu	37	15	89753607	89753607	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:89753607T>C	ENST00000268125.5	-	9	1302	c.863A>G	c.(862-864)gAc>gGc	p.D288G		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	288	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	GCCCCCGAAGTCAGAGGGCAG	0.562																																					p.D288G		Atlas-SNP	.											.	RLBP1	34	.	0			c.A863G						.						79.0	76.0	77.0					15																	89753607		2200	4299	6499	SO:0001583	missense	6017	exon9			CCGAAGTCAGAGG	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"""retinaldehyde-binding protein 1"""			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.863A>G	chr15.hg19:g.89753607T>C	ENSP00000268125:p.Asp288Gly	70.0	0.0		94.0	4.0	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	hg19	CCDS32324.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651773	0.88056	.	.	ENSG00000140522	ENST00000268125	T	0.75260	-0.92	5.21	5.21	0.72293	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.047924	0.85682	D	0.000000	D	0.83459	0.5259	M	0.66939	2.045	0.80722	D	1	D	0.57257	0.979	D	0.62955	0.909	D	0.85519	0.1202	10	0.72032	D	0.01	-15.3192	15.084	0.72135	0.0:0.0:0.0:1.0	.	288	P12271	RLBP1_HUMAN	G	288	ENSP00000268125:D288G	ENSP00000268125:D288G	D	-	2	0	RLBP1	87554611	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.668000	0.83897	1.974000	0.57490	0.454000	0.30748	GAC	.	.		0.562	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
POLG	5428	hgsc.bcm.edu	37	15	89876764	89876764	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:89876764C>A	ENST00000268124.5	-	2	555	c.222G>T	c.(220-222)ttG>ttT	p.L74F	POLG_ENST00000442287.2_Missense_Mutation_p.L74F|RP11-217B1.2_ENST00000569473.1_RNA|RP11-217B1.2_ENST00000562356.1_RNA|POLG_ENST00000525806.1_5'Flank	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	74					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			TCTGGATGTCCAATGGGTTGT	0.672								DNA polymerases (catalytic subunits)																													p.L74F	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.G222T						.						42.0	37.0	38.0					15																	89876764		2200	4299	6499	SO:0001583	missense	5428	exon2			GATGTCCAATGGG	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.222G>T	chr15.hg19:g.89876764C>A	ENSP00000268124:p.Leu74Phe	85.0	0.0		70.0	4.0	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	hg19	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324251	0.60634	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.96885	-4.16;-4.16	5.07	5.07	0.68467	.	0.066963	0.64402	D	0.000018	D	0.97148	0.9068	M	0.65975	2.015	0.48830	D	0.999712	D	0.76494	0.999	D	0.85130	0.997	D	0.96671	0.9496	10	0.56958	D	0.05	-13.0334	8.5579	0.33492	0.2756:0.583:0.1414:0.0	.	74	P54098	DPOG1_HUMAN	F	74	ENSP00000268124:L74F;ENSP00000399851:L74F	ENSP00000268124:L74F	L	-	3	2	POLG	87677768	1.000000	0.71417	0.968000	0.41197	0.801000	0.45260	1.317000	0.33631	2.359000	0.80004	0.561000	0.74099	TTG	.	.		0.672	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
PLIN1	5346	hgsc.bcm.edu	37	15	90210232	90210232	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:90210232A>G	ENST00000300055.5	-	8	1309	c.1144T>C	c.(1144-1146)Tcc>Ccc	p.S382P	PLIN1_ENST00000430628.2_Missense_Mutation_p.S382P	NM_002666.4	NP_002657.3	O60240	PLIN1_HUMAN	perilipin 1	382					lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)	lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(2)	13						TCTGATAGGGACATGGCCCTC	0.607																																					p.S382P		Atlas-SNP	.											.	PLIN1	36	.	0			c.T1144C						.						71.0	57.0	62.0					15																	90210232		2200	4299	6499	SO:0001583	missense	5346	exon8			ATAGGGACATGGC	AB005293	CCDS10353.1	15q26	2009-08-12	2009-08-12	2009-08-12	ENSG00000166819	ENSG00000166819		"""Perilipins"""	9076	protein-coding gene	gene with protein product		170290	"""perilipin"""	PLIN		9521880, 19638644	Standard	NM_002666		Approved		uc010upx.1	O60240	OTTHUMG00000149813	ENST00000300055.5:c.1144T>C	chr15.hg19:g.90210232A>G	ENSP00000300055:p.Ser382Pro	120.0	0.0		87.0	4.0	NM_001145311	Q8N5Y6	Missense_Mutation	SNP	ENST00000300055.5	hg19	CCDS10353.1	.	.	.	.	.	.	.	.	.	.	A	14.43	2.534171	0.45073	.	.	ENSG00000166819	ENST00000300055;ENST00000430628	T;T	0.06068	3.35;3.35	5.13	5.13	0.70059	.	1.710450	0.03407	N	0.204264	T	0.25827	0.0629	M	0.68317	2.08	0.32269	N	0.569184	D	0.76494	0.999	D	0.72338	0.977	T	0.00318	-1.1821	10	0.52906	T	0.07	-29.9343	9.4675	0.38822	0.806:0.194:0.0:0.0	.	382	O60240	PLIN1_HUMAN	P	382	ENSP00000300055:S382P;ENSP00000402167:S382P	ENSP00000300055:S382P	S	-	1	0	PLIN1	88011236	1.000000	0.71417	0.999000	0.59377	0.156000	0.22039	2.497000	0.45354	1.933000	0.56026	0.459000	0.35465	TCC	.	.		0.607	PLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313424.2	NM_002666	
ANPEP	290	hgsc.bcm.edu	37	15	90346884	90346884	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:90346884G>T	ENST00000300060.6	-	8	1744	c.1431C>A	c.(1429-1431)taC>taA	p.Y477*	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	477	Metalloprotease.	Transition state stabilizer.			angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GCACCTTGCTGTAGGAGATGG	0.667																																					p.Y477X	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C1431A						.						72.0	68.0	69.0					15																	90346884		2200	4298	6498	SO:0001587	stop_gained	290	exon8			CTTGCTGTAGGAG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1431C>A	chr15.hg19:g.90346884G>T	ENSP00000300060:p.Tyr477*	111.0	0.0		96.0	4.0	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Nonsense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	G	39	7.620069	0.98393	.	.	ENSG00000166825	ENST00000300060	.	.	.	4.58	2.68	0.31781	.	0.124363	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0156	0.30379	0.2021:0.0:0.7978:0.0	.	.	.	.	X	477	.	ENSP00000300060:Y477X	Y	-	3	2	ANPEP	88147888	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	3.527000	0.53517	0.922000	0.37019	0.305000	0.20034	TAC	.	.		0.667	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
ZNF710	374655	hgsc.bcm.edu	37	15	90610374	90610374	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:90610374A>G	ENST00000268154.4	+	2	256	c.5A>G	c.(4-6)gAg>gGg	p.E2G		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			CACGGGATGGAGGGCTTCATG	0.587																																					p.E2G		Atlas-SNP	.											.	ZNF710	50	.	0			c.A5G						.						53.0	36.0	42.0					15																	90610374		2200	4298	6498	SO:0001583	missense	374655	exon2			GGATGGAGGGCTT	AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"""Zinc fingers, C2H2-type"""	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.5A>G	chr15.hg19:g.90610374A>G	ENSP00000268154:p.Glu2Gly	104.0	0.0		86.0	42.0	NM_198526	A0AVS3|Q6ZMK9|Q8NDU0	Missense_Mutation	SNP	ENST00000268154.4	hg19	CCDS10358.1	.	.	.	.	.	.	.	.	.	.	A	14.66	2.601097	0.46423	.	.	ENSG00000140548	ENST00000268154	T	0.12569	2.67	5.28	5.28	0.74379	.	0.000000	0.39274	N	0.001419	T	0.11281	0.0275	L	0.27053	0.805	0.49687	D	0.999815	P	0.46987	0.888	B	0.39465	0.3	T	0.03148	-1.1067	10	0.87932	D	0	-26.3241	14.2008	0.65703	1.0:0.0:0.0:0.0	.	2	Q8N1W2	ZN710_HUMAN	G	2	ENSP00000268154:E2G	ENSP00000268154:E2G	E	+	2	0	ZNF710	88411378	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.966000	0.63715	2.217000	0.71921	0.533000	0.62120	GAG	.	.		0.587	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526	
BLM	641	hgsc.bcm.edu	37	15	91304196	91304196	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:91304196A>G	ENST00000355112.3	+	7	1711	c.1593A>G	c.(1591-1593)aaA>aaG	p.K531K	BLM_ENST00000560509.1_Silent_p.K531K	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	531	Necessary for interaction with SPIDR.				alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			CTGCTGTGAAAGATCAGAATA	0.353			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.K531K		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.A1593G						.						60.0	62.0	61.0					15																	91304196		2198	4298	6496	SO:0001819	synonymous_variant	641	exon7	Familial Cancer Database		TGTGAAAGATCAG	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.1593A>G	chr15.hg19:g.91304196A>G		112.0	0.0		93.0	4.0	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	hg19	CCDS10363.1																																																																																			.	.		0.353	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
FURIN	5045	hgsc.bcm.edu	37	15	91423173	91423173	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:91423173C>A	ENST00000268171.3	+	12	1614	c.1335C>A	c.(1333-1335)gcC>gcA	p.A445A		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	445					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CCACAGTGGCCCCCCAGCGGA	0.652																																					p.A445A		Atlas-SNP	.											.	FURIN	85	.	0			c.C1335A						.						28.0	30.0	30.0					15																	91423173		2198	4298	6496	SO:0001819	synonymous_variant	5045	exon12			AGTGGCCCCCCAG	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1335C>A	chr15.hg19:g.91423173C>A		117.0	0.0		68.0	4.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	C	7.250	0.603082	0.13939	.	.	ENSG00000140564	ENST00000535252	.	.	.	4.65	4.65	0.58169	.	.	.	.	.	T	0.58750	0.2144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64326	-0.6434	5	0.87932	D	0	-4.0563	3.3192	0.07044	0.2843:0.4838:0.1457:0.0861	.	.	.	.	H	44	.	ENSP00000439549:P44H	P	+	2	0	FURIN	89224177	0.651000	0.27340	1.000000	0.80357	0.734000	0.41952	-0.153000	0.10144	2.410000	0.81850	0.485000	0.47835	CCC	.	.		0.652	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
CHD2	1106	hgsc.bcm.edu	37	15	93498741	93498741	+	Splice_Site	SNP	A	A	G	rs397514739		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:93498741A>G	ENST00000394196.4	+	15	2876	c.1808A>G	c.(1807-1809)aAg>aGg	p.K603R	CHD2_ENST00000557381.1_Splice_Site_p.K603R	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	603	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTGAAAGATAAGGTGTGTAAT	0.348																																					p.K603R		Atlas-SNP	.											.	CHD2	280	.	0			c.A1808G						.						50.0	45.0	47.0					15																	93498741		2196	4294	6490	SO:0001630	splice_region_variant	1106	exon15			AAGATAAGGTGTG	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.1809+1A>G	chr15.hg19:g.93498741A>G		147.0	0.0		98.0	4.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	A	29.4	5.002609	0.93227	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.93426	-3.22;-3.22	5.16	5.16	0.70880	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.35677	U	0.003046	D	0.88869	0.6554	N	0.04636	-0.2	0.80722	D	1	P;P	0.49358	0.923;0.753	P;B	0.51055	0.657;0.288	D	0.91058	0.4883	10	0.51188	T	0.08	-21.7144	14.9865	0.71351	1.0:0.0:0.0:0.0	.	603;603	O14647;O14647-2	CHD2_HUMAN;.	R	603	ENSP00000377747:K603R;ENSP00000451366:K603R	ENSP00000377747:K603R	K	+	2	0	CHD2	91299745	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	9.331000	0.96430	1.926000	0.55796	0.528000	0.53228	AAG	.	.		0.348	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	Missense_Mutation
CHSY1	22856	hgsc.bcm.edu	37	15	101718547	101718547	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr15:101718547A>G	ENST00000254190.3	-	3	1930	c.1455T>C	c.(1453-1455)caT>caC	p.H485H	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	485					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CCAGCTCCTCATGCTCCACAA	0.478																																					p.H485H		Atlas-SNP	.											.	CHSY1	60	.	0			c.T1455C						.						51.0	51.0	51.0					15																	101718547		2203	4300	6503	SO:0001819	synonymous_variant	22856	exon3			CTCCTCATGCTCC	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.1455T>C	chr15.hg19:g.101718547A>G		93.0	0.0		81.0	4.0	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Silent	SNP	ENST00000254190.3	hg19	CCDS10390.1																																																																																			.	.		0.478	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
ITFG3	83986	hgsc.bcm.edu	37	16	312091	312091	+	Splice_Site	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:312091G>T	ENST00000399932.3	+	7	1159		c.e7-1		ITFG3_ENST00000600536.1_Splice_Site|ITFG3_ENST00000301679.2_Splice_Site|ITFG3_ENST00000450082.2_Splice_Site|ITFG3_ENST00000442458.2_Splice_Site|ITFG3_ENST00000301678.3_Splice_Site	NM_001284497.1	NP_001271426.1	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3							cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				TGTCATTGCAGGTTAGTGGCC	0.607																																					.		Atlas-SNP	.											.	ITFG3	42	.	0			c.709-1G>T						.						55.0	59.0	58.0					16																	312091		2171	4282	6453	SO:0001630	splice_region_variant	83986	exon7			ATTGCAGGTTAGT	AL136542	CCDS10402.1	16p13.3	2006-03-31	2006-03-31	2006-03-31	ENSG00000167930	ENSG00000167930			14163	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 9"""	C16orf9			Standard	XM_005255622		Approved	DKFZP761D0211, FLJ32603	uc002cgf.3	Q9H0X4	OTTHUMG00000060728	ENST00000399932.3:c.709-1G>T	chr16.hg19:g.312091G>T		243.0	0.0		113.0	5.0	NM_032039	D3DU45|Q7L416|Q96FR1|Q96MC7|Q96S30	Splice_Site	SNP	ENST00000399932.3	hg19	CCDS10402.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.020735	0.35606	.	.	ENSG00000167930	ENST00000399932;ENST00000301679;ENST00000442458;ENST00000449945;ENST00000301678;ENST00000450082	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8952	0.63766	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITFG3	252092	1.000000	0.71417	0.964000	0.40570	0.085000	0.17905	4.929000	0.63455	2.434000	0.82447	0.462000	0.41574	.	.	.		0.607	ITFG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134227.2	NM_032039	Intron
DECR2	26063	hgsc.bcm.edu	37	16	461574	461574	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:461574T>C	ENST00000219481.5	+	8	1013	c.875T>C	c.(874-876)cTc>cCc	p.L292P	DECR2_ENST00000424398.2_Missense_Mutation_p.L280P|DECR2_ENST00000461947.1_Intron	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	292					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				TCTGCTAAGCTCTAGGTGAGG	0.627																																					p.L292P		Atlas-SNP	.											.	DECR2	47	.	0			c.T875C						.						120.0	97.0	105.0					16																	461574		2202	4300	6502	SO:0001583	missense	26063	exon8			CTAAGCTCTAGGT	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	2754	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 17C, member 1"""	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.875T>C	chr16.hg19:g.461574T>C	ENSP00000219481:p.Leu292Pro	158.0	0.0		98.0	4.0	NM_020664	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	hg19	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.516322	0.64634	.	.	ENSG00000242612	ENST00000219481;ENST00000424398	D;T	0.82526	-1.62;-1.26	5.34	5.34	0.76211	.	0.514511	0.19597	N	0.110489	D	0.86707	0.5997	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87882	0.2678	10	0.87932	D	0	.	14.4897	0.67642	0.0:0.0:0.0:1.0	.	292	Q9NUI1	DECR2_HUMAN	P	292;280	ENSP00000219481:L292P;ENSP00000400374:L280P	ENSP00000219481:L292P	L	+	2	0	DECR2	401575	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	7.524000	0.81866	2.030000	0.59900	0.459000	0.35465	CTC	.	.		0.627	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664	
ATP6V0C	527	hgsc.bcm.edu	37	16	2564163	2564163	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:2564163C>A	ENST00000330398.4	+	1	293	c.59C>A	c.(58-60)tCg>tAg	p.S20*	ATP6V0C_ENST00000565223.1_5'Flank|ATP6C_ENST00000569317.1_Nonsense_Mutation_p.S20*|RP11-20I23.1_ENST00000564543.1_Intron|ATP6V0C_ENST00000568562.1_Intron	NM_001198569.1|NM_001694.3	NP_001185498.1|NP_001685.1	P27449	VATL_HUMAN	ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c	20					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|lung(1)|ovary(1)	3		Ovarian(90;0.17)				ATGGGCGCCTCGGCCGCCATG	0.731																																					p.S20X		Atlas-SNP	.											.	ATP6V0C	10	.	0			c.C59A						.						13.0	13.0	13.0					16																	2564163		2187	4284	6471	SO:0001587	stop_gained	527	exon2			GCGCCTCGGCCGC	M62762	CCDS10470.1	16p13.3	2010-04-21	2002-08-29	2002-05-10	ENSG00000185883	ENSG00000185883	3.6.3.14	"""ATPases / V-type"""	855	protein-coding gene	gene with protein product		108745	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) 16kD"""	ATPL, ATP6C, ATP6L		1709739, 8250920	Standard	NM_001694		Approved	VATL, Vma3	uc021tav.1	P27449	OTTHUMG00000128865	ENST00000330398.4:c.59C>A	chr16.hg19:g.2564163C>A	ENSP00000329757:p.Ser20*	98.0	0.0		88.0	5.0	NM_001198569	Q6FH26	Nonsense_Mutation	SNP	ENST00000330398.4	hg19	CCDS10470.1	.	.	.	.	.	.	.	.	.	.	C	40	8.243972	0.98722	.	.	ENSG00000185883	ENST00000330398	.	.	.	3.66	3.66	0.41972	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-13.4529	12.9649	0.58478	0.0:1.0:0.0:0.0	.	.	.	.	X	20	.	ENSP00000329757:S20X	S	+	2	0	ATP6V0C	2504164	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.136000	0.71703	1.892000	0.54788	0.543000	0.68304	TCG	.	.		0.731	ATP6V0C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250810.1	NM_001694	
SRRM2	23524	hgsc.bcm.edu	37	16	2818026	2818026	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:2818026T>C	ENST00000301740.8	+	11	8046	c.7497T>C	c.(7495-7497)ccT>ccC	p.P2499P	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2499	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TCCCTGCCCCTGGGGTGCCCC	0.642																																					p.P2499P		Atlas-SNP	.											.	SRRM2	263	.	0			c.T7497C						.						68.0	65.0	66.0					16																	2818026		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TGCCCCTGGGGTG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7497T>C	chr16.hg19:g.2818026T>C		121.0	0.0		80.0	4.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.642	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
THOC6	79228	hgsc.bcm.edu	37	16	3076554	3076554	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3076554T>C	ENST00000326266.8	+	7	745	c.449T>C	c.(448-450)tTg>tCg	p.L150S	HCFC1R1_ENST00000248089.3_5'Flank|HCFC1R1_ENST00000396916.1_5'Flank|HCFC1R1_ENST00000574980.1_5'Flank|HCFC1R1_ENST00000572355.1_5'Flank|HCFC1R1_ENST00000574151.1_5'Flank|THOC6_ENST00000253952.9_Missense_Mutation_p.L150S|THOC6_ENST00000575576.1_Missense_Mutation_p.L126S|THOC6_ENST00000574549.1_Missense_Mutation_p.L126S|HCFC1R1_ENST00000354679.3_5'Flank	NM_024339.3	NP_077315.2	Q86W42	THOC6_HUMAN	THO complex 6 homolog (Drosophila)	150					apoptotic process (GO:0006915)|central nervous system development (GO:0007417)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	13						GACTGTCAGTTGCACACTATG	0.547																																					p.L150S		Atlas-SNP	.											.	THOC6	40	.	0			c.T449C						.						86.0	78.0	81.0					16																	3076554		2198	4300	6498	SO:0001583	missense	79228	exon7			GTCAGTTGCACAC	BC050674	CCDS10491.1, CCDS45392.1	16p13.3	2013-02-11	2006-03-02	2006-03-02		ENSG00000131652		"""WD repeat domain containing"", ""THO complex subunits"""	28369	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 35"""	615403	"""WD repeat domain 58"""	WDR58		12477932	Standard	NM_024339		Approved	MGC2655, fSAP35	uc002ctb.2	Q86W42		ENST00000326266.8:c.449T>C	chr16.hg19:g.3076554T>C	ENSP00000326531:p.Leu150Ser	95.0	0.0		88.0	4.0	NM_001142350	B2RA85|Q8NBR1|Q9BTV9	Missense_Mutation	SNP	ENST00000326266.8	hg19	CCDS10491.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.570538	0.45798	.	.	ENSG00000131652	ENST00000326266;ENST00000253952	T;T	0.35421	1.31;1.31	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.127145	0.50627	D	0.000113	T	0.33702	0.0872	L	0.34521	1.04	0.42318	D	0.992244	P;P	0.49961	0.763;0.93	B;P	0.44860	0.293;0.462	T	0.19484	-1.0304	10	0.87932	D	0	-29.3651	13.9169	0.63905	0.0:0.0:0.0:1.0	.	150;150	Q86W42-3;Q86W42	.;THOC6_HUMAN	S	150	ENSP00000326531:L150S;ENSP00000253952:L150S	ENSP00000253952:L150S	L	+	2	0	THOC6	3016555	1.000000	0.71417	0.290000	0.24890	0.989000	0.77384	6.624000	0.74243	2.178000	0.69098	0.459000	0.35465	TTG	.	.		0.547	THOC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436981.1	NM_024339	
MEFV	4210	hgsc.bcm.edu	37	16	3306411	3306411	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3306411G>T	ENST00000219596.1	-	1	216	c.177C>A	c.(175-177)acC>acA	p.T59T	MEFV_ENST00000541159.1_Silent_p.T59T|MEFV_ENST00000339854.4_Silent_p.T59T|MEFV_ENST00000536379.1_Silent_p.T59T	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	59	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				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						CCCCATAGTAGGTGACCAGCA	0.632																																					p.T59T		Atlas-SNP	.											.	MEFV	170	.	0			c.C177A						.						81.0	79.0	79.0					16																	3306411		2197	4300	6497	SO:0001819	synonymous_variant	4210	exon1			ATAGTAGGTGACC	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.177C>A	chr16.hg19:g.3306411G>T		136.0	0.0		87.0	4.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	hg19	CCDS10498.1																																																																																			.	.		0.632	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
ZNF263	10127	hgsc.bcm.edu	37	16	3334126	3334126	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3334126A>G	ENST00000219069.5	+	1	1184	c.308A>G	c.(307-309)gAg>gGg	p.E103G	ZNF263_ENST00000573578.1_Missense_Mutation_p.E103G|ZNF263_ENST00000574253.1_Missense_Mutation_p.E103G|ZNF263_ENST00000538765.1_Intron	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	103	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						AGGGTGCAGGAGCTGCATCCG	0.582																																					p.E103G		Atlas-SNP	.											.	ZNF263	58	.	0			c.A308G						.						74.0	77.0	76.0					16																	3334126		2197	4300	6497	SO:0001583	missense	10127	exon1			TGCAGGAGCTGCA	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.308A>G	chr16.hg19:g.3334126A>G	ENSP00000219069:p.Glu103Gly	134.0	0.0		125.0	5.0	NM_005741	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	hg19	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	A	15.57	2.874040	0.51695	.	.	ENSG00000006194	ENST00000219069	T	0.05081	3.5	5.06	5.06	0.68205	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.53938	D	0.000046	T	0.09730	0.0239	N	0.25647	0.755	0.35551	D	0.803839	P;P	0.52577	0.954;0.954	P;P	0.54706	0.759;0.741	T	0.31888	-0.9927	10	0.34782	T	0.22	.	11.3814	0.49759	1.0:0.0:0.0:0.0	.	103;103	O14978;D3DUC1	ZN263_HUMAN;.	G	103	ENSP00000219069:E103G	ENSP00000219069:E103G	E	+	2	0	ZNF263	3274127	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.634000	0.24614	2.251000	0.74343	0.533000	0.62120	GAG	.	.		0.582	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2		
DNASE1	1773	hgsc.bcm.edu	37	16	3705477	3705477	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:3705477G>A	ENST00000246949.5	+	2	3312	c.103G>A	c.(103-105)Gag>Aag	p.E35K	DNASE1_ENST00000407479.1_Missense_Mutation_p.E35K|DNASE1_ENST00000414110.2_5'UTR	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I	35					apoptotic process (GO:0006915)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	deoxyribonuclease I activity (GO:0004530)			lung(1)	1		Ovarian(90;0.0261)		Kidney(780;0.0556)		GACATTTGGGGAGACCAAGAT	0.627																																					p.E35K		Atlas-SNP	.											.	DNASE1	16	.	0			c.G103A						.						79.0	66.0	71.0					16																	3705477		2197	4300	6497	SO:0001583	missense	1773	exon2			TTTGGGGAGACCA		CCDS10507.1	16p13.3	2008-02-05			ENSG00000213918	ENSG00000213918	3.1.21.1		2956	protein-coding gene	gene with protein product		125505		DNL1		2349940	Standard	XM_005255148		Approved		uc002cvr.3	P24855	OTTHUMG00000129426	ENST00000246949.5:c.103G>A	chr16.hg19:g.3705477G>A	ENSP00000246949:p.Glu35Lys	139.0	0.0		82.0	4.0	NM_005223	B4DV35|Q14UU9|Q14UV0	Missense_Mutation	SNP	ENST00000246949.5	hg19	CCDS10507.1	.	.	.	.	.	.	.	.	.	.	G	33	5.211441	0.95069	.	.	ENSG00000213918	ENST00000407479;ENST00000246949	T;T	0.59083	0.29;0.29	5.39	5.39	0.77823	Endonuclease/exonuclease/phosphatase (2);	0.284400	0.39475	N	0.001348	T	0.64843	0.2635	L	0.58669	1.825	0.80722	D	1	P	0.50066	0.931	P	0.52424	0.698	T	0.60826	-0.7186	10	0.27082	T	0.32	-26.2267	16.3008	0.82811	0.0:0.0:1.0:0.0	.	35	P24855	DNAS1_HUMAN	K	35	ENSP00000385905:E35K;ENSP00000246949:E35K	ENSP00000246949:E35K	E	+	1	0	DNASE1	3645478	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.992000	0.56980	2.543000	0.85770	0.561000	0.74099	GAG	.	.		0.627	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2		
MGRN1	23295	hgsc.bcm.edu	37	16	4715144	4715144	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:4715144T>C	ENST00000399577.5	+	7	763	c.670T>C	c.(670-672)Ttt>Ctt	p.F224L	MGRN1_ENST00000262370.7_Missense_Mutation_p.F224L|MGRN1_ENST00000586183.1_Missense_Mutation_p.F224L|MGRN1_ENST00000588994.1_Missense_Mutation_p.F224L|MGRN1_ENST00000415496.1_Missense_Mutation_p.F225L	NM_001142290.2	NP_001135762.1	O60291	MGRN1_HUMAN	mahogunin ring finger 1, E3 ubiquitin protein ligase	224					endosome to lysosome transport (GO:0008333)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						CTTGGCTGCCTTTGAAAAGGT	0.642																																					p.F224L		Atlas-SNP	.											.	MGRN1	66	.	0			c.T670C						.						54.0	60.0	58.0					16																	4715144		2056	4193	6249	SO:0001583	missense	23295	exon7			GCTGCCTTTGAAA	AB011116	CCDS42115.1, CCDS45401.1, CCDS45402.1, CCDS45401.2, CCDS59256.1	16p13	2012-02-23	2012-02-23					"""RING-type (C3HC4) zinc fingers"""	20254	protein-coding gene	gene with protein product		607559	"""mahogunin, ring finger 1"""			9628581	Standard	NM_015246		Approved	KIAA0544, RNF156	uc002cxa.3	O60291		ENST00000399577.5:c.670T>C	chr16.hg19:g.4715144T>C	ENSP00000382487:p.Phe224Leu	154.0	0.0		61.0	4.0	NM_001142291	A4URL3|A4URL4|Q86W76	Missense_Mutation	SNP	ENST00000399577.5	hg19	CCDS45402.1	.	.	.	.	.	.	.	.	.	.	t	19.62	3.862379	0.71949	.	.	ENSG00000102858	ENST00000262370;ENST00000399577;ENST00000415496;ENST00000536343	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	4.99	3.9	0.45041	.	0.047367	0.85682	N	0.000000	T	0.36413	0.0966	L	0.41356	1.27	0.58432	D	0.999994	D;D;D;D;P;D	0.76494	0.998;0.999;0.999;0.999;0.815;0.997	D;D;D;D;P;D	0.87578	0.998;0.99;0.97;0.978;0.646;0.995	T	0.04870	-1.0921	10	0.29301	T	0.29	-6.8499	8.5715	0.33572	0.0:0.088:0.0:0.912	.	224;224;224;225;224;224	O60291-4;O60291-3;B4DR12;E9PB19;O60291-2;O60291	.;.;.;.;.;MGRN1_HUMAN	L	224;224;225;224	ENSP00000262370:F224L;ENSP00000382487:F224L;ENSP00000393311:F225L;ENSP00000443810:F224L	ENSP00000262370:F224L	F	+	1	0	MGRN1	4655145	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	5.766000	0.68843	0.941000	0.37499	-0.259000	0.10710	TTT	.	.		0.642	MGRN1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432060.2		
GRIN2A	2903	hgsc.bcm.edu	37	16	9857312	9857312	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:9857312G>T	ENST00000396573.2	-	14	4398	c.4089C>A	c.(4087-4089)tcC>tcA	p.S1363S	GRIN2A_ENST00000396575.2_Silent_p.S1363S|GRIN2A_ENST00000562109.1_Intron|GRIN2A_ENST00000535259.1_Intron|GRIN2A_ENST00000404927.2_Intron|GRIN2A_ENST00000330684.3_Silent_p.S1363S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1363					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.S1363S(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AAGGGTTATCGGAGGTGTGGT	0.557																																					p.S1363S		Atlas-SNP	.											GRIN2A,NS,carcinoma,0,1	GRIN2A	366	.	1	Substitution - coding silent(1)	lung(1)	c.C4089A						.						72.0	68.0	69.0					16																	9857312		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon14			GTTATCGGAGGTG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.4089C>A	chr16.hg19:g.9857312G>T		120.0	0.0		63.0	4.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.557	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
GRIN2A	2903	hgsc.bcm.edu	37	16	9862782	9862782	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:9862782A>G	ENST00000396573.2	-	13	2830	c.2521T>C	c.(2521-2523)Ttc>Ctc	p.F841L	GRIN2A_ENST00000396575.2_Missense_Mutation_p.F841L|GRIN2A_ENST00000562109.1_Missense_Mutation_p.F841L|GRIN2A_ENST00000535259.1_Missense_Mutation_p.F684L|GRIN2A_ENST00000404927.2_Missense_Mutation_p.F841L|GRIN2A_ENST00000330684.3_Missense_Mutation_p.F841L	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	841					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TTCCAGTAGAAGAGGTGCTCC	0.582																																					p.F841L		Atlas-SNP	.											.	GRIN2A	366	.	0			c.T2521C						.						93.0	81.0	85.0					16																	9862782		2197	4300	6497	SO:0001583	missense	2903	exon13			AGTAGAAGAGGTG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2521T>C	chr16.hg19:g.9862782A>G	ENSP00000379818:p.Phe841Leu	77.0	0.0		55.0	5.0	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.862599	0.91511	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	4.3	4.3	0.51218	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.64170	0.2574	M	0.80746	2.51	0.80722	D	1	D;D;D	0.64830	0.992;0.994;0.979	D;D;D	0.73708	0.968;0.981;0.973	T	0.67971	-0.5532	9	.	.	.	.	12.9416	0.58348	1.0:0.0:0.0:0.0	.	684;841;841	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	L	841;841;684;841;841	ENSP00000379818:F841L;ENSP00000385872:F841L;ENSP00000441572:F684L;ENSP00000332549:F841L;ENSP00000379820:F841L	.	F	-	1	0	GRIN2A	9770283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.176000	0.94839	1.692000	0.51112	0.460000	0.39030	TTC	.	.		0.582	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
GRIN2A	2903	hgsc.bcm.edu	37	16	9943750	9943750	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:9943750G>T	ENST00000396573.2	-	6	1500	c.1191C>A	c.(1189-1191)tcC>tcA	p.S397S	GRIN2A_ENST00000396575.2_Silent_p.S397S|GRIN2A_ENST00000562109.1_Silent_p.S397S|GRIN2A_ENST00000535259.1_Silent_p.S240S|GRIN2A_ENST00000404927.2_Silent_p.S397S|GRIN2A_ENST00000330684.3_Silent_p.S397S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	397					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTCACAGTCGGAGAAGGACT	0.582																																					p.S397S		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C1191A						.						135.0	111.0	119.0					16																	9943750		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon6			ACAGTCGGAGAAG		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1191C>A	chr16.hg19:g.9943750G>T		120.0	0.0		62.0	4.0	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.		0.582	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
RSL1D1	26156	hgsc.bcm.edu	37	16	11935611	11935611	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:11935611A>G	ENST00000571133.1	-	7	868	c.796T>C	c.(796-798)Tcg>Ccg	p.S266P	RSL1D1_ENST00000542106.1_Missense_Mutation_p.S46P	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	266					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						CTGACAAACGAGGAAAAGATG	0.363																																					p.S266P		Atlas-SNP	.											.	RSL1D1	40	.	0			c.T796C						.						73.0	74.0	73.0					16																	11935611		2197	4300	6497	SO:0001583	missense	26156	exon7			CAAACGAGGAAAA	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.796T>C	chr16.hg19:g.11935611A>G	ENSP00000460871:p.Ser266Pro	135.0	0.0		122.0	5.0	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	hg19	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.393795	0.42410	.	.	ENSG00000171490	ENST00000355674;ENST00000396503;ENST00000542106	T	0.51817	0.69	4.91	4.91	0.64330	.	0.072138	0.56097	D	0.000021	T	0.65407	0.2688	M	0.78456	2.415	0.46927	D	0.999259	D;D	0.76494	0.999;0.999	D;D	0.70227	0.949;0.968	T	0.68938	-0.5277	10	0.66056	D	0.02	-7.6655	9.1436	0.36919	0.8164:0.1836:0.0:0.0	.	266;266	Q32Q62;O76021	.;RL1D1_HUMAN	P	265;266;46	ENSP00000347897:S265P	ENSP00000347897:S265P	S	-	1	0	RSL1D1	11843112	1.000000	0.71417	0.876000	0.34364	0.081000	0.17604	4.390000	0.59646	1.975000	0.57531	0.397000	0.26171	TCG	.	.		0.363	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659	
SMG1	23049	hgsc.bcm.edu	37	16	18863750	18863750	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:18863750C>A	ENST00000446231.2	-	32	5215	c.4803G>T	c.(4801-4803)ttG>ttT	p.L1601F	SMG1_ENST00000389467.3_Missense_Mutation_p.L1601F			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1601	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L1601F(1)|p.L1597F(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ACAACTGTCCCAAAATGAAGT	0.418																																					p.L1601F		Atlas-SNP	.											.	SMG1	401	.	2	Substitution - Missense(2)	lung(2)	c.G4803T						.						50.0	46.0	47.0					16																	18863750		1922	4146	6068	SO:0001583	missense	23049	exon32			CTGTCCCAAAATG	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.4803G>T	chr16.hg19:g.18863750C>A	ENSP00000402515:p.Leu1601Phe	109.0	0.0		88.0	4.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361432	0.61403	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01178	5.22;5.23	5.07	5.07	0.68467	PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.46758	D	0.000267	T	0.01523	0.0049	L	0.34521	1.04	0.44012	D	0.996726	P	0.41313	0.745	B	0.35413	0.202	T	0.69716	-0.5070	10	0.59425	D	0.04	.	18.8053	0.92034	0.0:1.0:0.0:0.0	.	1601	Q96Q15	SMG1_HUMAN	F	1601	ENSP00000402515:L1601F;ENSP00000374118:L1601F	ENSP00000374118:L1601F	L	-	3	2	SMG1	18771251	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.979000	0.49313	2.513000	0.84729	0.462000	0.41574	TTG	.	.		0.418	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
GTF3C1	2975	hgsc.bcm.edu	37	16	27506736	27506736	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:27506736G>T	ENST00000356183.4	-	15	2443	c.2428C>A	c.(2428-2430)Ctc>Atc	p.L810I	GTF3C1_ENST00000561623.1_Missense_Mutation_p.L810I	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	810					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CCGTAGATGAGGTACCACAGA	0.587																																					p.L810I		Atlas-SNP	.											.	GTF3C1	210	.	0			c.C2428A						.						45.0	39.0	41.0					16																	27506736		2197	4300	6497	SO:0001583	missense	2975	exon15			AGATGAGGTACCA	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.2428C>A	chr16.hg19:g.27506736G>T	ENSP00000348510:p.Leu810Ile	134.0	0.0		88.0	4.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.549773	0.65311	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.35973	1.28	5.55	4.4	0.53042	.	0.086693	0.48286	D	0.000186	T	0.32704	0.0838	L	0.48877	1.53	0.41008	D	0.98498	D;P	0.54397	0.966;0.886	P;P	0.45794	0.493;0.491	T	0.07790	-1.0754	10	0.48119	T	0.1	-20.3752	7.9264	0.29876	0.1224:0.0:0.7202:0.1574	.	810;810	Q12789;Q12789-3	TF3C1_HUMAN;.	I	810;808	ENSP00000348510:L810I	ENSP00000348510:L810I	L	-	1	0	GTF3C1	27414237	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	0.951000	0.29135	2.603000	0.88011	0.655000	0.94253	CTC	.	.		0.587	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
SH2B1	25970	hgsc.bcm.edu	37	16	28884047	28884047	+	Intron	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:28884047G>T	ENST00000322610.8	+	10	2336				SH2B1_ENST00000395532.4_Intron|SH2B1_ENST00000545570.1_Missense_Mutation_p.G330W|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000337120.5_Intron|SH2B1_ENST00000538342.1_Intron|SH2B1_ENST00000359285.5_Missense_Mutation_p.G640W			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1						blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						CAGGTCTGCAGGGGAGGAGGT	0.607																																					p.G640W		Atlas-SNP	.											.	SH2B1	160	.	0			c.G1918T						.						49.0	42.0	45.0					16																	28884047		2197	4300	6497	SO:0001627	intron_variant	25970	exon8			TCTGCAGGGGAGG	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	30417	protein-coding gene	gene with protein product	"""SH2-B homolog"""	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1897+21G>T	chr16.hg19:g.28884047G>T		181.0	0.0		96.0	4.0	NM_001145797	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	hg19	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	g	16.30	3.083218	0.55861	.	.	ENSG00000178188	ENST00000545570;ENST00000359285	T;T	0.46063	1.57;0.88	5.1	5.1	0.69264	.	.	.	.	.	T	0.46367	0.1389	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.45381	-0.9265	9	0.37606	T	0.19	.	14.0194	0.64545	0.0:0.0:1.0:0.0	.	330;640	F5GXU7;Q9NRF2-3	.;.	W	330;640	ENSP00000440354:G330W;ENSP00000352232:G640W	ENSP00000352232:G640W	G	+	1	0	SH2B1	28791548	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.294000	0.51787	2.363000	0.80096	0.558000	0.71614	GGG	.	.		0.607	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503	
ATP2A1	487	hgsc.bcm.edu	37	16	28914131	28914131	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:28914131C>A	ENST00000357084.3	+	19	2910	c.2643C>A	c.(2641-2643)acC>acA	p.T881T	ATP2A1_ENST00000395503.4_Silent_p.T881T|ATP2A1_ENST00000536376.1_Silent_p.T756T	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	881					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGACAACACCCACTTTGAGG	0.602																																					p.T881T		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C2643A						.						91.0	78.0	82.0					16																	28914131		2197	4300	6497	SO:0001819	synonymous_variant	487	exon19			CAACACCCACTTT		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.2643C>A	chr16.hg19:g.28914131C>A		160.0	0.0		121.0	5.0	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	hg19	CCDS10643.1																																																																																			.	.		0.602	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
CORO1A	11151	hgsc.bcm.edu	37	16	30196584	30196584	+	Silent	SNP	G	G	T	rs61736363		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:30196584G>T	ENST00000219150.5	+	2	359	c.54G>T	c.(52-54)ccG>ccT	p.P18P	RP11-455F5.5_ENST00000566144.1_RNA|CORO1A_ENST00000570045.1_Silent_p.P18P|CORO1A_ENST00000565497.1_Silent_p.P18P|RP11-455F5.5_ENST00000568506.1_RNA|CORO1A_ENST00000566619.1_3'UTR|RP11-455F5.5_ENST00000567153.1_RNA	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	18					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						TTGGACAGCCGGCCAAGGCCG	0.577																																					p.P18P		Atlas-SNP	.											.	CORO1A	36	.	0			c.G54T						.						95.0	83.0	87.0					16																	30196584		2197	4300	6497	SO:0001819	synonymous_variant	11151	exon2			ACAGCCGGCCAAG	X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"""Coronins"", ""WD repeat domain containing"""	2252	protein-coding gene	gene with protein product	"""Clabp TACO"""	605000	"""coronin, actin-binding protein, 1A"""			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.54G>T	chr16.hg19:g.30196584G>T		127.0	0.0		93.0	4.0	NM_007074	B2RBL1|Q2YD73	Silent	SNP	ENST00000219150.5	hg19	CCDS10673.1																																																																																			.	G|0.986;C|0.014		0.577	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074	
ZNF629	23361	hgsc.bcm.edu	37	16	30795164	30795164	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:30795164C>T	ENST00000262525.4	-	3	692	c.485G>A	c.(484-486)tGg>tAg	p.W162*		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			CAGCTTGGACCACTGGCTGAA	0.692																																					p.W162X		Atlas-SNP	.											.	ZNF629	44	.	0			c.G485A						.						31.0	33.0	33.0					16																	30795164		2197	4299	6496	SO:0001587	stop_gained	23361	exon3			TTGGACCACTGGC	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.485G>A	chr16.hg19:g.30795164C>T	ENSP00000262525:p.Trp162*	153.0	0.0		99.0	4.0	NM_001080417	Q15938	Nonsense_Mutation	SNP	ENST00000262525.4	hg19	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746570	0.89663	.	.	ENSG00000102870	ENST00000262525	.	.	.	4.89	4.89	0.63831	.	0.000000	0.42682	D	0.000674	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-19.9411	10.8269	0.46638	0.0:0.9108:0.0:0.0892	.	.	.	.	X	162	.	ENSP00000262525:W162X	W	-	2	0	ZNF629	30702665	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.009000	0.13219	2.416000	0.81992	0.561000	0.74099	TGG	.	.		0.692	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
ZNF646	9726	hgsc.bcm.edu	37	16	31088245	31088245	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:31088245C>T	ENST00000394979.2	+	1	1023	c.600C>T	c.(598-600)ccC>ccT	p.P200P	ZNF646_ENST00000300850.5_Silent_p.P200P|ZNF668_ENST00000300849.4_5'Flank|ZNF668_ENST00000564456.1_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	200					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CTCCTCTCCCCATCCCAGCCA	0.602																																					p.P200P		Atlas-SNP	.											.	ZNF646	133	.	0			c.C600T						.						45.0	50.0	48.0					16																	31088245		2196	4300	6496	SO:0001819	synonymous_variant	9726	exon2			TCTCCCCATCCCA	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.600C>T	chr16.hg19:g.31088245C>T		91.0	0.0		71.0	6.0	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	.		0.602	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
SLC5A2	6524	hgsc.bcm.edu	37	16	31499986	31499986	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:31499986G>T	ENST00000330498.3	+	10	1192	c.1173G>T	c.(1171-1173)atG>atT	p.M391I	AC026471.6_ENST00000565137.1_RNA	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	391					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)			endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	CCGCGCTCATGTCCTCGCTGG	0.706																																					p.M391I		Atlas-SNP	.											.	SLC5A2	58	.	0			c.G1173T						.						28.0	25.0	26.0					16																	31499986		2196	4299	6495	SO:0001583	missense	6524	exon10			GCTCATGTCCTCG		CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"""Solute carriers"""	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.1173G>T	chr16.hg19:g.31499986G>T	ENSP00000327943:p.Met391Ile	113.0	0.0		56.0	4.0	NM_003041	A2RRD2	Missense_Mutation	SNP	ENST00000330498.3	hg19	CCDS10714.1	.	.	.	.	.	.	.	.	.	.	G	32	5.107688	0.94292	.	.	ENSG00000140675	ENST00000330498	D	0.90955	-2.76	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.93350	0.7880	L	0.49455	1.56	0.80722	D	1	D	0.59357	0.985	D	0.72338	0.977	D	0.93607	0.6935	10	0.59425	D	0.04	.	15.2095	0.73209	0.0:0.0:1.0:0.0	.	391	P31639	SC5A2_HUMAN	I	391	ENSP00000327943:M391I	ENSP00000327943:M391I	M	+	3	0	SLC5A2	31407487	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.651000	0.98493	2.453000	0.82957	0.561000	0.74099	ATG	.	.		0.706	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2		
PHKB	5257	hgsc.bcm.edu	37	16	47545621	47545621	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:47545621T>C	ENST00000323584.5	+	5	475	c.451T>C	c.(451-453)Tct>Cct	p.S151P	PHKB_ENST00000566044.1_Missense_Mutation_p.S144P|PHKB_ENST00000455779.1_Missense_Mutation_p.S144P|PHKB_ENST00000299167.8_Missense_Mutation_p.S151P|PHKB_ENST00000567402.1_3'UTR	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	151					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				ATGTCTTCACTCTGTTTTCAA	0.333																																					p.S151P		Atlas-SNP	.											.	PHKB	298	.	0			c.T451C						.						144.0	125.0	132.0					16																	47545621		2201	4300	6501	SO:0001583	missense	5257	exon5			CTTCACTCTGTTT		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.451T>C	chr16.hg19:g.47545621T>C	ENSP00000313504:p.Ser151Pro	138.0	0.0		86.0	4.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	T	33	5.237119	0.95240	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91631	-2.88;-2.88	5.87	5.87	0.94306	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.96147	0.8744	M	0.81942	2.565	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.99;0.982	D	0.96562	0.9416	10	0.87932	D	0	-24.1279	16.5764	0.84681	0.0:0.0:0.0:1.0	.	144;151;144	B4DQ16;Q93100;Q93100-4	.;KPBB_HUMAN;.	P	144;144;151	ENSP00000414345:S144P;ENSP00000313504:S151P	ENSP00000299167:S144P	S	+	1	0	PHKB	46103122	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.795000	0.85887	2.371000	0.80710	0.533000	0.62120	TCT	.	.		0.333	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		
CBLN1	869	hgsc.bcm.edu	37	16	49313350	49313350	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:49313350A>G	ENST00000219197.6	-	3	912	c.547T>C	c.(547-549)Tcg>Ccg	p.S183P	CBLN1_ENST00000536749.1_Missense_Mutation_p.S183P	NM_004352.3	NP_004343.1	P23435	CBLN1_HUMAN	cerebellin 1 precursor	183	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Necessary for interaction with CBLN3, and homotrimerization. {ECO:0000250}.				cerebellar granule cell differentiation (GO:0021707)|heterophilic cell-cell adhesion (GO:0007157)|nervous system development (GO:0007399)|positive regulation of synapse assembly (GO:0051965)|protein secretion (GO:0009306)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|extracellular region (GO:0005576)|postsynaptic membrane (GO:0045211)				breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(37;0.0766)|all_lung(18;0.24)				GAGAAGGTCGAGTACTTCCAG	0.602																																					p.S183P		Atlas-SNP	.											.	CBLN1	26	.	0			c.T547C						.						109.0	103.0	105.0					16																	49313350		2200	4300	6500	SO:0001583	missense	869	exon3			AGGTCGAGTACTT	M58583	CCDS10736.1	16q12.1	2008-02-05			ENSG00000102924	ENSG00000102924			1543	protein-coding gene	gene with protein product		600432				7877445, 1704129	Standard	NM_004352		Approved		uc002efq.3	P23435	OTTHUMG00000133148	ENST00000219197.6:c.547T>C	chr16.hg19:g.49313350A>G	ENSP00000219197:p.Ser183Pro	214.0	0.0		133.0	6.0	NM_004352	B2RAN9|P02682|Q52M09	Missense_Mutation	SNP	ENST00000219197.6	hg19	CCDS10736.1	.	.	.	.	.	.	.	.	.	.	A	19.83	3.900943	0.72754	.	.	ENSG00000102924	ENST00000219197;ENST00000536749	T;T	0.44881	0.91;0.91	5.49	5.49	0.81192	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.064023	0.64402	D	0.000004	T	0.55226	0.1907	M	0.86805	2.84	0.58432	D	0.999999	B	0.20052	0.041	B	0.30716	0.119	T	0.59506	-0.7442	10	0.72032	D	0.01	-6.1619	15.88	0.79197	1.0:0.0:0.0:0.0	.	183	P23435	CBLN1_HUMAN	P	183	ENSP00000219197:S183P;ENSP00000444651:S183P	ENSP00000219197:S183P	S	-	1	0	CBLN1	47870851	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.183000	0.94887	2.193000	0.70182	0.533000	0.62120	TCG	.	.		0.602	CBLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256845.4	NM_004352	
ZNF423	23090	hgsc.bcm.edu	37	16	49670350	49670350	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:49670350G>T	ENST00000561648.1	-	4	2766	c.2713C>A	c.(2713-2715)Cgg>Agg	p.R905R	ZNF423_ENST00000563137.2_Silent_p.R845R|ZNF423_ENST00000562871.1_Silent_p.R845R|ZNF423_ENST00000535559.1_Silent_p.R788R|ZNF423_ENST00000262383.2_Silent_p.R905R|ZNF423_ENST00000562520.1_Silent_p.R845R|ZNF423_ENST00000567169.1_Silent_p.R788R	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	905					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				TCCCGCAGCCGGTGATTCTGC	0.602																																					p.R905R		Atlas-SNP	.											.	ZNF423	463	.	0			c.C2713A						.						64.0	61.0	62.0					16																	49670350		2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			GCAGCCGGTGATT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2713C>A	chr16.hg19:g.49670350G>T		95.0	0.0		81.0	4.0	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
NKD1	85407	hgsc.bcm.edu	37	16	50667325	50667325	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:50667325C>T	ENST00000268459.3	+	10	1270	c.1046C>T	c.(1045-1047)cCc>cTc	p.P349L		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	349					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GTGAGGTCCCCCAAGGCCCAG	0.667																																					p.P349L		Atlas-SNP	.											.	NKD1	43	.	0			c.C1046T						.						47.0	55.0	52.0					16																	50667325		2198	4300	6498	SO:0001583	missense	85407	exon10			GGTCCCCCAAGGC	AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"""EF-hand domain containing"""	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.1046C>T	chr16.hg19:g.50667325C>T	ENSP00000268459:p.Pro349Leu	275.0	0.0		149.0	7.0	NM_033119	B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	hg19	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364808	0.82463	.	.	ENSG00000140807	ENST00000268459	T	0.80994	-1.44	4.18	4.18	0.49190	.	0.000000	0.85682	D	0.000000	T	0.81283	0.4790	M	0.65975	2.015	0.80722	D	1	P	0.39250	0.665	B	0.43728	0.429	T	0.80781	-0.1229	10	0.33141	T	0.24	-24.5648	14.8623	0.70389	0.0:1.0:0.0:0.0	.	349	Q969G9	NKD1_HUMAN	L	349	ENSP00000268459:P349L	ENSP00000268459:P349L	P	+	2	0	NKD1	49224826	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.057000	0.76669	2.162000	0.67917	0.460000	0.39030	CCC	.	.		0.667	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1		
CHD9	80205	hgsc.bcm.edu	37	16	53358168	53358168	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:53358168G>A	ENST00000398510.3	+	38	8142	c.8055G>A	c.(8053-8055)ctG>ctA	p.L2685L	CHD9_ENST00000447540.1_Silent_p.L2670L|CHD9_ENST00000564845.1_Silent_p.L2669L|CHD9_ENST00000566029.1_Silent_p.L2669L			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2685					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TGCAGTCACTGCAAGTAACTG	0.483																																					p.L2669L		Atlas-SNP	.											.	CHD9	203	.	0			c.G8007A						.						78.0	77.0	77.0					16																	53358168		1894	4124	6018	SO:0001819	synonymous_variant	80205	exon39			GTCACTGCAAGTA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.8055G>A	chr16.hg19:g.53358168G>A		124.0	0.0		96.0	5.0	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	hg19																																																																																				.	.		0.483	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
LPCAT2	54947	hgsc.bcm.edu	37	16	55543151	55543151	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:55543151G>T	ENST00000262134.5	+	1	242	c.58G>T	c.(58-60)Ggg>Tgg	p.G20W		NM_017839.4	NP_060309.2	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	20					glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)	p.G20W(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	12						TGCCGGCGTCGGGAACGTGGG	0.726																																					p.G20W		Atlas-SNP	.											LPCAT2,NS,carcinoma,0,1	LPCAT2	35	.	1	Substitution - Missense(1)	lung(1)	c.G58T						.						4.0	6.0	5.0					16																	55543151		1880	3891	5771	SO:0001583	missense	54947	exon1			GGCGTCGGGAACG	AK000488	CCDS10753.1	16q12.2	2013-01-10	2007-12-17	2007-12-17	ENSG00000087253	ENSG00000087253		"""EF-hand domain containing"""	26032	protein-coding gene	gene with protein product		612040	"""acyltransferase like 1"""	AYTL1		16704971	Standard	NM_017839		Approved	FLJ20481	uc002eie.4	Q7L5N7	OTTHUMG00000133238	ENST00000262134.5:c.58G>T	chr16.hg19:g.55543151G>T	ENSP00000262134:p.Gly20Trp	91.0	0.0		36.0	2.0	NM_017839	A3KBM1|Q6MZJ6|Q9NX23	Missense_Mutation	SNP	ENST00000262134.5	hg19	CCDS10753.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.333120	0.41297	.	.	ENSG00000087253	ENST00000262134	T	0.74842	-0.88	4.69	3.66	0.41972	.	0.470628	0.22804	N	0.055437	T	0.78767	0.4335	L	0.54323	1.7	0.09310	N	0.999999	D	0.64830	0.994	D	0.64506	0.926	T	0.67624	-0.5623	10	0.72032	D	0.01	-9.5442	6.9664	0.24625	0.1269:0.0:0.8731:0.0	.	20	Q7L5N7	PCAT2_HUMAN	W	20	ENSP00000262134:G20W	ENSP00000262134:G20W	G	+	1	0	LPCAT2	54100652	0.708000	0.27876	0.080000	0.20451	0.010000	0.07245	0.837000	0.27558	2.436000	0.82500	0.643000	0.83706	GGG	.	.		0.726	LPCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256977.2	NM_017839	
CETP	1071	hgsc.bcm.edu	37	16	57007309	57007309	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:57007309G>T	ENST00000566128.1	+	9	889	c.622G>T	c.(622-624)Ggg>Tgg	p.G208W	CETP_ENST00000200676.3_Missense_Mutation_p.G273W|CETP_ENST00000379780.2_Intron					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CACACTGCTGGGGGACTCCCG	0.602																																					p.G273W		Atlas-SNP	.											.	CETP	50	.	0			c.G817T						.						79.0	75.0	76.0					16																	57007309		2198	4300	6498	SO:0001583	missense	1071	exon9			CTGCTGGGGGACT	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.622G>T	chr16.hg19:g.57007309G>T	ENSP00000456276:p.Gly208Trp	109.0	0.0		91.0	4.0	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.03	2.115257	0.37339	.	.	ENSG00000087237	ENST00000200676	T	0.08282	3.11	3.68	-1.51	0.08664	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.356298	0.25233	U	0.032142	T	0.05960	0.0155	L	0.27053	0.805	0.20764	N	0.999851	P	0.40230	0.708	P	0.45538	0.484	T	0.24476	-1.0159	10	0.72032	D	0.01	-2.0762	1.2121	0.01907	0.216:0.311:0.3149:0.1581	.	273	P11597	CETP_HUMAN	W	273	ENSP00000200676:G273W	ENSP00000200676:G273W	G	+	1	0	CETP	55564810	0.995000	0.38212	0.853000	0.33588	0.611000	0.37282	0.167000	0.16602	0.072000	0.16694	0.313000	0.20887	GGG	.	.		0.602	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
TK2	7084	hgsc.bcm.edu	37	16	66575828	66575828	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:66575828C>A	ENST00000451102.2	-	3	535	c.185G>T	c.(184-186)gGg>gTg	p.G62V	TK2_ENST00000563369.2_5'UTR|TK2_ENST00000544898.1_Missense_Mutation_p.G13V|TK2_ENST00000417693.3_Missense_Mutation_p.G62V|TK2_ENST00000527800.1_5'UTR|TK2_ENST00000545043.2_Intron|TK2_ENST00000299697.7_Missense_Mutation_p.G104V|TK2_ENST00000525974.1_5'UTR|TK2_ENST00000564917.1_Missense_Mutation_p.G62V|TK2_ENST00000527284.1_Missense_Mutation_p.G31V			O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial	62					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|DNA replication (GO:0006260)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|thymidine kinase activity (GO:0004797)			large_intestine(1)|lung(2)|urinary_tract(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)		TGTCGTCTTCCCACTTGCAAT	0.488																																					p.G62V		Atlas-SNP	.											.	TK2	17	.	0			c.G185T						.						137.0	109.0	118.0					16																	66575828		2201	4300	6501	SO:0001583	missense	7084	exon3			GTCTTCCCACTTG		CCDS10805.1, CCDS10805.2, CCDS54016.1, CCDS54017.1, CCDS54018.1, CCDS61955.1	16q22-q23.1	2012-10-02			ENSG00000166548	ENSG00000166548	2.7.1.21		11831	protein-coding gene	gene with protein product		188250					Standard	NM_004614		Approved		uc002eos.3	O00142	OTTHUMG00000137499	ENST00000451102.2:c.185G>T	chr16.hg19:g.66575828C>A	ENSP00000414334:p.Gly62Val	84.0	0.0		53.0	4.0	NM_001172645	B4DGJ7|B4DZK7|B7ZAB1|E9PH08|O15238	Missense_Mutation	SNP	ENST00000451102.2	hg19	CCDS10805.2	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661623	0.88154	.	.	ENSG00000166548	ENST00000299697;ENST00000417693;ENST00000451102;ENST00000527284;ENST00000544898	D;D;D;D;D	0.99931	-8.18;-8.18;-8.18;-8.18;-8.18	6.06	6.06	0.98353	.	0.097274	0.64402	D	0.000001	D	0.99941	0.9974	H	0.96175	3.78	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.998;1.0;1.0	D	0.96319	0.9235	10	0.87932	D	0	-40.5018	16.1399	0.81515	0.0:1.0:0.0:0.0	.	62;13;26;104;31	O00142;F5GYK4;A4IF54;E5KNQ5;O00142-2	KITM_HUMAN;.;.;.;.	V	104;62;62;31;13	ENSP00000299697:G104V;ENSP00000407469:G62V;ENSP00000414334:G62V;ENSP00000435312:G31V;ENSP00000440898:G13V	ENSP00000299697:G104V	G	-	2	0	TK2	65133329	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.121000	0.64691	2.880000	0.98712	0.650000	0.86243	GGG	.	.		0.488	TK2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268806.4		
RLTPR	146206	hgsc.bcm.edu	37	16	67685847	67685847	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:67685847G>T	ENST00000334583.6	+	26	2940	c.2612G>T	c.(2611-2613)gGg>gTg	p.G871V	RLTPR_ENST00000545661.1_Missense_Mutation_p.G835V	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	871					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TCAATCACGGGGACCTTGGCA	0.602																																					p.G871V		Atlas-SNP	.											.	RLTPR	124	.	0			c.G2612T						.						131.0	137.0	135.0					16																	67685847		2130	4237	6367	SO:0001583	missense	146206	exon26			TCACGGGGACCTT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.2612G>T	chr16.hg19:g.67685847G>T	ENSP00000334958:p.Gly871Val	78.0	0.0		62.0	4.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	G	8.766	0.924689	0.18056	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.12984	2.63;2.63	4.85	2.78	0.32641	.	0.534882	0.17245	N	0.181361	T	0.13756	0.0333	L	0.57536	1.79	0.24410	N	0.994663	B;B	0.27559	0.181;0.022	B;B	0.29267	0.1;0.006	T	0.14587	-1.0467	10	0.51188	T	0.08	-12.016	6.1459	0.20285	0.1038:0.2032:0.693:0.0	.	835;871	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	V	871;835	ENSP00000334958:G871V;ENSP00000441481:G835V	ENSP00000334958:G871V	G	+	2	0	RLTPR	66243348	0.856000	0.29760	0.841000	0.33234	0.549000	0.35272	2.433000	0.44793	1.256000	0.44068	0.655000	0.94253	GGG	.	.		0.602	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
THAP11	57215	hgsc.bcm.edu	37	16	67876832	67876832	+	Silent	SNP	G	G	A	rs141903290		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:67876832G>A	ENST00000303596.1	+	1	620	c.375G>A	c.(373-375)caG>caA	p.Q125Q	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	125	Gln-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		aacagcagcagcagcagcagc	0.677																																					p.Q125Q		Atlas-SNP	.											THAP11,NS,carcinoma,0,1	THAP11	27	.	0			c.G375A						.						33.0	39.0	37.0					16																	67876832		2053	4030	6083	SO:0001819	synonymous_variant	57215	exon1			GCAGCAGCAGCAG	AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"""THAP (C2CH-type zinc finger) domain containing"""	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.375G>A	chr16.hg19:g.67876832G>A		49.0	1.0		29.0	2.0	NM_020457	A4UCT5|A8K002|O94795	Silent	SNP	ENST00000303596.1	hg19	CCDS10847.1																																																																																			.	G|0.998;A|0.002		0.677	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268879.1	NM_020457	
ESRP2	80004	hgsc.bcm.edu	37	16	68265144	68265144	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:68265144G>T	ENST00000565858.1	-	12	1764	c.1678C>A	c.(1678-1680)Cga>Aga	p.R560R	ESRP2_ENST00000473183.2_Silent_p.R550R|RP11-96D1.11_ENST00000571197.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	560					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						ATCAGCACTCGGCTCATCTCC	0.632																																					p.R550R		Atlas-SNP	.											.	ESRP2	118	.	0			c.C1648A						.						89.0	71.0	77.0					16																	68265144		2198	4300	6498	SO:0001819	synonymous_variant	80004	exon12			GCACTCGGCTCAT	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"""RNA binding motif (RRM) containing"""	26152	protein-coding gene	gene with protein product		612960	"""RNA binding motif protein 35B"""	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.1678C>A	chr16.hg19:g.68265144G>T		110.0	0.0		98.0	4.0	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Silent	SNP	ENST00000565858.1	hg19																																																																																				.	.		0.632	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939	
COG4	25839	hgsc.bcm.edu	37	16	70546324	70546324	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:70546324C>T	ENST00000323786.5	-	5	577	c.556G>A	c.(556-558)Gat>Aat	p.D186N	COG4_ENST00000393612.4_Missense_Mutation_p.D182N|COG4_ENST00000564653.1_Intron	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	182					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				AGGTTGGCATCAATCATGCTC	0.463																																					p.D186N		Atlas-SNP	.											.	COG4	64	.	0			c.G556A						.						68.0	58.0	61.0					16																	70546324		2198	4300	6498	SO:0001583	missense	25839	exon5			TGGCATCAATCAT	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.556G>A	chr16.hg19:g.70546324C>T	ENSP00000315775:p.Asp186Asn	83.0	0.0		57.0	4.0	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	hg19	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	C	22.8	4.341999	0.81911	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612;ENST00000534772	T;T;T	0.49139	0.98;0.98;0.79	5.53	5.53	0.82687	.	0.089049	0.85682	D	0.000000	T	0.44540	0.1298	L	0.43152	1.355	0.80722	D	1	B;B	0.20671	0.021;0.047	B;B	0.17098	0.008;0.017	T	0.22556	-1.0213	10	0.34782	T	0.22	-15.4266	19.466	0.94939	0.0:1.0:0.0:0.0	.	181;182	Q6PIW8;Q9H9E3	.;COG4_HUMAN	N	186;182;182;109	ENSP00000315775:D186N;ENSP00000377236:D182N;ENSP00000461912:D109N	ENSP00000315775:D186N	D	-	1	0	COG4	69103825	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.550000	0.82173	2.607000	0.88179	0.655000	0.94253	GAT	.	.		0.463	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
ZFHX3	463	hgsc.bcm.edu	37	16	72992020	72992020	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:72992020C>T	ENST00000268489.5	-	2	2697	c.2025G>A	c.(2023-2025)aaG>aaA	p.K675K	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	675					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				GCCAGTTGCACTTGGGGCACT	0.602																																					p.K675K		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G2025A						.						45.0	49.0	48.0					16																	72992020		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			GTTGCACTTGGGG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2025G>A	chr16.hg19:g.72992020C>T		41.0	0.0		39.0	4.0	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
LDHD	197257	hgsc.bcm.edu	37	16	75149474	75149474	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:75149474G>T	ENST00000450168.2	-	2	207	c.157C>A	c.(157-159)Cag>Aag	p.Q53K	LDHD_ENST00000300051.4_Missense_Mutation_p.Q53K	NM_194436.2	NP_919417.1			lactate dehydrogenase D											endometrium(1)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	16						CGCCCGTGCTGCTCTCGGACC	0.647																																					p.Q53K		Atlas-SNP	.											.	LDHD	34	.	0			c.C157A						.						27.0	32.0	30.0					16																	75149474		2197	4300	6497	SO:0001583	missense	197257	exon2			CGTGCTGCTCTCG	AY092767	CCDS10913.1, CCDS45529.1	16q22.3	2011-01-27			ENSG00000166816	ENSG00000166816			19708	protein-coding gene	gene with protein product		607490				12127981	Standard	NM_153486		Approved		uc002fdm.3	Q86WU2	OTTHUMG00000137605	ENST00000450168.2:c.157C>A	chr16.hg19:g.75149474G>T	ENSP00000417011:p.Gln53Lys	153.0	0.0		101.0	5.0	NM_194436		Missense_Mutation	SNP	ENST00000450168.2	hg19	CCDS45529.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337595	0.81911	.	.	ENSG00000166816	ENST00000450168;ENST00000300051	T;T	0.41400	1.0;1.0	5.06	5.06	0.68205	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (1);	0.261864	0.38548	N	0.001647	T	0.46151	0.1378	L	0.53617	1.68	0.80722	D	1	P;P	0.48503	0.911;0.857	P;B	0.44359	0.447;0.333	T	0.51834	-0.8655	10	0.62326	D	0.03	-7.672	18.0365	0.89305	0.0:0.0:1.0:0.0	.	53;53	Q86WU2-2;Q86WU2	.;LDHD_HUMAN	K	53	ENSP00000417011:Q53K;ENSP00000300051:Q53K	ENSP00000300051:Q53K	Q	-	1	0	LDHD	73706975	1.000000	0.71417	0.355000	0.25773	0.535000	0.34838	8.832000	0.92079	2.371000	0.80710	0.561000	0.74099	CAG	.	.		0.647	LDHD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434651.1	NM_153486	
CHST6	4166	hgsc.bcm.edu	37	16	75513666	75513666	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:75513666G>A	ENST00000332272.4	-	3	240	c.61C>T	c.(61-63)Ctc>Ttc	p.L21F	RP11-77K12.4_ENST00000530512.3_RNA|CHST6_ENST00000390664.2_Missense_Mutation_p.L21F	NM_021615.4	NP_067628.1	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6	21					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AAGAGGAGGAGGAAGGTCTGC	0.697																																					p.L21F		Atlas-SNP	.											CHST6,colon,carcinoma,0,1	CHST6	57	.	0			c.C61T						.						13.0	15.0	15.0					16																	75513666		2183	4291	6474	SO:0001583	missense	4166	exon3			GGAGGAGGAAGGT	AF280086	CCDS10918.1	16q22	2008-02-05			ENSG00000183196	ENSG00000183196		"""Sulfotransferases, membrane-bound"""	6938	protein-coding gene	gene with protein product		605294		MCDC1		8644739, 11017086	Standard	NM_021615		Approved		uc002fef.3	Q9GZX3	OTTHUMG00000137612	ENST00000332272.4:c.61C>T	chr16.hg19:g.75513666G>A	ENSP00000328983:p.Leu21Phe	54.0	0.0		45.0	3.0	NM_021615	D3DUK3	Missense_Mutation	SNP	ENST00000332272.4	hg19	CCDS10918.1	.	.	.	.	.	.	.	.	.	.	G	5.371	0.253730	0.10185	.	.	ENSG00000183196	ENST00000332272;ENST00000390664	D;D	0.96856	-4.15;-4.15	5.01	1.82	0.25136	.	1.375640	0.04765	N	0.427071	D	0.89976	0.6871	N	0.17082	0.46	0.24533	N	0.994109	B	0.02656	0.0	B	0.04013	0.001	T	0.80759	-0.1239	10	0.10902	T	0.67	.	3.6852	0.08326	0.1772:0.0:0.4082:0.4146	.	21	Q9GZX3	CHST6_HUMAN	F	21	ENSP00000328983:L21F;ENSP00000375079:L21F	ENSP00000328983:L21F	L	-	1	0	CHST6	74071167	0.843000	0.29541	0.757000	0.31301	0.732000	0.41865	1.006000	0.29847	0.422000	0.26005	0.591000	0.81541	CTC	.	.		0.697	CHST6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435478.1	NM_021615	
PLCG2	5336	hgsc.bcm.edu	37	16	81972412	81972412	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:81972412G>A	ENST00000359376.3	+	29	3419	c.3205G>A	c.(3205-3207)Ggt>Agt	p.G1069S		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1069	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.G1069S(2)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CCAGGTTCTCGGTGCTCGCCA	0.542																																					p.G1069S		Atlas-SNP	.											PLCG2_ENST00000359376,NS,carcinoma,0,4	PLCG2	276	.	2	Substitution - Missense(2)	endometrium(2)	c.G3205A						.						88.0	84.0	86.0					16																	81972412		1943	4138	6081	SO:0001583	missense	5336	exon29			GTTCTCGGTGCTC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3205G>A	chr16.hg19:g.81972412G>A	ENSP00000352336:p.Gly1069Ser	152.0	0.0		99.0	4.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.033268	0.93575	.	.	ENSG00000197943	ENST00000359376	T	0.66638	-0.22	5.39	5.39	0.77823	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048118	0.85682	D	0.000000	T	0.64702	0.2622	N	0.05608	-0.01	0.80722	D	1	D	0.69078	0.997	P	0.59424	0.857	T	0.70163	-0.4947	10	0.42905	T	0.14	.	19.1452	0.93463	0.0:0.0:1.0:0.0	.	1069	P16885	PLCG2_HUMAN	S	1069	ENSP00000352336:G1069S	ENSP00000352336:G1069S	G	+	1	0	PLCG2	80529913	1.000000	0.71417	0.901000	0.35422	0.690000	0.40134	9.444000	0.97578	2.517000	0.84864	0.561000	0.74099	GGT	.	.		0.542	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
IRF8	3394	hgsc.bcm.edu	37	16	85946744	85946744	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:85946744T>C	ENST00000268638.5	+	5	877	c.455T>C	c.(454-456)gTg>gCg	p.V152A	IRF8_ENST00000562492.1_5'Flank	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	152					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CAGCCTTCTGTGGACGATTAC	0.577																																					p.V152A		Atlas-SNP	.											.	IRF8	65	.	0			c.T455C						.						111.0	117.0	115.0					16																	85946744		2198	4300	6498	SO:0001583	missense	3394	exon5			CTTCTGTGGACGA	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.455T>C	chr16.hg19:g.85946744T>C	ENSP00000268638:p.Val152Ala	132.0	0.0		68.0	4.0	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	hg19	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.818382	0.32145	.	.	ENSG00000140968	ENST00000268638	D	0.96967	-4.19	4.86	3.75	0.43078	.	0.655707	0.15813	N	0.243361	D	0.91945	0.7449	L	0.48642	1.525	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.83257	-0.0050	10	0.08179	T	0.78	-21.0783	6.6795	0.23113	0.0:0.0779:0.1554:0.7667	.	152	Q02556	IRF8_HUMAN	A	152	ENSP00000268638:V152A	ENSP00000268638:V152A	V	+	2	0	IRF8	84504245	0.998000	0.40836	0.901000	0.35422	0.968000	0.65278	1.156000	0.31712	0.798000	0.33994	0.459000	0.35465	GTG	.	.		0.577	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
SLC7A5	8140	hgsc.bcm.edu	37	16	87871523	87871523	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:87871523T>C	ENST00000261622.4	-	7	1133	c.1068A>G	c.(1066-1068)gaA>gaG	p.E356E	RP4-536B24.2_ENST00000563687.1_RNA|SLC7A5_ENST00000565644.1_Silent_p.E90E	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	356					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	GCAGGTGGCCTTCCCGGGACC	0.657																																					p.E356E		Atlas-SNP	.											.	SLC7A5	28	.	0			c.A1068G						.						114.0	92.0	99.0					16																	87871523		2198	4298	6496	SO:0001819	synonymous_variant	8140	exon7			GTGGCCTTCCCGG	AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"""CD molecules"", ""Solute carriers"""	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.1068A>G	chr16.hg19:g.87871523T>C		130.0	0.0		90.0	4.0	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Silent	SNP	ENST00000261622.4	hg19	CCDS10964.1																																																																																			.	.		0.657	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486	
PIEZO1	9780	hgsc.bcm.edu	37	16	88792799	88792799	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:88792799C>A	ENST00000301015.9	-	27	4107	c.3861G>T	c.(3859-3861)tgG>tgT	p.W1287C		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1287					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						AGACGCTGTCCCAGATGATGC	0.637																																					p.W1287C		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G3861T						.						90.0	98.0	96.0					16																	88792799		692	1591	2283	SO:0001583	missense	9780	exon27			GCTGTCCCAGATG	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.3861G>T	chr16.hg19:g.88792799C>A	ENSP00000301015:p.Trp1287Cys	155.0	0.0		96.0	4.0	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	hg19	CCDS54058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.09|15.09	2.730503|2.730503	0.48939|0.48939	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015	.|T	.|0.20332	.|2.08	4.46|4.46	2.4|2.4	0.29515|0.29515	.|.	.|0.288743	.|0.36167	.|N	.|0.002749	.|T	.|0.49813	.|0.1579	M|M	0.86864|0.86864	2.845|2.845	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	.|T	.|0.58825	.|-0.7568	.|10	.|0.72032	.|D	.|0.01	-12.6318|-12.6318	13.5937|13.5937	0.61975|0.61975	0.0:0.7025:0.2975:0.0|0.0:0.7025:0.2975:0.0	.|.	.|1287	.|Q92508	.|PIEZ1_HUMAN	X|C	1233|1287	.|ENSP00000301015:W1287C	.|ENSP00000301015:W1287C	G|W	-|-	1|3	0|0	FAM38A|FAM38A	87320300|87320300	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.612000|0.612000	0.37316|0.37316	6.988000|6.988000	0.76212|0.76212	0.561000|0.561000	0.29186|0.29186	0.484000|0.484000	0.47621|0.47621	GGA|TGG	.	.		0.637	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
PABPN1L	390748	hgsc.bcm.edu	37	16	88932215	88932215	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:88932215C>T	ENST00000419291.2	-	2	401	c.390G>A	c.(388-390)gtG>gtA	p.V130V	PABPN1L_ENST00000411789.2_Splice_Site_p.V130V|PABPN1L_ENST00000378358.4_Splice_Site_p.V130V|PABPN1L_ENST00000427766.1_Splice_Site_p.V130V	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	130						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						GGTTCCTACCCACGGTCTCAG	0.667																																					p.V130V		Atlas-SNP	.											.	PABPN1L	25	.	0			c.G390A						.						23.0	28.0	26.0					16																	88932215		1991	4153	6144	SO:0001630	splice_region_variant	390748	exon2			CCTACCCACGGTC		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.391+1G>A	chr16.hg19:g.88932215C>T		198.0	0.0		124.0	5.0	NM_001080487	A1L3B3|A2VDI2	Silent	SNP	ENST00000419291.2	hg19	CCDS45547.2																																																																																			.	.		0.667	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	Silent
SPG7	6687	hgsc.bcm.edu	37	16	89616941	89616941	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:89616941A>G	ENST00000268704.2	+	13	1718	c.1703A>G	c.(1702-1704)cAg>cGg	p.Q568R		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	568					anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		AAGGAAGAACAGAAAGTGGTT	0.592																																					p.Q568R		Atlas-SNP	.											.	SPG7	75	.	0			c.A1703G						.						116.0	107.0	110.0					16																	89616941		2198	4300	6498	SO:0001583	missense	6687	exon13			AAGAACAGAAAGT	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1703A>G	chr16.hg19:g.89616941A>G	ENSP00000268704:p.Gln568Arg	100.0	0.0		78.0	4.0	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	hg19	CCDS10977.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.222|1.222	-0.626757|-0.626757	0.03610|0.03610	.|.	.|.	ENSG00000197912|ENSG00000197912	ENST00000268704|ENST00000312613	T|.	0.80909|.	-1.43|.	5.84|5.84	3.53|3.53	0.40419|0.40419	Peptidase M41 (1);Peptidase M41, FtsH (2);|.	0.160396|.	0.56097|.	N|.	0.000027|.	T|T	0.07279|0.07279	0.0184|0.0184	N|N	0.00034|0.00034	-2.565|-2.565	0.80722|0.80722	D|D	1|1	B|.	0.06786|.	0.001|.	B|.	0.06405|.	0.002|.	T|T	0.10706|0.10706	-1.0618|-1.0618	10|6	0.06757|0.87932	T|D	0.87|0	.|.	3.2925|3.2925	0.06954|0.06954	0.5682:0.0:0.2664:0.1654|0.5682:0.0:0.2664:0.1654	.|.	568|.	Q9UQ90|.	SPG7_HUMAN|.	R|G	568|160	ENSP00000268704:Q568R|.	ENSP00000268704:Q568R|ENSP00000310320:R160G	Q|R	+|+	2|1	0|2	SPG7|SPG7	88144442|88144442	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.310000|0.310000	0.27922|0.27922	3.457000|3.457000	0.53007|0.53007	1.052000|1.052000	0.40392|0.40392	0.459000|0.459000	0.35465|0.35465	CAG|AGA	.	.		0.592	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
DEF8	54849	hgsc.bcm.edu	37	16	90023996	90023996	+	Silent	SNP	C	C	A	rs377269615		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr16:90023996C>A	ENST00000268676.7	+	5	572	c.483C>A	c.(481-483)ccC>ccA	p.P161P	DEF8_ENST00000418391.2_Silent_p.P100P|DEF8_ENST00000563594.1_Silent_p.P100P|DEF8_ENST00000569453.1_Silent_p.P100P|DEF8_ENST00000570182.1_Silent_p.P90P|DEF8_ENST00000563795.1_Silent_p.P100P|DEF8_ENST00000567874.1_Silent_p.P40P	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	161					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		TGGAGCTGCCCGAGCAGTCGG	0.682																																					p.P161P		Atlas-SNP	.											.	DEF8	28	.	0			c.C483A						.						33.0	29.0	31.0					16																	90023996		2188	4291	6479	SO:0001819	synonymous_variant	54849	exon5			GCTGCCCGAGCAG	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.483C>A	chr16.hg19:g.90023996C>A		421.0	0.0		273.0	232.0	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	hg19	CCDS10989.1																																																																																			.	.		0.682	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
INPP5K	51763	hgsc.bcm.edu	37	17	1399994	1399994	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:1399994G>T	ENST00000421807.2	-	9	1455	c.1067C>A	c.(1066-1068)cCc>cAc	p.P356H	INPP5K_ENST00000320345.6_Missense_Mutation_p.P280H|INPP5K_ENST00000397335.3_Missense_Mutation_p.P264H|INPP5K_ENST00000542125.1_Missense_Mutation_p.P260H|INPP5K_ENST00000406424.4_Missense_Mutation_p.P280H	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	356	Required for ruffle localization.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						CGGGCTGCTGGGGAAGTCCGA	0.582																																					p.P356H		Atlas-SNP	.											.	INPP5K	30	.	0			c.C1067A						.						132.0	108.0	116.0					17																	1399994		2203	4300	6503	SO:0001583	missense	51763	exon9			CTGCTGGGGAAGT		CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"""skeletal muscle and kidney enriched inositol phosphatase"""	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.1067C>A	chr17.hg19:g.1399994G>T	ENSP00000413937:p.Pro356His	165.0	0.0		145.0	6.0	NM_016532	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Missense_Mutation	SNP	ENST00000421807.2	hg19	CCDS11004.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.116506	0.37339	.	.	ENSG00000132376	ENST00000421807;ENST00000406424;ENST00000350761;ENST00000320345;ENST00000397335;ENST00000542125	D;D;D;D	0.97906	-4.6;-4.6;-4.54;-4.49	5.85	-1.1	0.09872	.	1.048160	0.07457	N	0.899909	D	0.93514	0.7930	L	0.31926	0.97	0.26738	N	0.970452	B;B	0.14438	0.01;0.003	B;B	0.10450	0.004;0.005	D	0.85590	0.1245	10	0.41790	T	0.15	-2.9489	3.4814	0.07603	0.3146:0.0:0.279:0.4063	.	260;356	F5GXZ0;Q9BT40	.;INP5K_HUMAN	H	280;280;356;280;264;260	ENSP00000385177:P280H;ENSP00000318476:P280H;ENSP00000380496:P264H;ENSP00000440147:P260H	ENSP00000318476:P280H	P	-	2	0	INPP5K	1346744	0.991000	0.36638	0.996000	0.52242	0.891000	0.51852	0.109000	0.15417	-0.125000	0.11703	0.650000	0.86243	CCC	.	.		0.582	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4		
DPH1	1801	hgsc.bcm.edu	37	17	1943643	1943643	+	Missense_Mutation	SNP	G	G	A	rs201983229		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:1943643G>A	ENST00000263083.6	+	8	941	c.896G>A	c.(895-897)cGc>cAc	p.R299H	OVCA2_ENST00000572195.1_5'Flank|DPH1_ENST00000570477.1_Missense_Mutation_p.R219H|RP11-667K14.4_ENST00000572404.1_RNA	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	299					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						ACTTTGGGCCGCCAGGGCAGT	0.602																																					p.R299H		Atlas-SNP	.											.	DPH1	32	.	0			c.G896A						.	G	HIS/ARG	2,3900		0,2,1949	49.0	50.0	49.0		896	5.1	1.0	17		49	0,8312		0,0,4156	yes	missense	DPH1	NM_001383.3	29	0,2,6105	AA,AG,GG		0.0,0.0513,0.0164	probably-damaging	299/444	1943643	2,12212	1951	4156	6107	SO:0001583	missense	1801	exon8			TGGGCCGCCAGGG	S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"""ovarian tumor suppressor candidate 1"""	603527	"""diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)"", ""DPH-like 1 (S. cerevisiae)"", ""DPH1 homolog (S. cerevisiae)"""	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.896G>A	chr17.hg19:g.1943643G>A	ENSP00000263083:p.Arg299His	76.0	0.0		86.0	4.0	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	hg19	CCDS42228.1	.	.	.	.	.	.	.	.	.	.	G	32	5.139864	0.94560	5.13E-4	0.0	ENSG00000108963	ENST00000263083	T	0.50548	0.74	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.71476	0.3344	M	0.89785	3.06	0.80722	D	1	D;D;D	0.67145	0.996;0.996;0.992	P;P;P	0.58928	0.848;0.848;0.848	T	0.79160	-0.1918	10	0.72032	D	0.01	-16.2111	17.1373	0.86743	0.0:0.0:1.0:0.0	.	309;309;299	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	H	299	ENSP00000263083:R299H	ENSP00000263083:R299H	R	+	2	0	DPH1	1890393	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.384000	0.79751	2.380000	0.81148	0.491000	0.48974	CGC	.	.		0.602	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
ZFP3	124961	hgsc.bcm.edu	37	17	4995559	4995559	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:4995559G>T	ENST00000318833.3	+	2	1096	c.760G>T	c.(760-762)Gaa>Taa	p.E254*		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	254					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						GAAACCATATGAATGTAATGA	0.393																																					p.E254X		Atlas-SNP	.											.	ZFP3	54	.	0			c.G760T						.						64.0	65.0	65.0					17																	4995559		2203	4300	6503	SO:0001587	stop_gained	124961	exon2			CCATATGAATGTA	BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"""Zinc fingers, C2H2-type"""	12861	protein-coding gene	gene with protein product		194480	"""zinc finger protein homologous to Zfp-3 in mouse"", ""zinc finger protein 3 homolog (mouse)"""				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.760G>T	chr17.hg19:g.4995559G>T	ENSP00000320347:p.Glu254*	54.0	0.0		69.0	4.0	NM_153018	A5PLL4	Nonsense_Mutation	SNP	ENST00000318833.3	hg19	CCDS11067.1	.	.	.	.	.	.	.	.	.	.	G	35	5.530654	0.96446	.	.	ENSG00000180787	ENST00000318833	.	.	.	3.93	2.96	0.34315	.	0.000000	0.37437	N	0.002089	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-15.6006	6.2313	0.20736	0.2204:0.0:0.7796:0.0	.	.	.	.	X	254	.	ENSP00000320347:E254X	E	+	1	0	ZFP3	4936283	0.000000	0.05858	0.771000	0.31576	0.971000	0.66376	-1.015000	0.03637	1.247000	0.43917	0.563000	0.77884	GAA	.	.		0.393	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018	
SLC13A5	284111	hgsc.bcm.edu	37	17	6597477	6597477	+	Silent	SNP	G	G	T	rs139660928		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:6597477G>T	ENST00000433363.2	-	8	1328	c.1095C>A	c.(1093-1095)acC>acA	p.T365T	SLC13A5_ENST00000293800.6_Silent_p.T348T|SLC13A5_ENST00000381074.4_Silent_p.T322T|SLC13A5_ENST00000573648.1_Silent_p.T365T	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	365					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)	p.T365T(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						TGAATAGCAGGGTGGCCACAA	0.522																																					p.T365T		Atlas-SNP	.											SLC13A5,NS,carcinoma,0,1	SLC13A5	57	.	1	Substitution - coding silent(1)	prostate(1)	c.C1095A						.						86.0	72.0	77.0					17																	6597477		2203	4300	6503	SO:0001819	synonymous_variant	284111	exon8			TAGCAGGGTGGCC	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"""Solute carriers"""	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.1095C>A	chr17.hg19:g.6597477G>T		65.0	0.0		80.0	4.0	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Silent	SNP	ENST00000433363.2	hg19	CCDS11079.1																																																																																			.	G|1.000;C|0.000		0.522	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550	
DLG4	1742	hgsc.bcm.edu	37	17	7097797	7097797	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:7097797T>C	ENST00000399506.2	-	12	1510	c.1319A>G	c.(1318-1320)gAc>gGc	p.D440G	DLG4_ENST00000302955.6_Missense_Mutation_p.D437G|DLG4_ENST00000399510.2_Missense_Mutation_p.D483G			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	440	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	CTTGGTCTTGTCGTAATCAAA	0.602																																					p.D483G		Atlas-SNP	.											.	DLG4	110	.	0			c.A1448G						.						32.0	37.0	36.0					17																	7097797		2067	4218	6285	SO:0001583	missense	1742	exon14			GTCTTGTCGTAAT	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1319A>G	chr17.hg19:g.7097797T>C	ENSP00000382425:p.Asp440Gly	56.0	0.0		56.0	4.0	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	hg19		.	.	.	.	.	.	.	.	.	.	T	27.3	4.815425	0.90790	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.50813	0.73;0.73;0.73	5.3	5.3	0.74995	Src homology-3 domain (4);	.	.	.	.	T	0.73984	0.3657	M	0.91561	3.22	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.989	D;D;D;D	0.91635	0.994;0.98;0.999;0.995	T	0.79964	-0.1581	9	0.66056	D	0.02	.	13.2525	0.60060	0.0:0.0:0.0:1.0	.	480;440;437;483	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	G	440;437;483;483;380;483	ENSP00000382425:D440G;ENSP00000307471:D437G;ENSP00000382428:D483G	ENSP00000293813:D483G	D	-	2	0	DLG4	7038521	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	6.077000	0.71275	2.235000	0.73313	0.533000	0.62120	GAC	.	.		0.602	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365	
DNAH9	1770	hgsc.bcm.edu	37	17	11661007	11661007	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:11661007C>T	ENST00000262442.4	+	35	7061	c.6993C>T	c.(6991-6993)acC>acT	p.T2331T	DNAH9_ENST00000454412.2_Silent_p.T2331T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2331	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CACTCAGAACCAGGTAGGCCA	0.463																																					p.T2331T		Atlas-SNP	.											.	DNAH9	695	.	0			c.C6993T						.						84.0	72.0	77.0					17																	11661007		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon35			CAGAACCAGGTAG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6993C>T	chr17.hg19:g.11661007C>T		148.0	0.0		143.0	6.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.		0.463	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ELAC2	60528	hgsc.bcm.edu	37	17	12899257	12899257	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:12899257C>A	ENST00000338034.4	-	18	1937	c.1698G>T	c.(1696-1698)ttG>ttT	p.L566F	ELAC2_ENST00000426905.3_Splice_Site_p.L526F|ELAC2_ENST00000395962.2_Splice_Site_p.L547F	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	566					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CCACACTTACCAAGGCGCGTT	0.557																																					p.L566F		Atlas-SNP	.											.	ELAC2	48	.	0			c.G1698T						.						89.0	67.0	75.0					17																	12899257		2203	4299	6502	SO:0001630	splice_region_variant	60528	exon18			ACTTACCAAGGCG	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1698+1G>T	chr17.hg19:g.12899257C>A		74.0	0.0		80.0	4.0	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.657201	0.29425	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962;ENST00000457438	T;T;T	0.76578	-1.03;-1.03;-1.03	5.17	5.17	0.71159	Beta-lactamase-like (1);	0.067543	0.64402	D	0.000010	T	0.71600	0.3359	L	0.29908	0.895	0.80722	D	1	B;B;B;B;B;B;B;B	0.31625	0.107;0.012;0.284;0.012;0.107;0.332;0.031;0.019	B;B;B;B;B;B;B;B	0.38954	0.152;0.034;0.188;0.021;0.152;0.286;0.092;0.037	T	0.67082	-0.5760	9	.	.	.	-19.2864	16.2022	0.82088	0.0:1.0:0.0:0.0	.	526;549;547;364;566;326;551;194	B4DPL9;E9PGJ0;G5E9D5;E7ES68;Q9BQ52;B3KSU9;B4DT15;Q9BQ52-3	.;.;.;.;RNZ2_HUMAN;.;.;.	F	526;566;547;244	ENSP00000405223:L526F;ENSP00000337445:L566F;ENSP00000379291:L547F	.	L	-	3	2	ELAC2	12839982	1.000000	0.71417	0.997000	0.53966	0.178000	0.23041	3.229000	0.51278	2.688000	0.91661	0.591000	0.81541	TTG	.	.		0.557	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		Missense_Mutation
CDRT15	146822	hgsc.bcm.edu	37	17	14139241	14139241	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:14139241A>G	ENST00000420162.2	-	3	514	c.499T>C	c.(499-501)Tgg>Cgg	p.W167R	CDRT15_ENST00000431716.2_Missense_Mutation_p.W101R	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	167										endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		ACCCGCATCCATGCCTGGAGG	0.612																																					p.W167R		Atlas-SNP	.											.	CDRT15	20	.	0			c.T499C						.						12.0	12.0	12.0					17																	14139241		1993	3893	5886	SO:0001583	missense	146822	exon3			GCATCCATGCCTG	AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.499T>C	chr17.hg19:g.14139241A>G	ENSP00000402355:p.Trp167Arg	311.0	0.0		357.0	81.0	NM_001007530	B2RUU5	Missense_Mutation	SNP	ENST00000420162.2	hg19	CCDS32569.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.962593	0.00461	.	.	ENSG00000223510	ENST00000431716;ENST00000420162	T	0.57907	0.37	.	.	.	.	.	.	.	.	T	0.42200	0.1192	N	0.14661	0.345	0.09310	N	1	D	0.54397	0.966	P	0.55667	0.781	T	0.32052	-0.9921	7	0.24483	T	0.36	.	.	.	.	.	167	Q96T59	CDRTF_HUMAN	R	101;167	ENSP00000402355:W167R	ENSP00000402355:W167R	W	-	1	0	CDRT15	14079966	0.019000	0.18553	0.011000	0.14972	0.011000	0.07611	0.140000	0.16056	0.103000	0.17682	0.102000	0.15555	TGG	.	.		0.612	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	
FAM83G	644815	hgsc.bcm.edu	37	17	18881095	18881095	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:18881095A>G	ENST00000388995.6	-	5	2107	c.1884T>C	c.(1882-1884)ccT>ccC	p.P628P	SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|FAM83G_ENST00000345041.4_Silent_p.P628P|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395643.2_Intron|FAM83G_ENST00000585154.2_Silent_p.P628P			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	628					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						GCCTCCGGAGAGGGACTGAGT	0.667																																					p.P628P		Atlas-SNP	.											.	FAM83G	51	.	0			c.T1884C						.						32.0	38.0	36.0					17																	18881095		2022	4180	6202	SO:0001819	synonymous_variant	644815	exon5			CCGGAGAGGGACT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.1884T>C	chr17.hg19:g.18881095A>G		65.0	0.0		86.0	4.0	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	hg19	CCDS42276.1																																																																																			.	.		0.667	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
SEZ6	124925	hgsc.bcm.edu	37	17	27286199	27286199	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:27286199C>T	ENST00000317338.12	-	10	2379	c.1951G>A	c.(1951-1953)Ggg>Agg	p.G651R	SEZ6_ENST00000442608.3_Missense_Mutation_p.G651R|SEZ6_ENST00000360295.9_Missense_Mutation_p.G651R|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	651	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	29	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			AGGTCATCCCCATCATAGAAG	0.612																																					p.G651R		Atlas-SNP	.											.	SEZ6	61	.	0			c.G1951A						.						39.0	44.0	42.0					17																	27286199		1946	4142	6088	SO:0001583	missense	124925	exon10			CATCCCCATCATA	AY038048	CCDS45638.1, CCDS45639.1	17q11.2	2008-03-06	2001-11-28		ENSG00000063015	ENSG00000063015			15955	protein-coding gene	gene with protein product			"""seizure related gene 6 (mouse) homolog"""			17086543	Standard	NM_178860		Approved		uc002hdp.2	Q53EL9	OTTHUMG00000168010	ENST00000317338.12:c.1951G>A	chr17.hg19:g.27286199C>T	ENSP00000312942:p.Gly651Arg	76.0	0.0		97.0	4.0	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	hg19	CCDS45639.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.627003	0.87560	.	.	ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381	T;T	0.26957	1.7;1.7	4.82	4.82	0.62117	CUB (5);	0.000000	0.85682	D	0.000000	T	0.58495	0.2126	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79784	0.982;0.993	T	0.67364	-0.5689	10	0.87932	D	0	.	15.8044	0.78481	0.0:1.0:0.0:0.0	.	651;651	Q53EL9-3;Q53EL9	.;SEZ6_HUMAN	R	651;651;526;651	ENSP00000403784:G651R;ENSP00000353440:G651R	ENSP00000312942:G526R	G	-	1	0	SEZ6	24310325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.680000	0.91292	0.655000	0.94253	GGG	.	.		0.612	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
TP53I13	90313	hgsc.bcm.edu	37	17	27896100	27896100	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:27896100C>T	ENST00000301057.7	+	2	252	c.137C>T	c.(136-138)cCg>cTg	p.P46L	RP11-68I3.4_ENST00000579050.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA|ABHD15_ENST00000307201.4_5'Flank	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	46						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		CCTCTGCCTCCGCAGGTAGGA	0.662																																					p.P46L		Atlas-SNP	.											.	TP53I13	17	.	0			c.C137T						.						10.0	14.0	13.0					17																	27896100		1982	4152	6134	SO:0001583	missense	90313	exon2			TGCCTCCGCAGGT	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.137C>T	chr17.hg19:g.27896100C>T	ENSP00000301057:p.Pro46Leu	27.0	0.0		80.0	4.0	NM_138349	Q7L5U3	Missense_Mutation	SNP	ENST00000301057.7	hg19	CCDS42289.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.074611	0.36566	.	.	ENSG00000167543	ENST00000301057	.	.	.	5.1	1.35	0.21983	.	0.576450	0.16267	N	0.221980	T	0.59088	0.2168	M	0.65975	2.015	0.46241	D	0.998941	D	0.57899	0.981	P	0.48063	0.565	T	0.63668	-0.6585	9	0.66056	D	0.02	-1.4311	10.6249	0.45502	0.5919:0.4081:0.0:0.0	.	46	Q8NBR0	P5I13_HUMAN	L	46	.	ENSP00000301057:P46L	P	+	2	0	TP53I13	24920226	0.004000	0.15560	1.000000	0.80357	0.599000	0.36880	0.057000	0.14279	0.630000	0.30394	0.456000	0.33151	CCG	.	.		0.662	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349	
NF1	4763	hgsc.bcm.edu	37	17	29676237	29676237	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:29676237A>G	ENST00000358273.4	+	49	7672	c.7289A>G	c.(7288-7290)gAa>gGa	p.E2430G	NF1_ENST00000444181.2_Missense_Mutation_p.E223G|NF1_ENST00000417592.2_Missense_Mutation_p.E143G|NF1_ENST00000356175.3_Missense_Mutation_p.E2409G	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2430					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GACAAATTTGAAGTGAATACA	0.353			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.E2430G		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.A7289G						.						89.0	81.0	84.0					17																	29676237		2203	4300	6503	SO:0001583	missense	4763	exon49	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	AATTTGAAGTGAA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7289A>G	chr17.hg19:g.29676237A>G	ENSP00000351015:p.Glu2430Gly	66.0	0.0		72.0	5.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.822818	0.90873	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181;ENST00000417592	T;T;T;T	0.66815	2.97;3.12;2.8;-0.23	5.78	5.78	0.91487	Armadillo-type fold (1);	0.114676	0.64402	D	0.000020	T	0.81024	0.4737	M	0.73962	2.25	0.58432	D	0.999999	D;D	0.63046	0.989;0.992	D;P	0.72982	0.979;0.864	T	0.80480	-0.1364	10	0.38643	T	0.18	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	2409;2430	P21359-2;P21359	.;NF1_HUMAN	G	2430;2409;2075;223;143	ENSP00000351015:E2430G;ENSP00000348498:E2409G;ENSP00000389907:E2075G;ENSP00000396481:E223G	ENSP00000348498:E2409G	E	+	2	0	NF1	26700363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.564000	0.90726	2.220000	0.72140	0.533000	0.62120	GAA	.	.		0.353	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
C17orf75	64149	hgsc.bcm.edu	37	17	30666839	30666839	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:30666839C>A	ENST00000577809.1	-	3	389	c.340G>T	c.(340-342)Gag>Tag	p.E114*	RP11-227G15.3_ENST00000581915.1_RNA|C17orf75_ENST00000225805.4_Nonsense_Mutation_p.E114*	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	114										ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TACTTTAGCTCCACAGATGCA	0.433																																					p.E114X		Atlas-SNP	.											.	C17orf75	23	.	0			c.G340T						.						149.0	145.0	146.0					17																	30666839		1933	4139	6072	SO:0001587	stop_gained	64149	exon3			TTAGCTCCACAGA	AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.340G>T	chr17.hg19:g.30666839C>A	ENSP00000464275:p.Glu114*	82.0	0.0		88.0	4.0	NM_022344	Q7Z2H4	Nonsense_Mutation	SNP	ENST00000577809.1	hg19	CCDS58537.1	.	.	.	.	.	.	.	.	.	.	C	34	5.381196	0.95945	.	.	ENSG00000108666	ENST00000225805	.	.	.	5.68	4.71	0.59529	.	0.098652	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-27.107	14.5631	0.68153	0.0:0.9298:0.0:0.0702	.	.	.	.	X	114	.	ENSP00000225805:E114X	E	-	1	0	C17orf75	27690952	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.265000	0.78442	1.396000	0.46663	0.650000	0.86243	GAG	.	.		0.433	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1	NM_022344	
LIG3	3980	hgsc.bcm.edu	37	17	33319691	33319691	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:33319691A>G	ENST00000378526.4	+	8	1568	c.1435A>G	c.(1435-1437)Aca>Gca	p.T479A	LIG3_ENST00000262327.5_Missense_Mutation_p.T479A	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	479					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	CTCGCTGATGACACCTGTGCA	0.607								Other BER factors																													p.T479A		Atlas-SNP	.											.	LIG3	164	.	0			c.A1435G						.						52.0	43.0	46.0					17																	33319691		2203	4300	6503	SO:0001583	missense	3980	exon8			CTGATGACACCTG		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"""ligase II, DNA, ATP-dependent"""	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.1435A>G	chr17.hg19:g.33319691A>G	ENSP00000367787:p.Thr479Ala	89.0	0.0		95.0	4.0	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	A	28.8	4.953740	0.92660	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	T;T	0.18810	2.19;2.19	5.5	5.5	0.81552	DNA ligase, ATP-dependent, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.38799	0.1054	M	0.73962	2.25	0.80722	D	1	P;P;P	0.45283	0.855;0.855;0.855	P;P;P	0.51355	0.667;0.667;0.667	T	0.18461	-1.0336	10	0.54805	T	0.06	-20.6633	14.9457	0.71029	1.0:0.0:0.0:0.0	.	479;479;479	E5KLB5;P49916;E5KLB6	.;DNLI3_HUMAN;.	A	479	ENSP00000367787:T479A;ENSP00000262327:T479A	ENSP00000262327:T479A	T	+	1	0	LIG3	30343804	1.000000	0.71417	0.978000	0.43139	0.955000	0.61496	8.914000	0.92735	2.308000	0.77769	0.533000	0.62120	ACA	.	.		0.607	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975	
GAS2L2	246176	hgsc.bcm.edu	37	17	34074044	34074044	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:34074044G>T	ENST00000254466.6	-	5	1103	c.1076C>A	c.(1075-1077)cCa>cAa	p.P359Q	GAS2L2_ENST00000587565.1_Missense_Mutation_p.P343Q	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	359					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTCAGGAATGGTGCCATCTC	0.587																																					p.P359Q		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C1076A						.						46.0	50.0	49.0					17																	34074044		2203	4300	6503	SO:0001583	missense	246176	exon5			AGGAATGGTGCCA	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1076C>A	chr17.hg19:g.34074044G>T	ENSP00000254466:p.Pro359Gln	86.0	0.0		80.0	5.0	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	hg19	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.098403	0.37048	.	.	ENSG00000132139	ENST00000254466	T	0.19938	2.11	4.54	3.57	0.40892	.	0.492528	0.18269	N	0.146396	T	0.22704	0.0548	L	0.56769	1.78	0.09310	N	1	P	0.44578	0.838	B	0.42422	0.387	T	0.11397	-1.0589	10	0.66056	D	0.02	-0.9574	8.404	0.32603	0.1065:0.0:0.8935:0.0	.	359	Q8NHY3	GA2L2_HUMAN	Q	359	ENSP00000254466:P359Q	ENSP00000254466:P359Q	P	-	2	0	GAS2L2	31098157	0.031000	0.19500	0.001000	0.08648	0.259000	0.26198	2.704000	0.47118	1.264000	0.44198	0.313000	0.20887	CCA	.	.		0.587	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
LHX1	3975	hgsc.bcm.edu	37	17	35300345	35300345	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:35300345T>C	ENST00000254457.5	+	5	2549	c.1138T>C	c.(1138-1140)Tcg>Ccg	p.S380P	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	380					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				CCCGCCCTTCTCGTCGCTGTC	0.716																																					p.S380P		Atlas-SNP	.											.	LHX1	48	.	0			c.T1138C						.						14.0	16.0	15.0					17																	35300345		2183	4260	6443	SO:0001583	missense	3975	exon5			CCCTTCTCGTCGC	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"""Homeoboxes / LIM class"""	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.1138T>C	chr17.hg19:g.35300345T>C	ENSP00000254457:p.Ser380Pro	68.0	0.0		82.0	5.0	NM_005568	Q3MIW0	Missense_Mutation	SNP	ENST00000254457.5	hg19	CCDS11316.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.110911	0.37242	.	.	ENSG00000132130	ENST00000254457	D	0.90676	-2.71	4.73	4.73	0.59995	.	0.075094	0.53938	D	0.000052	D	0.84106	0.5399	L	0.27053	0.805	0.44142	D	0.996931	B	0.06786	0.001	B	0.06405	0.002	T	0.79427	-0.1808	10	0.27785	T	0.31	.	14.3888	0.66963	0.0:0.0:0.0:1.0	.	380	P48742	LHX1_HUMAN	P	380	ENSP00000254457:S380P	ENSP00000254457:S380P	S	+	1	0	LHX1	32374458	1.000000	0.71417	0.991000	0.47740	0.933000	0.57130	4.015000	0.57152	1.988000	0.58038	0.459000	0.35465	TCG	.	.		0.716	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568	
HNF1B	6928	hgsc.bcm.edu	37	17	36070598	36070598	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:36070598G>T	ENST00000225893.4	-	5	1480	c.1119C>A	c.(1117-1119)gcC>gcA	p.A373A	HNF1B_ENST00000561193.1_Silent_p.A347A|HNF1B_ENST00000427275.2_Silent_p.A347A|HNF1B_ENST00000560016.1_Silent_p.A373A	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	373					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|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 initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			TGGTCACCATGGCGCTGTTGC	0.537																																					p.A373A	Colon(71;102 1179 9001 27917 43397)	Atlas-SNP	.											.	HNF1B	61	.	0			c.C1119A						.						79.0	71.0	74.0					17																	36070598		2203	4300	6503	SO:0001819	synonymous_variant	6928	exon5			CACCATGGCGCTG	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"""Homeoboxes / HNF class"""	11630	protein-coding gene	gene with protein product		189907	"""transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"""	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.1119C>A	chr17.hg19:g.36070598G>T		102.0	0.0		96.0	4.0	NM_000458	B4DKM3|E0YMJ9	Silent	SNP	ENST00000225893.4	hg19	CCDS11324.1																																																																																			.	.		0.537	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458	
HNF1B	6928	hgsc.bcm.edu	37	17	36091619	36091619	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:36091619G>A	ENST00000225893.4	-	4	1373	c.1012C>T	c.(1012-1014)Cag>Tag	p.Q338*	HNF1B_ENST00000561193.1_Nonsense_Mutation_p.Q312*|HNF1B_ENST00000427275.2_Nonsense_Mutation_p.Q312*|HNF1B_ENST00000560016.1_Nonsense_Mutation_p.Q338*	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	338					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|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 initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GAGCTGGGCTGGTGGTGGGGG	0.592																																					p.Q338X	Colon(71;102 1179 9001 27917 43397)	Atlas-SNP	.											.	HNF1B	61	.	0			c.C1012T						.						78.0	60.0	66.0					17																	36091619		2203	4300	6503	SO:0001587	stop_gained	6928	exon4			TGGGCTGGTGGTG	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"""Homeoboxes / HNF class"""	11630	protein-coding gene	gene with protein product		189907	"""transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"""	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.1012C>T	chr17.hg19:g.36091619G>A	ENSP00000225893:p.Gln338*	421.0	0.0		431.0	174.0	NM_000458	B4DKM3|E0YMJ9	Nonsense_Mutation	SNP	ENST00000225893.4	hg19	CCDS11324.1	.	.	.	.	.	.	.	.	.	.	G	38	7.176410	0.98114	.	.	ENSG00000108753	ENST00000225893;ENST00000427275;ENST00000544593;ENST00000539087	.	.	.	5.2	5.2	0.72013	.	0.163295	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-1.8848	17.4606	0.87619	0.0:0.0:1.0:0.0	.	.	.	.	X	338;312;338;226	.	ENSP00000225893:Q338X	Q	-	1	0	HNF1B	33165732	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.155000	0.94700	2.713000	0.92767	0.650000	0.86243	CAG	.	.		0.592	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458	
PIP4K2B	8396	hgsc.bcm.edu	37	17	36935671	36935671	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:36935671G>A	ENST00000269554.3	-	5	1099	c.619C>T	c.(619-621)Cat>Tat	p.H207Y	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	207	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GTGAGCCGATGGCTGAACACG	0.567																																					p.H207Y		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.C619T						.						183.0	139.0	154.0					17																	36935671		2203	4300	6503	SO:0001583	missense	8396	exon5			GCCGATGGCTGAA	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.619C>T	chr17.hg19:g.36935671G>A	ENSP00000269554:p.His207Tyr	74.0	0.0		98.0	4.0	NM_003559	Q5U0E8|Q8TBP2	Missense_Mutation	SNP	ENST00000269554.3	hg19	CCDS11329.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092795	0.76756	.	.	ENSG00000141720	ENST00000269554;ENST00000311500	T	0.30182	1.54	4.92	4.92	0.64577	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.60143	0.2246	M	0.87180	2.865	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.988	D;D;P	0.67382	0.951;0.918;0.871	T	0.66352	-0.5945	10	0.54805	T	0.06	-14.8159	16.8353	0.85955	0.0:0.0:1.0:0.0	.	207;207;207	C9JMM2;P78356-2;P78356	.;.;PI42B_HUMAN	Y	207	ENSP00000269554:H207Y	ENSP00000269554:H207Y	H	-	1	0	PIP4K2B	34189197	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.259000	0.95561	2.546000	0.85860	0.655000	0.94253	CAT	.	.		0.567	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	
TOP2A	7153	hgsc.bcm.edu	37	17	38561112	38561112	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:38561112A>G	ENST00000423485.1	-	17	2135	c.1977T>C	c.(1975-1977)gaT>gaC	p.D659D		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	659					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCTTTCGATCATCTATCTGTT	0.343																																					p.D659D		Atlas-SNP	.											.	TOP2A	124	.	0			c.T1977C						.						82.0	73.0	76.0					17																	38561112		1811	4077	5888	SO:0001819	synonymous_variant	7153	exon17			TCGATCATCTATC		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.1977T>C	chr17.hg19:g.38561112A>G		68.0	0.0		68.0	4.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.343	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39279994	39279994	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:39279994T>C	ENST00000394014.1	-	1	425	c.381A>G	c.(379-381)agA>agG	p.R127R		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	127	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].		Missing (in allele KAP4.12-v1). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcactggggtctgcagcagc	0.667																																					p.R127R		Atlas-SNP	.											KRTAP4-12,NS,carcinoma,0,1	KRTAP4-12	32	.	0			c.A381G						.						19.0	26.0	23.0					17																	39279994		2126	4172	6298	SO:0001819	synonymous_variant	83755	exon1			CTGGGGTCTGCAG	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.381A>G	chr17.hg19:g.39279994T>C		84.0	2.0		121.0	5.0	NM_031854	A3KMC5|Q495I0	Silent	SNP	ENST00000394014.1	hg19	CCDS32649.1																																																																																			.	.		0.667	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
DHX58	79132	hgsc.bcm.edu	37	17	40255722	40255722	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40255722T>C	ENST00000251642.3	-	12	1880	c.1658A>G	c.(1657-1659)cAg>cGg	p.Q553R		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	553	Repressor domain.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GCAGAGTAGCTGCACGTGCTC	0.642																																					p.Q553R		Atlas-SNP	.											.	DHX58	39	.	0			c.A1658G						.						72.0	59.0	64.0					17																	40255722		2203	4300	6503	SO:0001583	missense	79132	exon12			AGTAGCTGCACGT	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"""RNA helicase LGP2"""	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1658A>G	chr17.hg19:g.40255722T>C	ENSP00000251642:p.Gln553Arg	54.0	0.0		81.0	4.0	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	hg19	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.624609	0.28889	.	.	ENSG00000108771	ENST00000251642	T	0.40225	1.04	5.72	-0.744	0.11101	C-terminal domain of RIG-I (1);	0.398185	0.25903	N	0.027544	T	0.27027	0.0662	L	0.36672	1.1	0.09310	N	0.999999	B;B	0.11235	0.004;0.001	B;B	0.09377	0.004;0.004	T	0.25293	-1.0136	10	0.15499	T	0.54	.	10.7752	0.46346	0.0:0.5459:0.0:0.4541	.	546;553	B7Z455;Q96C10	.;DHX58_HUMAN	R	553	ENSP00000251642:Q553R	ENSP00000251642:Q553R	Q	-	2	0	DHX58	37509248	0.215000	0.23574	0.277000	0.24703	0.788000	0.44548	0.035000	0.13797	-0.102000	0.12197	0.454000	0.30748	CAG	.	.		0.642	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119	
STAT5A	6776	hgsc.bcm.edu	37	17	40460208	40460208	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40460208T>C	ENST00000345506.4	+	17	2561	c.1919T>C	c.(1918-1920)cTg>cCg	p.L640P	STAT5A_ENST00000452307.2_Missense_Mutation_p.L637P|STAT5A_ENST00000588868.1_Missense_Mutation_p.L609P|STAT5A_ENST00000590949.1_Missense_Mutation_p.L640P|STAT5A_ENST00000546010.2_Missense_Mutation_p.L610P|STAT5A_ENST00000587646.1_Missense_Mutation_p.L128P	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	640	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GAACGCAACCTGTGGAACCTG	0.547																																					p.L640P		Atlas-SNP	.											.	STAT5A	49	.	0			c.T1919C						.						79.0	71.0	74.0					17																	40460208		2203	4300	6503	SO:0001583	missense	6776	exon17			GCAACCTGTGGAA	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"""SH2 domain containing"""	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1919T>C	chr17.hg19:g.40460208T>C	ENSP00000341208:p.Leu640Pro	144.0	0.0		149.0	6.0	NM_003152	Q1KLZ6	Missense_Mutation	SNP	ENST00000345506.4	hg19	CCDS11424.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.710982	0.68730	.	.	ENSG00000126561	ENST00000345506;ENST00000546010;ENST00000540577;ENST00000452307	D;D;D	0.88664	-2.41;-2.41;-2.41	5.06	5.06	0.68205	SH2 motif (4);	0.147903	0.46145	D	0.000306	D	0.88108	0.6348	N	0.11064	0.09	0.80722	D	1	D;D;D;P;D	0.69078	0.997;0.997;0.997;0.529;0.997	D;D;D;P;D	0.69142	0.938;0.958;0.938;0.489;0.962	D	0.90804	0.4696	10	0.87932	D	0	-19.3234	14.4833	0.67597	0.0:0.0:0.0:1.0	.	640;637;610;611;640	A8K6I5;Q8WWS9;Q1KLZ6;Q59GY7;P42229	.;.;.;.;STA5A_HUMAN	P	640;610;611;637	ENSP00000341208:L640P;ENSP00000443107:L610P;ENSP00000400320:L637P	ENSP00000341208:L640P	L	+	2	0	STAT5A	37713734	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	6.927000	0.75840	1.919000	0.55581	0.459000	0.35465	CTG	.	.		0.547	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152	
HSD17B1	3292	hgsc.bcm.edu	37	17	40706435	40706435	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40706435C>T	ENST00000585807.1	+	5	4272	c.552C>T	c.(550-552)atC>atT	p.I184I	RP11-400F19.8_ENST00000585572.1_RNA|HSD17B1_ENST00000225929.5_Silent_p.I185I|RP11-400F19.6_ENST00000590513.1_RNA	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	184					bone development (GO:0060348)|cellular response to metal ion (GO:0071248)|estrogen biosynthetic process (GO:0006703)|estrogen metabolic process (GO:0008210)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			NS(1)|endometrium(1)|kidney(1)|lung(2)	5		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Equilin(DB02187)	TGAGCCTGATCGAGTGCGGCC	0.677																																					p.I184I		Atlas-SNP	.											.	HSD17B1	24	.	0			c.C552T						.						29.0	26.0	27.0					17																	40706435		2203	4299	6502	SO:0001819	synonymous_variant	3292	exon5			CCTGATCGAGTGC		CCDS11428.1	17q11-q21	2011-09-14					1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5210	protein-coding gene	gene with protein product	"""Estradiol 17-beta-dehydrogenase-1"", ""short chain dehydrogenase/reductase family 28CE, member 1"""	109684		EDHB17, EDH17B2		2330005, 19027726	Standard	NM_000413		Approved	HSD17, MGC138140, SDR28C1	uc002hzw.3	P14061		ENST00000585807.1:c.552C>T	chr17.hg19:g.40706435C>T		39.0	0.0		60.0	4.0	NM_000413	B3KXS1|Q2M2L8	Silent	SNP	ENST00000585807.1	hg19	CCDS11428.1																																																																																			.	.		0.677	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413	
PLEKHH3	79990	hgsc.bcm.edu	37	17	40823547	40823547	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:40823547A>G	ENST00000591022.1	-	8	1493	c.1106T>C	c.(1105-1107)cTg>cCg	p.L369P	PLEKHH3_ENST00000293349.6_Missense_Mutation_p.L369P|PLEKHH3_ENST00000412503.1_Missense_Mutation_p.L369P|PLEKHH3_ENST00000456950.2_5'UTR	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	369	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ATATTCCGCCAGTTCCGAGTC	0.637																																					p.L369P		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.T1106C						.						17.0	19.0	18.0					17																	40823547		2203	4300	6503	SO:0001583	missense	79990	exon8			TCCGCCAGTTCCG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1106T>C	chr17.hg19:g.40823547A>G	ENSP00000468678:p.Leu369Pro	74.0	0.0		77.0	4.0	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Missense_Mutation	SNP	ENST00000591022.1	hg19	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.817898	0.90790	.	.	ENSG00000068137	ENST00000456950;ENST00000293349;ENST00000412503	D;D	0.92495	-3.05;-3.05	4.7	4.7	0.59300	MyTH4 domain (2);	0.000000	0.34156	N	0.004212	D	0.88500	0.6453	N	0.02539	-0.55	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.972	D	0.89265	0.3600	10	0.31617	T	0.26	-4.1834	13.8699	0.63612	1.0:0.0:0.0:0.0	.	369;369	Q7Z736-2;Q7Z736	.;PKHH3_HUMAN	P	31;369;369	ENSP00000293349:L369P;ENSP00000411885:L369P	ENSP00000293349:L369P	L	-	2	0	PLEKHH3	38077073	1.000000	0.71417	0.995000	0.50966	0.956000	0.61745	9.287000	0.95975	1.760000	0.52011	0.459000	0.35465	CTG	.	.		0.637	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
C17orf104	284071	hgsc.bcm.edu	37	17	42744141	42744141	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:42744141T>C	ENST00000409122.2	+	5	1004	c.862T>C	c.(862-864)Tac>Cac	p.Y288H	C17orf104_ENST00000359945.3_Missense_Mutation_p.Y288H|C17orf104_ENST00000409464.1_Missense_Mutation_p.Y122H	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	288										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						AGTTGATATCTACCATTATGG	0.353																																					p.Y288H		Atlas-SNP	.											.	C17orf104	75	.	0			c.T862C						.						38.0	37.0	37.0					17																	42744141		2203	4299	6502	SO:0001583	missense	284071	exon5			GATATCTACCATT		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.862T>C	chr17.hg19:g.42744141T>C	ENSP00000386452:p.Tyr288His	74.0	0.0		100.0	4.0	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	T	4.722	0.134328	0.09032	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000456912;ENST00000409464	T;T;T;T	0.49432	0.8;0.78;0.97;0.79	5.37	4.28	0.50868	.	0.090041	0.48286	D	0.000195	T	0.33527	0.0866	L	0.27053	0.805	0.34532	D	0.709362	B;B;P	0.34639	0.166;0.166;0.461	B;B;B	0.34873	0.191;0.191;0.191	T	0.50915	-0.8771	10	0.49607	T	0.09	-9.9905	9.589	0.39534	0.0:0.0798:0.0:0.9202	.	288;288;122	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	H	288;288;122;122;122	ENSP00000353028:Y288H;ENSP00000386452:Y288H;ENSP00000399809:Y122H;ENSP00000386586:Y122H	ENSP00000353028:Y288H	Y	+	1	0	C17orf104	40099667	1.000000	0.71417	0.985000	0.45067	0.503000	0.33858	3.577000	0.53885	2.149000	0.67028	0.377000	0.23210	TAC	.	.		0.353	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080	
ITGB3	3690	hgsc.bcm.edu	37	17	45368371	45368371	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:45368371T>C	ENST00000559488.1	+	9	1193	c.1177T>C	c.(1177-1179)Tct>Cct	p.S393P	ITGB3_ENST00000435993.2_Missense_Mutation_p.S346P|ITGB3_ENST00000571680.1_Missense_Mutation_p.S393P|ITGB3_ENST00000560629.1_Missense_Mutation_p.V381A	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	393					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	TGAAGAGTTGTCTCTATCCTT	0.493																																					p.S393P		Atlas-SNP	.											.	ITGB3	157	.	0			c.T1177C						.						142.0	121.0	129.0					17																	45368371		2203	4300	6503	SO:0001583	missense	3690	exon9			GAGTTGTCTCTAT		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1177T>C	chr17.hg19:g.45368371T>C	ENSP00000452786:p.Ser393Pro	92.0	0.0		113.0	5.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.086976	0.55861	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	T	0.67171	-0.25	5.33	5.33	0.75918	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.293457	0.38663	N	0.001615	T	0.79782	0.4505	M	0.73962	2.25	0.53688	D	0.999978	D;D	0.65815	0.995;0.99	D;P	0.64042	0.921;0.82	T	0.82454	-0.0449	10	0.72032	D	0.01	.	14.26	0.66078	0.0:0.0:0.0:1.0	.	393;393	P05106;Q2YFE1	ITB3_HUMAN;.	P	393;346	ENSP00000407801:S346P	ENSP00000262017:S393P	S	+	1	0	C17orf57	42723370	1.000000	0.71417	0.983000	0.44433	0.630000	0.37929	1.750000	0.38329	2.013000	0.59113	0.374000	0.22700	TCT	.	.		0.493	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
SP6	80320	hgsc.bcm.edu	37	17	45925602	45925602	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:45925602T>C	ENST00000536300.1	-	2	525	c.194A>G	c.(193-195)cAg>cGg	p.Q65R	SP6_ENST00000342234.2_Missense_Mutation_p.Q65R	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	65					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(5)|prostate(1)|skin(1)	8						CTCATAGCCCTGCGAGAAGTC	0.697																																					p.Q65R		Atlas-SNP	.											SP6,NS,carcinoma,0,1	SP6	26	.	0			c.A194G						.						14.0	17.0	16.0					17																	45925602		2187	4289	6476	SO:0001583	missense	80320	exon2			TAGCCCTGCGAGA		CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	14530	protein-coding gene	gene with protein product	"""epiprofin"""	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.194A>G	chr17.hg19:g.45925602T>C	ENSP00000438209:p.Gln65Arg	33.0	0.0		69.0	3.0	NM_001258248	B3KXS4	Missense_Mutation	SNP	ENST00000536300.1	hg19	CCDS11520.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.825497	0.50739	.	.	ENSG00000189120	ENST00000342234;ENST00000536300	T;T	0.07444	3.19;3.19	4.29	4.29	0.51040	.	0.000000	0.41194	D	0.000924	T	0.04815	0.0130	N	0.08118	0	0.35986	D	0.836369	P	0.41232	0.743	B	0.38056	0.264	T	0.50065	-0.8871	10	0.38643	T	0.18	.	12.5416	0.56174	0.0:0.0:0.0:1.0	.	65	Q3SY56	SP6_HUMAN	R	65	ENSP00000340799:Q65R;ENSP00000438209:Q65R	ENSP00000340799:Q65R	Q	-	2	0	SP6	43280601	1.000000	0.71417	0.956000	0.39512	0.862000	0.49288	3.150000	0.50662	1.799000	0.52666	0.379000	0.24179	CAG	.	.		0.697	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262	
ITGA3	3675	hgsc.bcm.edu	37	17	48166578	48166578	+	3'UTR	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:48166578C>A	ENST00000320031.8	+	0	3622				ITGA3_ENST00000007722.7_Silent_p.P1050P	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)						blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GCACCCTGCCCACCAAGAAGC	0.602																																					p.P1050P		Atlas-SNP	.											.	ITGA3	128	.	0			c.C3150A						.						130.0	114.0	119.0					17																	48166578		2203	4300	6503	SO:0001624	3_prime_UTR_variant	3675	exon25			CCTGCCCACCAAG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.*136C>A	chr17.hg19:g.48166578C>A		110.0	0.0		87.0	4.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	hg19	CCDS11558.1																																																																																			.	.		0.602	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
MPO	4353	hgsc.bcm.edu	37	17	56355209	56355209	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:56355209G>A	ENST00000225275.3	-	7	1359	c.1183C>T	c.(1183-1185)Cgc>Tgc	p.R395C	MPO_ENST00000578493.1_5'UTR|MPO_ENST00000340482.3_Missense_Mutation_p.R427C	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	395					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	CAGGGGATGCGCGCTGAGCGG	0.622																																					p.R395C		Atlas-SNP	.											.	MPO	114	.	0			c.C1183T						.						58.0	60.0	59.0					17																	56355209		2203	4300	6503	SO:0001583	missense	4353	exon7			GGATGCGCGCTGA		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1183C>T	chr17.hg19:g.56355209G>A	ENSP00000225275:p.Arg395Cys	38.0	0.0		37.0	15.0	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	hg19	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	G	4.434	0.080249	0.08533	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.73363	-0.74;-0.74	4.8	-0.804	0.10882	.	1.422290	0.03913	N	0.282206	T	0.71082	0.3298	L	0.56340	1.77	0.09310	N	1	B	0.16396	0.017	B	0.13407	0.009	T	0.59118	-0.7514	10	0.66056	D	0.02	-2.9074	10.6686	0.45745	0.0:0.3017:0.3917:0.3066	.	395	P05164	PERM_HUMAN	C	427;395	ENSP00000344419:R427C;ENSP00000225275:R395C	ENSP00000225275:R395C	R	-	1	0	MPO	53710208	0.000000	0.05858	0.037000	0.18230	0.157000	0.22087	-0.360000	0.07622	-0.244000	0.09639	-3.360000	0.00041	CGC	.	.		0.622	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1		
TRIM37	4591	hgsc.bcm.edu	37	17	57058078	57058078	+	IGR	SNP	T	T	C	rs267604972		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:57058078T>C	ENST00000393066.3	-	0	3622				PPM1E_ENST00000308249.2_Silent_p.L652L	NM_001005207.2	NP_001005207.1	O94972	TRI37_HUMAN	tripartite motif containing 37						aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					CTGTTCAGGGTTGGAAAATGA	0.453									Mulibrey Nanism				T|||	1	0.000199681	0.0008	0.0	5008	,	,		19193	0.0		0.0	False		,,,				2504	0.0				p.L652L		Atlas-SNP	.											.	PPM1E	97	.	0			c.T1954C						.						161.0	170.0	167.0					17																	57058078		2203	4300	6503	SO:0001628	intergenic_variant	22843	exon7	Familial Cancer Database	Perheentupa syndrome	TCAGGGTTGGAAA	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	7523	protein-coding gene	gene with protein product	"""RING-B-box-coiled-coil protein"""	605073	"""tripartite motif-containing 37"""	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972			chr17.hg19:g.57058078T>C		92.0	0.0		100.0	4.0	NM_014906	Q7Z3E6|Q8IYF7|Q8WYF7	Silent	SNP	ENST00000393066.3	hg19	CCDS45746.1																																																																																			.	.		0.453	TRIM37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445928.1	NM_015294	
BCAS3	54828	hgsc.bcm.edu	37	17	59024696	59024696	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:59024696G>T	ENST00000390652.5	+	14	1235	c.1204G>T	c.(1204-1206)Gga>Tga	p.G402*	BCAS3_ENST00000588462.1_Nonsense_Mutation_p.G402*|BCAS3_ENST00000588874.1_Nonsense_Mutation_p.G173*|BCAS3_ENST00000585744.1_Nonsense_Mutation_p.G173*|BCAS3_ENST00000408905.3_Nonsense_Mutation_p.G402*|BCAS3_ENST00000589222.1_Nonsense_Mutation_p.G402*|BCAS3_ENST00000407086.3_Nonsense_Mutation_p.G402*	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3									p.G402*(1)		NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			TCTTCACAGGGGAGAAACTGA	0.413																																					p.G402X		Atlas-SNP	.											BCAS3,NS,carcinoma,0,1	BCAS3	90	.	1	Substitution - Nonsense(1)	lung(1)	c.G1204T						.						176.0	162.0	167.0					17																	59024696		1895	4127	6022	SO:0001587	stop_gained	54828	exon14			CACAGGGGAGAAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.1204G>T	chr17.hg19:g.59024696G>T	ENSP00000375067:p.Gly402*	78.0	0.0		65.0	4.0	NM_001099432		Nonsense_Mutation	SNP	ENST00000390652.5	hg19	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	G	40	7.913706	0.98557	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000405070;ENST00000408905;ENST00000360207;ENST00000405217	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.0192	0.97489	0.0:0.0:1.0:0.0	.	.	.	.	X	402;402;402;402;194;207	.	ENSP00000353336:G194X	G	+	1	0	BCAS3	56379478	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.463000	0.97652	2.722000	0.93159	0.591000	0.81541	GGA	.	.		0.413	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	
ACE	1636	hgsc.bcm.edu	37	17	61561702	61561702	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:61561702A>G	ENST00000290866.4	+	12	1745	c.1721A>G	c.(1720-1722)cAg>cGg	p.Q574R	ACE_ENST00000490216.2_5'Flank|ACE_ENST00000428043.1_Missense_Mutation_p.Q574R|ACE_ENST00000577647.1_5'Flank|ACE_ENST00000413513.3_5'Flank|ACE_ENST00000290863.6_5'Flank|ACE_ENST00000421982.2_5'Flank	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	574	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	AAGGTGCTGCAGGCTGGCTCC	0.657																																					p.Q574R		Atlas-SNP	.											.	ACE	187	.	0			c.A1721G						.						28.0	22.0	24.0					17																	61561702		2200	4292	6492	SO:0001583	missense	1636	exon12			TGCTGCAGGCTGG	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1721A>G	chr17.hg19:g.61561702A>G	ENSP00000290866:p.Gln574Arg	97.0	0.0		78.0	4.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	A	2.670	-0.277821	0.05679	.	.	ENSG00000159640	ENST00000290866;ENST00000428043	T;T	0.34072	1.38;1.38	4.97	1.49	0.22878	.	0.625902	0.18067	N	0.152745	T	0.23014	0.0556	L	0.28694	0.88	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.003	T	0.06058	-1.0848	10	0.23302	T	0.38	-10.2723	8.8603	0.35253	0.5885:0.0:0.4115:0.0	.	574;574	P12821-2;P12821	.;ACE_HUMAN	R	574	ENSP00000290866:Q574R;ENSP00000397593:Q574R	ENSP00000290866:Q574R	Q	+	2	0	ACE	58915434	0.830000	0.29337	0.307000	0.25127	0.023000	0.10783	1.317000	0.33631	0.064000	0.16427	0.379000	0.24179	CAG	.	.		0.657	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
DCAF7	10238	hgsc.bcm.edu	37	17	61666468	61666468	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:61666468G>T	ENST00000310827.4	+	8	1180	c.963G>T	c.(961-963)tgG>tgT	p.W321C	DCAF7_ENST00000415273.2_Missense_Mutation_p.W121C|DCAF7_ENST00000431926.1_Intron|DCAF7_ENST00000577702.1_3'UTR	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	321					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						ATGTGCAGTGGGCATCAACTC	0.567																																					p.W321C		Atlas-SNP	.											.	DCAF7	36	.	0			c.G963T						.						107.0	104.0	105.0					17																	61666468		2063	4198	6261	SO:0001583	missense	10238	exon8			GCAGTGGGCATCA	U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30915	protein-coding gene	gene with protein product	"""seven-WD-repeat protein of the AN11 family-1"", ""human anthocyanin"""	605973	"""WD repeat domain 68"""	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.963G>T	chr17.hg19:g.61666468G>T	ENSP00000308344:p.Trp321Cys	107.0	0.0		124.0	5.0	NM_005828	B4E039|D3DU14|O15491|Q9DAE4	Missense_Mutation	SNP	ENST00000310827.4	hg19		.	.	.	.	.	.	.	.	.	.	G	21.7	4.182068	0.78677	.	.	ENSG00000136485	ENST00000310827;ENST00000415273	T;T	0.61510	0.1;1.4	5.31	5.31	0.75309	WD40/YVTN repeat-like-containing domain (1);	0.113458	0.64402	D	0.000004	T	0.78610	0.4310	.	.	.	0.80722	D	1	D;D	0.89917	1.0;0.984	D;D	0.91635	0.999;0.929	T	0.80670	-0.1279	9	0.72032	D	0.01	-17.8074	19.1619	0.93537	0.0:0.0:1.0:0.0	.	121;321	B4E039;P61962	.;DCAF7_HUMAN	C	321;121	ENSP00000308344:W321C;ENSP00000403920:W121C	ENSP00000308344:W321C	W	+	3	0	DCAF7	59020200	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.657000	0.98554	2.758000	0.94735	0.563000	0.77884	TGG	.	.		0.567	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828	
SSTR2	6752	hgsc.bcm.edu	37	17	71166524	71166524	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:71166524A>G	ENST00000357585.2	+	2	1435	c.1066A>G	c.(1066-1068)Acc>Gcc	p.T356A	RP11-143K11.5_ENST00000580671.1_RNA|SSTR2_ENST00000315332.2_Intron	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	356				T -> A (in Ref. 5; BAG36594). {ECO:0000305}.	adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)			endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	GACCACGGAGACCCAGAGGAC	0.557																																					p.T356A		Atlas-SNP	.											.	SSTR2	27	.	0			c.A1066G						.						55.0	51.0	52.0					17																	71166524		2203	4300	6503	SO:0001583	missense	6752	exon2			ACGGAGACCCAGA		CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"""GPCR / Class A : Somatostatin receptors"""	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.1066A>G	chr17.hg19:g.71166524A>G	ENSP00000350198:p.Thr356Ala	73.0	0.0		86.0	5.0	NM_001050	A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Missense_Mutation	SNP	ENST00000357585.2	hg19	CCDS11691.1	.	.	.	.	.	.	.	.	.	.	A	11.41	1.630056	0.28978	.	.	ENSG00000180616	ENST00000357585	T	0.72394	-0.65	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.62429	0.2427	L	0.43152	1.355	0.80722	D	1	B	0.14805	0.011	B	0.16289	0.015	T	0.57705	-0.7765	10	0.18710	T	0.47	.	15.0092	0.71536	1.0:0.0:0.0:0.0	.	356	P30874	SSR2_HUMAN	A	356	ENSP00000350198:T356A	ENSP00000350198:T356A	T	+	1	0	SSTR2	68678119	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.905000	0.92613	2.084000	0.62774	0.533000	0.62120	ACC	.	.		0.557	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1		
TMEM104	54868	hgsc.bcm.edu	37	17	72815910	72815910	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:72815910G>T	ENST00000335464.5	+	9	820	c.658G>T	c.(658-660)Gga>Tga	p.G220*	TMEM104_ENST00000417024.2_Nonsense_Mutation_p.G233*|TMEM104_ENST00000582330.1_Nonsense_Mutation_p.G220*|TMEM104_ENST00000582773.1_Nonsense_Mutation_p.G220*	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	220						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					TCTCCTCCTCGGACCGTTCAC	0.562																																					p.G220X		Atlas-SNP	.											.	TMEM104	49	.	0			c.G658T						.						203.0	163.0	177.0					17																	72815910		2203	4300	6503	SO:0001587	stop_gained	54868	exon9			CTCCTCGGACCGT	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.658G>T	chr17.hg19:g.72815910G>T	ENSP00000334849:p.Gly220*	163.0	0.0		148.0	6.0	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Nonsense_Mutation	SNP	ENST00000335464.5	hg19	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	G	38	6.859352	0.97893	.	.	ENSG00000109066	ENST00000335464;ENST00000417024	.	.	.	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-5.8226	17.5725	0.87939	0.0:0.0:1.0:0.0	.	.	.	.	X	220;233	.	ENSP00000334849:G220X	G	+	1	0	TMEM104	70327505	1.000000	0.71417	0.829000	0.32907	0.946000	0.59487	8.796000	0.91877	2.506000	0.84524	0.561000	0.74099	GGA	.	.		0.562	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728	
HID1	283987	hgsc.bcm.edu	37	17	72955014	72955014	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:72955014A>G	ENST00000425042.2	-	9	1218	c.1141T>C	c.(1141-1143)Ttc>Ctc	p.F381L		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	381					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											ACCTTGTTGAAGTCGCAGAGC	0.617											OREG0024721	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F381L		Atlas-SNP	.											.	.	.	.	0			c.T1141C						.						56.0	44.0	48.0					17																	72955014		2203	4300	6503	SO:0001583	missense	283987	exon9			TGTTGAAGTCGCA		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"""downregulated in multiple cancer 1"""	605752	"""chromosome 17 open reading frame 28"""	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.1141T>C	chr17.hg19:g.72955014A>G	ENSP00000413520:p.Phe381Leu	103.0	0.0	1141	120.0	5.0	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	hg19	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585401	0.28268	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	4.97	3.87	0.44632	.	0.112112	0.64402	D	0.000009	T	0.29158	0.0725	N	0.05441	-0.05	0.37945	D	0.932478	B;B	0.09022	0.002;0.0	B;B	0.10450	0.005;0.004	T	0.10109	-1.0644	9	0.13108	T	0.6	-18.5177	11.0934	0.48130	0.8611:0.0:0.0:0.1389	.	380;381	Q8IV36-2;Q8IV36	.;CQ028_HUMAN	L	153;381;153	.	ENSP00000317795:F153L	F	-	1	0	C17orf28	70466609	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.643000	0.67895	0.725000	0.32318	0.369000	0.22263	TTC	.	.		0.617	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
KCTD2	23510	hgsc.bcm.edu	37	17	73059137	73059137	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73059137A>G	ENST00000322444.6	+	6	793	c.787A>G	c.(787-789)Atg>Gtg	p.M263V	KCTD2_ENST00000581589.1_Missense_Mutation_p.M64V	NM_015353.1	NP_056168.1	Q14681	KCTD2_HUMAN	potassium channel tetramerization domain containing 2	263					protein homooligomerization (GO:0051260)		protein complex binding (GO:0032403)			kidney(1)|lung(2)	3	all_lung(278;0.226)					AGGATCGCGGATGTAAACTAA	0.547																																					p.M263V		Atlas-SNP	.											.	KCTD2	15	.	0			c.A787G						.						74.0	63.0	67.0					17																	73059137		2203	4300	6503	SO:0001583	missense	23510	exon6			TCGCGGATGTAAA	BC033329	CCDS32728.1	17q25.2	2013-06-20	2013-06-20			ENSG00000180901			21294	protein-coding gene	gene with protein product		613422	"""potassium channel tetramerisation domain containing 2"""			12620391	Standard	XR_248405		Approved	KIAA0176	uc002jmp.3	Q14681		ENST00000322444.6:c.787A>G	chr17.hg19:g.73059137A>G	ENSP00000312814:p.Met263Val	64.0	0.0		125.0	5.0	NM_015353		Missense_Mutation	SNP	ENST00000322444.6	hg19	CCDS32728.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.903938	0.52333	.	.	ENSG00000180901	ENST00000322444;ENST00000375286	T	0.55234	0.53	4.73	4.73	0.59995	.	0.224065	0.52532	D	0.000076	T	0.42449	0.1203	L	0.31294	0.92	0.50039	D	0.999845	B	0.24721	0.11	B	0.24974	0.057	T	0.43376	-0.9395	10	0.72032	D	0.01	.	13.2495	0.60043	1.0:0.0:0.0:0.0	.	263	Q14681	KCTD2_HUMAN	V	263;245	ENSP00000312814:M263V	ENSP00000312814:M263V	M	+	1	0	KCTD2	70570732	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.458000	0.90364	2.108000	0.64289	0.533000	0.62120	ATG	.	.		0.547	KCTD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445538.1		
TSEN54	283989	hgsc.bcm.edu	37	17	73518036	73518036	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73518036G>T	ENST00000333213.6	+	8	910	c.874G>T	c.(874-876)Ggt>Tgt	p.G292C		NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	292					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CACGGGAGCCGGTAAGCGGCG	0.697																																					p.G292C		Atlas-SNP	.											.	TSEN54	27	.	0			c.G874T						.						16.0	19.0	18.0					17																	73518036		2195	4295	6490	SO:0001583	missense	283989	exon8			GGAGCCGGTAAGC	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"""tRNA splicing endonuclease subunits"""	27561	protein-coding gene	gene with protein product		608755	"""tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)"", ""tRNA splicing endonuclease 54 homolog (S. cerevisiae)"""			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.874G>T	chr17.hg19:g.73518036G>T	ENSP00000327487:p.Gly292Cys	82.0	0.0		72.0	4.0	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	hg19	CCDS11724.1	.	.	.	.	.	.	.	.	.	.	G	1.918	-0.449054	0.04572	.	.	ENSG00000182173	ENST00000333213	T	0.56776	0.44	4.96	-9.92	0.00455	.	1.215030	0.05564	N	0.569760	T	0.23133	0.0559	N	0.03115	-0.41	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43426	-0.9392	10	0.52906	T	0.07	16.6892	6.2324	0.20742	0.073:0.3457:0.3986:0.1826	.	292	Q7Z6J9	SEN54_HUMAN	C	292	ENSP00000327487:G292C	ENSP00000327487:G292C	G	+	1	0	TSEN54	71029631	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.717000	0.01876	-3.844000	0.00100	-0.333000	0.08304	GGT	.	.		0.697	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
LLGL2	3993	hgsc.bcm.edu	37	17	73566143	73566143	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73566143C>A	ENST00000392550.3	+	15	1798	c.1681C>A	c.(1681-1683)Cac>Aac	p.H561N	LLGL2_ENST00000167462.5_Missense_Mutation_p.H561N|LLGL2_ENST00000577200.1_Missense_Mutation_p.H561N	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	561					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CTGGAAGGGGCACGAGCGCCT	0.662																																					p.H561N		Atlas-SNP	.											.	LLGL2	155	.	0			c.C1681A						.						30.0	29.0	29.0					17																	73566143		2202	4298	6500	SO:0001583	missense	3993	exon15			AAGGGGCACGAGC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1681C>A	chr17.hg19:g.73566143C>A	ENSP00000376333:p.His561Asn	83.0	0.0		88.0	4.0	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	hg19	CCDS32733.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.091673	0.55968	.	.	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.50813	0.73;0.73	5.19	5.19	0.71726	.	0.049489	0.85682	D	0.000000	T	0.69788	0.3150	M	0.83312	2.635	0.58432	D	0.999997	P;P;P;P;D	0.69078	0.859;0.872;0.921;0.92;0.997	B;B;P;P;P	0.60949	0.406;0.396;0.601;0.73;0.881	T	0.75190	-0.3405	10	0.66056	D	0.02	0.2915	18.7672	0.91878	0.0:1.0:0.0:0.0	.	188;550;550;561;561	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	N	561;561;550	ENSP00000167462:H561N;ENSP00000376333:H561N	ENSP00000167462:H561N	H	+	1	0	LLGL2	71077738	1.000000	0.71417	0.936000	0.37596	0.899000	0.52679	7.620000	0.83070	2.431000	0.82371	0.549000	0.68633	CAC	.	.		0.662	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
UNK	85451	hgsc.bcm.edu	37	17	73811297	73811297	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73811297T>C	ENST00000589666.1	+	7	1034	c.924T>C	c.(922-924)tgT>tgC	p.C308C	UNK_ENST00000293218.3_Silent_p.C384C	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	308							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGGCAGCTGTCCCCGAGGAC	0.647																																					p.C308C		Atlas-SNP	.											.	UNK	87	.	0			c.T924C						.						147.0	158.0	154.0					17																	73811297		2095	4206	6301	SO:0001819	synonymous_variant	85451	exon7			CAGCTGTCCCCGA	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"""Zinc fingers, CCCH-type domain containing"""	29369	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 5"", ""zinc finger CCCH-type containing 5"", ""unkempt homolog (Drosophila)"""	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.924T>C	chr17.hg19:g.73811297T>C		116.0	0.0		97.0	4.0	NM_001080419		Silent	SNP	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.		0.647	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419	
FBF1	85302	hgsc.bcm.edu	37	17	73916127	73916127	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:73916127T>C	ENST00000586717.1	-	18	2123	c.1850A>G	c.(1849-1851)cAg>cGg	p.Q617R	FBF1_ENST00000389570.4_Missense_Mutation_p.Q617R|FBF1_ENST00000319129.5_Missense_Mutation_p.Q616R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	617					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGCCTGGTGCTGCTGCTGCAG	0.652																																					p.Q616R		Atlas-SNP	.											.	FBF1	48	.	0			c.A1847G						.						23.0	27.0	25.0					17																	73916127		1982	4165	6147	SO:0001583	missense	85302	exon18			TGGTGCTGCTGCT	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1850A>G	chr17.hg19:g.73916127T>C	ENSP00000465132:p.Gln617Arg	96.0	0.0		115.0	5.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.008	-1.929620	0.00488	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.15487	2.42;2.43	5.15	0.435	0.16544	.	.	.	.	.	T	0.04770	0.0129	N	0.01454	-0.855	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.0;0.001;0.002	T	0.41251	-0.9519	9	0.02654	T	1	-5.5969	9.2857	0.37755	0.0:0.6645:0.0:0.3355	.	631;617;616	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	R	617;617;616;630	ENSP00000374221:Q617R;ENSP00000324292:Q616R	ENSP00000324292:Q616R	Q	-	2	0	FBF1	71427722	0.033000	0.19621	0.393000	0.26258	0.099000	0.18886	0.456000	0.21859	0.104000	0.17725	-0.408000	0.06270	CAG	.	.		0.652	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
SRSF2	6427	hgsc.bcm.edu	37	17	74732955	74732955	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:74732955C>T	ENST00000392485.2	-	1	460	c.288G>A	c.(286-288)ccG>ccA	p.P96P	MFSD11_ENST00000586622.1_5'UTR|MFSD11_ENST00000590514.1_5'Flank|MIR636_ENST00000384825.1_RNA|MFSD11_ENST00000336509.4_5'Flank|MFSD11_ENST00000591864.1_5'UTR|MFSD11_ENST00000355954.3_5'Flank|SRSF2_ENST00000508921.3_Silent_p.P96P|SRSF2_ENST00000359995.5_Silent_p.P96P|MFSD11_ENST00000590393.1_5'Flank|MFSD11_ENST00000593181.1_5'Flank|RP11-318A15.7_ENST00000587459.1_Intron|MFSD11_ENST00000588460.1_5'UTR	NM_003016.4	NP_003007.2	Q01130	SRSF2_HUMAN	serine/arginine-rich splicing factor 2	96					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA biosynthetic process (GO:2001141)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)	p.P95_R102del(21)|p.P95_D97del(2)		haematopoietic_and_lymphoid_tissue(320)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)	329						GGTGTGAGTCCGGGGGGCGGC	0.741			Mis		"""MDS, CLL"""																																p.P96P		Atlas-SNP	.		Dom	yes		17	17q25	6427	serine/arginine-rich splicing factor 2		L	.	SRSF2	544	.	23	Deletion - In frame(23)	haematopoietic_and_lymphoid_tissue(23)	c.G288A						.						14.0	17.0	16.0					17																	74732955		2126	4192	6318	SO:0001819	synonymous_variant	6427	exon1			TGAGTCCGGGGGG	M90104	CCDS11749.1	17q25.2	2014-09-17	2010-06-22	2010-06-22	ENSG00000161547	ENSG00000161547		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10783	protein-coding gene	gene with protein product	"""SR splicing factor 2"""	600813	"""splicing factor, arginine/serine-rich 2"""	SFRS2		8530103, 20516191	Standard	NM_003016		Approved	SC-35, SC35, PR264, SFRS2A	uc002jsv.3	Q01130		ENST00000392485.2:c.288G>A	chr17.hg19:g.74732955C>T		33.0	0.0		38.0	4.0	NM_001195427	B3KWD5|B4DN89|H0YG49	Silent	SNP	ENST00000392485.2	hg19	CCDS11749.1																																																																																			.	.		0.741	SRSF2-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437489.1	NM_003016	
DNAH17	8632	hgsc.bcm.edu	37	17	76456313	76456313	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:76456313A>G	ENST00000585328.1	-	59	9475	c.9351T>C	c.(9349-9351)tgT>tgC	p.C3117C	DNAH17_ENST00000389840.5_Silent_p.C3108C|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3108	Stalk. {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)			GGTCTGTTTCACAGGCCTTTT	0.572																																					p.C3122C		Atlas-SNP	.											.	DNAH17	347	.	0			c.T9366C						.						65.0	58.0	60.0					17																	76456313		2203	4300	6503	SO:0001819	synonymous_variant	8632	exon59			TGTTTCACAGGCC	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.9351T>C	chr17.hg19:g.76456313A>G		96.0	0.0		116.0	5.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.		0.572	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
USP36	57602	hgsc.bcm.edu	37	17	76810529	76810529	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:76810529T>C	ENST00000542802.3	-	11	1572	c.1129A>G	c.(1129-1131)Agc>Ggc	p.S377G	USP36_ENST00000588467.1_5'UTR|USP36_ENST00000449938.2_Missense_Mutation_p.S77G|USP36_ENST00000312010.6_Missense_Mutation_p.S377G			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	377	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GCATGGCAGCTGTAGCCCGAG	0.527																																					p.S377G		Atlas-SNP	.											.	USP36	243	.	0			c.A1129G						.						92.0	68.0	76.0					17																	76810529		2203	4300	6503	SO:0001583	missense	57602	exon11			GGCAGCTGTAGCC	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.1129A>G	chr17.hg19:g.76810529T>C	ENSP00000441214:p.Ser377Gly	83.0	0.0		96.0	4.0	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	hg19	CCDS32755.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411169	0.83340	.	.	ENSG00000055483	ENST00000312010;ENST00000449938;ENST00000542802;ENST00000432878	T;T;T	0.06687	3.27;3.27;3.27	5.16	5.16	0.70880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.077885	0.85682	D	0.000000	T	0.24509	0.0594	L	0.53561	1.675	0.58432	D	0.999996	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.978	T	0.00565	-1.1668	10	0.87932	D	0	-32.9359	14.672	0.68951	0.0:0.0:0.0:1.0	.	377;377	Q9P275;Q9P275-2	UBP36_HUMAN;.	G	377;77;377;377	ENSP00000310590:S377G;ENSP00000401119:S77G;ENSP00000441214:S377G	ENSP00000310590:S377G	S	-	1	0	USP36	74322124	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.123000	0.57917	1.936000	0.56123	0.533000	0.62120	AGC	.	.		0.527	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
ENGASE	64772	hgsc.bcm.edu	37	17	77073755	77073755	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:77073755T>C	ENST00000579016.1	+	3	225	c.225T>C	c.(223-225)taT>taC	p.Y75Y	ENGASE_ENST00000539857.2_5'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	75						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						TTAGATATTATGACAAGGACA	0.433																																					p.Y75Y		Atlas-SNP	.											.	ENGASE	55	.	0			c.T225C						.						120.0	122.0	121.0					17																	77073755		1927	4129	6056	SO:0001819	synonymous_variant	64772	exon3			ATATTATGACAAG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.225T>C	chr17.hg19:g.77073755T>C		61.0	0.0		78.0	4.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	hg19	CCDS42394.1																																																																																			.	.		0.433	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
NPTX1	4884	hgsc.bcm.edu	37	17	78445639	78445639	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:78445639C>A	ENST00000306773.4	-	4	1127	c.970G>T	c.(970-972)Ggg>Tgg	p.G324W	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	324	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			TCCCAGACCCCGTCCCGGGTG	0.622																																					p.G324W		Atlas-SNP	.											.	NPTX1	28	.	0			c.G970T						.						56.0	45.0	49.0					17																	78445639		2203	4300	6503	SO:0001583	missense	4884	exon4			AGACCCCGTCCCG	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.970G>T	chr17.hg19:g.78445639C>A	ENSP00000307549:p.Gly324Trp	74.0	0.0		84.0	4.0	NM_002522	B3KXH3|Q5FWE6	Missense_Mutation	SNP	ENST00000306773.4	hg19	CCDS32762.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.889179	0.91889	.	.	ENSG00000171246	ENST00000306773;ENST00000535681	T	0.23348	1.91	5.02	5.02	0.67125	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.68412	0.2998	H	0.97940	4.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81699	-0.0814	10	0.87932	D	0	-31.6303	18.1318	0.89604	0.0:1.0:0.0:0.0	.	324	Q15818	NPTX1_HUMAN	W	324;86	ENSP00000307549:G324W	ENSP00000307549:G324W	G	-	1	0	NPTX1	76060234	1.000000	0.71417	0.996000	0.52242	0.965000	0.64279	7.582000	0.82546	2.607000	0.88179	0.561000	0.74099	GGG	.	.		0.622	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1		
PYCR1	5831	hgsc.bcm.edu	37	17	79892336	79892336	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:79892336T>C	ENST00000329875.8	-	6	727	c.663A>G	c.(661-663)gaA>gaG	p.E221E	PYCR1_ENST00000577756.1_Intron|PYCR1_ENST00000402252.2_Silent_p.E248E|PYCR1_ENST00000403172.4_Silent_p.E190E|PYCR1_ENST00000337943.5_Silent_p.E221E|RP11-498C9.13_ENST00000583521.1_RNA	NM_001282280.1|NM_001282281.1|NM_006907.2	NP_001269209.1|NP_001269210.1|NP_008838.2	P32322	P5CR1_HUMAN	pyrroline-5-carboxylate reductase 1	221					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to oxidative stress (GO:0034599)|L-proline biosynthetic process (GO:0055129)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|proline biosynthetic process (GO:0006561)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|pyrroline-5-carboxylate reductase activity (GO:0004735)			endometrium(2)|kidney(1)|lung(1)|prostate(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		L-Proline(DB00172)	CTGGGTGCTGTTCTGAGTGCA	0.647																																					p.E221E		Atlas-SNP	.											.	PYCR1	44	.	0			c.A663G						.						48.0	35.0	39.0					17																	79892336		2200	4296	6496	SO:0001819	synonymous_variant	5831	exon6			GTGCTGTTCTGAG		CCDS11794.1, CCDS11795.1, CCDS62365.1, CCDS62366.1	17q25.3	2013-09-23			ENSG00000183010	ENSG00000183010	1.5.1.2		9721	protein-coding gene	gene with protein product		179035				1730675	Standard	XM_005256381		Approved	P5C	uc002kcr.1	P32322	OTTHUMG00000178436	ENST00000329875.8:c.663A>G	chr17.hg19:g.79892336T>C		59.0	0.0		58.0	4.0	NM_153824	A6NFM2|B4DMU0|Q6FHI4|Q96DI6|Q9HBQ4	Silent	SNP	ENST00000329875.8	hg19	CCDS11795.1	.	.	.	.	.	.	.	.	.	.	T	7.318	0.616408	0.14129	.	.	ENSG00000183010	ENST00000403172	.	.	.	3.47	-1.76	0.08006	.	.	.	.	.	T	0.67382	0.2887	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68965	-0.5270	5	0.72032	D	0.01	.	10.5871	0.45288	0.0:0.6585:0.0:0.3415	.	.	.	.	A	222	.	ENSP00000385483:T222A	T	-	1	0	PYCR1	77485627	0.737000	0.28175	0.851000	0.33527	0.749000	0.42624	-0.089000	0.11180	-0.293000	0.08986	0.459000	0.35465	ACA	.	.		0.647	PYCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441953.1		
FASN	2194	hgsc.bcm.edu	37	17	80038328	80038328	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:80038328T>C	ENST00000306749.2	-	40	7183	c.6965A>G	c.(6964-6966)cAg>cGg	p.Q2322R	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2322	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CTGCTGGGCCTGCAGCTGGGA	0.662																																					p.Q2322R	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A6965G						.						18.0	18.0	18.0					17																	80038328		2177	4290	6467	SO:0001583	missense	2194	exon40			TGGGCCTGCAGCT	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6965A>G	chr17.hg19:g.80038328T>C	ENSP00000304592:p.Gln2322Arg	74.0	0.0		110.0	5.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.844098	0.91197	.	.	ENSG00000169710	ENST00000306749	T	0.27104	1.69	4.63	4.63	0.57726	Thioesterase (1);	0.068460	0.64402	D	0.000014	T	0.46014	0.1371	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.46470	-0.9189	10	0.87932	D	0	-29.5622	14.1766	0.65546	0.0:0.0:0.0:1.0	.	2322	P49327	FAS_HUMAN	R	2322	ENSP00000304592:Q2322R	ENSP00000304592:Q2322R	Q	-	2	0	FASN	77631617	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.681000	0.84073	1.955000	0.56771	0.482000	0.46254	CAG	.	.		0.662	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
TBCD	6904	hgsc.bcm.edu	37	17	80897247	80897247	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr17:80897247G>A	ENST00000355528.4	+	37	3504	c.3374G>A	c.(3373-3375)cGg>cAg	p.R1125Q	TBCD_ENST00000576691.1_3'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.R1163Q	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1125					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			TCCCAGATCCGGAAGACCACG	0.642																																					p.R1125Q		Atlas-SNP	.											.	TBCD	94	.	0			c.G3374A						.						86.0	92.0	90.0					17																	80897247		2203	4298	6501	SO:0001583	missense	6904	exon37			AGATCCGGAAGAC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.3374G>A	chr17.hg19:g.80897247G>A	ENSP00000347719:p.Arg1125Gln	75.0	0.0		70.0	4.0	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	hg19	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335358	0.81801	.	.	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000539345	T	0.59364	0.27	5.38	5.38	0.77491	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.81230	0.4779	M	0.91510	3.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.85190	0.1009	9	.	.	.	.	16.6114	0.84884	0.0:0.0:1.0:0.0	.	914;1125;1163	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	Q	1125;914;117	ENSP00000347719:R1125Q	.	R	+	2	0	TBCD	78490536	1.000000	0.71417	1.000000	0.80357	0.185000	0.23345	8.798000	0.91888	2.526000	0.85167	0.313000	0.20887	CGG	.	.		0.642	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
MYOM1	8736	hgsc.bcm.edu	37	18	3071875	3071875	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:3071875A>G	ENST00000356443.4	-	37	5054	c.4721T>C	c.(4720-4722)gTg>gCg	p.V1574A	MYOM1_ENST00000400569.3_Missense_Mutation_p.V1574A|MYOM1_ENST00000261606.7_Missense_Mutation_p.V1478A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1574	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						ACCTCCCAACACCCGGGCACG	0.547																																					p.V1574A		Atlas-SNP	.											.	MYOM1	192	.	0			c.T4721C						.						64.0	69.0	68.0					18																	3071875		2016	4196	6212	SO:0001583	missense	8736	exon37			CCCAACACCCGGG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4721T>C	chr18.hg19:g.3071875A>G	ENSP00000348821:p.Val1574Ala	86.0	0.0		95.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.185271	0.78677	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.53423	0.73;0.74;0.62	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.73249	0.3563	M	0.90595	3.13	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.77477	-0.2573	10	0.42905	T	0.14	.	14.9381	0.70973	1.0:0.0:0.0:0.0	.	1478;1574	P52179-2;P52179	.;MYOM1_HUMAN	A	1574;1574;1478	ENSP00000348821:V1574A;ENSP00000383413:V1574A;ENSP00000261606:V1478A	ENSP00000261606:V1478A	V	-	2	0	MYOM1	3061875	1.000000	0.71417	0.931000	0.37212	0.673000	0.39480	9.087000	0.94110	2.165000	0.68154	0.460000	0.39030	GTG	.	.		0.547	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
MYOM1	8736	hgsc.bcm.edu	37	18	3187546	3187546	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:3187546C>A	ENST00000356443.4	-	5	1194	c.861G>T	c.(859-861)acG>acT	p.T287T	MYOM1_ENST00000400569.3_Silent_p.T287T|MYOM1_ENST00000261606.7_Silent_p.T287T|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	287	Ig-like C2-type 1.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TCTCCCAAACCGTGTGGGAGC	0.428																																					p.T287T		Atlas-SNP	.											.	MYOM1	192	.	0			c.G861T						.						138.0	132.0	134.0					18																	3187546		1972	4149	6121	SO:0001819	synonymous_variant	8736	exon5			CCAAACCGTGTGG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.861G>T	chr18.hg19:g.3187546C>A		115.0	0.0		89.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.428	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
MYOM1	8736	hgsc.bcm.edu	37	18	3215059	3215059	+	Missense_Mutation	SNP	G	G	T	rs371866822		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:3215059G>T	ENST00000356443.4	-	2	496	c.163C>A	c.(163-165)Cgc>Agc	p.R55S	MYOM1_ENST00000400569.3_Missense_Mutation_p.R55S|MYOM1_ENST00000261606.7_Missense_Mutation_p.R55S|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	55					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GACTCCCGGCGGTGCGCGGCG	0.701																																					p.R55S		Atlas-SNP	.											MYOM1,NS,carcinoma,+1,1	MYOM1	192	.	0			c.C163A						.	G	SER/ARG,SER/ARG	1,4041		0,1,2020	26.0	33.0	30.0		163,163	5.7	1.0	18		30	0,8350		0,0,4175	no	missense,missense	MYOM1	NM_003803.3,NM_019856.1	110,110	0,1,6195	TT,TG,GG		0.0,0.0247,0.0081	probably-damaging,probably-damaging	55/1686,55/1590	3215059	1,12391	2021	4175	6196	SO:0001583	missense	8736	exon2			CCCGGCGGTGCGC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.163C>A	chr18.hg19:g.3215059G>T	ENSP00000348821:p.Arg55Ser	83.0	1.0		60.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.242192	0.58995	2.47E-4	0.0	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.58652	0.51;0.51;0.32	5.67	5.67	0.87782	.	0.396008	0.25316	N	0.031556	T	0.54415	0.1857	N	0.24115	0.695	0.43503	D	0.995752	D;P	0.61697	0.99;0.465	P;B	0.49665	0.618;0.095	T	0.59553	-0.7433	10	0.72032	D	0.01	.	16.7016	0.85350	0.0:0.0:1.0:0.0	.	55;55	P52179-2;P52179	.;MYOM1_HUMAN	S	55	ENSP00000348821:R55S;ENSP00000383413:R55S;ENSP00000261606:R55S	ENSP00000261606:R55S	R	-	1	0	MYOM1	3205059	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	5.850000	0.69473	2.673000	0.90976	0.655000	0.94253	CGC	.	.		0.701	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ZBTB14	7541	hgsc.bcm.edu	37	18	5291320	5291320	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:5291320T>C	ENST00000357006.4	-	4	1225	c.887A>G	c.(886-888)gAg>gGg	p.E296G	ZBTB14_ENST00000400143.3_Missense_Mutation_p.E296G	NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	296					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)										GTGGAGTTTCTCATGCTTCCT	0.478																																					p.E296G		Atlas-SNP	.											ZFP161,right_lower_lobe,carcinoma,0,1	.	.	.	0			c.A887G						.						100.0	91.0	94.0					18																	5291320		2203	4300	6503	SO:0001583	missense	7541	exon4			AGTTTCTCATGCT	D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12860	protein-coding gene	gene with protein product		602126	"""zinc finger protein 161 homolog (mouse)"", ""zinc finger protein 161"", ""ZFP161 zinc finger protein"""	ZFP161		9244432	Standard	NM_001243702		Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.887A>G	chr18.hg19:g.5291320T>C	ENSP00000349503:p.Glu296Gly	76.0	0.0		95.0	4.0	NM_001243702	O00403|Q2TB80	Missense_Mutation	SNP	ENST00000357006.4	hg19	CCDS11837.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287205	0.80803	.	.	ENSG00000198081	ENST00000357006;ENST00000400143	T;T	0.18657	2.2;2.2	5.8	5.8	0.92144	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.110120	0.64402	D	0.000015	T	0.41696	0.1170	L	0.54323	1.7	0.80722	D	1	D	0.69078	0.997	D	0.68765	0.96	T	0.12016	-1.0564	10	0.46703	T	0.11	-20.0105	16.143	0.81539	0.0:0.0:0.0:1.0	.	296	O43829	ZF161_HUMAN	G	296	ENSP00000349503:E296G;ENSP00000383009:E296G	ENSP00000349503:E296G	E	-	2	0	ZFP161	5281320	1.000000	0.71417	0.522000	0.27862	0.974000	0.67602	7.919000	0.87513	2.206000	0.71126	0.528000	0.53228	GAG	.	.		0.478	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254425.1	NM_003409	
TWSG1	57045	hgsc.bcm.edu	37	18	9337333	9337333	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:9337333A>G	ENST00000262120.5	+	2	297	c.106A>G	c.(106-108)Agc>Ggc	p.S36G	TWSG1_ENST00000581641.1_Missense_Mutation_p.S36G|RP11-888D10.3_ENST00000584509.1_lincRNA	NM_020648.5	NP_065699.1	Q9GZX9	TWSG1_HUMAN	twisted gastrulation BMP signaling modulator 1	36	Cys-rich.				BMP signaling pathway (GO:0030509)|camera-type eye development (GO:0043010)|cell differentiation (GO:0030154)|forebrain development (GO:0030900)|hemopoiesis (GO:0030097)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of BMP signaling pathway (GO:0030513)|salivary gland morphogenesis (GO:0007435)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|pancreas(2)	10						TAGTGATGTGAGCAAATGCCT	0.373																																					p.S36G		Atlas-SNP	.											.	TWSG1	23	.	0			c.A106G						.						141.0	124.0	129.0					18																	9337333		2203	4300	6503	SO:0001583	missense	57045	exon2			GATGTGAGCAAAT	AA486291	CCDS11844.1	18p11.3	2013-10-03	2013-10-03		ENSG00000128791	ENSG00000128791			12429	protein-coding gene	gene with protein product		605049	"""twisted gastrulation homolog 1 (Drosophila)"""			11260715	Standard	NM_020648		Approved	TSG	uc002knz.3	Q9GZX9	OTTHUMG00000131597	ENST00000262120.5:c.106A>G	chr18.hg19:g.9337333A>G	ENSP00000262120:p.Ser36Gly	35.0	0.0		44.0	4.0	NM_020648	B2RE08|D3DUH9|Q8NBI7|Q96K46	Missense_Mutation	SNP	ENST00000262120.5	hg19	CCDS11844.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.146938	0.77888	.	.	ENSG00000128791	ENST00000262120	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.67373	0.2886	M	0.74467	2.265	0.53688	D	0.99997	D	0.57899	0.981	P	0.51806	0.68	T	0.72600	-0.4244	9	0.87932	D	0	-27.5754	12.6797	0.56914	1.0:0.0:0.0:0.0	.	36	Q9GZX9	TWSG1_HUMAN	G	36	.	ENSP00000262120:S36G	S	+	1	0	TWSG1	9327333	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.345000	0.72995	2.242000	0.73789	0.533000	0.62120	AGC	.	.		0.373	TWSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254480.2		
CEP192	55125	hgsc.bcm.edu	37	18	13015339	13015339	+	5'UTR	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:13015339G>T	ENST00000325971.8	+	0	612				CEP192_ENST00000506447.1_Missense_Mutation_p.D178Y			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TGTTGTGCTTGATGCTGGAAA	0.378																																					p.D178Y		Atlas-SNP	.											.	CEP192	340	.	0			c.G532T						.						192.0	141.0	156.0					18																	13015339		692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon6			GTGCTTGATGCTG	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-982G>T	chr18.hg19:g.13015339G>T		89.0	0.0		89.0	4.0	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	G	9.907	1.208592	0.22205	.	.	ENSG00000101639	ENST00000506447	T	0.07444	3.19	4.37	3.49	0.39957	.	.	.	.	.	T	0.09113	0.0225	L	0.27053	0.805	0.22266	N	0.999246	P	0.48016	0.904	P	0.46253	0.509	T	0.18335	-1.0340	9	0.66056	D	0.02	.	10.2776	0.43519	0.0:0.2188:0.7812:0.0	.	178	E9PF99	.	Y	178	ENSP00000427550:D178Y	ENSP00000427550:D178Y	D	+	1	0	CEP192	13005339	0.047000	0.20315	0.002000	0.10522	0.015000	0.08874	2.120000	0.41968	1.184000	0.42957	0.563000	0.77884	GAT	.	.		0.378	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
MIB1	57534	hgsc.bcm.edu	37	18	19383906	19383906	+	Silent	SNP	T	T	C	rs144652547		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:19383906T>C	ENST00000261537.6	+	10	1674	c.1410T>C	c.(1408-1410)gcT>gcC	p.A470A	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	470					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			CTATGCAAGCTGCTAGTCAGA	0.333																																					p.A470A		Atlas-SNP	.											.	MIB1	87	.	0			c.T1410C						.	T		1,4405	2.1+/-5.4	0,1,2202	99.0	91.0	94.0		1410	3.3	1.0	18	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	MIB1	NM_020774.2		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		470/1007	19383906	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57534	exon10			GCAAGCTGCTAGT	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	21086	protein-coding gene	gene with protein product		608677	"""mindbomb homolog 1 (Drosophila)"""				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.1410T>C	chr18.hg19:g.19383906T>C		66.0	0.0		88.0	4.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Silent	SNP	ENST00000261537.6	hg19	CCDS11871.1																																																																																			.	T|1.000;C|0.000		0.333	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774	
LAMA3	3909	hgsc.bcm.edu	37	18	21355846	21355846	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:21355846A>G	ENST00000313654.9	+	10	1605	c.1364A>G	c.(1363-1365)gAg>gGg	p.E455G	LAMA3_ENST00000399516.3_Missense_Mutation_p.E455G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	455	Domain V.|Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GACAACTGTGAGAAGTGTGCA	0.498																																					p.E455G		Atlas-SNP	.											.	LAMA3	397	.	0			c.A1364G						.						83.0	79.0	81.0					18																	21355846		1963	4157	6120	SO:0001583	missense	3909	exon10			ACTGTGAGAAGTG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.1364A>G	chr18.hg19:g.21355846A>G	ENSP00000324532:p.Glu455Gly	122.0	0.0		101.0	5.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117370	0.77323	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669;ENST00000538801	T;T	0.64618	-0.11;-0.11	4.92	4.92	0.64577	EGF-like, laminin (4);	.	.	.	.	T	0.78464	0.4287	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	0.99;1.0;0.999	P;D;D	0.77557	0.894;0.986;0.99	T	0.81695	-0.0816	9	0.87932	D	0	.	13.6779	0.62465	1.0:0.0:0.0:0.0	.	455;455;455	F5H8G3;Q6VU67;Q16787	.;.;LAMA3_HUMAN	G	455;455;453;455	ENSP00000324532:E455G;ENSP00000382432:E455G	ENSP00000324532:E455G	E	+	2	0	LAMA3	19609844	1.000000	0.71417	0.999000	0.59377	0.756000	0.42949	7.578000	0.82498	2.072000	0.62099	0.482000	0.46254	GAG	.	.		0.498	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
TTC39C	125488	hgsc.bcm.edu	37	18	21660556	21660556	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:21660556C>T	ENST00000317571.3	+	5	704	c.468C>T	c.(466-468)atC>atT	p.I156I	RP11-403A21.3_ENST00000578443.1_RNA|TTC39C_ENST00000578150.1_3'UTR|TTC39C_ENST00000304621.6_Silent_p.I95I	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	156										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						TAGCTTATATCAAAGGTGGGT	0.348																																					p.I156I		Atlas-SNP	.											.	TTC39C	83	.	0			c.C468T						.						48.0	48.0	48.0					18																	21660556		2203	4300	6503	SO:0001819	synonymous_variant	125488	exon5			TTATATCAAAGGT	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.468C>T	chr18.hg19:g.21660556C>T		75.0	0.0		83.0	4.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Silent	SNP	ENST00000317571.3	hg19	CCDS45839.1																																																																																			.	.		0.348	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
SLC14A1	6563	hgsc.bcm.edu	37	18	43310402	43310402	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:43310402C>A	ENST00000321925.4	+	3	349	c.117C>A	c.(115-117)acC>acA	p.T39T	SLC14A1_ENST00000402943.2_Intron|SLC14A1_ENST00000502059.2_Intron|SLC14A1_ENST00000535474.1_Intron|SLC14A1_ENST00000591943.1_3'UTR|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000586142.1_Silent_p.T39T|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000589700.1_Silent_p.T39T|SLC14A1_ENST00000415427.3_Silent_p.T95T|SLC14A1_ENST00000436407.3_Silent_p.T95T	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	39					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						GCTATGTCACCGGTGACATGA	0.478																																					p.T95T		Atlas-SNP	.											.	SLC14A1	84	.	0			c.C285A						.						117.0	105.0	109.0					18																	43310402		2203	4300	6503	SO:0001819	synonymous_variant	6563	exon2			TGTCACCGGTGAC	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.117C>A	chr18.hg19:g.43310402C>A		99.0	0.0		97.0	5.0	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Silent	SNP	ENST00000321925.4	hg19	CCDS11925.1																																																																																			.	.		0.478	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
MAPK4	5596	hgsc.bcm.edu	37	18	48255833	48255833	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:48255833T>C	ENST00000400384.2	+	6	2409	c.1373T>C	c.(1372-1374)cTg>cCg	p.L458P	MAPK4_ENST00000592595.1_3'UTR|MAPK4_ENST00000540640.1_Missense_Mutation_p.L247P	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	458					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		AAGCTCATCCTGGACCTGTCG	0.716																																					p.L458P		Atlas-SNP	.											.	MAPK4	75	.	0			c.T1373C						.						6.0	8.0	7.0					18																	48255833		1977	4100	6077	SO:0001583	missense	5596	exon6			TCATCCTGGACCT	X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"""Mitogen-activated protein kinase cascade / Kinases"""	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.1373T>C	chr18.hg19:g.48255833T>C	ENSP00000383234:p.Leu458Pro	63.0	0.0		66.0	4.0	NM_002747	A1A4C4|Q0VG04	Missense_Mutation	SNP	ENST00000400384.2	hg19	CCDS42437.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.623861	0.87460	.	.	ENSG00000141639	ENST00000400384;ENST00000540640	T;T	0.77489	-1.1;0.86	5.36	5.36	0.76844	.	0.300400	0.23000	N	0.053089	T	0.78285	0.4259	N	0.24115	0.695	0.80722	D	1	D	0.63880	0.993	P	0.59056	0.851	T	0.81424	-0.0939	10	0.87932	D	0	-28.2539	14.3448	0.66654	0.0:0.0:0.0:1.0	.	458	P31152	MK04_HUMAN	P	458;247	ENSP00000383234:L458P;ENSP00000439231:L247P	ENSP00000383234:L458P	L	+	2	0	MAPK4	46509831	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.865000	0.87049	2.010000	0.58986	0.459000	0.35465	CTG	.	.		0.716	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747	
ZNF532	55205	hgsc.bcm.edu	37	18	56586800	56586800	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:56586800G>T	ENST00000336078.4	+	4	2057	c.1281G>T	c.(1279-1281)gcG>gcT	p.A427A	ZNF532_ENST00000591808.1_Silent_p.A427A|ZNF532_ENST00000591230.1_Silent_p.A427A|ZNF532_ENST00000591083.1_Silent_p.A427A|ZNF532_ENST00000589288.1_Silent_p.A427A	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	427					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TCCAGTCTGCGGTCGTGACCA	0.602																																					p.A427A		Atlas-SNP	.											ZNF532,caecum,carcinoma,0,1	ZNF532	108	.	0			c.G1281T						.						36.0	32.0	33.0					18																	56586800		2203	4300	6503	SO:0001819	synonymous_variant	55205	exon4			GTCTGCGGTCGTG	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.1281G>T	chr18.hg19:g.56586800G>T		103.0	0.0		97.0	4.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Silent	SNP	ENST00000336078.4	hg19	CCDS11969.1																																																																																			.	.		0.602	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
FAM69C	125704	hgsc.bcm.edu	37	18	72114420	72114420	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:72114420T>C	ENST00000343998.6	-	2	305	c.297A>G	c.(295-297)agA>agG	p.R99R	FAM69C_ENST00000400291.2_Intron	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	99						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|ovary(2)	5						CCTTCTTGCCTCTGTTGTAGT	0.667																																					p.R99R		Atlas-SNP	.											.	FAM69C	45	.	0			c.A297G						.						12.0	13.0	13.0					18																	72114420		689	1591	2280	SO:0001819	synonymous_variant	125704	exon2			CTTGCCTCTGTTG	BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"""chromosome 18 open reading frame 51"""	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.297A>G	chr18.hg19:g.72114420T>C		50.0	0.0		55.0	4.0	NM_001044369		Silent	SNP	ENST00000343998.6	hg19	CCDS42445.2																																																																																			.	.		0.667	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931	
CTDP1	9150	hgsc.bcm.edu	37	18	77488935	77488935	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr18:77488935T>C	ENST00000299543.7	+	11	2593	c.2446T>C	c.(2446-2448)Ttt>Ctt	p.F816L	CTDP1_ENST00000075430.7_Intron	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	816					exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		GCCGCAGATGTTTGGTGAAGA	0.547																																					p.F816L		Atlas-SNP	.											.	CTDP1	67	.	0			c.T2446C						.						183.0	201.0	195.0					18																	77488935		2203	4300	6503	SO:0001583	missense	9150	exon11			CAGATGTTTGGTG	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.2446T>C	chr18.hg19:g.77488935T>C	ENSP00000299543:p.Phe816Leu	63.0	0.0		73.0	4.0	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	hg19	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.286684	0.23478	.	.	ENSG00000060069	ENST00000299543	T	0.53423	0.62	5.26	2.75	0.32379	FCP1-like phosphatase, C-terminal (1);	0.764123	0.12984	N	0.423034	T	0.40694	0.1127	L	0.60455	1.87	0.80722	D	1	B;B	0.20550	0.01;0.046	B;B	0.22601	0.006;0.04	T	0.09292	-1.0681	10	0.21014	T	0.42	-2.5086	7.2897	0.26360	0.0:0.0794:0.1441:0.7765	.	697;816	Q9Y5B0-3;Q9Y5B0	.;CTDP1_HUMAN	L	816	ENSP00000299543:F816L	ENSP00000299543:F816L	F	+	1	0	CTDP1	75589923	1.000000	0.71417	0.969000	0.41365	0.033000	0.12548	2.202000	0.42743	0.280000	0.22209	0.496000	0.49642	TTT	.	.		0.547	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
SHC2	25759	hgsc.bcm.edu	37	19	422413	422413	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:422413C>A	ENST00000264554.6	-	11	1352	c.1353G>T	c.(1351-1353)gcG>gcT	p.A451A		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	451	CH1.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACGCCTGCCGCCACTGAGC	0.687																																					p.A451A		Atlas-SNP	.											.	SHC2	47	.	0			c.G1353T						.																																			SO:0001819	synonymous_variant	25759	exon11			GCCTGCCGCCACT	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"""SH2 domain containing"""	29869	protein-coding gene	gene with protein product	"""neuronal Shc adaptor homolog"""	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1353G>T	chr19.hg19:g.422413C>A		88.0	0.0		98.0	4.0	NM_012435	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	hg19	CCDS45891.1																																																																																			.	.		0.687	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3		
AP3D1	8943	hgsc.bcm.edu	37	19	2138617	2138617	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:2138617C>T	ENST00000345016.5	-	2	424		c.e2+1		AP3D1_ENST00000356926.4_Splice_Site|AP3D1_ENST00000350812.6_Splice_Site|AP3D1_ENST00000355272.6_Splice_Site	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit						anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCACTTACATACGTCAGC	0.537																																					.		Atlas-SNP	.											.	AP3D1	81	.	0			c.192+1G>A						.						104.0	110.0	108.0					19																	2138617		2179	4260	6439	SO:0001630	splice_region_variant	8943	exon3			CACTTACATACGT	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.192+1G>A	chr19.hg19:g.2138617C>T		72.0	0.0		101.0	7.0	NM_003938	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Splice_Site	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.673503	0.67928	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2978	0.90153	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AP3D1	2089617	1.000000	0.71417	0.110000	0.21437	0.587000	0.36485	7.379000	0.79691	2.633000	0.89246	0.563000	0.77884	.	.	.		0.537	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		Intron
CACTIN	58509	hgsc.bcm.edu	37	19	3626642	3626642	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:3626642C>T	ENST00000429344.2	-	1	171	c.119G>A	c.(118-120)cGg>cAg	p.R40Q	CACTIN_ENST00000221899.3_5'UTR|CACTIN_ENST00000248420.5_Missense_Mutation_p.R40Q	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	40					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)										CTCGTCCTCCCGGCGCCGTCG	0.761																																					p.R40Q		Atlas-SNP	.											.	.	.	.	0			c.G119A						.						4.0	6.0	5.0					19																	3626642		1821	3910	5731	SO:0001583	missense	58509	exon1			TCCTCCCGGCGCC	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.119G>A	chr19.hg19:g.3626642C>T	ENSP00000415078:p.Arg40Gln	29.0	0.0		35.0	5.0	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	hg19	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943503	0.53079	.	.	ENSG00000105298	ENST00000429344;ENST00000248420	.	.	.	4.74	3.68	0.42216	.	.	.	.	.	T	0.15478	0.0373	N	0.08118	0	0.26132	N	0.980404	B	0.32731	0.382	B	0.23018	0.043	T	0.06180	-1.0841	8	0.15499	T	0.54	.	9.4039	0.38449	0.0:0.8936:0.0:0.1064	.	40	Q8WUQ7	CS029_HUMAN	Q	40	.	ENSP00000248420:R40Q	R	-	2	0	C19orf29	3577642	0.999000	0.42202	1.000000	0.80357	0.935000	0.57460	2.971000	0.49248	2.352000	0.79861	0.555000	0.69702	CGG	.	.		0.761	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
SIRT6	51548	hgsc.bcm.edu	37	19	4179153	4179153	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:4179153A>G	ENST00000337491.2	-	3	389	c.325T>C	c.(325-327)Ttc>Ctc	p.F109L	SIRT6_ENST00000305232.6_Missense_Mutation_p.F109L|SIRT6_ENST00000381935.3_Missense_Mutation_p.F37L|SIRT6_ENST00000601488.1_Intron|SIRT6_ENST00000594279.1_Missense_Mutation_p.F37L	NM_016539.2	NP_057623.2	Q8N6T7	SIR6_HUMAN	sirtuin 6	109	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|protein ADP-ribosylation (GO:0006471)|regulation of double-strand break repair via homologous recombination (GO:0010569)	nuclear telomeric heterochromatin (GO:0005724)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|lung(4)|ovary(1)|skin(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.023)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGACCAGGAAGCGGAGGAGG	0.677																																					p.F109L		Atlas-SNP	.											.	SIRT6	16	.	0			c.T325C						.						25.0	23.0	23.0					19																	4179153		2203	4300	6503	SO:0001583	missense	51548	exon3			CCAGGAAGCGGAG	AF233396	CCDS12122.1, CCDS54199.1	19p13.3	2010-06-25	2010-06-25			ENSG00000077463			14934	protein-coding gene	gene with protein product		606211	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 6"", ""sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae)"""			10873683	Standard	NM_016539		Approved		uc002lzo.3	Q8N6T7		ENST00000337491.2:c.325T>C	chr19.hg19:g.4179153A>G	ENSP00000337332:p.Phe109Leu	67.0	0.0		93.0	5.0	NM_016539	B2RCD0|O75291|Q6IAF5|Q6PK99|Q8NCD2|Q9BSI5|Q9BWP3|Q9NRC7|Q9UQD1	Missense_Mutation	SNP	ENST00000337491.2	hg19	CCDS12122.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.587910	0.86851	.	.	ENSG00000077463	ENST00000337491;ENST00000305232;ENST00000381935	T;T;T	0.17370	2.28;2.28;2.28	4.97	4.97	0.65823	.	0.170832	0.53938	D	0.000060	T	0.27349	0.0671	L	0.41824	1.3	0.51767	D	0.999936	P;D;D	0.71674	0.882;0.991;0.998	P;P;D	0.65443	0.722;0.848;0.935	T	0.03443	-1.1036	10	0.11485	T	0.65	-27.9351	13.4809	0.61334	1.0:0.0:0.0:0.0	.	109;109;37	Q8N6T7-2;Q8N6T7;B7Z5U1	.;SIRT6_HUMAN;.	L	109;109;37	ENSP00000337332:F109L;ENSP00000305310:F109L;ENSP00000371360:F37L	ENSP00000305310:F109L	F	-	1	0	SIRT6	4130153	1.000000	0.71417	0.961000	0.40146	0.724000	0.41520	6.898000	0.75676	1.877000	0.54381	0.454000	0.30748	TTC	.	.		0.677	SIRT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457931.2		
PRR22	163154	hgsc.bcm.edu	37	19	5783322	5783322	+	Silent	SNP	C	C	A	rs188791439	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:5783322C>A	ENST00000419421.2	-	3	1040	c.936G>T	c.(934-936)ccG>ccT	p.P312P		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	312										endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						CAGGCAGGGCCGGCCCAGGGA	0.642																																					p.P312P		Atlas-SNP	.											.	PRR22	25	.	0			c.G936T						.						38.0	42.0	41.0					19																	5783322		2203	4297	6500	SO:0001819	synonymous_variant	163154	exon3			CAGGGCCGGCCCA	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.936G>T	chr19.hg19:g.5783322C>A		66.0	0.0		85.0	4.0	NM_001134316	E9PB31	Silent	SNP	ENST00000419421.2	hg19	CCDS45933.1																																																																																			.	C|0.997;T|0.003		0.642	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
XAB2	56949	hgsc.bcm.edu	37	19	7691045	7691045	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:7691045T>C	ENST00000358368.4	-	5	671	c.634A>G	c.(634-636)Aag>Gag	p.K212E	XAB2_ENST00000534844.1_Missense_Mutation_p.K209E	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	212					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						TTGCCGGCCTTAGACACGAAA	0.642								Direct reversal of damage;Nucleotide excision repair (NER)																													p.K212E		Atlas-SNP	.											.	XAB2	69	.	0			c.A634G						.						71.0	77.0	75.0					19																	7691045		2203	4299	6502	SO:0001583	missense	56949	exon5			CGGCCTTAGACAC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.634A>G	chr19.hg19:g.7691045T>C	ENSP00000351137:p.Lys212Glu	90.0	0.0		101.0	41.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	hg19	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	T	8.852	0.944764	0.18356	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.62941	-0.01;-0.01	4.96	3.95	0.45737	.	0.000000	0.85682	D	0.000000	T	0.54565	0.1866	M	0.63169	1.94	0.49299	D	0.999776	B	0.20780	0.048	B	0.13407	0.009	T	0.47736	-0.9094	10	0.28530	T	0.3	-47.5253	8.3945	0.32548	0.0:0.0911:0.0:0.9089	.	212	Q9HCS7	SYF1_HUMAN	E	212;209	ENSP00000351137:K212E;ENSP00000438225:K209E	ENSP00000351137:K212E	K	-	1	0	XAB2	7597045	1.000000	0.71417	0.993000	0.49108	0.025000	0.11179	7.454000	0.80714	0.756000	0.33013	-0.388000	0.06559	AAG	.	.		0.642	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
COL5A3	50509	hgsc.bcm.edu	37	19	10106242	10106242	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10106242T>C	ENST00000264828.3	-	16	1670	c.1585A>G	c.(1585-1587)Atg>Gtg	p.M529V	CTD-2553C6.1_ENST00000592332.1_RNA	NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	529	Collagen-like 2.|Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCACTCACCATCTTGCCCACT	0.552																																					p.M529V		Atlas-SNP	.											.	COL5A3	243	.	0			c.A1585G						.						75.0	59.0	64.0					19																	10106242		2203	4300	6503	SO:0001583	missense	50509	exon16			TCACCATCTTGCC	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.1585A>G	chr19.hg19:g.10106242T>C	ENSP00000264828:p.Met529Val	55.0	0.0		80.0	4.0	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.174270	0.38413	.	.	ENSG00000080573	ENST00000264828	D	0.89617	-2.54	5.06	3.93	0.45458	.	0.370933	0.26069	N	0.026526	T	0.78457	0.4286	N	0.16166	0.38	0.21675	N	0.999594	B	0.27013	0.166	B	0.28916	0.096	T	0.69359	-0.5166	10	0.48119	T	0.1	.	8.2267	0.31572	0.0:0.0:0.2636:0.7364	.	529	P25940	CO5A3_HUMAN	V	529	ENSP00000264828:M529V	ENSP00000264828:M529V	M	-	1	0	COL5A3	9967242	0.989000	0.36119	1.000000	0.80357	0.933000	0.57130	1.365000	0.34182	2.038000	0.60285	0.533000	0.62120	ATG	.	.		0.552	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
RDH8	50700	hgsc.bcm.edu	37	19	10131464	10131464	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10131464G>A	ENST00000171214.1	+	4	771	c.522G>A	c.(520-522)ctG>ctA	p.L174L	RDH8_ENST00000591589.1_Silent_p.L194L	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	174					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TCCAGCTGCTGCAGTTCAACA	0.567																																					p.L194L		Atlas-SNP	.											.	RDH8	51	.	0			c.G582A						.						67.0	54.0	58.0					19																	10131464		2203	4300	6503	SO:0001819	synonymous_variant	50700	exon4			GCTGCTGCAGTTC	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	14423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 28C, member 2"""	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.522G>A	chr19.hg19:g.10131464G>A		101.0	0.0		80.0	4.0	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	hg19																																																																																				.	.		0.567	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
TYK2	7297	hgsc.bcm.edu	37	19	10476357	10476357	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10476357G>A	ENST00000525621.1	-	7	1328	c.847C>T	c.(847-849)Ctg>Ttg	p.L283L	TYK2_ENST00000524462.1_Silent_p.L98L|TYK2_ENST00000529370.1_Silent_p.L283L|TYK2_ENST00000264818.6_Silent_p.L283L	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	283	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GCCTGGGCCAGCAGCCTCAGG	0.672																																					p.L283L		Atlas-SNP	.											.	TYK2	126	.	0			c.C847T						.						19.0	22.0	21.0					19																	10476357		2201	4296	6497	SO:0001819	synonymous_variant	7297	exon7			GGGCCAGCAGCCT		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.847C>T	chr19.hg19:g.10476357G>A		93.0	0.0		93.0	45.0	NM_003331	Q6QB10|Q96CH0	Silent	SNP	ENST00000525621.1	hg19	CCDS12236.1																																																																																			.	.		0.672	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
ILF3	3609	hgsc.bcm.edu	37	19	10793837	10793837	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:10793837G>T	ENST00000590261.1	+	13	1573	c.1573G>T	c.(1573-1575)Ggc>Tgc	p.G525C	ILF3_ENST00000250241.8_Missense_Mutation_p.G525C|ILF3_ENST00000589998.1_Missense_Mutation_p.G525C|ILF3_ENST00000449870.1_Missense_Mutation_p.G529C|ILF3_ENST00000407004.3_Missense_Mutation_p.G529C|ILF3_ENST00000592763.1_Missense_Mutation_p.G529C|ILF3_ENST00000420083.1_Missense_Mutation_p.G525C|ILF3_ENST00000588657.1_Missense_Mutation_p.G529C|ILF3_ENST00000318511.3_Missense_Mutation_p.G525C			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	525	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			GACAAAGCACGGCAAGAACCC	0.552																																					p.G529C		Atlas-SNP	.											.	ILF3	99	.	0			c.G1585T						.						95.0	98.0	97.0					19																	10793837		2203	4300	6503	SO:0001583	missense	3609	exon14			AAGCACGGCAAGA	U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 4"""	603182	"""interleukin enhancer binding factor 3, 90kD"""			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.1573G>T	chr19.hg19:g.10793837G>T	ENSP00000468156:p.Gly525Cys	84.0	0.0		99.0	4.0	NM_017620	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Missense_Mutation	SNP	ENST00000590261.1	hg19	CCDS12246.1	.	.	.	.	.	.	.	.	.	.	G	33	5.284864	0.95517	.	.	ENSG00000129351	ENST00000336059;ENST00000449870;ENST00000318511;ENST00000420083;ENST00000407004;ENST00000250241	T;T;T;T;T	0.19250	2.18;2.16;2.18;2.21;2.18	5.83	5.83	0.93111	Double-stranded RNA-binding (2);Double-stranded RNA-binding-like (1);	0.113792	0.64402	D	0.000011	T	0.54951	0.1890	M	0.87180	2.865	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D	0.97110	1.0;0.995;0.995;0.994;0.973;0.987	T	0.60403	-0.7270	10	0.87932	D	0	.	18.8865	0.92379	0.0:0.0:1.0:0.0	.	529;529;525;529;525;525	Q12906-4;G5E9M5;Q12906;Q12906-6;Q12906-2;Q12906-5	.;.;ILF3_HUMAN;.;.;.	C	525;529;525;525;529;525	ENSP00000404121:G529C;ENSP00000315205:G525C;ENSP00000405436:G525C;ENSP00000384660:G529C;ENSP00000250241:G525C	ENSP00000250241:G525C	G	+	1	0	ILF3	10654837	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	9.771000	0.98977	2.761000	0.94854	0.650000	0.86243	GGC	.	.		0.552	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1		
ZNF20	7568	hgsc.bcm.edu	37	19	12243683	12243683	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:12243683T>C	ENST00000334213.5	-	4	1542	c.1318A>G	c.(1318-1320)Ata>Gta	p.I440V	ZNF20_ENST00000485451.1_5'Flank|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000600335.1_Intron	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	440					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						CTTTCATGTATATGCAAGGAA	0.418																																					p.I440V		Atlas-SNP	.											.	ZNF20	86	.	0			c.A1318G						.						93.0	98.0	96.0					19																	12243683		2187	4295	6482	SO:0001583	missense	7568	exon4			CATGTATATGCAA	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"""Zinc fingers, C2H2-type"", ""-"""	12992	protein-coding gene	gene with protein product		194557	"""zinc finger protein 20 (KOX 13)"""				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.1318A>G	chr19.hg19:g.12243683T>C	ENSP00000335437:p.Ile440Val	75.0	0.0		89.0	4.0	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	hg19	CCDS45986.1	.	.	.	.	.	.	.	.	.	.	T	4.502	0.093141	0.08632	.	.	ENSG00000132010	ENST00000334213;ENST00000292241	T	0.07327	3.2	0.94	-0.317	0.12736	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03136	0.0092	N	0.04320	-0.23	0.09310	N	1	B	0.18461	0.028	B	0.20767	0.031	T	0.47560	-0.9108	9	0.19147	T	0.46	.	4.1968	0.10447	0.3019:0.0:0.0:0.6981	.	440	P17024	ZNF20_HUMAN	V	440	ENSP00000335437:I440V	ENSP00000292241:I440V	I	-	1	0	ZNF20	12104683	0.000000	0.05858	0.001000	0.08648	0.918000	0.54935	-7.956000	0.00027	-0.189000	0.10482	0.260000	0.18958	ATA	.	.		0.418	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143	
LPHN1	22859	hgsc.bcm.edu	37	19	14273762	14273762	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:14273762C>A	ENST00000340736.6	-	6	1163	c.866G>T	c.(865-867)cGg>cTg	p.R289L	CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.R284L|LPHN1_ENST00000591528.1_5'UTR	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	289	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CACCACCAGCCGCCCGTTGTT	0.632																																					p.R289L		Atlas-SNP	.											.	LPHN1	107	.	0			c.G866T						.						88.0	63.0	71.0					19																	14273762		2203	4300	6503	SO:0001583	missense	22859	exon6			ACCAGCCGCCCGT	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.866G>T	chr19.hg19:g.14273762C>A	ENSP00000340688:p.Arg289Leu	62.0	0.0		89.0	4.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	C	33	5.194948	0.94960	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	D;D	0.89050	-2.46;-2.46	5.27	5.27	0.74061	Olfactomedin-like (3);	0.000000	0.64402	D	0.000001	D	0.92067	0.7486	M	0.62016	1.91	0.80722	D	1	P;D	0.57571	0.888;0.98	P;P	0.56823	0.614;0.807	D	0.92831	0.6280	10	0.72032	D	0.01	.	16.3786	0.83431	0.0:1.0:0.0:0.0	.	284;289	O94910-2;O94910	.;LPHN1_HUMAN	L	289;284	ENSP00000340688:R289L;ENSP00000355328:R284L	ENSP00000340688:R289L	R	-	2	0	LPHN1	14134762	0.902000	0.30710	1.000000	0.80357	0.996000	0.88848	2.133000	0.42093	2.450000	0.82876	0.655000	0.94253	CGG	.	.		0.632	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
EMR3	84658	hgsc.bcm.edu	37	19	14765979	14765979	+	Splice_Site	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:14765979T>A	ENST00000253673.5	-	6	494		c.e6-2		EMR3_ENST00000344373.4_Splice_Site|EMR3_ENST00000443157.2_Intron|EMR3_ENST00000599900.1_Intron	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3						G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						CTTTTGCAGCTTTGAAGACAT	0.378																																					.		Atlas-SNP	.											.	EMR3	99	.	0			c.394-2A>T						.						80.0	78.0	79.0					19																	14765979		2202	4299	6501	SO:0001630	splice_region_variant	84658	exon7			TGCAGCTTTGAAG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.394-2A>T	chr19.hg19:g.14765979T>A		259.0	1.0		309.0	135.0	NM_032571		Splice_Site	SNP	ENST00000253673.5	hg19	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	T	14.57	2.574356	0.45902	.	.	ENSG00000131355	ENST00000253673;ENST00000344373	.	.	.	2.99	2.99	0.34606	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.835	0.29365	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EMR3	14626979	1.000000	0.71417	0.880000	0.34516	0.430000	0.31655	2.085000	0.41634	1.623000	0.50342	0.533000	0.62120	.	.	.		0.378	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	Intron
ZNF333	84449	hgsc.bcm.edu	37	19	14815924	14815924	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:14815924C>T	ENST00000292530.6	+	6	456	c.365C>T	c.(364-366)cCa>cTa	p.P122L	ZNF333_ENST00000601134.1_Silent_p.T62T|ZNF333_ENST00000536363.1_Missense_Mutation_p.P13L|ZNF333_ENST00000540689.2_Missense_Mutation_p.P122L	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	122					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						AGGGAGACACCATTGACTCGA	0.607																																					p.P122L	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.C365T						.						56.0	50.0	52.0					19																	14815924		2203	4300	6503	SO:0001583	missense	84449	exon6			AGACACCATTGAC		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"""Zinc fingers, C2H2-type"", ""-"""	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.365C>T	chr19.hg19:g.14815924C>T	ENSP00000292530:p.Pro122Leu	90.0	0.0		72.0	4.0	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Missense_Mutation	SNP	ENST00000292530.6	hg19	CCDS12316.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108868	0.37242	.	.	ENSG00000160961	ENST00000392987;ENST00000536363;ENST00000540689;ENST00000292530	T;T;T	0.05855	3.38;5.9;3.42	1.94	-1.49	0.08718	.	.	.	.	.	T	0.03348	0.0097	N	0.24115	0.695	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.10450	0.003;0.005	T	0.48352	-0.9043	9	0.08179	T	0.78	.	5.0306	0.14407	0.0:0.4861:0.0:0.5139	.	122;122	Q96JL9;Q6P2E6	ZN333_HUMAN;.	L	122;13;122;122	ENSP00000439749:P13L;ENSP00000438130:P122L;ENSP00000292530:P122L	ENSP00000292530:P122L	P	+	2	0	ZNF333	14676924	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.162000	0.10012	-0.288000	0.09051	-0.929000	0.02709	CCA	.	.		0.607	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433	
FCHO1	23149	hgsc.bcm.edu	37	19	17892040	17892040	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:17892040A>G	ENST00000596536.1	+	21	1911	c.1628A>G	c.(1627-1629)gAc>gGc	p.D543G	FCHO1_ENST00000389133.4_Splice_Site_p.D543G|FCHO1_ENST00000597512.1_Splice_Site_p.D550G|FCHO1_ENST00000252771.7_Splice_Site_p.D543G|FCHO1_ENST00000600676.1_Splice_Site_p.D543G|FCHO1_ENST00000539407.1_Splice_Site_p.D543G|FCHO1_ENST00000596951.1_Splice_Site_p.D543G|FCHO1_ENST00000594202.1_Splice_Site_p.D543G|FCHO1_ENST00000595033.1_Splice_Site_p.D493G	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	543	Pro-rich.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						TCGCTCCTAGACCTGATGCCT	0.627																																					p.D543G		Atlas-SNP	.											.	FCHO1	69	.	0			c.A1628G						.						65.0	69.0	68.0					19																	17892040		2203	4300	6503	SO:0001630	splice_region_variant	23149	exon20			TCCTAGACCTGAT	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.1628-1A>G	chr19.hg19:g.17892040A>G		49.0	0.0		74.0	4.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.262610	0.23051	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.34667	1.35;1.35;1.35	4.68	4.68	0.58851	.	2.071930	0.02799	U	0.122929	T	0.36082	0.0954	L	0.44542	1.39	0.09310	N	0.999997	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.21999	-1.0229	9	.	.	.	.	10.4931	0.44762	1.0:0.0:0.0:0.0	.	543;543	O14526;O14526-2	FCHO1_HUMAN;.	G	543	ENSP00000252771:D543G;ENSP00000373785:D543G;ENSP00000437978:D543G	.	D	+	2	0	FCHO1	17753040	0.678000	0.27586	0.085000	0.20634	0.217000	0.24651	1.511000	0.35801	1.741000	0.51731	0.402000	0.26972	GAC	.	.		0.627	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	Missense_Mutation
SLC5A5	6528	hgsc.bcm.edu	37	19	17988895	17988895	+	Missense_Mutation	SNP	C	C	A	rs149570759		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:17988895C>A	ENST00000222248.3	+	7	1309	c.962C>A	c.(961-963)cCa>cAa	p.P321Q		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	321					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)	p.P321L(1)		NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						ATCTCTGCCCCAGACCAGGTG	0.602																																					p.P321Q	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											SLC5A5,arm,malignant_melanoma,0,1	SLC5A5	67	.	1	Substitution - Missense(1)	skin(1)	c.C962A						.						64.0	52.0	56.0					19																	17988895		2203	4300	6503	SO:0001583	missense	6528	exon7			CTGCCCCAGACCA		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.962C>A	chr19.hg19:g.17988895C>A	ENSP00000222248:p.Pro321Gln	36.0	0.0		35.0	4.0	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	hg19	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344851	0.61073	.	.	ENSG00000105641	ENST00000222248	D	0.88124	-2.34	4.87	4.87	0.63330	.	0.172230	0.50627	D	0.000101	D	0.92309	0.7560	M	0.87097	2.86	0.80722	D	1	P	0.42078	0.77	P	0.52031	0.688	D	0.92576	0.6070	10	0.48119	T	0.1	.	15.607	0.76682	0.0:1.0:0.0:0.0	.	321	Q92911	SC5A5_HUMAN	Q	321	ENSP00000222248:P321Q	ENSP00000222248:P321Q	P	+	2	0	SLC5A5	17849895	0.988000	0.35896	0.983000	0.44433	0.145000	0.21501	5.721000	0.68477	2.557000	0.86248	0.555000	0.69702	CCA	.	.		0.602	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
UPF1	5976	hgsc.bcm.edu	37	19	18963017	18963017	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:18963017G>T	ENST00000599848.1	+	6	1093	c.884G>T	c.(883-885)cGg>cTg	p.R295L	UPF1_ENST00000262803.5_Missense_Mutation_p.R295L|UPF1_ENST00000600310.1_3'UTR			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	295	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GTCCTCCTGCGGTACGAGGAC	0.607																																					p.R295L		Atlas-SNP	.											.	UPF1	88	.	0			c.G884T						.						88.0	77.0	81.0					19																	18963017		2203	4300	6503	SO:0001583	missense	5976	exon6			TCCTGCGGTACGA	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.884G>T	chr19.hg19:g.18963017G>T	ENSP00000470142:p.Arg295Leu	121.0	0.0		117.0	5.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.6	4.432643	0.83776	.	.	ENSG00000005007	ENST00000262803	D	0.90324	-2.65	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.93400	0.7895	M	0.90425	3.115	0.80722	D	1	P;P	0.42871	0.689;0.792	B;B	0.43413	0.24;0.419	D	0.94873	0.8032	10	0.87932	D	0	-37.4037	17.4668	0.87634	0.0:0.0:1.0:0.0	.	295;295	Q92900;Q92900-2	RENT1_HUMAN;.	L	295	ENSP00000262803:R295L	ENSP00000262803:R295L	R	+	2	0	UPF1	18824017	1.000000	0.71417	0.822000	0.32727	0.390000	0.30446	9.429000	0.97481	2.362000	0.80069	0.561000	0.74099	CGG	.	.		0.607	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911	
NCAN	1463	hgsc.bcm.edu	37	19	19359573	19359573	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:19359573C>A	ENST00000252575.6	+	14	3801	c.3702C>A	c.(3700-3702)taC>taA	p.Y1234*	NCAN_ENST00000538881.1_Nonsense_Mutation_p.Y685*	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1234	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.			Y -> N (in Ref. 1; AAC80576). {ECO:0000305}.	axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	AGGCCAAGTACAATGTCCATG	0.577																																					p.Y1234X		Atlas-SNP	.											.	NCAN	277	.	0			c.C3702A						.						130.0	90.0	104.0					19																	19359573		2203	4300	6503	SO:0001587	stop_gained	1463	exon14			CAAGTACAATGTC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3702C>A	chr19.hg19:g.19359573C>A	ENSP00000252575:p.Tyr1234*	129.0	0.0		126.0	60.0	NM_004386	Q9UPK6	Nonsense_Mutation	SNP	ENST00000252575.6	hg19	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	C	36	5.830964	0.97003	.	.	ENSG00000130287	ENST00000539499;ENST00000252575;ENST00000538881	.	.	.	4.54	0.94	0.19513	.	0.273768	0.19634	N	0.109617	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.0681	0.25164	0.0:0.6342:0.0:0.3658	.	.	.	.	X	1248;1234;685	.	ENSP00000252575:Y1234X	Y	+	3	2	NCAN	19220573	0.974000	0.33945	0.989000	0.46669	0.867000	0.49689	0.350000	0.20079	0.056000	0.16144	-0.293000	0.09583	TAC	.	.		0.577	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
ZNF737	100129842	hgsc.bcm.edu	37	19	20727871	20727871	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:20727871A>G	ENST00000427401.4	-	4	1232	c.1138T>C	c.(1138-1140)Tgg>Cgg	p.W380R		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	380					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TGTGAGGACCAGTTGAAGGCT	0.418																																					p.W380R		Atlas-SNP	.											ZNF737,NS,carcinoma,+1,1	ZNF737	50	.	0			c.T1138C						.						44.0	42.0	43.0					19																	20727871		692	1591	2283	SO:0001583	missense	100129842	exon4			AGGACCAGTTGAA	BC015765	CCDS54238.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.1138T>C	chr19.hg19:g.20727871A>G	ENSP00000395733:p.Trp380Arg	49.0	0.0		50.0	2.0	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	hg19	CCDS54238.1	.	.	.	.	.	.	.	.	.	.	N	0.003	-2.411008	0.00191	.	.	ENSG00000237440	ENST00000427401	T	0.07327	3.2	0.801	0.801	0.18679	.	.	.	.	.	T	0.01523	0.0049	N	0.00155	-1.965	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.47071	-0.9145	9	0.13108	T	0.6	.	5.4149	0.16368	1.0:0.0:0.0:0.0	.	380	C9JHM3	.	R	380	ENSP00000395733:W380R	ENSP00000395733:W380R	W	-	1	0	ZNF737	20519711	0.000000	0.05858	0.789000	0.31954	0.791000	0.44710	-4.572000	0.00214	0.147000	0.19030	0.145000	0.16022	TGG	.	.		0.418	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289	
ZNF99	7652	hgsc.bcm.edu	37	19	22940398	22940398	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:22940398C>T	ENST00000596209.1	-	4	2403	c.2313G>A	c.(2311-2313)aaG>aaA	p.K771K	CTC-451A6.4_ENST00000442497.2_lincRNA|ZNF99_ENST00000397104.3_Silent_p.K680K	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	771					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CTGAGAAATGCTTAAAAGCTT	0.358																																					p.K771K		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	.	0			c.G2313A						.						30.0	32.0	32.0					19																	22940398		1951	4133	6084	SO:0001819	synonymous_variant	7652	exon4			GAAATGCTTAAAA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2313G>A	chr19.hg19:g.22940398C>T		32.0	0.0		44.0	3.0	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	hg19	CCDS59369.1																																																																																			.	.		0.358	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ANKRD27	84079	hgsc.bcm.edu	37	19	33140643	33140643	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:33140643A>G	ENST00000306065.4	-	3	316	c.158T>C	c.(157-159)tTt>tCt	p.F53S	ANKRD27_ENST00000587352.1_Missense_Mutation_p.F53S	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	53					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					GTAGGACTCAAACTGACAAGT	0.448																																					p.F53S		Atlas-SNP	.											.	ANKRD27	86	.	0			c.T158C						.						163.0	167.0	165.0					19																	33140643		2203	4300	6503	SO:0001583	missense	84079	exon3			GACTCAAACTGAC	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.158T>C	chr19.hg19:g.33140643A>G	ENSP00000304292:p.Phe53Ser	72.0	0.0		99.0	4.0	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030480	0.75504	.	.	ENSG00000105186	ENST00000306065	T	0.69926	-0.44	6.16	6.16	0.99307	.	0.000000	0.64402	D	0.000018	T	0.81654	0.4868	M	0.70275	2.135	0.48511	D	0.999661	D	0.89917	1.0	D	0.87578	0.998	T	0.83295	-0.0031	10	0.87932	D	0	-26.6583	16.8061	0.85666	1.0:0.0:0.0:0.0	.	53	Q96NW4	ANR27_HUMAN	S	53	ENSP00000304292:F53S	ENSP00000304292:F53S	F	-	2	0	ANKRD27	37832483	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	6.248000	0.72418	2.367000	0.80283	0.528000	0.53228	TTT	.	.		0.448	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
RHPN2	85415	hgsc.bcm.edu	37	19	33498926	33498926	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:33498926C>A	ENST00000254260.3	-	7	789	c.754G>T	c.(754-756)Gcc>Tcc	p.A252S	RHPN2_ENST00000400226.4_Missense_Mutation_p.A101S	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	252	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					ATACCTGCGGCTCTCTGAAAG	0.622																																					p.A252S		Atlas-SNP	.											.	RHPN2	107	.	0			c.G754T						.						30.0	26.0	27.0					19																	33498926		2203	4299	6502	SO:0001583	missense	85415	exon7			CTGCGGCTCTCTG	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.754G>T	chr19.hg19:g.33498926C>A	ENSP00000254260:p.Ala252Ser	118.0	0.0		159.0	60.0	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	hg19	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.013648	0.35511	.	.	ENSG00000131941	ENST00000254260;ENST00000400226	T;T	0.32023	1.47;1.47	4.21	4.21	0.49690	BRO1 domain (3);	0.163049	0.53938	D	0.000056	T	0.29976	0.0750	L	0.48362	1.52	0.53688	D	0.99997	P	0.36577	0.558	B	0.37267	0.245	T	0.08269	-1.0730	10	0.28530	T	0.3	-15.1431	16.9558	0.86259	0.0:1.0:0.0:0.0	.	252	Q8IUC4	RHPN2_HUMAN	S	252;101	ENSP00000254260:A252S;ENSP00000402244:A101S	ENSP00000254260:A252S	A	-	1	0	RHPN2	38190766	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	4.743000	0.62110	2.079000	0.62486	0.455000	0.32223	GCC	.	.		0.622	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
LSR	51599	hgsc.bcm.edu	37	19	35757273	35757273	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:35757273G>T	ENST00000361790.3	+	6	1093	c.934G>T	c.(934-936)Ggc>Tgc	p.G312C	LSR_ENST00000347609.4_Missense_Mutation_p.G275C|LSR_ENST00000354900.3_Missense_Mutation_p.G293C|USF2_ENST00000379134.3_5'Flank|USF2_ENST00000222305.3_5'Flank|LSR_ENST00000602122.1_Missense_Mutation_p.G293C|LSR_ENST00000360798.3_Missense_Mutation_p.G244C|USF2_ENST00000595068.1_5'Flank|AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000427250.1_Missense_Mutation_p.G156C|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000343550.5_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	312					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTATGCCGCCGGCAAAGCAGC	0.617																																					p.G312C		Atlas-SNP	.											.	LSR	60	.	0			c.G934T						.						85.0	86.0	85.0					19																	35757273		2203	4300	6503	SO:0001583	missense	51599	exon6			GCCGCCGGCAAAG	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29572	protein-coding gene	gene with protein product	"""lipolysis-stimulated remnant"", ""immunoglobulin-like domain containing receptor 3"""					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.934G>T	chr19.hg19:g.35757273G>T	ENSP00000354575:p.Gly312Cys	105.0	0.0		98.0	4.0	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	hg19	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.698566	0.68386	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	T;T;T;T;T	0.73681	-0.04;0.05;-0.51;0.07;-0.77	3.99	3.99	0.46301	.	0.000000	0.85682	D	0.000000	D	0.82337	0.5015	L	0.53249	1.67	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;0.996	D	0.84456	0.0591	10	0.87932	D	0	-27.9253	13.6187	0.62123	0.0:0.0:1.0:0.0	.	250;275;293;244;293;312	Q9BT33;Q86X29-2;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;.;LSR_HUMAN	C	312;293;244;275;156	ENSP00000354575:G312C;ENSP00000346976:G293C;ENSP00000354034:G244C;ENSP00000262627:G275C;ENSP00000394479:G156C	ENSP00000262627:G275C	G	+	1	0	LSR	40449113	1.000000	0.71417	0.937000	0.37676	0.716000	0.41182	7.524000	0.81866	2.025000	0.59659	0.462000	0.41574	GGC	.	.		0.617	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
GAPDHS	26330	hgsc.bcm.edu	37	19	36033226	36033226	+	Missense_Mutation	SNP	A	A	G	rs148474705	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:36033226A>G	ENST00000222286.4	+	5	571	c.455A>G	c.(454-456)gAg>gGg	p.E152G	AD000090.2_ENST00000590717.1_RNA|AD000090.2_ENST00000588286.1_RNA|AD000090.2_ENST00000590125.1_RNA|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000589137.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	152					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CACAGCAAAGAGCCCAAACAG	0.597																																					p.E152G		Atlas-SNP	.											.	GAPDHS	34	.	0			c.A455G						.						47.0	46.0	46.0					19																	36033226		2203	4300	6503	SO:0001583	missense	26330	exon5			GCAAAGAGCCCAA	AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.455A>G	chr19.hg19:g.36033226A>G	ENSP00000222286:p.Glu152Gly	82.0	0.0		121.0	5.0	NM_014364	B2RC82|O60823|Q6JTT9|Q9HCU6	Missense_Mutation	SNP	ENST00000222286.4	hg19	CCDS12465.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.260585	0.23051	.	.	ENSG00000105679	ENST00000222286	T	0.39997	1.05	4.47	2.27	0.28462	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain (2);NAD(P)-binding domain (1);	0.565559	0.18952	N	0.126644	T	0.32010	0.0815	L	0.39633	1.23	0.25093	N	0.990842	B	0.29212	0.237	B	0.33042	0.157	T	0.29792	-1.0000	10	0.87932	D	0	-4.4196	5.0327	0.14419	0.6245:0.1917:0.0:0.1838	.	152	O14556	G3PT_HUMAN	G	152	ENSP00000222286:E152G	ENSP00000222286:E152G	E	+	2	0	GAPDHS	40725066	0.997000	0.39634	0.965000	0.40720	0.028000	0.11728	4.661000	0.61518	0.294000	0.22547	-0.648000	0.03929	GAG	.	A|0.999;C|0.001		0.597	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364	
ZFP82	284406	hgsc.bcm.edu	37	19	36884281	36884281	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:36884281A>G	ENST00000392161.3	-	5	1203	c.961T>C	c.(961-963)Tgt>Cgt	p.C321R	ZFP82_ENST00000392171.1_Missense_Mutation_p.C321R	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CCAGAGCCACACAAAAAGGCC	0.453																																					p.C321R		Atlas-SNP	.											.	ZFP82	71	.	0			c.T961C						.						116.0	116.0	116.0					19																	36884281		2203	4300	6503	SO:0001583	missense	284406	exon5			AGCCACACAAAAA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"""Zinc fingers, C2H2-type"", ""-"""	28682	protein-coding gene	gene with protein product			"""zinc finger protein 545"", ""zinc finger protein 82 homolog (mouse)"", ""zinc finger protein 82"""	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.961T>C	chr19.hg19:g.36884281A>G	ENSP00000431265:p.Cys321Arg	92.0	0.0		117.0	5.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	A	9.204	1.029132	0.19512	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.07216	3.21;3.21	4.38	4.38	0.52667	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45361	D	0.000370	T	0.03095	0.0091	N	0.01009	-1.055	0.20873	N	0.99984	B	0.32324	0.364	B	0.37943	0.261	T	0.45644	-0.9247	10	0.22109	T	0.4	.	8.5849	0.33653	0.8282:0.0:0.0:0.1718	.	321	Q8N141	ZFP82_HUMAN	R	321	ENSP00000431265:C321R;ENSP00000446080:C321R	ENSP00000431265:C321R	C	-	1	0	ZFP82	41576121	0.000000	0.05858	1.000000	0.80357	0.988000	0.76386	-0.554000	0.06006	1.977000	0.57605	0.533000	0.62120	TGT	.	.		0.453	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466	
FAM98C	147965	hgsc.bcm.edu	37	19	38897603	38897603	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:38897603C>A	ENST00000252530.5	+	7	823	c.804C>A	c.(802-804)acC>acA	p.T268T	FAM98C_ENST00000343358.7_Intron|FAM98C_ENST00000588262.1_Missense_Mutation_p.P135T	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	268										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGGTTCTGACCCCAGAATCGG	0.617																																					p.T268T		Atlas-SNP	.											.	FAM98C	39	.	0			c.C804A						.						116.0	119.0	118.0					19																	38897603		2025	4178	6203	SO:0001819	synonymous_variant	147965	exon7			TCTGACCCCAGAA		CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.804C>A	chr19.hg19:g.38897603C>A		80.0	0.0		96.0	5.0	NM_174905	A6NMW3|Q66K45	Silent	SNP	ENST00000252530.5	hg19	CCDS42562.1																																																																																			.	.		0.617	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905	
RYR1	6261	hgsc.bcm.edu	37	19	38948829	38948829	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:38948829C>A	ENST00000359596.3	+	18	2064	c.2064C>A	c.(2062-2064)acC>acA	p.T688T	RYR1_ENST00000360985.3_Silent_p.T688T|RYR1_ENST00000355481.4_Silent_p.T688T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	688	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.T688T(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGGCCCTCACCGAGGGCTACA	0.627																																					p.T688T		Atlas-SNP	.											RYR1,right_upper_lobe,carcinoma,0,2	RYR1	708	.	1	Substitution - coding silent(1)	lung(1)	c.C2064A						.						56.0	52.0	53.0					19																	38948829		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon18			CCTCACCGAGGGC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2064C>A	chr19.hg19:g.38948829C>A		31.0	0.0		43.0	2.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.627	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
PLEKHG2	64857	hgsc.bcm.edu	37	19	39907025	39907025	+	Missense_Mutation	SNP	G	G	T	rs138517241		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:39907025G>T	ENST00000409794.3	+	5	1367	c.517G>T	c.(517-519)Ggg>Tgg	p.G173W	PLEKHG2_ENST00000409797.2_Missense_Mutation_p.G173W|PLEKHG2_ENST00000378550.1_Missense_Mutation_p.G173W|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.G173W|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.G114W	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	173	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CAGCAGCGCCGGGGGTATTGC	0.667																																					p.G173W		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G517T						.	G	TRP/GLY	0,4406		0,0,2203	67.0	76.0	73.0		517	3.6	0.9	19	dbSNP_134	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PLEKHG2	NM_022835.2	184	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	probably-damaging	173/1387	39907025	3,13003	2203	4300	6503	SO:0001583	missense	64857	exon5			AGCGCCGGGGGTA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.517G>T	chr19.hg19:g.39907025G>T	ENSP00000386733:p.Gly173Trp	125.0	0.0		100.0	4.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	19.01	3.742926	0.69418	0.0	3.49E-4	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000409797;ENST00000451354	T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;1.67	4.68	3.59	0.41128	Dbl homology (DH) domain (5);	0.224873	0.29106	N	0.013135	T	0.72415	0.3457	L	0.58354	1.805	0.39894	D	0.9738	D;D;D	0.76494	0.999;0.997;0.964	D;D;P	0.76071	0.986;0.987;0.883	T	0.73202	-0.4057	10	0.46703	T	0.11	.	11.1867	0.48660	0.0:0.3533:0.6467:0.0	.	173;114;173	Q9H7P9;E7ESZ3;Q9H7P9-2	PKHG2_HUMAN;.;.	W	173;173;173;114;173;174	ENSP00000386733:G173W;ENSP00000392906:G173W;ENSP00000367812:G173W;ENSP00000408857:G114W;ENSP00000386492:G173W;ENSP00000412818:G174W	ENSP00000367812:G173W	G	+	1	0	PLEKHG2	44598865	0.979000	0.34478	0.948000	0.38648	0.814000	0.46013	3.584000	0.53936	2.452000	0.82932	0.491000	0.48974	GGG	.	G|1.000;T|0.000		0.667	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39907052	39907052	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:39907052A>G	ENST00000409794.3	+	5	1394	c.544A>G	c.(544-546)Agg>Ggg	p.R182G	PLEKHG2_ENST00000409797.2_Missense_Mutation_p.R182G|PLEKHG2_ENST00000378550.1_Missense_Mutation_p.R182G|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R182G|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R123G	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	182	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTTCGTGCAGAGGGTGAGTGG	0.672																																					p.R182G		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.A544G						.						51.0	59.0	56.0					19																	39907052		2203	4299	6502	SO:0001583	missense	64857	exon5			GTGCAGAGGGTGA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.544A>G	chr19.hg19:g.39907052A>G	ENSP00000386733:p.Arg182Gly	83.0	0.0		97.0	4.0	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	A	20.4	3.987110	0.74589	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000409797;ENST00000451354	T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;1.52	4.68	2.53	0.30540	Dbl homology (DH) domain (5);	0.000000	0.64402	D	0.000008	T	0.79953	0.4535	M	0.80028	2.48	0.36209	D	0.851219	D;P;P	0.71674	0.998;0.953;0.942	D;D;P	0.80764	0.994;0.945;0.693	T	0.83170	-0.0094	10	0.72032	D	0.01	.	10.7161	0.46013	0.6954:0.3046:0.0:0.0	.	182;123;182	Q9H7P9;E7ESZ3;Q9H7P9-2	PKHG2_HUMAN;.;.	G	182;182;182;123;182;183	ENSP00000386733:R182G;ENSP00000392906:R182G;ENSP00000367812:R182G;ENSP00000408857:R123G;ENSP00000386492:R182G;ENSP00000412818:R183G	ENSP00000367812:R182G	R	+	1	2	PLEKHG2	44598892	0.996000	0.38824	1.000000	0.80357	0.956000	0.61745	2.022000	0.41030	0.282000	0.22254	-0.680000	0.03767	AGG	.	.		0.672	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
FCGBP	8857	hgsc.bcm.edu	37	19	40440523	40440523	+	Start_Codon_SNP	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:40440523C>A	ENST00000221347.6	-	1	10	c.3G>T	c.(1-3)atG>atT	p.M1I		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1						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)			ATAGGGCACCCATGGCTGCAG	0.567																																					p.M1I		Atlas-SNP	.											.	FCGBP	416	.	0			c.G3T						.						67.0	53.0	58.0					19																	40440523		2201	4299	6500	SO:0001582	initiator_codon_variant	8857	exon1			GGCACCCATGGCT	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.3G>T	chr19.hg19:g.40440523C>A	ENSP00000221347:p.Met1Ile	51.0	0.0		57.0	4.0	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.710422	0.30322	.	.	ENSG00000090920	ENST00000221347	T	0.17370	2.28	4.86	4.86	0.63082	.	0.414207	0.19677	U	0.108616	T	0.38214	0.1032	.	.	.	0.80722	D	1	P	0.49447	0.924	P	0.60682	0.878	T	0.08207	-1.0733	9	0.87932	D	0	.	13.7062	0.62641	0.0:1.0:0.0:0.0	.	1	Q9Y6R7	FCGBP_HUMAN	I	1	ENSP00000221347:M1I	ENSP00000221347:M1I	M	-	3	0	FCGBP	45132363	1.000000	0.71417	1.000000	0.80357	0.213000	0.24496	2.029000	0.41098	2.684000	0.91462	0.650000	0.86243	ATG	.	.		0.567	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	Missense_Mutation
CYP2B6	1555	hgsc.bcm.edu	37	19	41518302	41518302	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:41518302A>G	ENST00000324071.4	+	7	1071	c.1064A>G	c.(1063-1065)gAg>gGg	p.E355G	CYP2B6_ENST00000330446.5_Missense_Mutation_p.E155G|CYP2B6_ENST00000593831.1_Missense_Mutation_p.E119G	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	355					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)	GTCATCTATGAGATTCAGAGA	0.532																																					p.E355G		Atlas-SNP	.											.	CYP2B6	79	.	0			c.A1064G						.						121.0	96.0	104.0					19																	41518302		2203	4300	6503	SO:0001583	missense	1555	exon7			TCTATGAGATTCA	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.1064A>G	chr19.hg19:g.41518302A>G	ENSP00000324648:p.Glu355Gly	93.0	0.0		97.0	4.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	hg19	CCDS12570.1	.	.	.	.	.	.	.	.	.	.	.	16.78	3.217813	0.58560	.	.	ENSG00000197408	ENST00000324071;ENST00000330446	D;D	0.97114	-4.25;-4.25	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	D	0.98852	0.9612	H	0.96996	3.92	0.48975	D	0.999733	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99167	1.0863	10	0.87932	D	0	.	11.4609	0.50211	1.0:0.0:0.0:0.0	.	155;355	B4DWP3;P20813	.;CP2B6_HUMAN	G	355;155	ENSP00000324648:E355G;ENSP00000330650:E155G	ENSP00000324648:E355G	E	+	2	0	CYP2B6	46210142	1.000000	0.71417	0.981000	0.43875	0.303000	0.27691	8.505000	0.90515	1.800000	0.52685	0.248000	0.18094	GAG	.	.		0.532	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
ZNF221	7638	hgsc.bcm.edu	37	19	44471269	44471269	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:44471269T>C	ENST00000251269.5	+	6	1943	c.1615T>C	c.(1615-1617)Tgt>Cgt	p.C539R	ZNF221_ENST00000592350.1_Missense_Mutation_p.C539R|ZNF221_ENST00000587682.1_Missense_Mutation_p.C539R	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	539					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				ATGTGAGCAGTGTGAGAAGGG	0.428																																					p.C539R		Atlas-SNP	.											.	ZNF221	59	.	0			c.T1615C						.						97.0	90.0	92.0					19																	44471269		2203	4300	6503	SO:0001583	missense	7638	exon6			GAGCAGTGTGAGA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"""Zinc fingers, C2H2-type"", ""-"""	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1615T>C	chr19.hg19:g.44471269T>C	ENSP00000251269:p.Cys539Arg	87.0	0.0		91.0	4.0	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	t	17.52	3.409350	0.62399	.	.	ENSG00000159905	ENST00000251269	T	0.29655	1.56	2.81	2.81	0.32909	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.58906	0.2155	M	0.90595	3.13	0.53688	D	0.999971	D	0.89917	1.0	D	0.91635	0.999	T	0.65853	-0.6067	9	0.87932	D	0	.	10.1779	0.42950	0.0:0.0:0.0:1.0	.	539	Q9UK13	ZN221_HUMAN	R	539	ENSP00000251269:C539R	ENSP00000251269:C539R	C	+	1	0	ZNF221	49163109	1.000000	0.71417	0.155000	0.22561	0.235000	0.25334	7.212000	0.77941	1.271000	0.44313	0.379000	0.24179	TGT	.	.		0.428	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1		
ZNF223	7766	hgsc.bcm.edu	37	19	44570978	44570978	+	Nonsense_Mutation	SNP	A	A	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:44570978A>T	ENST00000434772.3	+	5	1252	c.997A>T	c.(997-999)Aag>Tag	p.K333*	ZNF223_ENST00000591793.1_Nonsense_Mutation_p.K443*	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GGATTTGTGTAAGCATCAGAC	0.443																																					p.K333X		Atlas-SNP	.											.	ZNF223	61	.	0			c.A997T						.						109.0	107.0	108.0					19																	44570978		2203	4300	6503	SO:0001587	stop_gained	7766	exon5			TTGTGTAAGCATC	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.997A>T	chr19.hg19:g.44570978A>T	ENSP00000401947:p.Lys333*	103.0	0.0		135.0	52.0	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Nonsense_Mutation	SNP	ENST00000434772.3	hg19	CCDS12635.1	.	.	.	.	.	.	.	.	.	.	A	37	6.246649	0.97408	.	.	ENSG00000178386	ENST00000434772	.	.	.	2.46	0.269	0.15631	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.6982	0.17867	0.5965:0.0:0.4035:0.0	.	.	.	.	X	333	.	ENSP00000401947:K333X	K	+	1	0	ZNF223	49262818	0.000000	0.05858	0.001000	0.08648	0.825000	0.46686	-1.667000	0.01961	0.188000	0.20168	0.260000	0.18958	AAG	.	.		0.443	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
ZNF225	7768	hgsc.bcm.edu	37	19	44635250	44635250	+	Silent	SNP	C	C	A	rs201221735		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:44635250C>A	ENST00000262894.6	+	5	763	c.483C>A	c.(481-483)tcC>tcA	p.S161S	ZNF225_ENST00000590612.1_Silent_p.S161S|ZNF225_ENST00000592780.1_3'UTR	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				GTGATGTCTCCGTCCTTGATC	0.413																																					p.S161S		Atlas-SNP	.											.	ZNF225	41	.	0			c.C483A						.						110.0	110.0	110.0					19																	44635250		2032	4213	6245	SO:0001819	synonymous_variant	7768	exon5			TGTCTCCGTCCTT	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"""Zinc fingers, C2H2-type"", ""-"""	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.483C>A	chr19.hg19:g.44635250C>A		103.0	0.0		121.0	5.0	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Silent	SNP	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	C|1.000;T|0.000		0.413	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1		
MARK4	57787	hgsc.bcm.edu	37	19	45801087	45801087	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:45801087T>C	ENST00000262891.4	+	15	2083	c.1752T>C	c.(1750-1752)ggT>ggC	p.G584G	MARK4_ENST00000300843.4_Silent_p.G584G	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	584					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GTGGGGGTGGTGGGGGTGTGC	0.731																																					p.G584G		Atlas-SNP	.											.	MARK4	132	.	0			c.T1752C						.						2.0	3.0	3.0					19																	45801087		1796	3555	5351	SO:0001819	synonymous_variant	57787	exon15			GGGTGGTGGGGGT	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"""MAP/microtubule affinity-regulating kinase like 1"""	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1752T>C	chr19.hg19:g.45801087T>C		46.0	0.0		88.0	7.0	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Silent	SNP	ENST00000262891.4	hg19	CCDS56097.1																																																																																			.	.		0.731	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417	
RSPH6A	81492	hgsc.bcm.edu	37	19	46307718	46307718	+	Missense_Mutation	SNP	C	C	A	rs139803225		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:46307718C>A	ENST00000221538.3	-	3	1587	c.1445G>T	c.(1444-1446)cGg>cTg	p.R482L	RSPH6A_ENST00000600188.1_Missense_Mutation_p.R218L|RSPH6A_ENST00000597055.1_Missense_Mutation_p.R482L	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	482						intracellular (GO:0005622)		p.R482P(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						TATCTGGGCCCGCAGGTAGTT	0.622																																					p.R482L		Atlas-SNP	.											RSPH6A,NS,carcinoma,0,1	RSPH6A	70	.	1	Substitution - Missense(1)	lung(1)	c.G1445T						.						55.0	50.0	52.0					19																	46307718		2203	4300	6503	SO:0001583	missense	81492	exon3			TGGGCCCGCAGGT	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.1445G>T	chr19.hg19:g.46307718C>A	ENSP00000221538:p.Arg482Leu	113.0	0.0		113.0	6.0	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150863	0.78001	.	.	ENSG00000104941	ENST00000221538	T	0.34072	1.38	3.8	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.66346	0.2780	M	0.91818	3.245	0.48135	D	0.99959	D	0.89917	1.0	D	0.91635	0.999	T	0.75249	-0.3384	10	0.87932	D	0	-5.2906	14.008	0.64478	0.0:1.0:0.0:0.0	.	482	Q9H0K4	RSH6A_HUMAN	L	482	ENSP00000221538:R482L	ENSP00000221538:R482L	R	-	2	0	RSPH6A	50999558	1.000000	0.71417	0.988000	0.46212	0.658000	0.38924	7.298000	0.78815	2.428000	0.82296	0.456000	0.33151	CGG	.	C|1.000;G|0.000		0.622	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		
CCDC9	26093	hgsc.bcm.edu	37	19	47764057	47764057	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:47764057T>C	ENST00000221922.6	+	5	645	c.423T>C	c.(421-423)tcT>tcC	p.S141S		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	141	Gly-rich.						poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		CTCACCTCTCTGGAGCTGGAG	0.642																																					p.S141S		Atlas-SNP	.											.	CCDC9	37	.	0			c.T423C						.						36.0	37.0	37.0					19																	47764057		2203	4297	6500	SO:0001819	synonymous_variant	26093	exon5			CCTCTCTGGAGCT	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.423T>C	chr19.hg19:g.47764057T>C		146.0	0.0		143.0	6.0	NM_015603		Silent	SNP	ENST00000221922.6	hg19	CCDS12698.1																																																																																			.	.		0.642	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
LIG1	3978	hgsc.bcm.edu	37	19	48630537	48630537	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:48630537T>C	ENST00000263274.7	-	21	2420	c.2001A>G	c.(1999-2001)ggA>ggG	p.G667G	LIG1_ENST00000536218.1_Silent_p.G599G|CTC-453G23.5_ENST00000596839.1_RNA|LIG1_ENST00000427526.2_Silent_p.G636G|CTC-453G23.5_ENST00000596563.1_RNA	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	667					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	AACTCACCTCTCCATTGAGGT	0.602								Nucleotide excision repair (NER)																													p.G667G		Atlas-SNP	.											.	LIG1	151	.	0			c.A2001G						.						175.0	128.0	144.0					19																	48630537		2203	4300	6503	SO:0001819	synonymous_variant	3978	exon21			CACCTCTCCATTG		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.2001A>G	chr19.hg19:g.48630537T>C		89.0	0.0		98.0	4.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	hg19	CCDS12711.1																																																																																			.	.		0.602	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
FUT1	2523	hgsc.bcm.edu	37	19	49253770	49253770	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49253770C>T	ENST00000310160.3	-	4	1743	c.769G>A	c.(769-771)Gtt>Att	p.V257I	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	257					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		ACCACGAAAACGGGGGCTTCG	0.612																																					p.V257I		Atlas-SNP	.											FUT1,caecum,carcinoma,0,1	FUT1	44	.	0			c.G769A						.						108.0	96.0	100.0					19																	49253770		2203	4300	6503	SO:0001583	missense	2523	exon4			CGAAAACGGGGGC		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"""Blood group antigens"", ""Fucosyltransferases"""	4012	protein-coding gene	gene with protein product		211100	"""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)"", ""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"""	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.769G>A	chr19.hg19:g.49253770C>T	ENSP00000312021:p.Val257Ile	41.0	0.0		48.0	2.0	NM_000148	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	hg19	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	C	4.015	0.000199	0.07819	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.96587	-4.06	4.46	0.0669	0.14363	.	0.649436	0.13918	N	0.353746	D	0.88187	0.6369	N	0.08118	0	0.24263	N	0.995272	B	0.13594	0.008	B	0.12156	0.007	T	0.77864	-0.2429	10	0.22109	T	0.4	-2.9453	8.1744	0.31272	0.0:0.5508:0.0:0.4492	.	257	P19526	FUT1_HUMAN	I	257;247	ENSP00000312021:V257I	ENSP00000312021:V257I	V	-	1	0	FUT1	53945582	0.000000	0.05858	0.861000	0.33841	0.006000	0.05464	-1.446000	0.02398	0.056000	0.16144	-0.484000	0.04775	GTT	.	.		0.612	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148	
TULP2	7288	hgsc.bcm.edu	37	19	49401098	49401098	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49401098T>C	ENST00000221399.3	-	2	172	c.28A>G	c.(28-30)Aga>Gga	p.R10G	NUCB1_ENST00000405315.4_5'Flank|NUCB1_ENST00000407032.1_5'Flank|NUCB1_ENST00000263273.5_5'Flank	NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	10					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		ACTCACTCTCTCATCAATGTG	0.522																																					p.R10G		Atlas-SNP	.											.	TULP2	60	.	0			c.A28G						.						188.0	149.0	162.0					19																	49401098		2203	4300	6503	SO:0001583	missense	7288	exon2			ACTCTCTCATCAA	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.28A>G	chr19.hg19:g.49401098T>C	ENSP00000221399:p.Arg10Gly	63.0	0.0		83.0	4.0	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	hg19	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	T	8.126	0.782051	0.16189	.	.	ENSG00000104804	ENST00000221399;ENST00000518572;ENST00000522945	D;T;T	0.82893	-1.66;2.23;1.46	4.03	4.03	0.46877	.	0.819393	0.10887	N	0.623123	T	0.68952	0.3057	N	0.19112	0.55	0.21105	N	0.999787	B	0.23650	0.089	B	0.17098	0.017	T	0.53005	-0.8499	10	0.13108	T	0.6	.	9.64	0.39833	0.0:0.0:0.0:1.0	.	10	O00295	TULP2_HUMAN	G	10	ENSP00000221399:R10G;ENSP00000428420:R10G;ENSP00000430040:R10G	ENSP00000221399:R10G	R	-	1	2	TULP2	54092910	0.232000	0.23762	0.390000	0.26220	0.004000	0.04260	2.132000	0.42083	2.063000	0.61619	0.448000	0.29417	AGA	.	.		0.522	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
PPFIA3	8541	hgsc.bcm.edu	37	19	49640052	49640052	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49640052G>T	ENST00000334186.4	+	15	2086	c.1737G>T	c.(1735-1737)gaG>gaT	p.E579D	PPFIA3_ENST00000602351.1_Missense_Mutation_p.E579D	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	579					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GCTCCGATGAGGAGGAGGCAG	0.647																																					p.E579D		Atlas-SNP	.											.	PPFIA3	71	.	0			c.G1737T						.						38.0	33.0	35.0					19																	49640052		2198	4300	6498	SO:0001583	missense	8541	exon15			CGATGAGGAGGAG	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"""Sterile alpha motif (SAM) domain containing"""	9247	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3"", ""liprin-alpha 3"", ""liprin"""	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.1737G>T	chr19.hg19:g.49640052G>T	ENSP00000335614:p.Glu579Asp	75.0	0.0		109.0	5.0	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	hg19	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	G	8.109	0.778381	0.16120	.	.	ENSG00000177380	ENST00000334186;ENST00000421230	T	0.52983	0.64	3.31	-0.258	0.12975	.	0.000000	0.47455	U	0.000236	T	0.32882	0.0844	L	0.47078	1.49	0.42488	D	0.992888	B;B;B	0.20261	0.043;0.0;0.0	B;B;B	0.24006	0.05;0.005;0.0	T	0.08249	-1.0731	10	0.13853	T	0.58	-17.3817	6.9779	0.24686	0.5916:0.0:0.4084:0.0	.	503;579;579	B4DEU8;O75145-2;O75145	.;.;LIPA3_HUMAN	D	579;503	ENSP00000335614:E579D	ENSP00000335614:E579D	E	+	3	2	PPFIA3	54331864	0.902000	0.30710	0.998000	0.56505	0.795000	0.44927	-0.020000	0.12525	0.042000	0.15717	0.542000	0.68232	GAG	.	.		0.647	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660	
CD37	951	hgsc.bcm.edu	37	19	49842011	49842011	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:49842011A>G	ENST00000323906.4	+	6	643	c.502A>G	c.(502-504)Aga>Gga	p.R168G	CD37_ENST00000426897.2_Missense_Mutation_p.R100G|CD37_ENST00000598095.1_Missense_Mutation_p.R100G|CTC-301O7.4_ENST00000358234.4_lincRNA|CD37_ENST00000535669.2_Missense_Mutation_p.R168G	NM_001774.2	NP_001765.1	P11049	CD37_HUMAN	CD37 molecule	168					defense response to protozoan (GO:0042832)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|positive regulation of immunoglobulin production (GO:0002639)|regulation of defense response to virus (GO:0050688)|regulation of humoral immune response (GO:0002920)	extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	11		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)		CCTCATCCTGAGAGGTAACGG	0.607																																					p.R168G		Atlas-SNP	.											.	CD37	33	.	0			c.A502G						.						74.0	64.0	67.0					19																	49842011		2203	4300	6503	SO:0001583	missense	951	exon6			ATCCTGAGAGGTA		CCDS12760.1, CCDS46139.1	19p13-q13.4	2013-02-14	2006-03-28			ENSG00000104894		"""CD molecules"", ""Tetraspanins"""	1666	protein-coding gene	gene with protein product		151523	"""CD37 antigen"""			8436422	Standard	XM_005259435		Approved	TSPAN26	uc002pnd.3	P11049		ENST00000323906.4:c.502A>G	chr19.hg19:g.49842011A>G	ENSP00000325708:p.Arg168Gly	76.0	0.0		85.0	4.0	NM_001774	B4DVC1|Q3KPF9	Missense_Mutation	SNP	ENST00000323906.4	hg19	CCDS12760.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217901	0.39201	.	.	ENSG00000104894	ENST00000323906;ENST00000426897;ENST00000535669	T;T;T	0.79247	-1.25;-1.25;-1.25	3.95	2.83	0.33086	Tetraspanin, EC2 domain (1);	1.119980	0.06880	N	0.802384	T	0.71264	0.3319	L	0.50333	1.59	0.09310	N	1	P;B;B;B	0.37276	0.589;0.27;0.27;0.072	B;B;B;B	0.36030	0.216;0.136;0.136;0.067	T	0.61048	-0.7141	10	0.41790	T	0.15	.	6.874	0.24137	0.7627:0.2373:0.0:0.0	.	100;168;168;168	B4DVC1;B7ZAN3;B4DW15;P11049	.;.;.;CD37_HUMAN	G	168;100;168	ENSP00000325708:R168G;ENSP00000413151:R100G;ENSP00000441037:R168G	ENSP00000325708:R168G	R	+	1	2	CD37	54533823	0.074000	0.21230	0.246000	0.24233	0.107000	0.19398	0.809000	0.27168	1.561000	0.49584	0.402000	0.26972	AGA	.	.		0.607	CD37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465532.1		
MYH14	79784	hgsc.bcm.edu	37	19	50775107	50775107	+	Splice_Site	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:50775107A>G	ENST00000596571.1	+	23	3050	c.3050A>G	c.(3049-3051)gAg>gGg	p.E1017G	MYH14_ENST00000262269.8_Splice_Site_p.E1058G|MYH14_ENST00000440075.2_Splice_Site_p.E1058G|MYH14_ENST00000376970.2_Splice_Site_p.E1050G|MYH14_ENST00000425460.1_Splice_Site_p.E1025G|MYH14_ENST00000601313.1_Splice_Site_p.E1058G|MYH14_ENST00000598205.1_Splice_Site_p.E1025G			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1017					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		ACCCCTCAGGAGCGGAAGCTG	0.562																																					p.E1058G		Atlas-SNP	.											.	MYH14	261	.	0			c.A3173G						.						30.0	33.0	32.0					19																	50775107		1997	4159	6156	SO:0001630	splice_region_variant	79784	exon26			CTCAGGAGCGGAA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.3049-1A>G	chr19.hg19:g.50775107A>G		73.0	0.0		90.0	4.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.65|19.65	3.866778|3.866778	0.72065|0.72065	.|.	.|.	ENSG00000105357|ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000262269|ENST00000301415;ENST00000376965	D;D;D;D|.	0.86694|.	-2.16;-2.16;-2.16;-2.16|.	3.14|3.14	3.14|3.14	0.36123|0.36123	.|.	.|.	.|.	.|.	.|.	T|T	0.78729|0.78729	0.4329|0.4329	M|M	0.90977|0.90977	3.165|3.165	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.81914|.	0.992;0.989;0.995|.	T|T	0.81890|0.81890	-0.0725|-0.0725	9|5	0.87932|.	D|.	0|.	.|.	10.0111|10.0111	0.41986|0.41986	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1058;1017;1025|.	Q7Z406-2;Q7Z406;Q7Z406-6|.	.;MYH14_HUMAN;.|.	G|G	1058;1050;1025;1058|1017	ENSP00000406273:E1058G;ENSP00000366169:E1050G;ENSP00000407879:E1025G;ENSP00000262269:E1058G|.	ENSP00000262269:E1058G|.	E|S	+|+	2|1	0|0	MYH14|MYH14	55466919|55466919	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.836000|0.836000	0.47400|0.47400	8.595000|8.595000	0.90840|0.90840	1.674000|1.674000	0.50907|0.50907	0.482000|0.482000	0.46254|0.46254	GAG|AGC	.	.		0.562	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	Missense_Mutation
FAM71E1	112703	hgsc.bcm.edu	37	19	50971076	50971076	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:50971076A>G	ENST00000600100.1	-	4	914	c.550T>C	c.(550-552)Ttg>Ctg	p.L184L	FAM71E1_ENST00000595790.1_Silent_p.L168L			Q6IPT2	F71E1_HUMAN	family with sequence similarity 71, member E1	184										breast(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		ACGAACTTCAAGGGGAACAGC	0.637																																					p.L168L		Atlas-SNP	.											.	FAM71E1	21	.	0			c.T502C						.						25.0	24.0	24.0					19																	50971076		2203	4300	6503	SO:0001819	synonymous_variant	112703	exon4			ACTTCAAGGGGAA		CCDS33081.1	19q13.33	2007-11-20				ENSG00000142530			25107	protein-coding gene	gene with protein product							Standard	XM_005258472		Approved		uc002psg.3	Q6IPT2		ENST00000600100.1:c.550T>C	chr19.hg19:g.50971076A>G		61.0	0.0		77.0	4.0	NM_138411	Q96EJ5|Q9BSM9	Silent	SNP	ENST00000600100.1	hg19																																																																																				.	.		0.637	FAM71E1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464754.2		
ZNF610	162963	hgsc.bcm.edu	37	19	52856964	52856964	+	Silent	SNP	C	C	T	rs375754279		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:52856964C>T	ENST00000403906.3	+	4	549	c.93C>T	c.(91-93)atC>atT	p.I31I	ZNF610_ENST00000601151.1_Silent_p.I31I|ZNF610_ENST00000327920.8_Silent_p.I31I|ZNF610_ENST00000321287.8_Silent_p.I31I	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	31	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I31I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		ACGTGGCCATCGAATTCTCTC	0.438																																					p.I31I		Atlas-SNP	.											ZNF610,NS,carcinoma,0,1	ZNF610	84	.	1	Substitution - coding silent(1)	ovary(1)	c.C93T						.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	98.0	98.0	98.0		93,93,93,93	-2.9	0.9	19		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	,,,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,,,	31/463,31/463,31/420,31/463	52856964	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	162963	exon4			GGCCATCGAATTC	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.93C>T	chr19.hg19:g.52856964C>T		66.0	0.0		73.0	4.0	NM_001161427	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	hg19	CCDS12851.1																																																																																			.	.		0.438	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
ZNF845	91664	hgsc.bcm.edu	37	19	53856000	53856000	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:53856000A>G	ENST00000595091.1	+	5	2291	c.2072A>G	c.(2071-2073)tAc>tGc	p.Y691C	ZNF845_ENST00000458035.1_Missense_Mutation_p.Y691C			Q96IR2	ZN845_HUMAN	zinc finger protein 845	691				Missing (in Ref. 1; BAG58121). {ECO:0000305}.	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						GAGAAACCTTACAAGTGTAAT	0.418																																					p.Y691C		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2072G						.						67.0	69.0	68.0					19																	53856000		692	1591	2283	SO:0001583	missense	91664	exon4			AACCTTACAAGTG	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.2072A>G	chr19.hg19:g.53856000A>G	ENSP00000470005:p.Tyr691Cys	77.0	0.0		94.0	4.0	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	hg19	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.486382	0.26686	.	.	ENSG00000213799	ENST00000458035	T	0.25414	1.8	2.07	2.07	0.26955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36496	0.0969	M	0.64676	1.99	0.09310	N	1	D	0.55172	0.97	P	0.56788	0.806	T	0.12477	-1.0546	9	0.66056	D	0.02	.	4.8789	0.13670	0.5432:0.0:0.0:0.4568	.	691	Q96IR2	ZN845_HUMAN	C	691	ENSP00000388311:Y691C	ENSP00000388311:Y691C	Y	+	2	0	ZNF845	58547812	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-0.258000	0.08733	0.956000	0.37904	0.378000	0.23410	TAC	.	.		0.418	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
TMC4	147798	hgsc.bcm.edu	37	19	54664261	54664261	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:54664261C>A	ENST00000376591.4	-	14	2144	c.2013G>T	c.(2011-2013)gtG>gtT	p.V671V	LENG1_ENST00000222224.3_5'Flank|TMC4_ENST00000416963.1_Silent_p.V253V|TMC4_ENST00000301187.4_Silent_p.V665V	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	671					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					tagccagAGCCACAGTGTACG	0.582																																					p.V671V		Atlas-SNP	.											.	TMC4	89	.	0			c.G2013T						.						60.0	57.0	58.0					19																	54664261		2203	4300	6503	SO:0001819	synonymous_variant	147798	exon14			CAGAGCCACAGTG	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.2013G>T	chr19.hg19:g.54664261C>A		88.0	0.0		100.0	4.0	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	hg19	CCDS46174.1																																																																																			.	.		0.582	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
LILRA5	353514	hgsc.bcm.edu	37	19	54822783	54822783	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:54822783T>C	ENST00000301219.3	-	5	732	c.613A>G	c.(613-615)Acc>Gcc	p.T205A	LILRA5_ENST00000446712.3_Missense_Mutation_p.T193A|LILRA5_ENST00000346508.3_Missense_Mutation_p.T193A|AC008984.2_ENST00000507363.1_RNA|LILRA5_ENST00000432233.3_Missense_Mutation_p.T205A	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	205	Ig-like C2-type 2.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGCTGGGGGTCACAGGGCCC	0.597																																					p.T205A		Atlas-SNP	.											.	LILRA5	49	.	0			c.A613G						.						56.0	58.0	57.0					19																	54822783		2203	4300	6503	SO:0001583	missense	353514	exon5			TGGGGGTCACAGG	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.613A>G	chr19.hg19:g.54822783T>C	ENSP00000301219:p.Thr205Ala	157.0	0.0		132.0	6.0	NM_181879	A6NHI3	Missense_Mutation	SNP	ENST00000301219.3	hg19	CCDS12888.1	.	.	.	.	.	.	.	.	.	.	T	12.55	1.971507	0.34754	.	.	ENSG00000187116	ENST00000301219;ENST00000346508;ENST00000446712;ENST00000432233	T;T;T;T	0.03635	3.86;3.86;3.86;3.86	3.14	0.665	0.17896	Immunoglobulin-like fold (1);	1.446230	0.05063	U	0.480129	T	0.12050	0.0293	M	0.90542	3.125	0.09310	N	1	B;P;B;P	0.40931	0.408;0.733;0.199;0.705	B;B;B;P	0.46110	0.138;0.27;0.155;0.504	T	0.25433	-1.0132	10	0.72032	D	0.01	.	3.0226	0.06080	0.0:0.1505:0.2548:0.5948	.	193;205;193;205	A6NI73-4;A6NI73-3;A6NI73-2;A6NI73	.;.;.;LIRA5_HUMAN	A	205;193;193;205	ENSP00000301219:T205A;ENSP00000302948:T193A;ENSP00000389499:T193A;ENSP00000404236:T205A	ENSP00000301219:T205A	T	-	1	0	LILRA5	59514595	0.000000	0.05858	0.001000	0.08648	0.494000	0.33585	-0.073000	0.11468	0.260000	0.21731	0.172000	0.16884	ACC	.	.		0.597	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985	
NLRP9	338321	hgsc.bcm.edu	37	19	56244026	56244026	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr19:56244026G>T	ENST00000332836.2	-	2	1198	c.1171C>A	c.(1171-1173)Cga>Aga	p.R391R		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	391	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CTTTTTAGTCGGGCTCTGTTC	0.418																																					p.R391R		Atlas-SNP	.											.	NLRP9	163	.	0			c.C1171A						.						88.0	89.0	89.0					19																	56244026		2203	4298	6501	SO:0001819	synonymous_variant	338321	exon2			TTAGTCGGGCTCT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22941	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"""	609663	"""NACHT, leucine rich repeat and PYD containing 9"""	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.1171C>A	chr19.hg19:g.56244026G>T		62.0	0.0		90.0	4.0	NM_176820	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	hg19	CCDS12934.1																																																																																			.	.		0.418	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820	
TRIB3	57761	hgsc.bcm.edu	37	20	376998	376998	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:376998G>T	ENST00000217233.3	+	4	1294	c.741G>T	c.(739-741)ctG>ctT	p.L247L	TRIB3_ENST00000422053.2_Silent_p.L274L	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		TCTGGAGCCTGGGCGTGGCGC	0.657																																					p.L247L	Melanoma(101;421 2374 19538)	Atlas-SNP	.											.	TRIB3	50	.	0			c.G741T						.						40.0	37.0	38.0					20																	376998		2203	4299	6502	SO:0001819	synonymous_variant	57761	exon4			GAGCCTGGGCGTG	AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"""chromosome 20 open reading frame 97"", ""tribbles homolog 3 (Drosophila)"""	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.741G>T	chr20.hg19:g.376998G>T		98.0	0.0		96.0	4.0	NM_021158	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Silent	SNP	ENST00000217233.3	hg19	CCDS12997.1																																																																																			.	.		0.657	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158	
ADAM33	80332	hgsc.bcm.edu	37	20	3655209	3655209	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:3655209T>C	ENST00000356518.2	-	6	783	c.542A>G	c.(541-543)cAc>cGc	p.H181R	ADAM33_ENST00000350009.2_Missense_Mutation_p.H181R|ADAM33_ENST00000379861.4_Missense_Mutation_p.H181R|ADAM33_ENST00000466620.1_5'Flank	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	181					proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						AGGATCCCTGTGGCCACAGGT	0.592																																					p.H181R		Atlas-SNP	.											.	ADAM33	76	.	0			c.A542G						.						76.0	81.0	79.0					20																	3655209		2203	4300	6503	SO:0001583	missense	80332	exon6			TCCCTGTGGCCAC	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"""ADAM metallopeptidase domain containing"""	15478	protein-coding gene	gene with protein product		607114	"""a disintegrin and metalloproteinase domain 33"", ""chromosome 20 open reading frame 153"""	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.542A>G	chr20.hg19:g.3655209T>C	ENSP00000348912:p.His181Arg	48.0	0.0		57.0	4.0	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	hg19	CCDS13058.1	.	.	.	.	.	.	.	.	.	.	T	12.85	2.062992	0.36373	.	.	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000439201	T;T;T	0.01538	4.79;4.8;4.83	4.77	4.77	0.60923	.	.	.	.	.	T	0.04318	0.0119	L	0.32530	0.975	0.37575	D	0.919572	D;D;D;D;D	0.67145	0.996;0.984;0.985;0.975;0.975	P;P;P;P;P	0.61070	0.883;0.575;0.756;0.575;0.575	T	0.63175	-0.6696	9	0.25751	T	0.34	.	13.5427	0.61684	0.0:0.0:0.0:1.0	.	181;193;181;181;181	B4DTZ3;B4E1Y6;Q9BZ11-2;Q9BZ11;A2A2L3	.;.;.;ADA33_HUMAN;.	R	181	ENSP00000348912:H181R;ENSP00000369190:H181R;ENSP00000322550:H181R	ENSP00000322550:H181R	H	-	2	0	ADAM33	3603209	0.731000	0.28111	0.267000	0.24556	0.096000	0.18686	2.444000	0.44890	2.137000	0.66172	0.533000	0.62120	CAC	.	.		0.592	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3670895	3670895	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:3670895G>T	ENST00000344754.4	-	18	4607	c.4608C>A	c.(4606-4608)ccC>ccA	p.P1536P	SIGLEC1_ENST00000202578.4_Silent_p.P1536P	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1536	Ig-like C2-type 16.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CCATCATGGTGGGCGTCTTGG	0.602																																					p.P1536P		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4608A						.						9.0	6.0	7.0					20																	3670895		2111	4144	6255	SO:0001819	synonymous_variant	6614	exon18			CATGGTGGGCGTC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4608C>A	chr20.hg19:g.3670895G>T		46.0	0.0		47.0	4.0	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	hg19	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	G	4.313	0.057463	0.08339	.	.	ENSG00000088827	ENST00000419548	.	.	.	5.48	-0.652	0.11450	.	.	.	.	.	T	0.43897	0.1268	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	T	0.30119	-0.9989	4	.	.	.	.	4.1016	0.10015	0.4441:0.1778:0.3781:0.0	.	.	.	.	N	350	.	.	H	-	1	0	SIGLEC1	3618895	0.011000	0.17503	0.956000	0.39512	0.527000	0.34593	-0.145000	0.10265	0.290000	0.22444	0.561000	0.74099	CAC	.	.		0.602	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
KIF16B	55614	hgsc.bcm.edu	37	20	16492142	16492142	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:16492142T>C	ENST00000354981.2	-	6	634	c.477A>G	c.(475-477)agA>agG	p.R159R	KIF16B_ENST00000408042.1_Silent_p.R159R|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Silent_p.R159R	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	159	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GAAGTAGATCTCTCACACGTT	0.338																																					p.R159R		Atlas-SNP	.											.	KIF16B	305	.	0			c.A477G						.						70.0	69.0	69.0					20																	16492142		2203	4300	6503	SO:0001819	synonymous_variant	55614	exon6			TAGATCTCTCACA	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.477A>G	chr20.hg19:g.16492142T>C		106.0	0.0		94.0	4.0	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	hg19	CCDS13122.1																																																																																			.	.		0.338	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
MYLK2	85366	hgsc.bcm.edu	37	20	30419870	30419870	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:30419870C>A	ENST00000375994.2	+	11	1914	c.1641C>A	c.(1639-1641)gcC>gcA	p.A547A	MYLK2_ENST00000375985.4_Silent_p.A547A|MYLK2_ENST00000468730.1_3'UTR			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	547					cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CGGAGAAAGCCAAACGCTGTA	0.602																																					p.A547A		Atlas-SNP	.											.	MYLK2	76	.	0			c.C1641A						.						46.0	36.0	40.0					20																	30419870		2203	4300	6503	SO:0001819	synonymous_variant	85366	exon12			GAAAGCCAAACGC	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"""skeletal muscle myosin light chain kinase"""	606566	"""myosin light chain kinase 2, skeletal muscle"""				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.1641C>A	chr20.hg19:g.30419870C>A		77.0	0.0		98.0	6.0	NM_033118	Q569L1|Q96I84	Silent	SNP	ENST00000375994.2	hg19	CCDS13191.1																																																																																			.	.		0.602	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118	
CEP250	11190	hgsc.bcm.edu	37	20	34067549	34067549	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:34067549G>T	ENST00000397527.1	+	19	3087	c.2367G>T	c.(2365-2367)caG>caT	p.Q789H	RP3-477O4.14_ENST00000444933.1_RNA|CEP250_ENST00000342580.4_Missense_Mutation_p.Q789H|RP3-477O4.14_ENST00000416260.1_RNA|RP3-477O4.14_ENST00000453914.1_RNA	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	789	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CCAAGGGGCAGCTGGAGGTCC	0.488																																					p.Q789H		Atlas-SNP	.											.	CEP250	141	.	0			c.G2367T						.						104.0	103.0	104.0					20																	34067549		2203	4300	6503	SO:0001583	missense	11190	exon19			GGGGCAGCTGGAG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.2367G>T	chr20.hg19:g.34067549G>T	ENSP00000380661:p.Gln789His	170.0	0.0		127.0	41.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.404417	0.62288	.	.	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.16597	2.33;2.33	5.15	0.996	0.19844	.	0.000000	0.56097	D	0.000035	T	0.38374	0.1038	M	0.87180	2.865	0.33820	D	0.628968	D	0.89917	1.0	D	0.87578	0.998	T	0.46816	-0.9164	10	0.45353	T	0.12	.	5.1638	0.15075	0.3723:0.0:0.4954:0.1323	.	789	Q9BV73	CP250_HUMAN	H	789	ENSP00000380661:Q789H;ENSP00000341541:Q789H	ENSP00000341541:Q789H	Q	+	3	2	CEP250	33530963	0.985000	0.35326	1.000000	0.80357	0.997000	0.91878	0.006000	0.13152	0.354000	0.24105	0.655000	0.94253	CAG	.	.		0.488	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
CEP250	11190	hgsc.bcm.edu	37	20	34086433	34086433	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:34086433G>T	ENST00000397527.1	+	27	4385	c.3665G>T	c.(3664-3666)gGa>gTa	p.G1222V	CEP250_ENST00000342580.4_Missense_Mutation_p.G1166V	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1222	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GACCAGAATGGAGCTAGGAGC	0.527																																					p.G1222V		Atlas-SNP	.											.	CEP250	141	.	0			c.G3665T						.						75.0	80.0	78.0					20																	34086433		2203	4300	6503	SO:0001583	missense	11190	exon27			AGAATGGAGCTAG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.3665G>T	chr20.hg19:g.34086433G>T	ENSP00000380661:p.Gly1222Val	42.0	0.0		54.0	4.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872338	0.51695	.	.	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.10860	2.86;2.83	4.18	2.05	0.26809	.	0.625363	0.15036	N	0.284178	T	0.12732	0.0309	M	0.65975	2.015	0.39236	D	0.963764	P	0.39480	0.675	B	0.41813	0.367	T	0.11690	-1.0577	10	0.30854	T	0.27	.	4.7449	0.13033	0.3708:0.0:0.6292:0.0	.	1222	Q9BV73	CP250_HUMAN	V	1222;1166	ENSP00000380661:G1222V;ENSP00000341541:G1166V	ENSP00000341541:G1166V	G	+	2	0	CEP250	33549847	0.029000	0.19370	0.536000	0.28039	0.848000	0.48234	0.483000	0.22292	0.455000	0.26910	0.455000	0.32223	GGA	.	.		0.527	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
KIAA1755	85449	hgsc.bcm.edu	37	20	36851952	36851952	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:36851952A>G	ENST00000279024.4	-	9	2527	c.2256T>C	c.(2254-2256)ccT>ccC	p.P752P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	752										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GCATCCCCCCAGGGGGGTCGG	0.617																																					p.P752P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.T2256C						.						37.0	35.0	36.0					20																	36851952		2203	4300	6503	SO:0001819	synonymous_variant	85449	exon9			CCCCCCAGGGGGG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2256T>C	chr20.hg19:g.36851952A>G		66.0	0.0		79.0	4.0	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	hg19	CCDS33467.1																																																																																			.	.		0.617	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
SNAI1	6615	hgsc.bcm.edu	37	20	48600493	48600493	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:48600493T>C	ENST00000244050.2	+	2	276	c.215T>C	c.(214-216)aTt>aCt	p.I72T		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	72					cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GCCCAGCCAATTGCCTGGGCC	0.662																																					p.I72T		Atlas-SNP	.											.	SNAI1	28	.	0			c.T215C						.						44.0	50.0	48.0					20																	48600493		2203	4300	6503	SO:0001583	missense	6615	exon2			AGCCAATTGCCTG	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.215T>C	chr20.hg19:g.48600493T>C	ENSP00000244050:p.Ile72Thr	72.0	0.0		86.0	5.0	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	hg19	CCDS13423.1	.	.	.	.	.	.	.	.	.	.	T	1.677	-0.507608	0.04231	.	.	ENSG00000124216	ENST00000244050	T	0.21734	1.99	4.09	1.77	0.24775	.	1.733090	0.02986	N	0.146262	T	0.13243	0.0321	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24728	-1.0152	10	0.15066	T	0.55	1.2354	5.9026	0.18976	0.0:0.16:0.1486:0.6914	.	72	O95863	SNAI1_HUMAN	T	72	ENSP00000244050:I72T	ENSP00000244050:I72T	I	+	2	0	SNAI1	48033900	0.000000	0.05858	0.000000	0.03702	0.651000	0.38670	0.378000	0.20569	0.234000	0.21139	-0.410000	0.06199	ATT	.	.		0.662	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1		
SLC2A4RG	56731	hgsc.bcm.edu	37	20	62373570	62373570	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr20:62373570C>T	ENST00000266077.2	+	5	719	c.667C>T	c.(667-669)Ctg>Ttg	p.L223L	RP4-583P15.10_ENST00000447343.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					ACACATCCGCCTGGTGCACCT	0.706																																					p.L223L		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.C667T						.						16.0	20.0	18.0					20																	62373570		2171	4269	6440	SO:0001819	synonymous_variant	56731	exon5			ATCCGCCTGGTGC	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"""GLUT4 enhancer factor"", ""Huntington's disease gene regulatory region-binding protein 1"""	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.667C>T	chr20.hg19:g.62373570C>T		126.0	0.0		137.0	62.0	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Silent	SNP	ENST00000266077.2	hg19	CCDS13537.1																																																																																			.	.		0.706	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062	
CXADR	1525	hgsc.bcm.edu	37	21	18919456	18919456	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:18919456C>A	ENST00000284878.7	+	2	903	c.155C>A	c.(154-156)cCg>cAg	p.P52Q	CXADR_ENST00000400169.1_Missense_Mutation_p.P52Q|CXADR_ENST00000306618.10_Missense_Mutation_p.P52Q|CXADR_ENST00000400166.1_Missense_Mutation_p.P52Q|CXADR_ENST00000356275.6_Missense_Mutation_p.P52Q|CXADR_ENST00000400165.1_Missense_Mutation_p.P52Q	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	52	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)			endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		GACCAGGGACCGCTGGACATC	0.468																																					p.P52Q		Atlas-SNP	.											.	CXADR	44	.	0			c.C155A						.						91.0	77.0	82.0					21																	18919456		2203	4300	6503	SO:0001583	missense	1525	exon2			AGGGACCGCTGGA	Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.155C>A	chr21.hg19:g.18919456C>A	ENSP00000284878:p.Pro52Gln	67.0	0.0		57.0	4.0	NM_001207065	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	hg19	CCDS33519.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153859	0.57259	.	.	ENSG00000154639	ENST00000284878;ENST00000400166;ENST00000356275;ENST00000400169;ENST00000400165;ENST00000306618	T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.11	4.21	0.49690	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.145075	0.64402	D	0.000006	D	0.84960	0.5588	M	0.72894	2.215	0.54753	D	0.999982	D;D;D;D;D	0.89917	0.974;1.0;0.998;0.989;1.0	P;D;D;P;D	0.75020	0.768;0.978;0.977;0.905;0.985	T	0.82470	-0.0441	10	0.13853	T	0.58	.	14.7428	0.69469	0.1461:0.8539:0.0:0.0	.	52;52;52;52;52	P78310-3;P78310-4;B7WPI3;P78310;P78310-5	.;.;.;CXAR_HUMAN;.	Q	52	ENSP00000284878:P52Q;ENSP00000383030:P52Q;ENSP00000348620:P52Q;ENSP00000383033:P52Q;ENSP00000383029:P52Q;ENSP00000303395:P52Q	ENSP00000284878:P52Q	P	+	2	0	CXADR	17841327	0.998000	0.40836	0.635000	0.29338	0.466000	0.32739	6.588000	0.74076	1.449000	0.47699	0.655000	0.94253	CCG	.	.		0.468	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1		
ADAMTS5	11096	hgsc.bcm.edu	37	21	28296553	28296553	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:28296553C>A	ENST00000284987.5	-	8	2733	c.2612G>T	c.(2611-2613)gGa>gTa	p.G871V	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	871	Spacer.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						AGTGTGTGATCCCACTTTATT	0.522																																					p.G871V	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G2612T						.						108.0	103.0	105.0					21																	28296553		2203	4300	6503	SO:0001583	missense	11096	exon8			TGTGATCCCACTT	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.2612G>T	chr21.hg19:g.28296553C>A	ENSP00000284987:p.Gly871Val	104.0	0.0		133.0	51.0	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	hg19	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	0.265	-0.996879	0.02145	.	.	ENSG00000154736	ENST00000284987	T	0.63096	-0.02	5.54	2.69	0.31865	.	0.846026	0.10799	N	0.632875	T	0.34629	0.0904	N	0.04203	-0.255	0.34851	D	0.741686	B	0.02656	0.0	B	0.04013	0.001	T	0.30208	-0.9986	10	0.30078	T	0.28	.	3.8348	0.08889	0.3709:0.392:0.1617:0.0755	.	871	Q9UNA0	ATS5_HUMAN	V	871	ENSP00000284987:G871V	ENSP00000284987:G871V	G	-	2	0	ADAMTS5	27218424	0.343000	0.24818	0.416000	0.26546	0.125000	0.20455	1.929000	0.40114	0.401000	0.25424	-0.274000	0.10170	GGA	.	.		0.522	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
SLC37A1	54020	hgsc.bcm.edu	37	21	43979198	43979198	+	Splice_Site	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:43979198C>A	ENST00000352133.2	+	11	1962	c.980C>A	c.(979-981)cCa>cAa	p.P327Q	AP001625.6_ENST00000442605.1_RNA|SLC37A1_ENST00000398341.3_Splice_Site_p.P327Q			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	327					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						TTGAAAATTCCAGTAAGTAAA	0.557																																					p.P327Q		Atlas-SNP	.											.	SLC37A1	48	.	0			c.C980A						.						38.0	40.0	39.0					21																	43979198		2203	4300	6503	SO:0001630	splice_region_variant	54020	exon12			AAATTCCAGTAAG	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.981+1C>A	chr21.hg19:g.43979198C>A		37.0	0.0		51.0	5.0	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365300	0.61513	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.63096	-0.02;-0.02	5.7	5.7	0.88788	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.80618	0.4657	M	0.82193	2.58	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.82659	-0.0348	10	0.66056	D	0.02	-17.2009	16.7639	0.85519	0.0:1.0:0.0:0.0	.	327	P57057	GLPT_HUMAN	Q	327	ENSP00000381383:P327Q;ENSP00000344648:P327Q	ENSP00000344648:P327Q	P	+	2	0	SLC37A1	42852267	0.997000	0.39634	0.652000	0.29579	0.003000	0.03518	5.609000	0.67661	2.688000	0.91661	0.655000	0.94253	CCA	.	.		0.557	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		Missense_Mutation
WDR4	10785	hgsc.bcm.edu	37	21	44274711	44274711	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:44274711A>G	ENST00000398208.2	-	8	811	c.752T>C	c.(751-753)tTc>tCc	p.F251S	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Missense_Mutation_p.F251S	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		CTGGCACCAGAATGCAATCCT	0.607																																					p.F251S		Atlas-SNP	.											.	WDR4	35	.	0			c.T752C						.						36.0	36.0	36.0					21																	44274711		2203	4300	6503	SO:0001583	missense	10785	exon8			CACCAGAATGCAA	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.752T>C	chr21.hg19:g.44274711A>G	ENSP00000381266:p.Phe251Ser	51.0	0.0		55.0	4.0	NM_018669		Missense_Mutation	SNP	ENST00000398208.2	hg19	CCDS13691.1	.	.	.	.	.	.	.	.	.	.	A	5.960	0.361096	0.11296	.	.	ENSG00000160193	ENST00000330317;ENST00000398208	T;T	0.36878	1.23;1.23	3.46	2.28	0.28536	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.321965	0.29791	N	0.011181	T	0.22360	0.0539	L	0.29908	0.895	0.29659	N	0.843374	B;B	0.15141	0.012;0.009	B;B	0.16289	0.015;0.006	T	0.10567	-1.0624	10	0.44086	T	0.13	-19.9255	5.1598	0.15054	0.406:0.0:0.0:0.594	.	250;251	P57081-2;P57081	.;WDR4_HUMAN	S	251	ENSP00000328671:F251S;ENSP00000381266:F251S	ENSP00000328671:F251S	F	-	2	0	WDR4	43147780	0.996000	0.38824	0.432000	0.26747	0.382000	0.30200	1.487000	0.35540	0.508000	0.28173	0.482000	0.46254	TTC	.	.		0.607	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
TSPEAR	54084	hgsc.bcm.edu	37	21	45953608	45953608	+	Missense_Mutation	SNP	C	C	T	rs370848096	byFrequency	TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:45953608C>T	ENST00000323084.4	-	3	567	c.502G>A	c.(502-504)Gtc>Atc	p.V168I	TSPEAR_ENST00000397916.1_Missense_Mutation_p.V100I	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	168	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						AGGGAGAAGACGCCTGCGGAC	0.697													C|||	2	0.000399361	0.0	0.0	5008	,	,		12838	0.0		0.0	False		,,,				2504	0.002				p.V168I		Atlas-SNP	.											.	TSPEAR	110	.	0			c.G502A						.						25.0	25.0	25.0					21																	45953608		2192	4291	6483	SO:0001583	missense	54084	exon3			AGAAGACGCCTGC	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.502G>A	chr21.hg19:g.45953608C>T	ENSP00000321987:p.Val168Ile	124.0	0.0		188.0	74.0	NM_144991		Missense_Mutation	SNP	ENST00000323084.4	hg19	CCDS13712.1	.	.	.	.	.	.	.	.	.	.	c	1.389	-0.581309	0.03854	.	.	ENSG00000175894	ENST00000323084;ENST00000397916;ENST00000341581	T;T	0.43688	0.94;0.94	4.99	-0.667	0.11395	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.779066	0.12485	N	0.464779	T	0.15912	0.0383	N	0.03608	-0.345	0.09310	N	1	B	0.18741	0.03	B	0.09377	0.004	T	0.26155	-1.0111	10	0.16896	T	0.51	3.2862	6.7678	0.23576	0.4228:0.2357:0.0:0.3415	.	168	Q8WU66	TSEAR_HUMAN	I	168;100;168	ENSP00000321987:V168I;ENSP00000381012:V100I	ENSP00000321987:V168I	V	-	1	0	TSPEAR	44778036	0.995000	0.38212	0.012000	0.15200	0.000000	0.00434	3.040000	0.49799	-0.754000	0.04715	-2.269000	0.00276	GTC	.	.		0.697	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
ITGB2	3689	hgsc.bcm.edu	37	21	46321640	46321640	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:46321640A>G	ENST00000397850.2	-	7	960	c.508T>C	c.(508-510)Tcc>Ccc	p.S170P	ITGB2_ENST00000397854.3_Missense_Mutation_p.S113P|ITGB2_ENST00000355153.4_Missense_Mutation_p.S170P|ITGB2_ENST00000397857.1_Missense_Mutation_p.S170P|ITGB2_ENST00000397852.1_Missense_Mutation_p.S170P|ITGB2_ENST00000302347.5_Missense_Mutation_p.S170P			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	170	VWFA.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	TCCACGAAGGACCCGAAGCCT	0.637																																					p.S170P		Atlas-SNP	.											.	ITGB2	107	.	0			c.T508C						.						60.0	54.0	56.0					21																	46321640		2203	4300	6503	SO:0001583	missense	3689	exon6			CGAAGGACCCGAA	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.508T>C	chr21.hg19:g.46321640A>G	ENSP00000380948:p.Ser170Pro	63.0	0.0		67.0	5.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017791	0.54576	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414;ENST00000320216	D;D;D;D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51	4.14	4.14	0.48551	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	.	.	.	.	D	0.97751	0.9262	H	0.95470	3.675	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.78314	0.991;0.991	D	0.98047	1.0385	9	0.62326	D	0.03	.	11.1595	0.48507	1.0:0.0:0.0:0.0	.	113;170	A8MYE6;P05107	.;ITB2_HUMAN	P	170;170;113;170;170;170;113;161	ENSP00000380950:S170P;ENSP00000380955:S170P;ENSP00000380952:S113P;ENSP00000347279:S170P;ENSP00000380948:S170P;ENSP00000303242:S170P;ENSP00000317697:S161P	ENSP00000303242:S170P	S	-	1	0	ITGB2	45146068	1.000000	0.71417	0.977000	0.42913	0.053000	0.15095	5.377000	0.66184	1.750000	0.51863	0.454000	0.30748	TCC	.	.		0.637	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
ITGB2	3689	hgsc.bcm.edu	37	21	46330223	46330223	+	Silent	SNP	G	G	T	rs375907746		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr21:46330223G>T	ENST00000397850.2	-	4	575	c.123C>A	c.(121-123)ccC>ccA	p.P41P	ITGB2_ENST00000397854.3_Silent_p.P41P|ITGB2_ENST00000355153.4_Silent_p.P41P|ITGB2_ENST00000397857.1_Silent_p.P41P|ITGB2_ENST00000397852.1_Silent_p.P41P|ITGB2_ENST00000397846.3_Silent_p.P41P|ITGB2_ENST00000302347.5_Silent_p.P41P|ITGB2_ENST00000523126.1_5'UTR			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	41					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGGTGCAGCCGGGCCCCGACT	0.662																																					p.P41P		Atlas-SNP	.											.	ITGB2	107	.	0			c.C123A						.						47.0	44.0	45.0					21																	46330223		2203	4300	6503	SO:0001819	synonymous_variant	3689	exon3			GCAGCCGGGCCCC	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.123C>A	chr21.hg19:g.46330223G>T		104.0	0.0		143.0	6.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	hg19	CCDS13716.1																																																																																			.	.		0.662	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
CCT8L2	150160	hgsc.bcm.edu	37	22	17072001	17072001	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:17072001C>A	ENST00000359963.3	-	1	1699	c.1440G>T	c.(1438-1440)gtG>gtT	p.V480V		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	480					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTTCAGTTCCCACACCCATTA	0.512																																					p.V480V		Atlas-SNP	.											CCT8L2,bladder,carcinoma,0,1	CCT8L2	150	.	0			c.G1440T						.						145.0	141.0	143.0					22																	17072001		2203	4300	6503	SO:0001819	synonymous_variant	150160	exon1			AGTTCCCACACCC	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1440G>T	chr22.hg19:g.17072001C>A		285.0	0.0		155.0	113.0	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	hg19	CCDS13738.1																																																																																			.	.		0.512	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
CLTCL1	8218	hgsc.bcm.edu	37	22	19222036	19222036	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:19222036G>T	ENST00000263200.10	-	7	1235	c.1163C>A	c.(1162-1164)cCa>cAa	p.P388Q	CLTCL1_ENST00000353891.5_Missense_Mutation_p.P388Q|CLTCL1_ENST00000427926.1_Missense_Mutation_p.P388Q	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	388	Globular terminal domain.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TATCACCTTTGGTGCAGACGC	0.428			T	?	ALCL																																p.P388Q		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.C1163A						.						38.0	37.0	38.0					22																	19222036		1884	4117	6001	SO:0001583	missense	8218	exon7			ACCTTTGGTGCAG		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.1163C>A	chr22.hg19:g.19222036G>T	ENSP00000445677:p.Pro388Gln	138.0	0.0		83.0	4.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.873517	0.72180	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.52754	0.65;0.65;0.65	3.29	3.29	0.37713	Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.72269	0.3439	M	0.88842	2.985	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.997;1.0	T	0.79971	-0.1578	10	0.66056	D	0.02	-6.0763	15.0953	0.72229	0.0:0.0:1.0:0.0	.	388;388	P53675-2;P53675	.;CLH2_HUMAN	Q	388	ENSP00000439662:P388Q;ENSP00000445677:P388Q;ENSP00000441158:P388Q	ENSP00000445677:P388Q	P	-	2	0	CLTCL1	17602036	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	8.619000	0.90938	1.847000	0.53656	0.460000	0.39030	CCA	.	.		0.428	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
C22orf29	79680	hgsc.bcm.edu	37	22	19839039	19839039	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:19839039A>G	ENST00000405640.1	-	2	1414	c.746T>C	c.(745-747)gTa>gCa	p.V249A	GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.V249A|C22orf29_ENST00000407472.1_Missense_Mutation_p.V249A|GNB1L_ENST00000403325.1_Intron|GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000460402.1_Intron|C22orf29_ENST00000484072.1_Intron			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	249					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)				NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					ACTTCTAGATACAGAGTTGGA	0.592																																					p.V249A		Atlas-SNP	.											.	C22orf29	23	.	0			c.T746C						.						66.0	70.0	69.0					22																	19839039		2203	4300	6503	SO:0001583	missense	79680	exon3			CTAGATACAGAGT	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.746T>C	chr22.hg19:g.19839039A>G	ENSP00000384924:p.Val249Ala	102.0	0.0		88.0	4.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	A	6.930	0.541218	0.13250	.	.	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640	T;T;T	0.26957	1.7;1.7;1.7	3.72	-7.43	0.01383	.	7.488640	0.01795	N	0.032529	T	0.10337	0.0253	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	10	0.21540	T	0.41	.	3.99	0.09533	0.5967:0.1215:0.1589:0.1228	.	249	Q7L3V2	CV029_HUMAN	A	249	ENSP00000386111:V249A;ENSP00000330596:V249A;ENSP00000384924:V249A	ENSP00000330596:V249A	V	-	2	0	C22orf29	18219039	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.175000	0.03102	-1.792000	0.01259	-1.338000	0.01255	GTA	.	.		0.592	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627	
SNAP29	9342	hgsc.bcm.edu	37	22	21235375	21235375	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:21235375C>T	ENST00000215730.7	+	3	601	c.473C>T	c.(472-474)gCa>gTa	p.A158V		NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	158					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			GAACAGGAAGCAAAGTACCAG	0.403																																					p.A158V		Atlas-SNP	.											.	SNAP29	22	.	0			c.C473T						.						84.0	73.0	76.0					22																	21235375		2203	4300	6503	SO:0001583	missense	9342	exon3			AGGAAGCAAAGTA	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"""soluble 29 kDa NSF attachment protein"""	604202	"""synaptosomal-associated protein, 29kD"""			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.473C>T	chr22.hg19:g.21235375C>T	ENSP00000215730:p.Ala158Val	209.0	1.0		153.0	107.0	NM_004782		Missense_Mutation	SNP	ENST00000215730.7	hg19	CCDS13784.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.748021	0.30955	.	.	ENSG00000099940	ENST00000215730;ENST00000439214	.	.	.	4.79	-0.269	0.12930	SNAP-25 (1);	0.768768	0.12064	N	0.502901	T	0.26593	0.0650	N	0.22421	0.69	0.09310	N	1	B	0.30068	0.267	B	0.29942	0.109	T	0.19386	-1.0307	9	0.30078	T	0.28	-0.6118	10.2209	0.43196	0.4547:0.4386:0.1067:0.0	.	158	O95721	SNP29_HUMAN	V	158;65	.	ENSP00000215730:A158V	A	+	2	0	SNAP29	19565375	0.156000	0.22821	0.309000	0.25155	0.988000	0.76386	0.979000	0.29500	0.201000	0.20466	0.491000	0.48974	GCA	.	.		0.403	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782	
AIFM3	150209	hgsc.bcm.edu	37	22	21329042	21329042	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:21329042C>A	ENST00000399167.2	+	8	897	c.657C>A	c.(655-657)tcC>tcA	p.S219S	AIFM3_ENST00000399163.2_Silent_p.S219S|AIFM3_ENST00000465606.1_3'UTR|AIFM3_ENST00000333607.6_Silent_p.S219S|AIFM3_ENST00000405089.1_Silent_p.S225S|AIFM3_ENST00000440238.2_Silent_p.S219S|AIFM3_ENST00000335375.5_Silent_p.S207S	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	219					cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			AGGGCTTCTCCGACCGGATCG	0.642																																					p.S225S		Atlas-SNP	.											AIFM3,colon,carcinoma,0,1	AIFM3	49	.	0			c.C675A						.						68.0	63.0	64.0					22																	21329042		2203	4300	6503	SO:0001819	synonymous_variant	150209	exon8			CTTCTCCGACCGG	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.657C>A	chr22.hg19:g.21329042C>A		115.0	1.0		67.0	3.0	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Silent	SNP	ENST00000399167.2	hg19	CCDS13786.1																																																																																			.	.		0.642	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704	
EWSR1	2130	hgsc.bcm.edu	37	22	29692342	29692342	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:29692342C>A	ENST00000397938.2	+	12	1597	c.1278C>A	c.(1276-1278)gcC>gcA	p.A426A	EWSR1_ENST00000332050.6_Silent_p.A353A|EWSR1_ENST00000406548.1_Silent_p.A425A|EWSR1_ENST00000332035.6_Silent_p.A370A|EWSR1_ENST00000331029.7_Silent_p.A388A|EWSR1_ENST00000414183.2_Silent_p.A431A	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	426	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCAAGGCTGCCGTGGAATGGT	0.502			T	"""FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"""	"""Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"""																																p.A431A		Atlas-SNP	.		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"""L, M"""	.	EWSR1	104	.	0			c.C1293A						.						114.0	91.0	99.0					22																	29692342		2203	4300	6503	SO:0001819	synonymous_variant	2130	exon13			GGCTGCCGTGGAA		CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944		"""RNA binding motif (RRM) containing"""	3508	protein-coding gene	gene with protein product		133450	"""Ewing sarcoma breakpoint region 1"""			1522903	Standard	NM_005243		Approved	EWS	uc003aev.3	Q01844	OTTHUMG00000151107	ENST00000397938.2:c.1278C>A	chr22.hg19:g.29692342C>A		102.0	0.0		82.0	4.0	NM_013986	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Silent	SNP	ENST00000397938.2	hg19	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	C	5.371	0.253678	0.10185	.	.	ENSG00000182944	ENST00000360091	.	.	.	5.52	-11.0	0.00169	.	.	.	.	.	T	0.58221	0.2107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71020	-0.4713	4	.	.	.	.	14.8813	0.70534	0.0782:0.2555:0.0:0.6663	.	.	.	.	S	82	.	.	R	+	1	0	EWSR1	28022342	0.000000	0.05858	0.081000	0.20488	0.814000	0.46013	-4.087000	0.00297	-2.355000	0.00614	-1.578000	0.00866	CGT	.	.		0.502	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1	NM_005243	
MORC2	22880	hgsc.bcm.edu	37	22	31333570	31333570	+	Splice_Site	SNP	C	C	T	rs201852637		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:31333570C>T	ENST00000397641.3	-	15	1906	c.1498G>A	c.(1498-1500)Gat>Aat	p.D500N	MORC2_ENST00000469915.1_Intron|MORC2_ENST00000215862.4_Splice_Site_p.D438N			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	500						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CCCAACTCACCGCACTGGATG	0.552																																					p.D438N		Atlas-SNP	.											MORC2,caecum,carcinoma,0,1	MORC2	78	.	0			c.G1312A						.						68.0	70.0	69.0					22																	31333570		2203	4300	6503	SO:0001630	splice_region_variant	22880	exon16			ACTCACCGCACTG	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 1"", ""zinc finger, CW type with coiled-coil domain 1"""	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1498+1G>A	chr22.hg19:g.31333570C>T		55.0	0.0		28.0	2.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	C	29.5	5.011379	0.93346	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.15139	2.46;2.45	5.4	5.4	0.78164	Zinc finger, CW-type (2);	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54649	-0.8262	9	.	.	.	.	19.5178	0.95171	0.0:1.0:0.0:0.0	.	500	Q9Y6X9	MORC2_HUMAN	N	500;438	ENSP00000380763:D500N;ENSP00000215862:D438N	.	D	-	1	0	MORC2	29663570	1.000000	0.71417	1.000000	0.80357	0.464000	0.32679	7.442000	0.80503	2.681000	0.91329	0.555000	0.69702	GAT	.	C|0.999;T|0.001		0.552	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941	Missense_Mutation
PATZ1	23598	hgsc.bcm.edu	37	22	31724792	31724792	+	Silent	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:31724792G>A	ENST00000266269.5	-	4	2255	c.1626C>T	c.(1624-1626)gcC>gcT	p.A542A	PATZ1_ENST00000351933.4_Intron|PATZ1_ENST00000405309.3_Nonsense_Mutation_p.Q521*|RP3-400N23.6_ENST00000440456.1_RNA	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	542					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						CATAGGTCCTGGCGCAGTGGA	0.617																																					p.Q521X		Atlas-SNP	.											.	PATZ1	24	.	0			c.C1561T						.						70.0	58.0	62.0					22																	31724792		2203	4300	6503	SO:0001819	synonymous_variant	23598	exon4			GGTCCTGGCGCAG	AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13071	protein-coding gene	gene with protein product		605165	"""zinc finger protein 278"""	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.1626C>T	chr22.hg19:g.31724792G>A		105.0	0.0		73.0	4.0	NM_032052	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Nonsense_Mutation	SNP	ENST00000266269.5	hg19	CCDS13894.1	.	.	.	.	.	.	.	.	.	.	G	43	10.223038	0.99362	.	.	ENSG00000100105	ENST00000405309	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	0.1094	17.4491	0.87587	0.0:0.0:1.0:0.0	.	.	.	.	X	521	.	ENSP00000384173:Q521X	Q	-	1	0	PATZ1	30054792	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.130000	0.89598	2.447000	0.82792	0.462000	0.41574	CAG	.	.		0.617	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052	
SFI1	9814	hgsc.bcm.edu	37	22	31969140	31969140	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:31969140A>G	ENST00000400288.2	+	9	967	c.862A>G	c.(862-864)Aga>Gga	p.R288G	SFI1_ENST00000540643.1_Missense_Mutation_p.R264G|SFI1_ENST00000443326.1_Missense_Mutation_p.R206G|SFI1_ENST00000400289.1_Missense_Mutation_p.R206G|SFI1_ENST00000443011.1_Missense_Mutation_p.R135G|SFI1_ENST00000414585.1_Missense_Mutation_p.R135G|SFI1_ENST00000432498.1_Missense_Mutation_p.R288G	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	288					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GCAAAAACGGAGATTTCTAAA	0.502											OREG0003525	type=REGULATORY REGION|Gene=SFI1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R288G		Atlas-SNP	.											.	SFI1	78	.	0			c.A862G						.						81.0	81.0	81.0					22																	31969140		1903	4134	6037	SO:0001583	missense	9814	exon9			AAACGGAGATTTC	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.862A>G	chr22.hg19:g.31969140A>G	ENSP00000383145:p.Arg288Gly	51.0	0.0	828	53.0	4.0	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	hg19	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	A	11.18	1.562377	0.27915	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288	T;T;T;T;T;T;T	0.37058	1.22;1.22;1.22;2.73;2.71;1.22;1.22	5.87	3.62	0.41486	.	0.712062	0.14740	N	0.301244	T	0.35451	0.0932	N	0.08118	0	0.09310	N	1	P;P;D;P;P;D	0.76494	0.835;0.835;0.999;0.95;0.897;0.967	B;B;D;P;P;P	0.71414	0.311;0.311;0.973;0.487;0.465;0.74	T	0.18840	-1.0324	10	0.31617	T	0.26	.	10.2417	0.43316	0.6827:0.3173:0.0:0.0	.	264;206;206;288;288;264	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;.;.;SFI1_HUMAN;.	G	288;264;206;264;135;135;206;288	ENSP00000402679:R288G;ENSP00000443025:R264G;ENSP00000416469:R206G;ENSP00000397148:R135G;ENSP00000401199:R135G;ENSP00000383146:R206G;ENSP00000383145:R288G	ENSP00000383145:R288G	R	+	1	2	SFI1	30299140	0.004000	0.15560	0.002000	0.10522	0.005000	0.04900	1.848000	0.39309	1.008000	0.39264	0.533000	0.62120	AGA	.	.		0.502	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
DEPDC5	9681	hgsc.bcm.edu	37	22	32217607	32217607	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:32217607C>T	ENST00000382112.3	+	22	2060	c.1990C>T	c.(1990-1992)Cat>Tat	p.H664Y	DEPDC5_ENST00000400248.2_Missense_Mutation_p.H664Y|DEPDC5_ENST00000266091.3_Missense_Mutation_p.H664Y|DEPDC5_ENST00000400249.2_Missense_Mutation_p.H664Y|DEPDC5_ENST00000382111.2_Missense_Mutation_p.H664Y|DEPDC5_ENST00000400246.1_Missense_Mutation_p.H664Y|DEPDC5_ENST00000536766.1_Intron|DEPDC5_ENST00000382105.2_Intron|DEPDC5_ENST00000535622.1_Intron	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	664					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GTTAGCATATCATGAAGCTGC	0.542																																					p.H664Y		Atlas-SNP	.											.	DEPDC5	266	.	0			c.C1990T						.						128.0	135.0	133.0					22																	32217607		2116	4242	6358	SO:0001583	missense	9681	exon22			GCATATCATGAAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1990C>T	chr22.hg19:g.32217607C>T	ENSP00000371546:p.His664Tyr	88.0	0.0		74.0	4.0	NM_001136029	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.18|19.18	3.777990|3.777990	0.70107|0.70107	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000266091;ENST00000400249;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248|ENST00000433147	T;T;T;T;T;T|.	0.24151|.	1.89;1.91;1.87;1.91;1.87;1.91|.	5.91|5.91	4.83|4.83	0.62350|0.62350	.|.	0.151077|.	0.64402|.	D|.	0.000018|.	T|T	0.69646|0.69646	0.3134|0.3134	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	P;P;B;P|.	0.47604|.	0.867;0.898;0.031;0.837|.	B;B;B;B|.	0.43867|.	0.317;0.434;0.01;0.335|.	T|T	0.66858|0.66858	-0.5817|-0.5817	10|5	0.40728|.	T|.	0.16|.	.|.	14.9866|14.9866	0.71353|0.71353	0.143:0.857:0.0:0.0|0.143:0.857:0.0:0.0	.|.	664;664;664;664|.	B9EGN9;O75140-4;A8MPX9;O75140|.	.;.;.;DEPD5_HUMAN|.	Y|L	664|61	ENSP00000266091:H664Y;ENSP00000383108:H664Y;ENSP00000383105:H664Y;ENSP00000371546:H664Y;ENSP00000371545:H664Y;ENSP00000383107:H664Y|.	ENSP00000266091:H664Y|.	H|S	+|+	1|2	0|0	DEPDC5|DEPDC5	30547607|30547607	1.000000|1.000000	0.71417|0.71417	0.916000|0.916000	0.36221|0.36221	0.997000|0.997000	0.91878|0.91878	5.554000|5.554000	0.67294|0.67294	2.801000|2.801000	0.96364|0.96364	0.655000|0.655000	0.94253|0.94253	CAT|TCA	.	.		0.542	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
SSTR3	6753	hgsc.bcm.edu	37	22	37602782	37602782	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:37602782T>C	ENST00000328544.3	-	2	1594	c.1061A>G	c.(1060-1062)gAg>gGg	p.E354G	SSTR3_ENST00000402501.1_Missense_Mutation_p.E354G	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	354	Glu-rich (acidic).				cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	atcctcctcctcctcatcctc	0.701																																					p.E354G		Atlas-SNP	.											.	SSTR3	42	.	0			c.A1061G						.						30.0	31.0	30.0					22																	37602782		2203	4300	6503	SO:0001583	missense	6753	exon2			TCCTCCTCCTCAT		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1061A>G	chr22.hg19:g.37602782T>C	ENSP00000330138:p.Glu354Gly	41.0	0.0		44.0	4.0	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	T	9.129	1.010998	0.19277	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.73047	-0.71;-0.71	5.17	5.17	0.71159	.	1.685100	0.02858	N	0.129966	T	0.70868	0.3273	L	0.50333	1.59	0.50467	D	0.999873	B	0.02656	0.0	B	0.06405	0.002	T	0.27054	-1.0085	10	0.25751	T	0.34	.	14.9968	0.71439	0.0:0.0:0.0:1.0	.	354	P32745	SSR3_HUMAN	G	354	ENSP00000330138:E354G;ENSP00000384904:E354G	ENSP00000330138:E354G	E	-	2	0	SSTR3	35932728	0.823000	0.29233	0.300000	0.25030	0.021000	0.10359	2.080000	0.41586	1.942000	0.56320	0.459000	0.35465	GAG	.	.		0.701	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
TOMM22	56993	hgsc.bcm.edu	37	22	39078943	39078943	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:39078943T>C	ENST00000216034.4	+	3	327	c.296T>C	c.(295-297)gTt>gCt	p.V99A	RP3-508I15.9_ENST00000412067.1_RNA|RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000431924.2_RNA	NM_020243.4	NP_064628.1	Q9NS69	TOM22_HUMAN	translocase of outer mitochondrial membrane 22 homolog (yeast)	99	TMD; necessary for mitochondrion outer membrane localization and integration in the TOM complex. {ECO:0000250}.				cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			large_intestine(1)|lung(2)	3	Melanoma(58;0.04)					GTTCTTCCCGTTGTCTTTGAG	0.542																																					p.V99A		Atlas-SNP	.											.	TOMM22	10	.	0			c.T296C						.						143.0	130.0	135.0					22																	39078943		2203	4300	6503	SO:0001583	missense	56993	exon3			TTCCCGTTGTCTT	AB040119	CCDS13975.1	22q12-q13	2010-07-29			ENSG00000100216	ENSG00000100216			18002	protein-coding gene	gene with protein product		607046				10982837, 10900208	Standard	NM_020243		Approved	TOM22	uc003awe.3	Q9NS69	OTTHUMG00000150991	ENST00000216034.4:c.296T>C	chr22.hg19:g.39078943T>C	ENSP00000216034:p.Val99Ala	130.0	0.0		95.0	4.0	NM_020243		Missense_Mutation	SNP	ENST00000216034.4	hg19	CCDS13975.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.562765	0.86335	.	.	ENSG00000100216	ENST00000216034	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.80497	0.4634	M	0.86864	2.845	0.80722	D	1	D	0.63046	0.992	D	0.63488	0.915	D	0.84407	0.0563	9	0.72032	D	0.01	-22.5999	15.351	0.74384	0.0:0.0:0.0:1.0	.	99	Q9NS69	TOM22_HUMAN	A	99	.	ENSP00000216034:V99A	V	+	2	0	TOMM22	37408889	1.000000	0.71417	0.999000	0.59377	0.717000	0.41224	7.501000	0.81600	2.024000	0.59613	0.460000	0.39030	GTT	.	.		0.542	TOMM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320842.1		
SUN2	25777	hgsc.bcm.edu	37	22	39147022	39147022	+	Missense_Mutation	SNP	C	C	A	rs373600095		TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:39147022C>A	ENST00000405510.1	-	5	663	c.305G>T	c.(304-306)cGg>cTg	p.R102L	SUN2_ENST00000216064.4_Missense_Mutation_p.R102L|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000405018.1_Missense_Mutation_p.R102L|SUN2_ENST00000411587.2_Intron|SUN2_ENST00000406622.1_Missense_Mutation_p.R102L	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	102	LMNA-binding. {ECO:0000250}.|Poly-Arg.|Ser-rich.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						TCTCCTCCTCCGCACCCGCAG	0.657																																					p.R102L		Atlas-SNP	.											.	SUN2	59	.	0			c.G305T						.						30.0	28.0	29.0					22																	39147022		2203	4300	6503	SO:0001583	missense	25777	exon5			CTCCTCCGCACCC	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"""unc-84 homolog B (C. elegans)"""	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.305G>T	chr22.hg19:g.39147022C>A	ENSP00000385740:p.Arg102Leu	52.0	0.0		53.0	4.0	NM_001199580	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Missense_Mutation	SNP	ENST00000405510.1	hg19	CCDS13978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.995441|3.995441	0.74703|0.74703	.|.	.|.	ENSG00000100242|ENSG00000100242	ENST00000417332|ENST00000405510;ENST00000216064;ENST00000405018;ENST00000406622;ENST00000456894;ENST00000452294;ENST00000433561	.|T;T;T;T;T;T;T	.|0.43688	.|2.57;2.57;2.23;2.57;0.94;0.98;1.1	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	.|0.126644	.|0.42420	.|D	.|0.000713	.|T	.|0.51618	.|0.1685	L|L	0.27053|0.27053	0.805|0.805	0.39641|0.39641	D|D	0.970326|0.970326	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.81914	.|0.995;0.995;0.995;0.995	.|T	.|0.53975	.|-0.8362	.|10	0.87932|0.42905	D|T	0|0.14	-25.0041|-25.0041	16.4198|16.4198	0.83754|0.83754	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|137;102;102;102	.|B4E2A6;Q2T9F7;B0QY62;Q9UH99	.|.;.;.;SUN2_HUMAN	X|L	122|102	.|ENSP00000385740:R102L;ENSP00000216064:R102L;ENSP00000385616:R102L;ENSP00000383992:R102L;ENSP00000415588:R102L;ENSP00000414950:R102L;ENSP00000411615:R102L	ENSP00000412928:G122X|ENSP00000216064:R102L	G|R	-|-	1|2	0|0	SUN2|SUN2	37476968|37476968	0.963000|0.963000	0.33076|0.33076	0.998000|0.998000	0.56505|0.56505	0.595000|0.595000	0.36748|0.36748	4.507000|4.507000	0.60434|0.60434	2.299000|2.299000	0.77371|0.77371	0.563000|0.563000	0.77884|0.77884	GGA|CGG	.	.		0.657	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332	
CACNA1I	8911	hgsc.bcm.edu	37	22	39994207	39994207	+	Silent	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:39994207T>C	ENST00000402142.3	+	2	288	c.288T>C	c.(286-288)ctT>ctC	p.L96L	CACNA1I_ENST00000401624.1_Silent_p.L96L|CACNA1I_ENST00000407673.1_Silent_p.L96L|CACNA1I_ENST00000400164.3_Silent_p.L96L|CACNA1I_ENST00000404898.1_Silent_p.L96L|CACNA1I_ENST00000336649.4_Silent_p.L96L	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	96					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	GCGTGACACTTGGCATGTACC	0.642																																					p.L96L		Atlas-SNP	.											.	CACNA1I	264	.	0			c.T288C						.						74.0	80.0	78.0					22																	39994207		2163	4255	6418	SO:0001819	synonymous_variant	8911	exon2			GACACTTGGCATG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.288T>C	chr22.hg19:g.39994207T>C		140.0	0.0		98.0	4.0	NM_001003406	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	hg19	CCDS46710.1																																																																																			.	.		0.642	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
EP300	2033	hgsc.bcm.edu	37	22	41572904	41572904	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:41572904C>A	ENST00000263253.7	+	31	6408	c.5189C>A	c.(5188-5190)tCt>tAt	p.S1730Y	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1730	Binding region for E1A adenovirus.				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)	p.S1730F(1)		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						CCAGGCGATTCTCGCCGCCTG	0.542			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.S1730Y		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	EP300,NS,carcinoma,0,1	EP300	367	.	1	Substitution - Missense(1)	lung(1)	c.C5189A						.						77.0	71.0	73.0					22																	41572904		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	GCGATTCTCGCCG	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.5189C>A	chr22.hg19:g.41572904C>A	ENSP00000263253:p.Ser1730Tyr	95.0	0.0		92.0	4.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.418313	0.62622	.	.	ENSG00000100393	ENST00000263253	D	0.85013	-1.93	5.75	5.75	0.90469	Zinc finger, TAZ-type (4);	0.000000	0.48286	D	0.000194	D	0.92782	0.7705	M	0.77103	2.36	0.58432	D	0.999999	D	0.71674	0.998	D	0.80764	0.994	D	0.92983	0.6408	10	0.87932	D	0	-8.2686	19.9469	0.97185	0.0:1.0:0.0:0.0	.	1730	Q09472	EP300_HUMAN	Y	1730	ENSP00000263253:S1730Y	ENSP00000263253:S1730Y	S	+	2	0	EP300	39902850	1.000000	0.71417	0.995000	0.50966	0.805000	0.45488	4.851000	0.62896	2.714000	0.92807	0.650000	0.86243	TCT	.	.		0.542	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
CHADL	150356	hgsc.bcm.edu	37	22	41634867	41634867	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:41634867T>C	ENST00000216241.9	-	3	261	c.209A>G	c.(208-210)cAg>cGg	p.Q70R		NM_138481.1	NP_612490.1	Q6NUI6	CHADL_HUMAN	chondroadherin-like	70						proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(1)|skin(1)	4						CAAATTGCCCTGCAGGTCCAG	0.662																																					p.Q70R		Atlas-SNP	.											.	CHADL	20	.	0			c.A209G						.						10.0	14.0	13.0					22																	41634867		692	1590	2282	SO:0001583	missense	150356	exon3			TTGCCCTGCAGGT	BC012882	CCDS46715.1	22q13.2	2008-10-31			ENSG00000100399	ENSG00000100399			25165	protein-coding gene	gene with protein product						12477932	Standard	NM_138481		Approved	SLRR4B	uc003azq.4	Q6NUI6	OTTHUMG00000150936	ENST00000216241.9:c.209A>G	chr22.hg19:g.41634867T>C	ENSP00000216241:p.Gln70Arg	89.0	0.0		56.0	4.0	NM_138481	Q05CY2|Q4G0S0|Q5JY13|Q86XY1|Q96E60	Missense_Mutation	SNP	ENST00000216241.9	hg19	CCDS46715.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.654|5.654	0.305258|0.305258	0.10678|0.10678	.|.	.|.	ENSG00000100399|ENSG00000100399	ENST00000216241|ENST00000417999	T|.	0.55930|.	0.49|.	4.9|4.9	2.76|2.76	0.32466|0.32466	.|.	0.220792|.	0.36591|.	N|.	0.002509|.	T|T	0.25827|0.25827	0.0629|0.0629	N|N	0.26042|0.26042	0.785|0.785	0.24963|0.24963	N|N	0.991712|0.991712	B;B|.	0.16603|.	0.013;0.018|.	B;B|.	0.20577|.	0.022;0.03|.	T|T	0.21518|0.21518	-1.0243|-1.0243	10|5	0.02654|.	T|.	1|.	.|.	7.1332|7.1332	0.25512|0.25512	0.0:0.4217:0.0:0.5783|0.0:0.4217:0.0:0.5783	.|.	70;70|.	Q6NUI6-2;Q6NUI6|.	.;CHADL_HUMAN|.	R|G	70|68	ENSP00000216241:Q70R|.	ENSP00000216241:Q70R|.	Q|R	-|-	2|1	0|2	CHADL|CHADL	39964813|39964813	0.997000|0.997000	0.39634|0.39634	0.998000|0.998000	0.56505|0.56505	0.451000|0.451000	0.32288|0.32288	1.894000|1.894000	0.39768|0.39768	0.235000|0.235000	0.21160|0.21160	-0.464000|-0.464000	0.05259|0.05259	CAG|AGG	.	.		0.662	CHADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320597.1	NM_138481	
CCDC134	79879	hgsc.bcm.edu	37	22	42205910	42205910	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:42205910G>T	ENST00000255784.5	+	3	235	c.131G>T	c.(130-132)cGg>cTg	p.R44L	CCDC134_ENST00000402061.3_Missense_Mutation_p.R44L	NM_024821.2	NP_079097.1	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134	44						extracellular region (GO:0005576)|membrane (GO:0016020)				large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						GTGAAGCGGCGGGAGCAGCTG	0.522																																					p.R44L		Atlas-SNP	.											.	CCDC134	19	.	0			c.G131T						.						66.0	59.0	62.0					22																	42205910		2203	4300	6503	SO:0001583	missense	79879	exon3			AGCGGCGGGAGCA	AL021453	CCDS33654.1	22q13.2	2010-12-24			ENSG00000100147	ENSG00000100147			26185	protein-coding gene	gene with protein product						18087676	Standard	NM_024821		Approved	FLJ22349	uc003bbh.1	Q9H6E4	OTTHUMG00000151262	ENST00000255784.5:c.131G>T	chr22.hg19:g.42205910G>T	ENSP00000255784:p.Arg44Leu	131.0	0.0		95.0	4.0	NM_024821		Missense_Mutation	SNP	ENST00000255784.5	hg19	CCDS33654.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607388	0.66558	.	.	ENSG00000100147	ENST00000402061;ENST00000255784;ENST00000429249	.	.	.	4.84	3.82	0.43975	.	0.057402	0.64402	D	0.000003	T	0.35885	0.0947	L	0.38175	1.15	0.43326	D	0.995359	P;P	0.47191	0.761;0.891	B;B	0.43950	0.437;0.331	T	0.21724	-1.0237	9	0.66056	D	0.02	-23.4126	4.5115	0.11914	0.2863:0.0:0.7137:0.0	.	44;44	B0QY51;Q9H6E4	.;CC134_HUMAN	L	44	.	ENSP00000255784:R44L	R	+	2	0	CCDC134	40535856	1.000000	0.71417	0.673000	0.29887	0.468000	0.32798	6.717000	0.74707	2.683000	0.91414	0.655000	0.94253	CGG	.	.		0.522	CCDC134-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321964.1	NM_024821	
SEPT3	55964	hgsc.bcm.edu	37	22	42377812	42377812	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:42377812C>A	ENST00000396426.3	+	2	429	c.174C>A	c.(172-174)acC>acA	p.T58T	SEPT3_ENST00000396425.3_Silent_p.T58T|SEPT3_ENST00000291236.11_Intron|CTA-250D10.19_ENST00000424613.1_RNA|SEPT3_ENST00000328414.8_Silent_p.T58T|SEPT3_ENST00000406029.1_Intron	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3	58	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)			breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						CCATGAAGACCGGTTTCGACT	0.572																																					p.T58T		Atlas-SNP	.											.	SEPT3	53	.	0			c.C174A						.						126.0	99.0	109.0					22																	42377812		2203	4300	6503	SO:0001819	synonymous_variant	55964	exon2			GAAGACCGGTTTC	AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"""Septins"""	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.174C>A	chr22.hg19:g.42377812C>A		83.0	0.0		72.0	6.0	NM_019106	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Silent	SNP	ENST00000396426.3	hg19	CCDS14026.2																																																																																			.	.		0.572	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1	NM_145734	
TCF20	6942	hgsc.bcm.edu	37	22	42607070	42607070	+	Silent	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:42607070C>A	ENST00000359486.3	-	1	4378	c.4242G>T	c.(4240-4242)tcG>tcT	p.S1414S	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Silent_p.S1414S	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						TGACTAGGTCCGAAGCCACCT	0.502																																					p.S1414S		Atlas-SNP	.											.	TCF20	164	.	0			c.G4242T						.						121.0	119.0	120.0					22																	42607070		2203	4300	6503	SO:0001819	synonymous_variant	6942	exon1			TAGGTCCGAAGCC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.4242G>T	chr22.hg19:g.42607070C>A		112.0	0.0		82.0	4.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	hg19	CCDS14033.1																																																																																			.	.		0.502	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
LDOC1L	84247	hgsc.bcm.edu	37	22	44893427	44893427	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:44893427G>A	ENST00000341255.3	-	2	519	c.10C>T	c.(10-12)Ccg>Tcg	p.P4S		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	4										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		GACGTCTGCGGCTGCACCATG	0.617																																					p.P4S		Atlas-SNP	.											.	LDOC1L	24	.	0			c.C10T						.						37.0	26.0	30.0					22																	44893427		2202	4296	6498	SO:0001583	missense	84247	exon2			TCTGCGGCTGCAC	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.10C>T	chr22.hg19:g.44893427G>A	ENSP00000340434:p.Pro4Ser	119.0	0.0		66.0	4.0	NM_032287	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	hg19	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.429699	0.83776	.	.	ENSG00000188636	ENST00000341255	T	0.28666	1.6	2.95	2.95	0.34219	.	.	.	.	.	T	0.30262	0.0759	N	0.08118	0	0.33260	D	0.559666	D	0.60575	0.988	D	0.65140	0.932	T	0.43458	-0.9390	9	0.87932	D	0	-17.9232	9.6217	0.39725	0.0:0.0:1.0:0.0	.	4	Q6ICC9	LDOCL_HUMAN	S	4	ENSP00000340434:P4S	ENSP00000340434:P4S	P	-	1	0	LDOC1L	43272091	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	4.044000	0.57361	1.969000	0.57287	0.467000	0.42956	CCG	.	.		0.617	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287	
PHF21B	112885	hgsc.bcm.edu	37	22	45291935	45291935	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:45291935A>G	ENST00000313237.5	-	6	1010	c.860T>C	c.(859-861)cTg>cCg	p.L287P	PHF21B_ENST00000403565.1_Missense_Mutation_p.L83P|PHF21B_ENST00000447824.3_Missense_Mutation_p.L233P|PHF21B_ENST00000396103.3_Missense_Mutation_p.L245P|PHF21B_ENST00000404079.2_Missense_Mutation_p.L233P	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	287							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		CGTGGTAACCAGGCCTAGCGC	0.522																																					p.L287P		Atlas-SNP	.											.	PHF21B	61	.	0			c.T860C						.						215.0	186.0	196.0					22																	45291935		2203	4300	6503	SO:0001583	missense	112885	exon6			GTAACCAGGCCTA	AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"""Zinc fingers, PHD-type"""	25161	protein-coding gene	gene with protein product			"""PHD finger protein 4"""	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.860T>C	chr22.hg19:g.45291935A>G	ENSP00000324403:p.Leu287Pro	139.0	0.0		98.0	67.0	NM_138415	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Missense_Mutation	SNP	ENST00000313237.5	hg19	CCDS14061.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.254463	0.80135	.	.	ENSG00000056487	ENST00000403565;ENST00000313237;ENST00000396103;ENST00000404079;ENST00000447824;ENST00000414269	T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01	5.23	5.23	0.72850	.	0.000000	0.52532	D	0.000062	T	0.75466	0.3853	L	0.57536	1.79	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.999;0.999;0.999	T	0.77846	-0.2436	10	0.66056	D	0.02	-21.6784	14.1049	0.65083	1.0:0.0:0.0:0.0	.	233;245;233;287;83	B7Z657;Q96EK2-3;B7Z4F8;Q96EK2;B1AHC5	.;.;.;PF21B_HUMAN;.	P	83;287;245;233;233;83	ENSP00000385053:L83P;ENSP00000324403:L287P;ENSP00000379410:L245P;ENSP00000385105:L233P;ENSP00000388619:L233P;ENSP00000401091:L83P	ENSP00000324403:L287P	L	-	2	0	PHF21B	43670599	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.799000	0.85936	1.954000	0.56735	0.460000	0.39030	CTG	.	.		0.522	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415	
FBLN1	2192	hgsc.bcm.edu	37	22	45943008	45943008	+	Silent	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:45943008C>T	ENST00000327858.6	+	12	1460	c.1365C>T	c.(1363-1365)gcC>gcT	p.A455A	FBLN1_ENST00000348697.2_Silent_p.A455A|FBLN1_ENST00000402984.3_Silent_p.A493A|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000262722.7_Silent_p.A455A|FBLN1_ENST00000340923.5_Silent_p.A455A|FBLN1_ENST00000442170.2_Silent_p.A455A	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	455	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		AGGAGTGTGCCAACGTCTACG	0.587																																					p.A455A		Atlas-SNP	.											.	FBLN1	143	.	0			c.C1365T						.						102.0	82.0	89.0					22																	45943008		2203	4300	6503	SO:0001819	synonymous_variant	2192	exon12			GTGTGCCAACGTC		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"""Fibulins"""	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1365C>T	chr22.hg19:g.45943008C>T		80.0	0.0		45.0	33.0	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Silent	SNP	ENST00000327858.6	hg19	CCDS14067.1																																																																																			.	.		0.587	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486	
MLC1	23209	hgsc.bcm.edu	37	22	50515343	50515343	+	Splice_Site	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:50515343T>C	ENST00000311597.5	-	7	1132		c.e7-2		MLC1_ENST00000431262.2_Splice_Site|MLC1_ENST00000395876.2_Splice_Site|MLC1_ENST00000450140.2_Splice_Site|MLC1_ENST00000538737.1_Splice_Site|MLC1_ENST00000535444.1_Splice_Site	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1						caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CATGGAGCCCTACGAAGAAAC	0.577																																					.		Atlas-SNP	.											.	MLC1	48	.	0			c.526-2A>G						.						92.0	93.0	93.0					22																	50515343		2203	4300	6503	SO:0001630	splice_region_variant	23209	exon8			GAGCCCTACGAAG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.526-2A>G	chr22.hg19:g.50515343T>C		134.0	0.0		99.0	4.0	NM_139202	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Splice_Site	SNP	ENST00000311597.5	hg19	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.178820	0.38511	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140;ENST00000442311	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9803	0.53115	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MLC1	48857470	0.997000	0.39634	0.031000	0.17742	0.007000	0.05969	4.190000	0.58365	1.793000	0.52555	0.533000	0.62120	.	.	.		0.577	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	Intron
PANX2	56666	hgsc.bcm.edu	37	22	50609290	50609290	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:50609290T>C	ENST00000395842.2	+	1	131	c.131T>C	c.(130-132)cTg>cCg	p.L44P	PANX2_ENST00000159647.5_Missense_Mutation_p.L44P	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	44					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CTTCTGCAGCTGAAGCTGGAG	0.682																																					p.L44P		Atlas-SNP	.											.	PANX2	69	.	0			c.T131C						.						8.0	8.0	8.0					22																	50609290		2143	4196	6339	SO:0001583	missense	56666	exon1			TGCAGCTGAAGCT		CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"""Ion channels / Pannexins"""	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.131T>C	chr22.hg19:g.50609290T>C	ENSP00000379183:p.Leu44Pro	88.0	0.0		55.0	4.0	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	hg19	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	T	12.53	1.965566	0.34659	.	.	ENSG00000073150	ENST00000159647;ENST00000395842	T;T	0.33438	1.41;1.41	3.42	3.42	0.39159	.	0.000000	0.64402	U	0.000011	T	0.38692	0.1050	N	0.24115	0.695	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.74023	0.982;0.979	T	0.32693	-0.9897	10	0.87932	D	0	-6.376	11.9315	0.52849	0.0:0.0:0.0:1.0	.	44;44	Q96RD6-1;Q96RD6	.;PANX2_HUMAN	P	44	ENSP00000159647:L44P;ENSP00000379183:L44P	ENSP00000159647:L44P	L	+	2	0	PANX2	48951417	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	6.904000	0.75708	1.205000	0.43262	0.248000	0.18094	CTG	.	.		0.682	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839	
CPT1B	1375	hgsc.bcm.edu	37	22	51008052	51008052	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr22:51008052T>C	ENST00000360719.2	-	18	2325	c.2188A>G	c.(2188-2190)Aac>Gac	p.N730D	CPT1B_ENST00000395650.2_Missense_Mutation_p.N730D|CPT1B_ENST00000457250.1_Missense_Mutation_p.N696D|CPT1B_ENST00000405237.3_Missense_Mutation_p.N730D|CPT1B_ENST00000440709.1_Missense_Mutation_p.N649D|CPT1B_ENST00000312108.7_Missense_Mutation_p.N730D|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000434492.2_Missense_Mutation_p.N525D	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	730					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		AAGATCGTGTTCTCGCCTGCA	0.517																																					p.N730D	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.A2188G						.						146.0	124.0	132.0					22																	51008052		2203	4300	6503	SO:0001583	missense	1375	exon18			TCGTGTTCTCGCC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.2188A>G	chr22.hg19:g.51008052T>C	ENSP00000353945:p.Asn730Asp	138.0	0.0		97.0	4.0	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	hg19	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	T	10.32	1.318010	0.23994	.	.	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	T;T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	N	0.17872	0.535	0.80722	D	1	P;B;B;B	0.43938	0.822;0.011;0.018;0.049	B;B;B;B	0.42625	0.393;0.023;0.06;0.101	T	0.63060	-0.6721	10	0.18276	T	0.48	-33.1143	13.0547	0.58973	0.0:0.0:0.0:1.0	.	649;696;525;730	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	D	730;730;730;696;649;525;730	ENSP00000385486:N730D;ENSP00000312189:N730D;ENSP00000353945:N730D;ENSP00000409342:N696D;ENSP00000414713:N649D;ENSP00000410966:N525D;ENSP00000379011:N730D	ENSP00000312189:N730D	N	-	1	0	CPT1B	49354918	1.000000	0.71417	0.947000	0.38551	0.395000	0.30598	3.095000	0.50235	1.963000	0.57068	0.459000	0.35465	AAC	.	.		0.517	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
GYG2	8908	hgsc.bcm.edu	37	X	2774545	2774545	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:2774545A>G	ENST00000381163.3	+	7	869	c.587A>G	c.(586-588)gAc>gGc	p.D196G	GYG2_ENST00000542787.1_Missense_Mutation_p.D196G|GYG2_ENST00000381161.1_3'UTR|GYG2-AS1_ENST00000445107.1_RNA|GYG2_ENST00000398806.3_Missense_Mutation_p.D165G|GYG2_ENST00000338623.5_Missense_Mutation_p.D196G	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	196					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GTAGGGGCAGACCAAGGCTTA	0.448																																					p.D196G		Atlas-SNP	.											.	GYG2	39	.	0			c.A587G						.						114.0	93.0	100.0					X																	2774545		2203	4299	6502	SO:0001583	missense	8908	exon7			GGGCAGACCAAGG	U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.587A>G	chrX.hg19:g.2774545A>G	ENSP00000370555:p.Asp196Gly	108.0	0.0		80.0	4.0	NM_003918	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	hg19	CCDS14121.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204566	0.38905	.	.	ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787	T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48	3.34	3.34	0.38264	.	0.000000	0.64402	D	0.000020	D	0.92974	0.7764	H	0.98629	4.285	0.51482	D	0.999926	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.94089	0.7351	10	0.87932	D	0	.	11.4252	0.50007	1.0:0.0:0.0:0.0	.	196;196;156;165;165;196	O15488-6;O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.;.;.;.;.;GLYG2_HUMAN	G	165;196;196;196	ENSP00000381786:D165G;ENSP00000370555:D196G;ENSP00000341273:D196G;ENSP00000446092:D196G	ENSP00000341273:D196G	D	+	2	0	GYG2	2784545	1.000000	0.71417	0.145000	0.22337	0.006000	0.05464	7.242000	0.78210	1.191000	0.43056	0.425000	0.28330	GAC	.	.		0.448	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918	
RPGR	6103	hgsc.bcm.edu	37	X	38145015	38145015	+	Intron	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:38145015C>A	ENST00000339363.3	-	14	2688				RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.R1079S|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						CTCCATCCTGCCTTTCATTCT	0.423																																					p.R1079S		Atlas-SNP	.											.	RPGR	175	.	0			c.G3237T						.						408.0	328.0	355.0					X																	38145015		2202	4300	6502	SO:0001627	intron_variant	6103	exon15			ATCCTGCCTTTCA	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1331G>T	chrX.hg19:g.38145015C>A		832.0	1.0		745.0	365.0	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	hg19		.	.	.	.	.	.	.	.	.	.	c	9.446	1.089200	0.20390	.	.	ENSG00000156313	ENST00000378505	T	0.02197	4.4	2.56	1.49	0.22878	.	1.292120	0.05640	U	0.583284	T	0.02304	0.0071	L	0.48642	1.525	0.40039	D	0.975626	P	0.37233	0.588	B	0.20955	0.032	T	0.50939	-0.8768	10	0.87932	D	0	.	5.1985	0.15250	0.3421:0.6579:0.0:0.0	.	1079	E9PE28	.	S	1079	ENSP00000367766:R1079S	ENSP00000367766:R1079S	R	-	3	2	RPGR	38029959	0.000000	0.05858	0.035000	0.18076	0.523000	0.34469	-0.557000	0.05985	1.252000	0.44001	0.339000	0.21740	AGG	.	.		0.423	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ARAF	369	hgsc.bcm.edu	37	X	47430811	47430811	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:47430811T>A	ENST00000377045.4	+	16	1970	c.1776T>A	c.(1774-1776)gaT>gaA	p.D592E	ARAF_ENST00000470206.1_Intron	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	592					cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	CCCAGGCCGATGAGTTGCCTG	0.647																																					p.D595E		Atlas-SNP	.											.	ARAF	67	.	0			c.T1785A						.						57.0	39.0	45.0					X																	47430811		2203	4300	6503	SO:0001583	missense	369	exon16			GGCCGATGAGTTG	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"""v-raf murine sarcoma 3611 viral oncogene homolog 1"""	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.1776T>A	chrX.hg19:g.47430811T>A	ENSP00000366244:p.Asp592Glu	137.0	0.0		146.0	73.0	NM_001256196	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	hg19	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	t	3.051	-0.195418	0.06259	.	.	ENSG00000078061	ENST00000377045	T	0.72942	-0.7	5.26	-6.7	0.01766	.	0.059749	0.64402	D	0.000004	T	0.27384	0.0672	N	0.02011	-0.69	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41142	-0.9525	10	0.02654	T	1	.	5.3103	0.15828	0.1124:0.5063:0.1977:0.1836	.	592	P10398	ARAF_HUMAN	E	592	ENSP00000366244:D592E	ENSP00000366244:D592E	D	+	3	2	ARAF	47315755	0.969000	0.33509	0.946000	0.38457	0.994000	0.84299	0.003000	0.13083	-1.053000	0.03218	0.427000	0.28365	GAT	.	.		0.647	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1		
WDR13	64743	hgsc.bcm.edu	37	X	48458757	48458757	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:48458757T>C	ENST00000218056.5	+	5	1079	c.574T>C	c.(574-576)Tca>Cca	p.S192P	WDR13_ENST00000376729.5_Missense_Mutation_p.S192P	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	192						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						GGCCTGCTGCTCACTCGACGG	0.632																																					p.S192P		Atlas-SNP	.											.	WDR13	96	.	0			c.T574C						.						88.0	61.0	70.0					X																	48458757		2203	4300	6503	SO:0001583	missense	64743	exon5			TGCTGCTCACTCG	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"""WD repeat domain containing"""	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.574T>C	chrX.hg19:g.48458757T>C	ENSP00000218056:p.Ser192Pro	69.0	0.0		61.0	4.0	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	hg19	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.684538	0.88639	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.71103	-0.54;-0.54	4.93	4.93	0.64822	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.82416	0.5032	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.84370	0.0543	10	0.87932	D	0	.	11.6068	0.51037	0.0:0.0:0.0:1.0	.	70;192	B4DVQ7;Q9H1Z4	.;WDR13_HUMAN	P	192	ENSP00000365919:S192P;ENSP00000218056:S192P	ENSP00000218056:S192P	S	+	1	0	WDR13	48343701	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	7.034000	0.76511	1.641000	0.50575	0.356000	0.21956	TCA	.	.		0.632	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2		
IQSEC2	23096	hgsc.bcm.edu	37	X	53277936	53277936	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:53277936T>C	ENST00000375368.5	-	5	2596	c.2396A>G	c.(2395-2397)aAc>aGc	p.N799S	IQSEC2_ENST00000375365.2_Missense_Mutation_p.N604S|IQSEC2_ENST00000396435.3_Missense_Mutation_p.N809S			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	799	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						CTTCTGCCGGTTCCCTAGGAA	0.597																																					p.N809S		Atlas-SNP	.											.	IQSEC2	195	.	0			c.A2426G						.						100.0	75.0	83.0					X																	53277936		2203	4300	6503	SO:0001583	missense	23096	exon6			TGCCGGTTCCCTA	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2396A>G	chrX.hg19:g.53277936T>C	ENSP00000364517:p.Asn799Ser	111.0	0.0		95.0	4.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.77	3.215009	0.58452	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.53423	0.62;0.62;0.62	5.6	5.6	0.85130	.	0.193919	0.53938	D	0.000056	T	0.41213	0.1149	L	0.38175	1.15	0.58432	D	0.999998	B;P	0.40970	0.229;0.734	B;B	0.39531	0.159;0.302	T	0.42498	-0.9448	10	0.72032	D	0.01	.	13.7602	0.62961	0.0:0.0:0.0:1.0	.	809;604	Q5JU85-2;Q5JU85-3	.;.	S	809;799;604	ENSP00000379712:N809S;ENSP00000364517:N799S;ENSP00000364514:N604S	ENSP00000364514:N604S	N	-	2	0	IQSEC2	53294661	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.893000	0.54813	0.430000	0.28490	AAC	.	.		0.597	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
WNK3	65267	hgsc.bcm.edu	37	X	54335737	54335737	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:54335737C>A	ENST00000375159.2	-	3	721	c.722G>T	c.(721-723)cGa>cTa	p.R241L	WNK3_ENST00000375169.3_Missense_Mutation_p.R241L|WNK3_ENST00000354646.2_Missense_Mutation_p.R241L			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						GACTTTAAATCGTTTTAAGTA	0.358																																					p.R241L		Atlas-SNP	.											.	WNK3	218	.	0			c.G722T						.						49.0	42.0	44.0					X																	54335737		2203	4300	6503	SO:0001583	missense	65267	exon4			TTAAATCGTTTTA	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.722G>T	chrX.hg19:g.54335737C>A	ENSP00000364301:p.Arg241Leu	78.0	0.0		60.0	4.0	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586794	0.86851	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.66995	-0.24;-0.24;-0.24	4.93	4.93	0.64822	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40469	N	0.001090	T	0.79919	0.4529	M	0.64170	1.965	0.51012	D	0.999902	D;D	0.89917	0.999;1.0	D;D	0.85130	0.99;0.997	T	0.82436	-0.0458	10	0.87932	D	0	-7.7154	16.24	0.82402	0.0:1.0:0.0:0.0	.	241;241	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	L	241	ENSP00000364312:R241L;ENSP00000346667:R241L;ENSP00000364301:R241L	ENSP00000346667:R241L	R	-	2	0	WNK3	54352462	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.688000	0.84153	2.175000	0.68902	0.422000	0.28245	CGA	.	.		0.358	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
ITIH6	347365	hgsc.bcm.edu	37	X	54784888	54784888	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:54784888T>C	ENST00000218436.6	-	8	1648	c.1619A>G	c.(1618-1620)aAc>aGc	p.N540S		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	540					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTGGCTGTTGTTGGTGGCCCC	0.627																																					p.N540S		Atlas-SNP	.											.	.	.	.	0			c.A1619G						.						15.0	15.0	15.0					X																	54784888		2200	4290	6490	SO:0001583	missense	347365	exon8			CTGTTGTTGGTGG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1619A>G	chrX.hg19:g.54784888T>C	ENSP00000218436:p.Asn540Ser	77.0	0.0		98.0	4.0	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	hg19	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	T	9.673	1.147282	0.21288	.	.	ENSG00000102313	ENST00000218436	T	0.10763	2.84	3.7	2.22	0.28083	.	1.294390	0.05575	U	0.571857	T	0.13286	0.0322	M	0.67953	2.075	0.29653	N	0.843819	B	0.17852	0.024	B	0.21546	0.035	T	0.47898	-0.9081	10	0.09084	T	0.74	.	7.9866	0.30216	0.0:0.1363:0.0:0.8637	.	540	Q6UXX5	ITH5L_HUMAN	S	540	ENSP00000218436:N540S	ENSP00000218436:N540S	N	-	2	0	ITIH5L	54801613	0.000000	0.05858	0.996000	0.52242	0.206000	0.24218	0.061000	0.14366	1.162000	0.42619	0.483000	0.47432	AAC	.	.		0.627	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
AR	367	hgsc.bcm.edu	37	X	66766306	66766306	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:66766306A>G	ENST00000374690.3	+	1	1842	c.1318A>G	c.(1318-1320)Aca>Gca	p.T440A	AR_ENST00000504326.1_Missense_Mutation_p.T440A|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.T440A	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	438	Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|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 transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CACTCTCTTCACAGCCGAAGA	0.746									Androgen Insensitivity Syndrome																												p.T440A		Atlas-SNP	.											.	AR	249	.	0			c.A1318G						.						4.0	4.0	4.0					X																	66766306		1370	2920	4290	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CTCTTCACAGCCG	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1318A>G	chrX.hg19:g.66766306A>G	ENSP00000363822:p.Thr440Ala	45.0	0.0		43.0	4.0	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	13.33	2.205347	0.39003	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	D;D;D	0.95035	-3.59;-3.59;-3.59	5.06	2.67	0.31697	.	0.840433	0.10974	N	0.613442	D	0.92545	0.7632	M	0.74881	2.28	0.27541	N	0.9508	B;B;P	0.43701	0.01;0.005;0.815	B;B;B	0.42214	0.074;0.042;0.38	D	0.84511	0.0622	10	0.29301	T	0.29	.	4.8744	0.13650	0.6413:0.0:0.3587:0.0	.	440;440;438	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	A	250;440;440;440;432	ENSP00000363822:T440A;ENSP00000421155:T440A;ENSP00000379359:T440A	ENSP00000363822:T440A	T	+	1	0	AR	66683031	0.991000	0.36638	0.950000	0.38849	0.951000	0.60555	0.992000	0.29667	0.759000	0.33084	0.414000	0.27820	ACA	.	.		0.746	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
PJA1	64219	hgsc.bcm.edu	37	X	68381880	68381880	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:68381880T>C	ENST00000361478.1	-	2	1579	c.1202A>G	c.(1201-1203)gAg>gGg	p.E401G	PJA1_ENST00000477231.1_5'Flank|PJA1_ENST00000374571.4_Missense_Mutation_p.E346G|PJA1_ENST00000374583.1_Missense_Mutation_p.E401G|PJA1_ENST00000374584.3_Missense_Mutation_p.E213G	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	401					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						AGGTTCCCGCTCTTCTTTCCC	0.642																																					p.E401G		Atlas-SNP	.											.	PJA1	106	.	0			c.A1202G						.						28.0	30.0	29.0					X																	68381880		2203	4300	6503	SO:0001583	missense	64219	exon2			TCCCGCTCTTCTT	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.1202A>G	chrX.hg19:g.68381880T>C	ENSP00000355014:p.Glu401Gly	74.0	0.0		93.0	4.0	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Missense_Mutation	SNP	ENST00000361478.1	hg19	CCDS14393.1	.	.	.	.	.	.	.	.	.	.	t	18.46	3.627998	0.66901	.	.	ENSG00000181191	ENST00000396010;ENST00000374584;ENST00000374583;ENST00000361478;ENST00000374571	T;T;T;T	0.06294	3.32;3.32;3.32;3.32	3.59	3.59	0.41128	.	0.000000	0.53938	U	0.000056	T	0.17280	0.0415	L	0.61218	1.895	0.42671	D	0.993515	D;D	0.63046	0.97;0.992	P;P	0.62740	0.749;0.906	T	0.00520	-1.1692	10	0.87932	D	0	-12.4008	9.8043	0.40783	0.0:0.0:0.0:1.0	.	401;213	Q8NG27;Q8NG27-2	PJA1_HUMAN;.	G	316;213;401;401;346	ENSP00000363712:E213G;ENSP00000363711:E401G;ENSP00000355014:E401G;ENSP00000363699:E346G	ENSP00000355014:E401G	E	-	2	0	PJA1	68298605	1.000000	0.71417	0.068000	0.19968	0.023000	0.10783	5.616000	0.67709	1.672000	0.50884	0.438000	0.28831	GAG	.	.		0.642	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
ZMYM3	9203	hgsc.bcm.edu	37	X	70465850	70465850	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:70465850A>G	ENST00000353904.2	-	16	2858	c.2671T>C	c.(2671-2673)Tcg>Ccg	p.S891P	ZMYM3_ENST00000373988.1_Missense_Mutation_p.S893P|ZMYM3_ENST00000373984.3_Missense_Mutation_p.S893P|ZMYM3_ENST00000314425.5_Missense_Mutation_p.S891P|ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373998.1_Missense_Mutation_p.S879P	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	891					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(7)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(17)|ovary(1)|prostate(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(35;0.156)					ATAGGCATCGAGAAAGGCACC	0.572																																					p.S891P		Atlas-SNP	.											.	ZMYM3	137	.	0			c.T2671C						.						122.0	99.0	107.0					X																	70465850		2203	4300	6503	SO:0001583	missense	9203	exon16			GCATCGAGAAAGG	AB002383	CCDS14409.1, CCDS55443.1, CCDS55444.1	Xq13.1	2013-01-08	2005-12-19	2005-12-19	ENSG00000147130	ENSG00000147130		"""Zinc fingers, MYM type"""	13054	protein-coding gene	gene with protein product		300061	"""zinc finger protein 261"""	ZNF261		10486218	Standard	NM_201599		Approved	ZNF198L2, DXS6673E, KIAA0385, MYM	uc004dzh.2	Q14202	OTTHUMG00000021799	ENST00000353904.2:c.2671T>C	chrX.hg19:g.70465850A>G	ENSP00000343909:p.Ser891Pro	96.0	0.0		89.0	4.0	NM_005096	D3DVV3|O15089|Q96E26	Missense_Mutation	SNP	ENST00000353904.2	hg19	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	a	15.19	2.760658	0.49468	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373984;ENST00000373988	T;T;T;T;T	0.41400	1.61;1.0;1.61;1.61;1.61	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000008	T	0.42449	0.1203	N	0.15975	0.35	0.41935	D	0.990581	D;D	0.67145	0.996;0.994	D;P	0.65010	0.931;0.854	T	0.27706	-1.0066	10	0.15952	T	0.53	-7.3014	14.089	0.64977	1.0:0.0:0.0:0.0	.	879;891	Q14202-2;Q14202	.;ZMYM3_HUMAN	P	891;879;891;893;893	ENSP00000322845:S891P;ENSP00000363110:S879P;ENSP00000343909:S891P;ENSP00000363096:S893P;ENSP00000363100:S893P	ENSP00000322845:S891P	S	-	1	0	ZMYM3	70382575	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	2.833000	0.48159	1.902000	0.55061	0.427000	0.28365	TCG	.	.		0.572	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599	
DACH2	117154	hgsc.bcm.edu	37	X	85404070	85404070	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:85404070G>T	ENST00000373125.4	+	1	446	c.446G>T	c.(445-447)aGg>aTg	p.R149M	DACH2_ENST00000373131.1_Missense_Mutation_p.R149M	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	149	DACHbox-N.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						CTCATCACCAGGAAAGACTTC	0.557																																					p.R149M		Atlas-SNP	.											.	DACH2	263	.	0			c.G446T						.						46.0	47.0	46.0					X																	85404070		2203	4300	6503	SO:0001583	missense	117154	exon1			TCACCAGGAAAGA	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"""dachshund homolog 2 (Drosophila)"""				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.446G>T	chrX.hg19:g.85404070G>T	ENSP00000362217:p.Arg149Met	61.0	0.0		59.0	4.0	NM_001139514	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.958200	0.73902	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125	D;D	0.84370	-1.84;-1.84	4.5	4.5	0.54988	DNA binding domain, putative (1);Transforming protein Ski (2);	0.000000	0.56097	D	0.000037	D	0.92166	0.7516	M	0.81497	2.545	0.80722	D	1	D;D	0.76494	0.991;0.999	D;D	0.77557	0.984;0.99	D	0.92951	0.6380	10	0.54805	T	0.06	.	16.1211	0.81357	0.0:0.0:1.0:0.0	.	149;149	Q96NX9-2;Q96NX9	.;DACH2_HUMAN	M	149	ENSP00000362223:R149M;ENSP00000362217:R149M	ENSP00000345134:R149M	R	+	2	0	DACH2	85290726	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.806000	0.91930	2.071000	0.62044	0.544000	0.68410	AGG	.	.		0.557	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281	
MUM1L1	139221	hgsc.bcm.edu	37	X	105450466	105450466	+	Silent	SNP	A	A	G			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:105450466A>G	ENST00000357175.2	+	4	1690	c.1041A>G	c.(1039-1041)gaA>gaG	p.E347E	MUM1L1_ENST00000337685.2_Silent_p.E347E|MUM1L1_ENST00000372552.1_Silent_p.E347E	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	347						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						ATTTTGAAGAACTTGAGGAAG	0.408																																					p.E347E		Atlas-SNP	.											.	MUM1L1	166	.	0			c.A1041G						.						23.0	21.0	21.0					X																	105450466		1849	4080	5929	SO:0001819	synonymous_variant	139221	exon5			TGAAGAACTTGAG	AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.1041A>G	chrX.hg19:g.105450466A>G		104.0	0.0		100.0	4.0	NM_152423	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Silent	SNP	ENST00000357175.2	hg19	CCDS55469.1																																																																																			.	.		0.408	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423	
RNF128	79589	hgsc.bcm.edu	37	X	105970375	105970375	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:105970375G>T	ENST00000255499.2	+	1	482	c.232G>T	c.(232-234)Gag>Tag	p.E78*	RNF128_ENST00000324342.3_Intron	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	78	PA.				negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						CTCGCCGCTGGAGCCTGTGGC	0.677																																					p.E78X		Atlas-SNP	.											.	RNF128	74	.	0			c.G232T						.						15.0	13.0	14.0					X																	105970375		2146	4174	6320	SO:0001587	stop_gained	79589	exon1			CCGCTGGAGCCTG	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"""RING-type (C3HC4) zinc fingers"""	21153	protein-coding gene	gene with protein product		300439	"""ring finger protein 128"""				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.232G>T	chrX.hg19:g.105970375G>T	ENSP00000255499:p.Glu78*	192.0	0.0		208.0	75.0	NM_194463	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Nonsense_Mutation	SNP	ENST00000255499.2	hg19	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	g	40	8.078396	0.98643	.	.	ENSG00000133135	ENST00000255499	.	.	.	4.7	4.7	0.59300	.	0.763681	0.12066	N	0.502641	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	10.5584	0.45131	0.0:0.1912:0.8088:0.0	.	.	.	.	X	78	.	ENSP00000255499:E78X	E	+	1	0	RNF128	105857031	0.996000	0.38824	0.985000	0.45067	0.975000	0.68041	1.794000	0.38774	2.082000	0.62665	0.509000	0.49947	GAG	.	.		0.677	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539	
MID2	11043	hgsc.bcm.edu	37	X	107097839	107097839	+	Splice_Site	SNP	C	C	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:107097839C>T	ENST00000262843.6	+	3	1269	c.721C>T	c.(721-723)Caa>Taa	p.Q241*	MID2_ENST00000443968.2_Splice_Site_p.Q241*	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	241					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						GCGATGACAGCAAACTCTGGA	0.463																																					p.Q241X		Atlas-SNP	.											.	MID2	122	.	0			c.C721T						.						129.0	106.0	114.0					X																	107097839		2203	4300	6503	SO:0001630	splice_region_variant	11043	exon3			TGACAGCAAACTC		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.721-1C>T	chrX.hg19:g.107097839C>T		106.0	0.0		101.0	5.0	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Nonsense_Mutation	SNP	ENST00000262843.6	hg19	CCDS14532.2	.	.	.	.	.	.	.	.	.	.	C	43	10.251219	0.99368	.	.	ENSG00000080561	ENST00000262843;ENST00000443968	.	.	.	5.17	5.17	0.71159	.	0.059879	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8595	0.70369	0.0:1.0:0.0:0.0	.	.	.	.	X	241	.	.	Q	+	1	0	MID2	106984495	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.021000	0.76425	2.388000	0.81334	0.600000	0.82982	CAA	.	.		0.463	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216	Nonsense_Mutation
DOCK11	139818	hgsc.bcm.edu	37	X	117744275	117744275	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:117744275T>C	ENST00000276202.7	+	28	3053	c.2990T>C	c.(2989-2991)gTc>gCc	p.V997A	DOCK11_ENST00000276204.6_Missense_Mutation_p.V997A	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	997					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TATCATCATGTCTTACATTCA	0.423																																					p.V997A		Atlas-SNP	.											.	DOCK11	185	.	0			c.T2990C						.						153.0	121.0	132.0					X																	117744275		2203	4300	6503	SO:0001583	missense	139818	exon28			ATCATGTCTTACA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.2990T>C	chrX.hg19:g.117744275T>C	ENSP00000276202:p.Val997Ala	88.0	0.0		99.0	4.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	T	4.159	0.028049	0.08054	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.03580	3.88;3.88	5.14	5.14	0.70334	.	0.174630	0.49916	D	0.000134	T	0.01592	0.0051	N	0.03608	-0.345	0.29348	N	0.865558	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40961	-0.9535	10	0.07482	T	0.82	-7.7299	7.1266	0.25475	0.0:0.1496:0.0:0.8504	.	997;997	A6NIW2;Q5JSL3	.;DOC11_HUMAN	A	997	ENSP00000276204:V997A;ENSP00000276202:V997A	ENSP00000276202:V997A	V	+	2	0	DOCK11	117628303	0.953000	0.32496	1.000000	0.80357	0.812000	0.45895	1.804000	0.38873	1.817000	0.53016	0.481000	0.45027	GTC	.	.		0.423	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
ZNF75D	7626	hgsc.bcm.edu	37	X	134426381	134426381	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:134426381C>A	ENST00000370766.3	-	4	3139	c.430G>T	c.(430-432)Gga>Tga	p.G144*	ZNF75D_ENST00000370764.1_Intron|ZNF75D_ENST00000494295.1_Intron	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	144					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GCCTCCTTTCCCAGCTCATGG	0.522																																					p.G144X		Atlas-SNP	.											.	ZNF75D	65	.	0			c.G430T						.						74.0	67.0	70.0					X																	134426381		2203	4300	6503	SO:0001587	stop_gained	7626	exon3			CCTTTCCCAGCTC	S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13145	protein-coding gene	gene with protein product		314997	"""zinc finger protein 75 (D8C6)"""	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.430G>T	chrX.hg19:g.134426381C>A	ENSP00000359802:p.Gly144*	90.0	0.0		82.0	4.0	NM_007131	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Nonsense_Mutation	SNP	ENST00000370766.3	hg19	CCDS14648.1	.	.	.	.	.	.	.	.	.	.	C	54	22.293001	0.99947	.	.	ENSG00000186376	ENST00000370766	.	.	.	2.3	-0.642	0.11486	.	.	.	.	.	.	.	.	.	.	.	0.19775	N	0.999954	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	2.7469	0.05270	0.0:0.4105:0.2511:0.3384	.	.	.	.	X	144	.	ENSP00000359802:G144X	G	-	1	0	ZNF75D	134254047	0.362000	0.24980	0.059000	0.19551	0.570000	0.35934	-0.047000	0.11963	-0.314000	0.08716	-0.355000	0.07637	GGA	.	.		0.522	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131	
MMGT1	93380	hgsc.bcm.edu	37	X	135053250	135053250	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:135053250T>A	ENST00000305963.2	-	2	486	c.99A>T	c.(97-99)ttA>ttT	p.L33F	MMGT1_ENST00000433339.2_Missense_Mutation_p.L98F	NM_173470.1	NP_775741.1	Q8N4V1	MMGT1_HUMAN	membrane magnesium transporter 1	33					magnesium ion transport (GO:0015693)	early endosome (GO:0005769)|ER membrane protein complex (GO:0072546)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|endometrium(1)|kidney(1)	3						CTTTTTCTGTTAATCGCATAT	0.294																																					p.L33F		Atlas-SNP	.											.	MMGT1	14	.	0			c.A99T						.						161.0	153.0	156.0					X																	135053250		2203	4300	6503	SO:0001583	missense	93380	exon2			TTCTGTTAATCGC	AL157477	CCDS14653.1	Xq26.3	2012-05-23	2008-11-21	2008-11-21	ENSG00000169446	ENSG00000169446			28100	protein-coding gene	gene with protein product	"""ER membrane protein complex subunit 5"""		"""transmembrane protein 32"""	TMEM32		18057121, 22119785	Standard	NM_173470		Approved	EMC5	uc004ezi.1	Q8N4V1	OTTHUMG00000022499	ENST00000305963.2:c.99A>T	chrX.hg19:g.135053250T>A	ENSP00000306220:p.Leu33Phe	578.0	0.0		484.0	245.0	NM_173470	B2R625|B4DIY3|D3DWG7|Q5JPP7	Missense_Mutation	SNP	ENST00000305963.2	hg19	CCDS14653.1	.	.	.	.	.	.	.	.	.	.	T	17.61	3.431485	0.62844	.	.	ENSG00000169446	ENST00000305963;ENST00000433339	.	.	.	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000001	T	0.69878	0.3160	M	0.62266	1.93	0.58432	D	0.999997	D;D	0.89917	1.0;0.958	D;P	0.91635	0.999;0.815	T	0.71276	-0.4641	9	0.52906	T	0.07	.	8.5328	0.33344	0.0:0.0932:0.0:0.9068	.	98;33	Q8N4V1-2;Q8N4V1	.;MMGT1_HUMAN	F	33;98	.	ENSP00000306220:L33F	L	-	3	2	MMGT1	134880916	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.536000	0.36072	1.832000	0.53329	0.481000	0.45027	TTA	.	.		0.294	MMGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058453.3	NM_173470	
SOX3	6658	hgsc.bcm.edu	37	X	139587141	139587141	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:139587141G>T	ENST00000370536.2	-	1	84	c.85C>A	c.(85-87)Ccc>Acc	p.P29T		NM_005634.2	NP_005625.2	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	29					central nervous system development (GO:0007417)|face development (GO:0060324)|hypothalamus development (GO:0021854)|negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|sensory organ development (GO:0007423)|Sertoli cell development (GO:0060009)|sex determination (GO:0007530)|spermatid differentiation (GO:0048515)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	10	Acute lymphoblastic leukemia(192;7.65e-05)					GGCGGGAAGGGTAGGCTTATC	0.652																																					p.P29T		Atlas-SNP	.											.	SOX3	44	.	0			c.C85A						.						10.0	10.0	10.0					X																	139587141		2193	4281	6474	SO:0001583	missense	6658	exon1			GGAAGGGTAGGCT		CCDS14669.1	Xq27.1	2013-10-17			ENSG00000134595	ENSG00000134595		"""SRY (sex determining region Y)-boxes"""	11199	protein-coding gene	gene with protein product		313430	"""panhypopituitarism"""	PHP		15800844	Standard	NM_005634		Approved		uc004fbd.1	P41225	OTTHUMG00000022544	ENST00000370536.2:c.85C>A	chrX.hg19:g.139587141G>T	ENSP00000359567:p.Pro29Thr	126.0	0.0		125.0	31.0	NM_005634	P35714|Q5JWI3|Q9NP49	Missense_Mutation	SNP	ENST00000370536.2	hg19	CCDS14669.1	.	.	.	.	.	.	.	.	.	.	g	11.55	1.672375	0.29693	.	.	ENSG00000134595	ENST00000370536	D	0.98493	-4.96	3.67	1.8	0.24995	.	.	.	.	.	D	0.93455	0.7912	N	0.19112	0.55	0.23879	N	0.996589	B	0.24186	0.099	B	0.22753	0.041	D	0.86525	0.1818	8	.	.	.	.	5.0479	0.14494	0.1311:0.2109:0.658:0.0	.	29	P41225	SOX3_HUMAN	T	29	ENSP00000359567:P29T	.	P	-	1	0	SOX3	139414807	0.050000	0.20438	0.229000	0.23960	0.689000	0.40095	0.143000	0.16115	0.179000	0.19938	0.525000	0.51046	CCC	.	.		0.652	SOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058577.1		
GPR50	9248	hgsc.bcm.edu	37	X	150345211	150345211	+	Silent	SNP	G	G	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chrX:150345211G>T	ENST00000218316.3	+	1	87	c.18G>T	c.(16-18)gcG>gcT	p.A6A	GPR50-AS1_ENST00000454196.1_RNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	6					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CCACCCTAGCGGTTCCCACCC	0.557																																					p.A6A		Atlas-SNP	.											.	GPR50	195	.	0			c.G18T						.						67.0	70.0	69.0					X																	150345211		1931	4111	6042	SO:0001819	synonymous_variant	9248	exon1			CCTAGCGGTTCCC	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.18G>T	chrX.hg19:g.150345211G>T		104.0	0.0		98.0	4.0	NM_004224	Q0VGG3|Q3ZAR0	Silent	SNP	ENST00000218316.3	hg19	CCDS44012.1																																																																																			.	.		0.557	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
SPATA31A1	647060	hgsc.bcm.edu	37	9	39361559	39361559	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:39361559delC	ENST00000377647.3	+	4	3826	c.3797delC	c.(3796-3798)gccfs	p.A1266fs		NM_001085452.1	NP_001078921.1	Q5TZJ5	S31A1_HUMAN	SPATA31 subfamily A, member 1	1266					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGCTATGCAGCCAGCAGTCAA	0.502																																					p.A1266fs		Atlas-INDEL	.											.	.	.	.	0			c.3796delG						.						0.0	1.0	1.0					9																	39361559		0	1	1	SO:0001589	frameshift_variant	647060	exon4			.		CCDS43808.1	9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000204849	ENSG00000204849			23394	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 36"", ""family with sequence similarity 75, member A1"""	C9orf36, FAM75A1		20850414	Standard	XM_006716851		Approved	DKFZP434B204, C9orf36A, OTTHUMG00000013156		Q5TZJ5	OTTHUMG00000013156	ENST00000377647.3:c.3797delC	chr9.hg19:g.39361559delC	ENSP00000366875:p.Ala1266fs	36.0	0.0		38.0	14.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000377647.3	hg19	CCDS43808.1																																																																																			.	.		0.502	SPATA31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036910.1	NM_001085452	
ARID1A	8289	hgsc.bcm.edu	37	1	27106505	27106506	+	Frame_Shift_Ins	INS	-	-	T			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr1:27106505_27106506insT	ENST00000324856.7	+	20	6487_6488	c.6116_6117insT	c.(6115-6120)caagggfs	p.QG2039fs	ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.QG1822fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.QG1656fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.QG367fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2039					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GAACAGGACCAAGGGGTGAGCT	0.569			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.Q2039fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.6116_6117insT						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	Exception_encountered	chr1.hg19:g.27106505_27106506insT	ENSP00000320485:p.Gln2039fs	276.0	0.0		171.0	126.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.569	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
CADM2	253559	hgsc.bcm.edu	37	3	85932563	85932563	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr3:85932563delA	ENST00000407528.2	+	3	396	c.334delA	c.(334-336)aaafs	p.K112fs	CADM2_ENST00000405615.2_Frame_Shift_Del_p.K114fs|CADM2_ENST00000383699.3_Frame_Shift_Del_p.K121fs	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	112	Ig-like V-type.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		AATGCCTGTCAAAACTTCCAA	0.413																																					p.V120fs		Atlas-Indel,Pindel	.											CADM2_ENST00000383699,NS,carcinoma,+2,2	CADM2	195	.	0			c.360delC						.						97.0	80.0	86.0					3																	85932563		2203	4300	6503	SO:0001589	frameshift_variant	253559	exon4			.	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	29849	protein-coding gene	gene with protein product	"""nectin-like 3"""	609938	"""immunoglobulin superfamily, member 4D"""	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.334delA	chr3.hg19:g.85932563delA	ENSP00000384575:p.Lys112fs	160.0	0.0		125.0	29.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Frame_Shift_Del	DEL	ENST00000407528.2	hg19	CCDS54614.1																																																																																			.	.		0.413	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
SPATA31A2	642265	hgsc.bcm.edu	37	9	39890810	39890810	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EP-A2KB-01A-11D-A183-10	TCGA-EP-A2KB-10A-01D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	305a5074-5384-45a0-985d-289b178d09f6	87df7481-7da6-412b-9452-d7ce62844ef4	g.chr9:39890810delC	ENST00000456183.2	+	4	3826	c.3797delC	c.(3796-3798)gccfs	p.A1266fs		NM_001040065.1	NP_001035154.1	Q5RGS2	S31A2_HUMAN	SPATA31 subfamily A, member 2	1266					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGCTATGCAGCCAGCAGTCAA	0.502																																					p.A1266fs		Atlas-INDEL	.											.	.	.	.	0			c.3796delG						.																																			SO:0001589	frameshift_variant	647060	exon4			.			9p13.1	2012-10-15	2012-10-12	2012-10-12	ENSG00000204848				32002	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A2"""	FAM75A2		20850414	Standard			Approved	OTTHUMG00000013563	uc004abm.3	Q5RGS2	OTTHUMG00000013563	ENST00000456183.2:c.3797delC	chr9.hg19:g.39890810delC	ENSP00000406957:p.Ala1266fs	19.0	0.0		65.0	21.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000456183.2	hg19	CCDS43809.1																																																																																			.	.		0.502	SPATA31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037739.1	NM_001040065	
