#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
DVL1	1855	hgsc.bcm.edu	37	1	1273715	1273715	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:1273715G>A	ENST00000378888.5	-	13	1725	c.1441C>T	c.(1441-1443)Cgg>Tgg	p.R481W	DVL1_ENST00000378891.5_Missense_Mutation_p.R456W			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	481	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	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)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ACCGTGTGCCGCAGGAAGCCG	0.647																																					p.R456W		Atlas-SNP	.											.	DVL1	36	.	0			c.C1366T						.						61.0	55.0	57.0					1																	1273715		2203	4298	6501	SO:0001583	missense	1855	exon13			TGTGCCGCAGGAA	AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404		"""Dishevelled homologs"""	3084	protein-coding gene	gene with protein product		601365	"""dishevelled 1 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 1 (Drosophila)"""			8817329	Standard	NM_004421		Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.1441C>T	chr1.hg19:g.1273715G>A	ENSP00000368166:p.Arg481Trp	88.0	0.0		67.0	27.0	NM_004421	Q5TA33|Q5TA35	Missense_Mutation	SNP	ENST00000378888.5	hg19		.	.	.	.	.	.	.	.	.	.	G	17.12	3.308401	0.60305	.	.	ENSG00000107404	ENST00000378891;ENST00000378888;ENST00000345100;ENST00000263743	T;T	0.23552	1.9;1.9	3.48	0.306	0.15806	DEP domain (6);Winged helix-turn-helix transcription repressor DNA-binding (2);	0.065039	0.64402	D	0.000013	T	0.54679	0.1873	M	0.90595	3.13	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.997;0.989;0.981	T	0.63453	-0.6634	10	0.87932	D	0	.	13.219	0.59877	0.0:0.0:0.2627:0.7373	.	139;481;456;456	G3XA93;O14640;P54792;O14640-2	.;DVL1_HUMAN;DVL1L_HUMAN;.	W	456;481;230;139	ENSP00000368169:R456W;ENSP00000368166:R481W	ENSP00000263743:R139W	R	-	1	2	DVL1	1263578	0.963000	0.33076	0.998000	0.56505	0.987000	0.75469	0.169000	0.16641	-0.032000	0.13758	-0.513000	0.04457	CGG	.	.		0.647	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421	
C1orf174	339448	hgsc.bcm.edu	37	1	3807306	3807306	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:3807306C>T	ENST00000361605.3	-	3	543	c.445G>A	c.(445-447)Gga>Aga	p.G149R	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	149						nucleus (GO:0005634)				endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		TCTTCTGCTCCGGACCCGGCA	0.552																																					p.G149R		Atlas-SNP	.											.	C1orf174	20	.	0			c.G445A						.						98.0	89.0	92.0					1																	3807306		2203	4300	6503	SO:0001583	missense	339448	exon3			CTGCTCCGGACCC	BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.445G>A	chr1.hg19:g.3807306C>T	ENSP00000355306:p.Gly149Arg	123.0	0.0		93.0	38.0	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Missense_Mutation	SNP	ENST00000361605.3	hg19	CCDS53.1	.	.	.	.	.	.	.	.	.	.	C	7.306	0.614107	0.14129	.	.	ENSG00000198912	ENST00000361605	T	0.06218	3.33	5.56	3.67	0.42095	.	0.776019	0.11796	N	0.528623	T	0.08537	0.0212	L	0.43152	1.355	0.09310	N	1	D	0.53619	0.961	P	0.46885	0.53	T	0.21759	-1.0236	10	0.14656	T	0.56	-5.474	11.4202	0.49976	0.0:0.8484:0.0:0.1516	.	149	Q8IYL3	CA174_HUMAN	R	149	ENSP00000355306:G149R	ENSP00000355306:G149R	G	-	1	0	C1orf174	3797166	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-2.141000	0.01300	1.337000	0.45525	0.563000	0.77884	GGA	.	.		0.552	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356	
CHD5	26038	hgsc.bcm.edu	37	1	6202186	6202186	+	Splice_Site	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6202186A>G	ENST00000262450.3	-	15	2536		c.e15+1		CHD5_ENST00000378021.1_Splice_Site	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5						tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCGAGCCCTCACCTTCATACG	0.597																																					.		Atlas-SNP	.											.	CHD5	267	.	0			c.2436+2T>C						.						143.0	136.0	138.0					1																	6202186		2203	4300	6503	SO:0001630	splice_region_variant	26038	exon16			GCCCTCACCTTCA	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2436+1T>C	chr1.hg19:g.6202186A>G		122.0	0.0		120.0	43.0	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Splice_Site	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	A	15.10	2.734198	0.48939	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	.	.	.	4.07	4.07	0.47477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3346	0.60509	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHD5	6124773	1.000000	0.71417	0.980000	0.43619	0.512000	0.34134	6.186000	0.72026	1.609000	0.50190	0.459000	0.35465	.	.	.		0.597	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	Intron
PLEKHG5	57449	hgsc.bcm.edu	37	1	6531575	6531575	+	Silent	SNP	G	G	A	rs139904931	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6531575G>A	ENST00000400915.3	-	13	1488	c.1422C>T	c.(1420-1422)ccC>ccT	p.P474P	PLEKHG5_ENST00000340850.5_Silent_p.P418P|PLEKHG5_ENST00000400913.1_Silent_p.P418P|PLEKHG5_ENST00000537245.1_Silent_p.P497P|PLEKHG5_ENST00000535355.1_Silent_p.P487P|PLEKHG5_ENST00000377732.1_Silent_p.P455P|PLEKHG5_ENST00000377728.3_Silent_p.P418P|PLEKHG5_ENST00000377737.2_Silent_p.P418P|PLEKHG5_ENST00000377748.1_Silent_p.P495P|PLEKHG5_ENST00000544978.1_Silent_p.P418P|PLEKHG5_ENST00000377725.1_Silent_p.P418P|PLEKHG5_ENST00000377740.3_Silent_p.P495P	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	474	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)	p.P495P(1)		liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GGAAGTCCCCGGGCTGTAGCA	0.711																																					p.P497P		Atlas-SNP	.											PLEKHG5_ENST00000377748,NS,carcinoma,0,1	PLEKHG5	66	.	1	Substitution - coding silent(1)	prostate(1)	c.C1491T						.						14.0	18.0	17.0					1																	6531575		2198	4283	6481	SO:0001819	synonymous_variant	57449	exon13			GTCCCCGGGCTGT	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"""Pleckstrin homology (PH) domain containing"""	29105	protein-coding gene	gene with protein product	"""synectin-binding guanine exchange factor"""	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.1422C>T	chr1.hg19:g.6531575G>A		181.0	0.0		140.0	55.0	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	hg19	CCDS41241.1																																																																																			.	G|0.997;C|0.003		0.711	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	
ZBTB48	3104	hgsc.bcm.edu	37	1	6642238	6642238	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6642238C>T	ENST00000377674.4	+	3	969	c.811C>T	c.(811-813)Ctg>Ttg	p.L271L		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	271					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)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		TGAGCCAGCCCTGAGCGCGGG	0.552																																					p.L271L	Esophageal Squamous(125;1449 1657 4031 29866 49542)	Atlas-SNP	.											.	ZBTB48	33	.	0			c.C811T						.						69.0	68.0	68.0					1																	6642238		2203	4300	6503	SO:0001819	synonymous_variant	3104	exon3			CCAGCCCTGAGCG	BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	4930	protein-coding gene	gene with protein product		165270	"""GLI-Kruppel family member HKR3"""	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.811C>T	chr1.hg19:g.6642238C>T		200.0	0.0		164.0	59.0	NM_005341	Q5SY19	Silent	SNP	ENST00000377674.4	hg19	CCDS84.1																																																																																			.	.		0.552	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341	
DNAJC11	55735	hgsc.bcm.edu	37	1	6697322	6697322	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:6697322T>C	ENST00000377577.5	-	14	1583	c.1460A>G	c.(1459-1461)gAc>gGc	p.D487G	DNAJC11_ENST00000542246.1_Missense_Mutation_p.D449G|DNAJC11_ENST00000377573.5_Missense_Mutation_p.D397G|DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000465508.1_5'UTR|DNAJC11_ENST00000294401.7_Missense_Mutation_p.D435G	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	487						extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		CACAGTCACGTCAATCACCTT	0.547																																					p.D487G		Atlas-SNP	.											.	DNAJC11	93	.	0			c.A1460G						.						271.0	203.0	226.0					1																	6697322		2203	4300	6503	SO:0001583	missense	55735	exon14			GTCACGTCAATCA	AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"""Heat shock proteins / DNAJ (HSP40)"""	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.1460A>G	chr1.hg19:g.6697322T>C	ENSP00000366800:p.Asp487Gly	126.0	0.0		107.0	40.0	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	hg19	CCDS87.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837986	0.91117	.	.	ENSG00000007923	ENST00000377577;ENST00000294401;ENST00000542246;ENST00000377573	T;T;T;T	0.63096	0.82;0.72;0.44;-0.02	5.54	5.54	0.83059	DnaJ-like protein C11, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84534	0.5493	H	0.94886	3.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.986;0.999;0.999	D	0.88947	0.3384	10	0.87932	D	0	-8.1167	14.8693	0.70444	0.0:0.0:0.0:1.0	.	397;435;487	B4DGD5;Q9NVH1-3;Q9NVH1	.;.;DJC11_HUMAN	G	487;435;449;397	ENSP00000366800:D487G;ENSP00000294401:D435G;ENSP00000444020:D449G;ENSP00000366796:D397G	ENSP00000294401:D435G	D	-	2	0	DNAJC11	6619909	1.000000	0.71417	0.918000	0.36340	0.991000	0.79684	7.502000	0.81614	2.107000	0.64212	0.533000	0.62120	GAC	.	.		0.547	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
PER3	8863	hgsc.bcm.edu	37	1	7854025	7854025	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:7854025C>T	ENST00000361923.2	+	5	773	c.598C>T	c.(598-600)Cgg>Tgg	p.R200W	PER3_ENST00000377541.1_Missense_Mutation_p.R200W|PER3_ENST00000377532.3_Missense_Mutation_p.R201W	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	200					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		AGCAGCTGCACGGTATGAATG	0.428																																					p.R200W		Atlas-SNP	.											.	PER3	95	.	0			c.C598T						.						158.0	154.0	155.0					1																	7854025		2203	4300	6503	SO:0001583	missense	8863	exon5			GCTGCACGGTATG	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.598C>T	chr1.hg19:g.7854025C>T	ENSP00000355031:p.Arg200Trp	111.0	0.0		134.0	64.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	hg19	CCDS89.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212237	0.79240	.	.	ENSG00000049246	ENST00000377541;ENST00000377532;ENST00000361923	T;T;T	0.31510	1.49;2.92;2.92	4.41	4.41	0.53225	.	0.616314	0.15113	N	0.279841	T	0.34629	0.0904	N	0.08118	0	0.29974	N	0.818265	D;D;D;D	0.76494	0.999;0.992;0.995;0.999	P;P;D;P	0.65233	0.82;0.859;0.933;0.82	T	0.39121	-0.9629	10	0.52906	T	0.07	.	16.1524	0.81632	0.0:1.0:0.0:0.0	.	200;201;201;200	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	200;201;200	ENSP00000366764:R200W;ENSP00000366755:R201W;ENSP00000355031:R200W	ENSP00000355031:R200W	R	+	1	2	PER3	7776612	0.077000	0.21312	0.006000	0.13384	0.002000	0.02628	3.621000	0.54210	2.273000	0.75805	0.591000	0.81541	CGG	.	.		0.428	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
PER3	8863	hgsc.bcm.edu	37	1	7887318	7887318	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:7887318C>T	ENST00000361923.2	+	17	2480	c.2305C>T	c.(2305-2307)Ccc>Tcc	p.P769S	PER3_ENST00000377532.3_Missense_Mutation_p.P777S|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	769	Pro-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GAACGCACAGCCCTGCTGCCC	0.682																																					p.P769S		Atlas-SNP	.											.	PER3	95	.	0			c.C2305T						.						38.0	44.0	42.0					1																	7887318		2203	4299	6502	SO:0001583	missense	8863	exon17			GCACAGCCCTGCT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2305C>T	chr1.hg19:g.7887318C>T	ENSP00000355031:p.Pro769Ser	150.0	0.0		160.0	68.0	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	hg19	CCDS89.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.366043	0.24684	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.09723	2.95;2.95	4.33	1.33	0.21861	.	2.473990	0.01395	N	0.013374	T	0.17365	0.0417	L	0.37507	1.11	0.09310	N	1	D;P;P;D	0.76494	0.999;0.473;0.607;0.999	D;B;B;D	0.64144	0.922;0.145;0.28;0.922	T	0.44605	-0.9317	10	0.07030	T	0.85	.	4.4648	0.11684	0.0:0.4257:0.3652:0.209	.	769;777;777;769	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	S	777;769	ENSP00000366755:P777S;ENSP00000355031:P769S	ENSP00000355031:P769S	P	+	1	0	PER3	7809905	0.037000	0.19845	0.015000	0.15790	0.025000	0.11179	1.031000	0.30165	0.105000	0.17753	0.561000	0.74099	CCC	.	.		0.682	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
CLSTN1	22883	hgsc.bcm.edu	37	1	9795966	9795966	+	Missense_Mutation	SNP	C	C	T	rs201640412		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:9795966C>T	ENST00000377298.4	-	12	2503	c.1711G>A	c.(1711-1713)Gaa>Aaa	p.E571K	CLSTN1_ENST00000361311.4_Missense_Mutation_p.E561K|CLSTN1_ENST00000377288.3_Missense_Mutation_p.E552K|CLSTN1_ENST00000477264.1_5'Flank	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	571					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)	p.E571K(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-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;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CCACTGTCTTCGAGGACCTGC	0.597																																					p.E571K		Atlas-SNP	.											CLSTN1,colon,carcinoma,0,1	CLSTN1	88	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1711A						.	C	LYS/GLU,LYS/GLU	0,4406		0,0,2203	65.0	65.0	65.0		1711,1681	5.8	0.1	1		65	4,8596	3.7+/-12.6	0,4,4296	no	missense,missense	CLSTN1	NM_001009566.1,NM_014944.3	56,56	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	possibly-damaging,possibly-damaging	571/982,561/972	9795966	4,13002	2203	4300	6503	SO:0001583	missense	22883	exon12			TGTCTTCGAGGAC	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1711G>A	chr1.hg19:g.9795966C>T	ENSP00000366513:p.Glu571Lys	83.0	0.0		96.0	31.0	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	hg19	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.085223	0.55861	0.0	4.65E-4	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.77	5.77	0.91146	.	0.152343	0.64402	D	0.000017	T	0.45034	0.1322	L	0.55481	1.735	0.58432	D	0.99999	P;D;D	0.58620	0.95;0.983;0.971	B;P;B	0.47981	0.164;0.563;0.359	T	0.23833	-1.0177	10	0.39692	T	0.17	-13.2539	19.9983	0.97395	0.0:1.0:0.0:0.0	.	552;561;571	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	K	571;561;372;552;552	ENSP00000366513:E571K;ENSP00000354997:E561K;ENSP00000401934:E372K;ENSP00000366502:E552K	ENSP00000354997:E561K	E	-	1	0	CLSTN1	9718553	1.000000	0.71417	0.057000	0.19452	0.313000	0.28021	4.859000	0.62954	2.724000	0.93272	0.561000	0.74099	GAA	.	C|0.999;T|0.001		0.597	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
CASZ1	54897	hgsc.bcm.edu	37	1	10713986	10713986	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:10713986G>T	ENST00000377022.3	-	11	2445	c.2128C>A	c.(2128-2130)Ctg>Atg	p.L710M	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.L710M	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	710					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TTGGCGCCCAGCAGCGAGGGC	0.657																																					p.L710M		Atlas-SNP	.											.	CASZ1	150	.	0			c.C2128A						.						47.0	49.0	48.0					1																	10713986		2203	4300	6503	SO:0001583	missense	54897	exon11			CGCCCAGCAGCGA	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2128C>A	chr1.hg19:g.10713986G>T	ENSP00000366221:p.Leu710Met	108.0	0.0		112.0	46.0	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	hg19	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170630	0.78452	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.84	4.84	0.62591	.	0.366421	0.27495	N	0.019106	T	0.63651	0.2529	L	0.29908	0.895	0.38147	D	0.938617	D;D;D	0.76494	0.999;0.996;0.98	D;P;P	0.68192	0.956;0.9;0.788	T	0.67526	-0.5648	9	0.54805	T	0.06	-6.3503	13.7821	0.63089	0.0:0.0:0.8462:0.1537	.	734;710;710	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	M	710	.	ENSP00000339445:L710M	L	-	1	2	CASZ1	10636573	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.391000	0.59652	2.619000	0.88677	0.561000	0.74099	CTG	.	.		0.657	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
C1orf127	148345	hgsc.bcm.edu	37	1	11009719	11009719	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:11009719G>A	ENST00000377008.4	-	10	1197	c.751C>T	c.(751-753)Cgg>Tgg	p.R251W	C1orf127_ENST00000377004.4_Missense_Mutation_p.R418W			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	251	Pro-rich.									NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		AGGAGGTCCCGAGAAAGCCAT	0.632																																					p.R418W		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1252T						.						42.0	36.0	38.0					1																	11009719		2199	4300	6499	SO:0001583	missense	148345	exon11			GGTCCCGAGAAAG	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.751C>T	chr1.hg19:g.11009719G>A	ENSP00000366207:p.Arg251Trp	132.0	0.0		118.0	45.0	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	hg19		.	.	.	.	.	.	.	.	.	.	G	6.613	0.481543	0.12581	.	.	ENSG00000175262	ENST00000377004;ENST00000377008	T;T	0.30981	1.51;1.51	3.16	-0.889	0.10580	.	2.454000	0.01735	N	0.029072	T	0.18718	0.0449	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.31806	-0.9930	10	0.59425	D	0.04	1.1221	8.5329	0.33346	0.3534:0.0:0.6466:0.0	.	269;251	B7ZLG7;Q8N9H9	.;CA127_HUMAN	W	418;251	ENSP00000366203:R418W;ENSP00000366207:R251W	ENSP00000366203:R418W	R	-	1	2	C1orf127	10932306	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	0.229000	0.17833	-0.441000	0.07201	-1.583000	0.00853	CGG	.	.		0.632	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
EXOSC10	5394	hgsc.bcm.edu	37	1	11151567	11151567	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:11151567A>G	ENST00000376936.4	-	4	509	c.460T>C	c.(460-462)Tcc>Ccc	p.S154P	EXOSC10_ENST00000544779.1_Missense_Mutation_p.S154P|EXOSC10_ENST00000304457.7_Missense_Mutation_p.S154P	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	154					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		TTCCAGCTGGACACTACCGTT	0.458																																					p.S154P	Colon(179;105 1987 14326 27364 29542)	Atlas-SNP	.											.	EXOSC10	59	.	0			c.T460C						.						72.0	71.0	71.0					1																	11151567		2203	4300	6503	SO:0001583	missense	5394	exon4			AGCTGGACACTAC	BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 2 (100kD)"""	605960	"""polymyositis/scleroderma autoantigen 2, 100kDa"""	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.460T>C	chr1.hg19:g.11151567A>G	ENSP00000366135:p.Ser154Pro	123.0	0.0		132.0	38.0	NM_001001998	B1AKQ0|B1AKQ1|Q15158	Missense_Mutation	SNP	ENST00000376936.4	hg19	CCDS30584.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.216668	0.79352	.	.	ENSG00000171824	ENST00000376936;ENST00000304457;ENST00000544779	.	.	.	6.03	4.9	0.64082	.	0.050617	0.85682	N	0.000000	T	0.76535	0.4001	M	0.77616	2.38	0.58432	D	0.999999	D;D	0.69078	0.997;0.995	D;D	0.68192	0.956;0.929	T	0.76846	-0.2808	9	0.46703	T	0.11	-19.1249	11.155	0.48482	0.9288:0.0:0.0712:0.0	.	154;154	Q01780-2;Q01780	.;EXOSX_HUMAN	P	154	.	ENSP00000307307:S154P	S	-	1	0	EXOSC10	11074154	1.000000	0.71417	0.994000	0.49952	0.629000	0.37895	8.534000	0.90620	1.113000	0.41760	0.454000	0.30748	TCC	.	.		0.458	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1	NM_001001998	
MIIP	60672	hgsc.bcm.edu	37	1	12082888	12082888	+	Splice_Site	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:12082888A>G	ENST00000235332.4	+	4	631		c.e4-1		MIIP_ENST00000466860.1_Splice_Site|Y_RNA_ENST00000365591.1_RNA|MIIP_ENST00000436478.2_Splice_Site	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein											autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						TTCCTTCCTCAGCCCAGGGTG	0.567																																					.		Atlas-SNP	.											.	MIIP	34	.	0			c.463-2A>G						.						57.0	48.0	51.0					1																	12082888		2203	4300	6503	SO:0001630	splice_region_variant	60672	exon4			TTCCTCAGCCCAG	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"""invasion inhibitory protein 45"""	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.463-1A>G	chr1.hg19:g.12082888A>G		77.0	0.0		57.0	19.0	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Splice_Site	SNP	ENST00000235332.4	hg19	CCDS143.1	.	.	.	.	.	.	.	.	.	.	A	9.245	1.039384	0.19669	.	.	ENSG00000116691	ENST00000235332;ENST00000436478	.	.	.	3.54	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.776	0.34762	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MIIP	12005475	0.988000	0.35896	0.947000	0.38551	0.340000	0.28889	2.501000	0.45389	1.831000	0.53308	0.254000	0.18369	.	.	.		0.567	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933	Intron
TMEM51	55092	hgsc.bcm.edu	37	1	15541641	15541641	+	Missense_Mutation	SNP	G	G	T	rs147062114		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:15541641G>T	ENST00000428417.1	+	2	504	c.58G>T	c.(58-60)Ggg>Tgg	p.G20W	TMEM51_ENST00000434578.2_Missense_Mutation_p.G20W|TMEM51_ENST00000376008.2_Missense_Mutation_p.G20W|TMEM51_ENST00000376014.3_Missense_Mutation_p.G20W|TMEM51_ENST00000400796.3_Missense_Mutation_p.G20W	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	20						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CATCGGCCTGGGGATGCTGGT	0.607																																					p.G20W		Atlas-SNP	.											.	TMEM51	28	.	0			c.G58T						.	G	TRP/GLY,TRP/GLY,TRP/GLY,TRP/GLY	1,4405	2.1+/-5.4	0,1,2202	95.0	98.0	97.0		58,58,58,58	5.5	1.0	1	dbSNP_134	97	0,8600		0,0,4300	no	missense,missense,missense,missense	TMEM51	NM_001136216.1,NM_001136217.1,NM_001136218.1,NM_018022.2	184,184,184,184	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	20/254,20/254,20/254,20/254	15541641	1,13005	2203	4300	6503	SO:0001583	missense	55092	exon2			GGCCTGGGGATGC	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 72"""	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.58G>T	chr1.hg19:g.15541641G>T	ENSP00000394899:p.Gly20Trp	44.0	0.0		65.0	29.0	NM_018022	A8K819	Missense_Mutation	SNP	ENST00000428417.1	hg19	CCDS154.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891637	0.91889	2.27E-4	0.0	ENSG00000171729	ENST00000428417;ENST00000376014;ENST00000451326;ENST00000434578;ENST00000400796;ENST00000376008;ENST00000303840	T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.81866	0.4913	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83408	0.0026	10	0.87932	D	0	11.5582	18.4425	0.90671	0.0:0.0:1.0:0.0	.	20;20	Q9BSA0;Q9NW97	.;TMM51_HUMAN	W	20	ENSP00000394899:G20W;ENSP00000365182:G20W;ENSP00000412298:G20W;ENSP00000409665:G20W;ENSP00000383600:G20W;ENSP00000365176:G20W	ENSP00000303666:G20W	G	+	1	0	TMEM51	15414228	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.744000	0.91596	2.612000	0.88384	0.655000	0.94253	GGG	.	G|1.000;T|0.000		0.607	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022	
FHAD1	114827	hgsc.bcm.edu	37	1	15702219	15702219	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:15702219T>A	ENST00000375998.4	+	26	3632	c.3632T>A	c.(3631-3633)aTc>aAc	p.I1211N	FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Missense_Mutation_p.I464N|FHAD1_ENST00000375999.3_Missense_Mutation_p.I1211N|FHAD1_ENST00000417793.1_Missense_Mutation_p.I1175N|FHAD1_ENST00000358897.4_Missense_Mutation_p.I1211N			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1211										skin(1)|stomach(1)	2						AGAATAGAGATCCTAGCGGTA	0.453																																					p.I1211N		Atlas-SNP	.											.	FHAD1	78	.	0			c.T3632A						.						99.0	81.0	86.0					1																	15702219		692	1591	2283	SO:0001583	missense	114827	exon27			TAGAGATCCTAGC	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.3632T>A	chr1.hg19:g.15702219T>A	ENSP00000365166:p.Ile1211Asn	117.0	0.0		93.0	34.0	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.580|9.580	1.123313|1.123313	0.20959|0.20959	.|.	.|.	ENSG00000142621|ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668|ENST00000444385	T;T;T;T;T;T;T|.	0.52526|.	0.67;0.68;0.66;0.67;0.69;0.7;0.69|.	4.9|4.9	-0.25|-0.25	0.13007|0.13007	.|.	.|.	.|.	.|.	.|.	T|T	0.39708|0.39708	0.1088|0.1088	M|M	0.65975|0.65975	2.015|2.015	0.09310|0.09310	N|N	1|1	B;P|.	0.41265|.	0.01;0.744|.	B;B|.	0.30943|.	0.016;0.122|.	T|T	0.38929|0.38929	-0.9638|-0.9638	9|5	0.44086|.	T|.	0.13|.	.|.	1.404|1.404	0.02276|0.02276	0.1986:0.0957:0.3235:0.3823|0.1986:0.0957:0.3235:0.3823	.|.	464;1211|.	B7WPP2;B1AJZ9|.	.;FHAD1_HUMAN|.	N|T	1211;1175;1211;1211;482;464;446|530	ENSP00000351770:I1211N;ENSP00000407615:I1175N;ENSP00000365167:I1211N;ENSP00000365166:I1211N;ENSP00000434909:I482N;ENSP00000322979:I464N;ENSP00000318812:I446N|.	ENSP00000318812:I446N|.	I|S	+|+	2|1	0|0	FHAD1|FHAD1	15574806|15574806	0.096000|0.096000	0.21769|0.21769	0.192000|0.192000	0.23308|0.23308	0.625000|0.625000	0.37756|0.37756	0.157000|0.157000	0.16402|0.16402	0.042000|0.042000	0.15717|0.15717	0.533000|0.533000	0.62120|0.62120	ATC|TCC	.	.		0.453	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
CLCNKB	1188	hgsc.bcm.edu	37	1	16377520	16377520	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:16377520C>A	ENST00000375679.4	+	12	1315	c.1204C>A	c.(1204-1206)Ctt>Att	p.L402I	CLCNKB_ENST00000375667.3_Missense_Mutation_p.L233I	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	402					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|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)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CTTTGGGACCCTTGCCTTCTT	0.642																																					p.L402I		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1204A						.						77.0	84.0	82.0					1																	16377520		2203	4300	6503	SO:0001583	missense	1188	exon12			GGGACCCTTGCCT	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1204C>A	chr1.hg19:g.16377520C>A	ENSP00000364831:p.Leu402Ile	142.0	0.0		132.0	59.0	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Missense_Mutation	SNP	ENST00000375679.4	hg19	CCDS168.1	.	.	.	.	.	.	.	.	.	.	c	17.44	3.390206	0.62066	.	.	ENSG00000184908	ENST00000375679;ENST00000331579;ENST00000375667	D;D	0.96136	-3.92;-3.92	4.59	4.59	0.56863	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.96849	0.8971	M	0.81497	2.545	0.49582	D	0.999808	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95358	0.8453	10	0.27082	T	0.32	.	8.1502	0.31137	0.0:0.8827:0.0:0.1173	.	233;402	Q5T5Q7;P51801	.;CLCKB_HUMAN	I	402;274;233	ENSP00000364831:L402I;ENSP00000364819:L233I	ENSP00000332055:L274I	L	+	1	0	CLCNKB	16250107	0.996000	0.38824	0.993000	0.49108	0.989000	0.77384	3.671000	0.54576	2.090000	0.63153	0.561000	0.74099	CTT	.	.		0.642	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
ATP13A2	23400	hgsc.bcm.edu	37	1	17328825	17328825	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17328825G>A	ENST00000326735.8	-	7	634	c.601C>T	c.(601-603)Cgc>Tgc	p.R201C	ATP13A2_ENST00000341676.5_Missense_Mutation_p.R196C|ATP13A2_ENST00000452699.1_Missense_Mutation_p.R196C|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000502860.1_5'Flank			Q9NQ11	AT132_HUMAN	ATPase type 13A2	201					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGGCCATGGCGGGAGCGGTGG	0.672																																					p.R201C		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C601T						.						40.0	34.0	36.0					1																	17328825		2203	4299	6502	SO:0001583	missense	23400	exon7			CATGGCGGGAGCG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.601C>T	chr1.hg19:g.17328825G>A	ENSP00000327214:p.Arg201Cys	334.0	0.0		342.0	156.0	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	hg19	CCDS175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.344|6.344	0.431639|0.431639	0.12045|0.12045	.|.	.|.	ENSG00000159363|ENSG00000159363	ENST00000510069;ENST00000508222;ENST00000509619|ENST00000326735;ENST00000341676;ENST00000452699;ENST00000511957	.|D;D;D;D	.|0.89123	.|-2.47;-2.47;-2.47;-2.47	4.89|4.89	-3.19|-3.19	0.05171|0.05171	.|ATPase, P-type cation-transporter, N-terminal (1);	.|0.418143	.|0.28718	.|N	.|0.014368	T|T	0.77811|0.77811	0.4186|0.4186	L|L	0.33624|0.33624	1.015|1.015	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B;B	.|0.17268	.|0.021;0.005;0.002	.|B;B;B	.|0.10450	.|0.005;0.002;0.003	T|T	0.64622|0.64622	-0.6364|-0.6364	5|10	.|0.48119	.|T	.|0.1	-2.4527|-2.4527	6.0407|6.0407	0.19732|0.19732	0.1704:0.0:0.3217:0.508|0.1704:0.0:0.3217:0.508	.|.	.|196;196;201	.|Q5JXY1;Q6S9Z9;Q9NQ11	.|.;.;AT132_HUMAN	L|C	175;107;187|201;196;196;105	.|ENSP00000327214:R201C;ENSP00000341115:R196C;ENSP00000413307:R196C;ENSP00000427241:R105C	.|ENSP00000327214:R201C	P|R	-|-	2|1	0|0	ATP13A2|ATP13A2	17201412|17201412	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.037000|0.037000	0.13140|0.13140	0.090000|0.090000	0.15025|0.15025	-0.312000|-0.312000	0.08741|0.08741	0.561000|0.561000	0.74099|0.74099	CCG|CGC	.	.		0.672	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
PADI2	11240	hgsc.bcm.edu	37	1	17418998	17418998	+	Missense_Mutation	SNP	C	C	A	rs372515836		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17418998C>A	ENST00000375486.4	-	6	623	c.560G>T	c.(559-561)cGg>cTg	p.R187L	PADI2_ENST00000444885.2_Intron|PADI2_ENST00000375481.1_Missense_Mutation_p.R187L	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	187					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GCCTTTGGTCCGCAGGATCAT	0.527																																					p.R187L		Atlas-SNP	.											.	PADI2	72	.	0			c.G560T						.						76.0	70.0	72.0					1																	17418998		2203	4300	6503	SO:0001583	missense	11240	exon6			TTGGTCCGCAGGA	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.560G>T	chr1.hg19:g.17418998C>A	ENSP00000364635:p.Arg187Leu	119.0	0.0		111.0	14.0	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	hg19	CCDS177.1	.	.	.	.	.	.	.	.	.	.	C	35	5.452748	0.96223	.	.	ENSG00000117115	ENST00000375486;ENST00000375481	T;T	0.19669	2.13;2.13	5.59	5.59	0.84812	Protein-arginine deiminase (PAD), central domain (2);	0.000000	0.85682	D	0.000000	T	0.45696	0.1355	M	0.79011	2.435	0.80722	D	1	P	0.50943	0.94	P	0.57776	0.827	T	0.37596	-0.9699	10	0.54805	T	0.06	-32.5878	18.1583	0.89701	0.0:1.0:0.0:0.0	.	187	Q9Y2J8	PADI2_HUMAN	L	187	ENSP00000364635:R187L;ENSP00000364630:R187L	ENSP00000364630:R187L	R	-	2	0	PADI2	17291585	1.000000	0.71417	0.990000	0.47175	0.997000	0.91878	5.239000	0.65371	2.642000	0.89623	0.561000	0.74099	CGG	.	.		0.527	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17983183	17983183	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17983183C>A	ENST00000361221.3	+	25	2999	c.2840C>A	c.(2839-2841)gCt>gAt	p.A947D	ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A720D|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A650D|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A908D|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A908D|ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.A942D|ARHGEF10L_ENST00000469726.1_3'UTR	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	947						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GGGACCCTTGCTGCTTACCCT	0.647																																					p.A947D		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.C2840A						.						45.0	45.0	45.0					1																	17983183		2203	4300	6503	SO:0001583	missense	55160	exon25			CCCTTGCTGCTTA	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.2840C>A	chr1.hg19:g.17983183C>A	ENSP00000355060:p.Ala947Asp	161.0	0.0		151.0	38.0	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	hg19	CCDS182.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.924970	0.73213	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T;T	0.63580	3.33;3.33;-0.05;3.33;3.33;3.33	4.72	4.72	0.59763	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.311872	0.34676	N	0.003775	T	0.80513	0.4637	M	0.85462	2.755	0.44570	D	0.99753	D;D;D;D;D;D;D	0.76494	0.984;0.998;0.995;0.992;0.995;0.999;0.996	P;D;D;P;D;D;D	0.74023	0.811;0.979;0.933;0.899;0.948;0.982;0.959	D	0.84243	0.0473	10	0.72032	D	0.01	-26.1294	15.1562	0.72743	0.0:1.0:0.0:0.0	.	720;942;650;708;903;908;947	Q5VXI4;Q9HCE6-5;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;ARGAL_HUMAN	D	947;908;942;908;720;720;650	ENSP00000355060:A947D;ENSP00000399401:A908D;ENSP00000394621:A942D;ENSP00000364564:A908D;ENSP00000364557:A720D;ENSP00000167825:A650D	ENSP00000167825:A650D	A	+	2	0	ARHGEF10L	17855770	0.960000	0.32886	1.000000	0.80357	0.913000	0.54294	2.350000	0.44063	2.161000	0.67846	0.555000	0.69702	GCT	.	.		0.647	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
CDA	978	hgsc.bcm.edu	37	1	20931423	20931423	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:20931423T>C	ENST00000375071.3	+	2	339	c.157T>C	c.(157-159)Tgc>Cgc	p.C53R	CDA_ENST00000461985.1_3'UTR	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	53	CMP/dCMP deaminase zinc-binding.				cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	CTTCTCAGGGTGCAACATAGA	0.522																																					p.C53R	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.T157C						.						90.0	78.0	82.0					1																	20931423		2203	4300	6503	SO:0001583	missense	978	exon2			TCAGGGTGCAACA	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.157T>C	chr1.hg19:g.20931423T>C	ENSP00000364212:p.Cys53Arg	142.0	0.0		124.0	39.0	NM_001785		Missense_Mutation	SNP	ENST00000375071.3	hg19	CCDS210.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.297091	0.81025	.	.	ENSG00000158825	ENST00000375071	T	0.42131	0.98	5.75	5.75	0.90469	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.000000	0.85682	D	0.000000	T	0.78641	0.4315	H	0.99286	4.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86682	0.1917	10	0.87932	D	0	.	12.4468	0.55654	0.0:0.0:0.0:1.0	.	53	P32320	CDD_HUMAN	R	53	ENSP00000364212:C53R	ENSP00000364212:C53R	C	+	1	0	CDA	20804010	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.790000	0.75115	2.192000	0.70111	0.459000	0.35465	TGC	.	.		0.522	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785	
EPHA8	2046	hgsc.bcm.edu	37	1	22928128	22928128	+	Missense_Mutation	SNP	G	G	A	rs139543017		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:22928128G>A	ENST00000166244.3	+	17	2984	c.2912G>A	c.(2911-2913)cGc>cAc	p.R971H		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	971	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGGGACGTGCGCGCCCTGGGC	0.697																																					p.R971H		Atlas-SNP	.											.	EPHA8	221	.	0			c.G2912A						.	G	HIS/ARG	0,4380		0,0,2190	17.0	19.0	18.0		2912	5.2	1.0	1	dbSNP_134	18	1,8575		0,1,4287	no	missense	EPHA8	NM_020526.3	29	0,1,6477	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	971/1006	22928128	1,12955	2190	4288	6478	SO:0001583	missense	2046	exon17			ACGTGCGCGCCCT	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2912G>A	chr1.hg19:g.22928128G>A	ENSP00000166244:p.Arg971His	213.0	0.0		168.0	66.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	hg19	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137159	0.37728	0.0	1.17E-4	ENSG00000070886	ENST00000166244	T	0.51574	0.7	5.23	5.23	0.72850	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.071675	0.56097	D	0.000030	T	0.60894	0.2304	L	0.59436	1.845	0.80722	D	1	D	0.64830	0.994	P	0.58780	0.845	T	0.60073	-0.7334	10	0.48119	T	0.1	.	16.319	0.82939	0.0:0.0:1.0:0.0	.	971	P29322	EPHA8_HUMAN	H	971	ENSP00000166244:R971H	ENSP00000166244:R971H	R	+	2	0	EPHA8	22800715	0.953000	0.32496	0.960000	0.40013	0.004000	0.04260	2.257000	0.43240	2.722000	0.93159	0.491000	0.48974	CGC	.	G|1.000;A|0.000		0.697	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
C1QA	712	hgsc.bcm.edu	37	1	22965607	22965607	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:22965607G>A	ENST00000374642.3	+	3	649	c.445G>A	c.(445-447)Ggc>Agc	p.G149S	C1QA_ENST00000402322.1_Missense_Mutation_p.G149S	NM_015991.2	NP_057075.1	P02745	C1QA_HUMAN	complement component 1, q subcomponent, A chain	149	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cell-cell signaling (GO:0007267)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|liver(1)|lung(3)|skin(1)	6		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.41e-27)|Colorectal(126;1.52e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.63e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000541)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GAACCACTCCGGCCGATTCGT	0.592																																					p.G149S		Atlas-SNP	.											.	C1QA	31	.	0			c.G445A						.						84.0	75.0	78.0					1																	22965607		2203	4300	6503	SO:0001583	missense	712	exon3			CACTCCGGCCGAT	AF135157	CCDS226.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173372	ENSG00000173372		"""Complement system"""	1241	protein-coding gene	gene with protein product		120550	"""complement component 1, q subcomponent, alpha polypeptide"""			1537612	Standard	NM_015991		Approved		uc001bfy.3	P02745	OTTHUMG00000002893	ENST00000374642.3:c.445G>A	chr1.hg19:g.22965607G>A	ENSP00000363773:p.Gly149Ser	232.0	0.0		201.0	82.0	NM_015991	B2R4X2|Q5T963	Missense_Mutation	SNP	ENST00000374642.3	hg19	CCDS226.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907539	0.52333	.	.	ENSG00000173372	ENST00000374642;ENST00000438241;ENST00000402322	T;T;T	0.66995	-0.24;-0.24;-0.24	5.67	4.76	0.60689	Tumour necrosis factor-like (2);Complement C1q protein (4);	.	.	.	.	T	0.78830	0.4345	M	0.73598	2.24	0.47547	D	0.999458	D	0.71674	0.998	D	0.63113	0.911	T	0.80495	-0.1357	9	0.52906	T	0.07	0.1645	13.3906	0.60823	0.0763:0.0:0.9237:0.0	.	149	P02745	C1QA_HUMAN	S	149	ENSP00000363773:G149S;ENSP00000416841:G149S;ENSP00000385564:G149S	ENSP00000363773:G149S	G	+	1	0	C1QA	22838194	1.000000	0.71417	0.132000	0.22025	0.022000	0.10575	5.948000	0.70249	1.419000	0.47118	0.561000	0.74099	GGC	.	.		0.592	C1QA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008087.2	NM_015991	
EPHB2	2048	hgsc.bcm.edu	37	1	23191427	23191427	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:23191427T>A	ENST00000400191.3	+	5	1043	c.1025T>A	c.(1024-1026)cTg>cAg	p.L342Q	EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000374630.3_Missense_Mutation_p.L342Q|EPHB2_ENST00000374632.3_Missense_Mutation_p.L342Q|EPHB2_ENST00000374627.1_Missense_Mutation_p.L336Q|MIR4253_ENST00000581187.1_RNA|EPHB2_ENST00000544305.1_Missense_Mutation_p.L342Q	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	342	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		TCCCTCATGCTGGAGTGGACC	0.677																																					p.L342Q		Atlas-SNP	.											.	EPHB2	257	.	0			c.T1025A						.						58.0	65.0	63.0					1																	23191427		2203	4300	6503	SO:0001583	missense	2048	exon5			TCATGCTGGAGTG	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1025T>A	chr1.hg19:g.23191427T>A	ENSP00000383053:p.Leu342Gln	174.0	0.0		214.0	84.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	hg19		.	.	.	.	.	.	.	.	.	.	T	24.1	4.492364	0.84962	.	.	ENSG00000133216	ENST00000374625;ENST00000544305;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.26	5.26	0.73747	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000008	D	0.87063	0.6084	H	0.96239	3.79	0.54753	D	0.999989	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.984;0.998;0.996;0.994	D	0.90943	0.4799	10	0.87932	D	0	.	14.1516	0.65389	0.0:0.0:0.0:1.0	.	342;342;360;342	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	Q	342;342;342;342;342;336	ENSP00000444174:L342Q;ENSP00000363761:L342Q;ENSP00000383053:L342Q;ENSP00000363763:L342Q;ENSP00000363758:L336Q	ENSP00000363755:L342Q	L	+	2	0	EPHB2	23064014	1.000000	0.71417	0.957000	0.39632	0.987000	0.75469	7.868000	0.87116	2.208000	0.71279	0.460000	0.39030	CTG	.	.		0.677	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
ASAP3	55616	hgsc.bcm.edu	37	1	23763464	23763464	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:23763464G>A	ENST00000336689.3	-	15	1460	c.1416C>T	c.(1414-1416)ggC>ggT	p.G472G	ASAP3_ENST00000437606.2_Silent_p.G463G|ASAP3_ENST00000495646.1_5'Flank	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	472	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						AAAAGCGCACGCCCAGTTCGC	0.677																																					p.G472G		Atlas-SNP	.											.	ASAP3	65	.	0			c.C1416T						.						23.0	23.0	23.0					1																	23763464		2202	4298	6500	SO:0001819	synonymous_variant	55616	exon15			GCGCACGCCCAGT	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	14987	protein-coding gene	gene with protein product	"""centaurin, beta 6"""		"""development and differentiation enhancing factor-like 1"""	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.1416C>T	chr1.hg19:g.23763464G>A		116.0	0.0		129.0	52.0	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Silent	SNP	ENST00000336689.3	hg19	CCDS235.1																																																																																			.	.		0.677	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707	
SRRM1	10250	hgsc.bcm.edu	37	1	24995828	24995828	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:24995828C>T	ENST00000323848.9	+	14	2269	c.1954C>T	c.(1954-1956)Cgt>Tgt	p.R652C	SRRM1_ENST00000447431.2_Missense_Mutation_p.R664C|SRRM1_ENST00000479034.1_3'UTR|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000374389.4_Missense_Mutation_p.R661C	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	652	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CACCAAGAGACGTTCACCTTC	0.557																																					p.R652C	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											SRRM1,NS,carcinoma,0,1	SRRM1	81	.	0			c.C1954T						.						79.0	77.0	78.0					1																	24995828		2203	4300	6503	SO:0001583	missense	10250	exon14			AAGAGACGTTCAC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1954C>T	chr1.hg19:g.24995828C>T	ENSP00000326261:p.Arg652Cys	222.0	0.0		222.0	84.0	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	hg19	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165145	0.78339	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.34275	1.37;1.37;1.37	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000007	T	0.58192	0.2105	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.83275	0.996;0.535	T	0.57236	-0.7846	10	0.87932	D	0	-1.3183	20.1542	0.98100	0.0:1.0:0.0:0.0	.	664;652	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	C	652;664;661	ENSP00000326261:R652C;ENSP00000391430:R664C;ENSP00000363510:R661C	ENSP00000326261:R652C	R	+	1	0	SRRM1	24868415	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	6.904000	0.75708	2.767000	0.95098	0.563000	0.77884	CGT	.	.		0.557	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
CEP85	64793	hgsc.bcm.edu	37	1	26586251	26586251	+	Silent	SNP	G	G	A	rs534974823		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:26586251G>A	ENST00000252992.4	+	7	1430	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	CEP85_ENST00000451429.2_Silent_p.A382A	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	433						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						TCAAAGTGGCGTTGCAGAAGC	0.463													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21547	0.0		0.0	False		,,,				2504	0.0				p.A433A		Atlas-SNP	.											.	CEP85	61	.	0			c.G1299A						.						119.0	118.0	118.0					1																	26586251		2203	4300	6503	SO:0001819	synonymous_variant	64793	exon7			AGTGGCGTTGCAG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.1299G>A	chr1.hg19:g.26586251G>A		218.0	0.0		223.0	69.0	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Silent	SNP	ENST00000252992.4	hg19	CCDS277.1	.	.	.	.	.	.	.	.	.	.	G	8.413	0.844673	0.16963	.	.	ENSG00000130695	ENST00000453146	.	.	.	6.07	-5.35	0.02697	.	.	.	.	.	T	0.40423	0.1116	.	.	.	0.37854	D	0.929493	.	.	.	.	.	.	T	0.46857	-0.9161	4	.	.	.	-5.7386	4.8867	0.13706	0.2822:0.0792:0.4595:0.1791	.	.	.	.	H	107	.	.	R	+	2	0	CEP85	26458838	0.000000	0.05858	0.053000	0.19242	0.858000	0.48976	-2.122000	0.01321	-0.445000	0.07159	-0.290000	0.09829	CGT	.	.		0.463	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
UBXN11	91544	hgsc.bcm.edu	37	1	26609381	26609381	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:26609381C>T	ENST00000374222.1	-	14	1589	c.1125G>A	c.(1123-1125)acG>acA	p.T375T	UBXN11_ENST00000374221.3_Silent_p.T375T|UBXN11_ENST00000314675.7_Silent_p.T255T|UBXN11_ENST00000374223.1_Silent_p.T132T|UBXN11_ENST00000357089.4_Silent_p.T342T|UBXN11_ENST00000374217.2_Silent_p.T342T			Q5T124	UBX11_HUMAN	UBX domain protein 11	375						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						CCAAGGTGGGCGTCTCCACCA	0.642																																					p.T375T		Atlas-SNP	.											.	UBXN11	54	.	0			c.G1125A						.						67.0	78.0	75.0					1																	26609381		2102	4237	6339	SO:0001819	synonymous_variant	91544	exon14			GGTGGGCGTCTCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1125G>A	chr1.hg19:g.26609381C>T		99.0	0.0		96.0	23.0	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	hg19	CCDS41288.1																																																																																			.	.		0.642	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
FCN3	8547	hgsc.bcm.edu	37	1	27697179	27697179	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:27697179T>A	ENST00000270879.4	-	7	571	c.566A>T	c.(565-567)aAc>aTc	p.N189I	FCN3_ENST00000354982.2_Missense_Mutation_p.N178I	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	189	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	7		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;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GAAAGTACGGTTACCATTAAA	0.582																																					p.N189I		Atlas-SNP	.											.	FCN3	30	.	0			c.A566T						.						153.0	157.0	155.0					1																	27697179		2203	4300	6503	SO:0001583	missense	8547	exon7			GTACGGTTACCAT	D88587	CCDS300.1, CCDS301.1	1p36.11	2014-09-17	2013-09-12		ENSG00000142748	ENSG00000142748		"""Fibrinogen C domain containing"""	3625	protein-coding gene	gene with protein product	"""Hakata antigen"""	604973	"""ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)"""			9694814, 10330454	Standard	NM_003665		Approved	FCNH, HAKA1	uc001boa.3	O75636	OTTHUMG00000005722	ENST00000270879.4:c.566A>T	chr1.hg19:g.27697179T>A	ENSP00000270879:p.Asn189Ile	168.0	0.0		106.0	48.0	NM_003665	Q6IBJ5|Q8WW86	Missense_Mutation	SNP	ENST00000270879.4	hg19	CCDS300.1	.	.	.	.	.	.	.	.	.	.	T	15.68	2.903872	0.52333	.	.	ENSG00000142748	ENST00000270879;ENST00000354982;ENST00000498393	T;T	0.23552	1.9;1.9	4.62	-4.0	0.04057	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.938058	0.08880	N	0.880214	T	0.18964	0.0455	L	0.41961	1.31	0.09310	N	1	B;B	0.21606	0.015;0.058	B;B	0.26202	0.045;0.067	T	0.36792	-0.9733	10	0.51188	T	0.08	.	5.4862	0.16751	0.0:0.3113:0.2594:0.4293	.	178;189	Q6UXM4;O75636	.;FCN3_HUMAN	I	189;178;67	ENSP00000270879:N189I;ENSP00000347077:N178I	ENSP00000270879:N189I	N	-	2	0	FCN3	27569766	0.000000	0.05858	0.000000	0.03702	0.823000	0.46562	-0.277000	0.08502	-0.855000	0.04125	0.456000	0.33151	AAC	.	.		0.582	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1		
AHDC1	27245	hgsc.bcm.edu	37	1	27876444	27876444	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:27876444C>T	ENST00000247087.5	-	5	2779	c.2183G>A	c.(2182-2184)cGg>cAg	p.R728Q	AHDC1_ENST00000374011.2_Missense_Mutation_p.R728Q			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	728	Gly-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		TACCTCCCCCCGGCCCCGTTT	0.647																																					p.R728Q		Atlas-SNP	.											.	AHDC1	98	.	0			c.G2183A						.						33.0	31.0	32.0					1																	27876444		2203	4300	6503	SO:0001583	missense	27245	exon6			TCCCCCCGGCCCC	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2183G>A	chr1.hg19:g.27876444C>T	ENSP00000247087:p.Arg728Gln	250.0	0.0		174.0	65.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	hg19	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342280	0.81911	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.52983	0.64;0.64	5.38	5.38	0.77491	.	0.244715	0.27846	U	0.017619	T	0.52773	0.1755	N	0.24115	0.695	0.37859	D	0.929645	D	0.71674	0.998	P	0.59012	0.85	T	0.60870	-0.7177	10	0.66056	D	0.02	-9.3255	17.8971	0.88892	0.0:1.0:0.0:0.0	.	728	Q5TGY3	AHDC1_HUMAN	Q	728	ENSP00000247087:R728Q;ENSP00000363123:R728Q	ENSP00000247087:R728Q	R	-	2	0	AHDC1	27749031	0.987000	0.35691	1.000000	0.80357	0.988000	0.76386	3.961000	0.56759	2.512000	0.84698	0.555000	0.69702	CGG	.	.		0.647	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
SESN2	83667	hgsc.bcm.edu	37	1	28598852	28598852	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:28598852C>A	ENST00000253063.3	+	4	733	c.412C>A	c.(412-414)Cag>Aag	p.Q138K		NM_031459.4	NP_113647.1	P58004	SESN2_HUMAN	sestrin 2	138					autophagy (GO:0006914)|fatty acid beta-oxidation (GO:0006635)|glucose import (GO:0046323)|mitochondrial DNA metabolic process (GO:0032042)|protein kinase B signaling (GO:0043491)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of response to reactive oxygen species (GO:1901031)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	27		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)		CGAGTTTCTGCAGACTGGTGG	0.622																																					p.Q138K		Atlas-SNP	.											.	SESN2	51	.	0			c.C412A						.						67.0	71.0	69.0					1																	28598852		2203	4300	6503	SO:0001583	missense	83667	exon4			TTTCTGCAGACTG	AY123223	CCDS321.1	1p35.2	2008-02-05			ENSG00000130766	ENSG00000130766			20746	protein-coding gene	gene with protein product		607767				12607115, 12203114	Standard	NM_031459		Approved	SES2, DKFZp761M0212, HI95, SEST2	uc001bps.3	P58004	OTTHUMG00000003532	ENST00000253063.3:c.412C>A	chr1.hg19:g.28598852C>A	ENSP00000253063:p.Gln138Lys	73.0	0.0		83.0	33.0	NM_031459	Q5T7D0|Q96SI5	Missense_Mutation	SNP	ENST00000253063.3	hg19	CCDS321.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530154	0.27387	.	.	ENSG00000130766	ENST00000253063	T	0.21932	1.98	5.46	5.46	0.80206	.	0.277061	0.36167	N	0.002744	T	0.21267	0.0512	L	0.37630	1.12	0.58432	D	0.999992	B	0.29481	0.245	B	0.37550	0.253	T	0.02208	-1.1195	10	0.06099	T	0.92	-32.1059	18.9052	0.92458	0.0:1.0:0.0:0.0	.	138	P58004	SESN2_HUMAN	K	138	ENSP00000253063:Q138K	ENSP00000253063:Q138K	Q	+	1	0	SESN2	28471439	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	5.723000	0.68492	2.568000	0.86640	0.591000	0.81541	CAG	.	.		0.622	SESN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009840.1		
GMEB1	10691	hgsc.bcm.edu	37	1	29010172	29010172	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:29010172A>G	ENST00000294409.2	+	2	138	c.48A>G	c.(46-48)gtA>gtG	p.V16V	GMEB1_ENST00000480454.1_3'UTR|GMEB1_ENST00000361872.4_Silent_p.V16V|GMEB1_ENST00000373816.1_Silent_p.V16V	NM_006582.3	NP_006573.2	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding protein 1	16					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)|transcription coactivator activity (GO:0003713)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)	11		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTTGTGGTACCTACTGAAG	0.478																																					p.V16V		Atlas-SNP	.											.	GMEB1	28	.	0			c.A48G						.						193.0	172.0	179.0					1																	29010172		2203	4300	6503	SO:0001819	synonymous_variant	10691	exon2			TGTGGTACCTACT	AF099013	CCDS327.1, CCDS328.1	1p35	2008-02-05			ENSG00000162419	ENSG00000162419			4370	protein-coding gene	gene with protein product		604409				10386584, 10523663	Standard	NM_006582		Approved	P96PIF, PIF96	uc001bra.3	Q9Y692	OTTHUMG00000003647	ENST00000294409.2:c.48A>G	chr1.hg19:g.29010172A>G		154.0	0.0		131.0	38.0	NM_006582	B1AT48|Q9NWH1|Q9UKD0	Silent	SNP	ENST00000294409.2	hg19	CCDS327.1																																																																																			.	.		0.478	GMEB1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000010333.1	NM_006582	
CSMD2	114784	hgsc.bcm.edu	37	1	34083155	34083155	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:34083155G>A	ENST00000373380.1	-	17	2729	c.2509C>T	c.(2509-2511)Cgc>Tgc	p.R837C	CSMD2_ENST00000373388.2_Missense_Mutation_p.R63C|CSMD2_ENST00000373377.1_Missense_Mutation_p.R63C|CSMD2_ENST00000373381.4_Missense_Mutation_p.R1964C			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1924	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ACCAAGTAGCGCTCGCCAGTC	0.567																																					p.R1924C		Atlas-SNP	.											.	CSMD2	946	.	0			c.C5770T						.						112.0	86.0	95.0					1																	34083155		2203	4300	6503	SO:0001583	missense	114784	exon38			AGTAGCGCTCGCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2509C>T	chr1.hg19:g.34083155G>A	ENSP00000362478:p.Arg837Cys	97.0	0.0		81.0	46.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.8	4.457652	0.84317	.	.	ENSG00000121904	ENST00000373381;ENST00000373380;ENST00000373377;ENST00000373388	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	5.67	5.67	0.87782	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	M	0.83603	2.65	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	T	0.57470	-0.7806	10	0.66056	D	0.02	.	13.3258	0.60459	0.0:0.0:0.842:0.158	.	837;1924;1964	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	C	1964;837;63;63	ENSP00000362479:R1964C;ENSP00000362478:R837C;ENSP00000362475:R63C;ENSP00000362486:R63C	ENSP00000241312:R1924C	R	-	1	0	CSMD2	33855742	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	2.739000	0.47409	2.676000	0.91093	0.655000	0.94253	CGC	.	.		0.567	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
CSMD2	114784	hgsc.bcm.edu	37	1	34090759	34090759	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:34090759G>A	ENST00000373380.1	-	13	2231	c.2011C>T	c.(2011-2013)Cgc>Tgc	p.R671C	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373377.1_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.R1798C			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1758	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CATTCGAAGCGGACGATGGCC	0.652																																					p.R1758C		Atlas-SNP	.											.	CSMD2	946	.	0			c.C5272T						.						76.0	67.0	70.0					1																	34090759		2203	4300	6503	SO:0001583	missense	114784	exon34			CGAAGCGGACGAT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2011C>T	chr1.hg19:g.34090759G>A	ENSP00000362478:p.Arg671Cys	200.0	0.0		168.0	70.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.8	4.674746	0.88445	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.66815	-0.23;-0.23	6.17	6.17	0.99709	Complement control module (2);Sushi/SCR/CCP (3);	0.117450	0.64402	D	0.000014	D	0.86104	0.5853	M	0.92367	3.3	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.70016	0.828;0.932;0.967	D	0.85728	0.1329	10	0.38643	T	0.18	.	19.4432	0.94831	0.0:0.0:1.0:0.0	.	671;1758;1798	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	C	1798;671	ENSP00000362479:R1798C;ENSP00000362478:R671C	ENSP00000241312:R1758C	R	-	1	0	CSMD2	33863346	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	4.566000	0.60843	2.941000	0.99782	0.655000	0.94253	CGC	.	.		0.652	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
GJB4	127534	hgsc.bcm.edu	37	1	35227148	35227148	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:35227148G>A	ENST00000339480.1	+	2	663	c.293G>A	c.(292-294)cGc>cAc	p.R98H	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	98					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GTGGCCTACCGCGAGGAACGC	0.637																																					p.R98H		Atlas-SNP	.											GJB4,NS,haematopoietic_neoplasm,0,1	GJB4	51	.	0			c.G293A						.						86.0	65.0	72.0					1																	35227148		2203	4300	6503	SO:0001583	missense	127534	exon2			CCTACCGCGAGGA		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.293G>A	chr1.hg19:g.35227148G>A	ENSP00000345868:p.Arg98His	90.0	1.0		75.0	28.0	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	hg19	CCDS383.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.423700	0.83559	.	.	ENSG00000189433	ENST00000339480	D	0.99129	-5.46	5.73	4.82	0.62117	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98902	0.9628	M	0.77103	2.36	0.42241	D	0.991933	D	0.76494	0.999	P	0.57204	0.815	D	0.99100	1.0843	10	0.52906	T	0.07	.	14.3259	0.66521	0.0717:0.0:0.9283:0.0	.	98	Q9NTQ9	CXB4_HUMAN	H	98	ENSP00000345868:R98H	ENSP00000345868:R98H	R	+	2	0	GJB4	34999735	0.868000	0.29978	0.878000	0.34440	0.479000	0.33129	4.164000	0.58190	1.445000	0.47624	0.655000	0.94253	CGC	.	.		0.637	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
GJA4	2701	hgsc.bcm.edu	37	1	35260244	35260244	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:35260244C>T	ENST00000342280.4	+	2	518	c.430C>T	c.(430-432)Cgc>Tgc	p.R144C		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	144					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				AGAAGATGGTCGCCTGCGCAT	0.657																																					p.R144C		Atlas-SNP	.											.	GJA4	25	.	0			c.C430T						.						33.0	36.0	35.0					1																	35260244		2203	4300	6503	SO:0001583	missense	2701	exon2			GATGGTCGCCTGC	M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"""Ion channels / Gap junction proteins (connexins)"""	4278	protein-coding gene	gene with protein product	"""connexin 37"""	121012	"""gap junction protein, alpha 4, 37kD (connexin 37)"", ""gap junction protein, alpha 4, 37kDa (connexin 37)"""			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.430C>T	chr1.hg19:g.35260244C>T	ENSP00000343676:p.Arg144Cys	43.0	0.0		45.0	13.0	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	hg19	CCDS30669.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191990	0.38707	.	.	ENSG00000187513	ENST00000342280;ENST00000450137;ENST00000543143	D;D	0.97870	-4.56;-4.58	5.48	4.57	0.56435	.	0.754074	0.12461	N	0.466846	D	0.96975	0.9012	L	0.50333	1.59	0.52501	D	0.999951	D;D	0.65815	0.995;0.994	P;P	0.52343	0.696;0.451	D	0.95143	0.8265	10	0.87932	D	0	.	9.2276	0.37416	0.1443:0.7827:0.0:0.073	.	144;144	Q5JW71;P35212	.;CXA4_HUMAN	C	144	ENSP00000343676:R144C;ENSP00000409186:R144C	ENSP00000343676:R144C	R	+	1	0	GJA4	35032831	0.033000	0.19621	0.064000	0.19789	0.072000	0.16883	2.660000	0.46749	1.295000	0.44724	-0.140000	0.14226	CGC	.	.		0.657	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060	
AGO3	192669	hgsc.bcm.edu	37	1	36521336	36521336	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:36521336A>G	ENST00000373191.4	+	19	2922	c.2573A>G	c.(2572-2574)tAc>tGc	p.Y858C	AGO3_ENST00000246314.6_Missense_Mutation_p.Y624C	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	858					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)										CGCACAATGTACTTCGCTTAA	0.423																																					p.Y858C		Atlas-SNP	.											.	.	.	.	0			c.A2573G						.						149.0	123.0	132.0					1																	36521336		2203	4300	6503	SO:0001583	missense	192669	exon19			CAATGTACTTCGC	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.2573A>G	chr1.hg19:g.36521336A>G	ENSP00000362287:p.Tyr858Cys	74.0	0.0		100.0	6.0	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	hg19	CCDS399.1	.	.	.	.	.	.	.	.	.	.	A	19.66	3.869021	0.72065	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.15718	2.41;2.4	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.41373	0.1156	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.29792	-1.0000	10	0.87932	D	0	-58.0065	15.4359	0.75146	1.0:0.0:0.0:0.0	.	858	Q9H9G7	AGO3_HUMAN	C	858;624	ENSP00000362287:Y858C;ENSP00000246314:Y624C	ENSP00000246314:Y624C	Y	+	2	0	EIF2C3	36293923	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.287000	0.95975	2.194000	0.70268	0.533000	0.62120	TAC	.	.		0.423	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
OSCP1	127700	hgsc.bcm.edu	37	1	36915910	36915910	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:36915910G>T	ENST00000356637.5	-	1	124	c.61C>A	c.(61-63)Ctc>Atc	p.L21I	OSCP1_ENST00000235532.5_Missense_Mutation_p.L21I|OSCP1_ENST00000354267.3_Missense_Mutation_p.L21I|OSCP1_ENST00000315643.9_Missense_Mutation_p.L21I			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	21					transport (GO:0006810)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						CGTTGGTCGAGGATGTAAAGC	0.667											OREG0013369	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L21I		Atlas-SNP	.											.	OSCP1	48	.	0			c.C61A						.						45.0	46.0	46.0					1																	36915910		2203	4300	6503	SO:0001583	missense	127700	exon1			GGTCGAGGATGTA		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"""oxidored nitro domain containing protein"""	608854	"""chromosome 1 open reading frame 102"""	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.61C>A	chr1.hg19:g.36915910G>T	ENSP00000349052:p.Leu21Ile	296.0	0.0	866	327.0	105.0	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	hg19		.	.	.	.	.	.	.	.	.	.	G	22.1	4.238260	0.79800	.	.	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000315643;ENST00000354267	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	4.56	3.64	0.41730	.	0.000000	0.64402	D	0.000003	T	0.45074	0.1324	L	0.45744	1.44	0.52099	D	0.999946	P;P;P	0.51147	0.932;0.706;0.942	P;P;P	0.55824	0.523;0.589;0.785	T	0.38112	-0.9676	10	0.54805	T	0.06	.	11.8718	0.52525	0.086:0.0:0.914:0.0	.	21;21;21	Q8WVF1-4;Q8WVF1-3;Q8WVF1	.;.;OSCP1_HUMAN	I	21	ENSP00000235532:L21I;ENSP00000349052:L21I;ENSP00000314541:L21I;ENSP00000346216:L21I	ENSP00000235532:L21I	L	-	1	0	OSCP1	36688497	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.097000	0.50251	1.033000	0.39918	0.655000	0.94253	CTC	.	.		0.667	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
RHBDL2	54933	hgsc.bcm.edu	37	1	39352294	39352294	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:39352294A>G	ENST00000289248.2	-	8	1802	c.794T>C	c.(793-795)tTt>tCt	p.F265S	RHBDL2_ENST00000372990.1_Missense_Mutation_p.F265S|RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000538156.1_Missense_Mutation_p.F332S|RHBDL2_ENST00000372985.3_Missense_Mutation_p.F345S			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			AAAGCAGCTAAACACCGTGTA	0.408																																					p.F265S		Atlas-SNP	.											.	RHBDL2	28	.	0			c.T794C						.						124.0	118.0	120.0					1																	39352294		2203	4300	6503	SO:0001583	missense	54933	exon8			CAGCTAAACACCG	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"""rhomboid (veinlet, Drosophila)-like 2"""				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.794T>C	chr1.hg19:g.39352294A>G	ENSP00000289248:p.Phe265Ser	108.0	0.0		99.0	37.0	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Missense_Mutation	SNP	ENST00000289248.2	hg19	CCDS30680.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.823707	0.90873	.	.	ENSG00000158315	ENST00000372990;ENST00000289248;ENST00000538156;ENST00000372985	T;T;T;T	0.13196	2.61;2.61;2.61;2.61	6.03	6.03	0.97812	Peptidase S54, rhomboid domain (1);	0.000000	0.85682	D	0.000000	T	0.39759	0.1090	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72338	0.977;0.977	T	0.24977	-1.0145	10	0.87932	D	0	-20.5891	15.5407	0.76043	1.0:0.0:0.0:0.0	.	345;265	B7Z1Y9;Q9NX52	.;RHBL2_HUMAN	S	265;265;332;345	ENSP00000362081:F265S;ENSP00000289248:F265S;ENSP00000439227:F332S;ENSP00000362076:F345S	ENSP00000289248:F265S	F	-	2	0	RHBDL2	39124881	1.000000	0.71417	0.995000	0.50966	0.950000	0.60333	7.907000	0.87430	2.308000	0.77769	0.533000	0.62120	TTT	.	.		0.408	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821	
MACF1	23499	hgsc.bcm.edu	37	1	39827077	39827077	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:39827077A>G	ENST00000372915.3	+	48	12601	c.12514A>G	c.(12514-12516)Acc>Gcc	p.T4172A	MACF1_ENST00000545844.1_Missense_Mutation_p.T2105A|MACF1_ENST00000564288.1_Missense_Mutation_p.T4167A|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000289893.4_Missense_Mutation_p.T2607A|MACF1_ENST00000539005.1_Missense_Mutation_p.T2105A|MACF1_ENST00000567887.1_Missense_Mutation_p.T4204A|MACF1_ENST00000361689.2_Missense_Mutation_p.T2105A|MACF1_ENST00000317713.7_Missense_Mutation_p.T2105A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4172					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTTGGAGGCCACCCGTGAGAT	0.532																																					p.T2105A		Atlas-SNP	.											.	MACF1	909	.	0			c.A6313G						.						76.0	73.0	74.0					1																	39827077		2203	4300	6503	SO:0001583	missense	23499	exon45			GAGGCCACCCGTG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.12514A>G	chr1.hg19:g.39827077A>G	ENSP00000362006:p.Thr4172Ala	249.0	0.0		242.0	68.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.5|28.5	4.923491|4.923491	0.92319|0.92319	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.34072	.|1.38;1.43;1.38;1.38;1.38;1.38	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	T|T	0.57784|0.57784	0.2077|0.2077	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	.|D;B;D;P	.|0.89917	.|1.0;0.198;0.997;0.841	.|D;B;D;P	.|0.85130	.|0.997;0.155;0.969;0.62	T|T	0.52997|0.52997	-0.8500|-0.8500	5|10	.|0.32370	.|T	.|0.25	.|.	16.5885|16.5885	0.84745|0.84745	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|4172;2105;2105;2070	.|Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|MACF1_HUMAN;.;.;.	R|A	1238|2105;4172;2105;2105;2105;2607	.|ENSP00000439537:T2105A;ENSP00000362006:T4172A;ENSP00000354573:T2105A;ENSP00000313438:T2105A;ENSP00000444364:T2105A;ENSP00000289893:T2607A	.|ENSP00000289893:T2607A	H|T	+|+	2|1	0|0	MACF1|MACF1	39599664|39599664	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	8.962000|8.962000	0.93254|0.93254	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	CAC|ACC	.	.		0.532	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
COL9A2	1298	hgsc.bcm.edu	37	1	40771858	40771858	+	Splice_Site	SNP	C	C	G	rs199502479		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:40771858C>G	ENST00000372748.3	-	20	1106	c.1010G>C	c.(1009-1011)gGt>gCt	p.G337A	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	337	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			GCCTGGCACACCCTGCAGAAA	0.587																																					p.G337A		Atlas-SNP	.											.	COL9A2	63	.	0			c.G1010C						.						62.0	57.0	58.0					1																	40771858		2203	4300	6503	SO:0001630	splice_region_variant	1298	exon20			GGCACACCCTGCA	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.1009-1G>C	chr1.hg19:g.40771858C>G		60.0	0.0		68.0	34.0	NM_001852	B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	hg19	CCDS450.1	.	.	.	.	.	.	.	.	.	.	.	19.16	3.774406	0.70107	.	.	ENSG00000049089	ENST00000372748	D	0.99329	-5.75	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.99515	0.9827	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98249	1.0492	10	0.87932	D	0	.	14.4487	0.67370	0.0:1.0:0.0:0.0	.	337	Q14055	CO9A2_HUMAN	A	337	ENSP00000361834:G337A	ENSP00000361834:G337A	G	-	2	0	COL9A2	40544445	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.269000	0.72558	2.479000	0.83701	0.655000	0.94253	GGT	.	C|0.999;G|0.001		0.587	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	Missense_Mutation
TMEM125	128218	hgsc.bcm.edu	37	1	43738760	43738760	+	Missense_Mutation	SNP	G	G	C	rs143350378	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:43738760G>C	ENST00000432792.2	+	4	937	c.367G>C	c.(367-369)Gtg>Ctg	p.V123L	TMEM125_ENST00000439858.1_Missense_Mutation_p.V123L			Q96AQ2	TM125_HUMAN	transmembrane protein 125	123						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGTGGCCTCGTGCTGCTGGT	0.721																																					p.V123L		Atlas-SNP	.											.	TMEM125	18	.	0			c.G367C						.						22.0	24.0	23.0					1																	43738760		2198	4293	6491	SO:0001583	missense	128218	exon4			GGCCTCGTGCTGC	BC016858	CCDS480.1	1p34.2	2006-02-16			ENSG00000179178	ENSG00000179178			28275	protein-coding gene	gene with protein product							Standard	NM_144626		Approved	MGC17299	uc021oml.1	Q96AQ2	OTTHUMG00000007288	ENST00000432792.2:c.367G>C	chr1.hg19:g.43738760G>C	ENSP00000429275:p.Val123Leu	81.0	0.0		81.0	32.0	NM_144626	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	hg19	CCDS480.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.366544	0.61513	.	.	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.43294	0.95;0.95	5.24	5.24	0.73138	.	0.350030	0.29059	N	0.013275	T	0.25791	0.0628	N	0.17082	0.46	0.30566	N	0.764038	B	0.29253	0.239	B	0.21360	0.034	T	0.17592	-1.0364	10	0.35671	T	0.21	.	12.2066	0.54355	0.0783:0.0:0.9217:0.0	.	123	Q96AQ2	TM125_HUMAN	L	123	ENSP00000429775:V123L;ENSP00000429275:V123L	ENSP00000429275:V123L	V	+	1	0	TMEM125	43511347	0.980000	0.34600	0.929000	0.37066	0.676000	0.39594	2.566000	0.45948	2.446000	0.82766	0.455000	0.32223	GTG	.	G|0.997;A|0.003		0.721	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626	
TIE1	7075	hgsc.bcm.edu	37	1	43772515	43772515	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:43772515C>A	ENST00000372476.3	+	4	568	c.489C>A	c.(487-489)tcC>tcA	p.S163S	TIE1_ENST00000538015.1_Silent_p.S163S|TIE1_ENST00000441333.2_Silent_p.S163S|TIE1_ENST00000433781.2_5'Flank	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	163					angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CCCCAGGATCCTACTTCTACA	0.577																																					p.S163S		Atlas-SNP	.											.	TIE1	132	.	0			c.C489A						.						94.0	90.0	91.0					1																	43772515		2203	4300	6503	SO:0001819	synonymous_variant	7075	exon4			AGGATCCTACTTC	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11809	protein-coding gene	gene with protein product		600222	"""tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"""	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.489C>A	chr1.hg19:g.43772515C>A		57.0	0.0		35.0	16.0	NM_005424	B5A949|B5A950	Silent	SNP	ENST00000372476.3	hg19	CCDS482.1																																																																																			.	.		0.577	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424	
SZT2	23334	hgsc.bcm.edu	37	1	43895374	43895374	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:43895374C>T	ENST00000562955.1	+	28	3996	c.3996C>T	c.(3994-3996)agC>agT	p.S1332S	SZT2_ENST00000372442.1_Splice_Site_p.S490S	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1389					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						AACCATTCAGCATAGAGACCG	0.537																																					p.S1332S		Atlas-SNP	.											.	SZT2	383	.	0			c.C3996T						.						88.0	86.0	87.0					1																	43895374		2203	4300	6503	SO:0001630	splice_region_variant	23334	exon28			ATTCAGCATAGAG	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.3996-1C>T	chr1.hg19:g.43895374C>T		81.0	0.0		91.0	36.0	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	hg19	CCDS30694.2																																																																																			.	.		0.537	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	Silent
TOE1	114034	hgsc.bcm.edu	37	1	45806886	45806886	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:45806886C>T	ENST00000372090.5	+	2	777	c.194C>T	c.(193-195)aCg>aTg	p.T65M	TOE1_ENST00000539779.1_Intron|MUTYH_ENST00000529984.1_5'Flank|MUTYH_ENST00000528332.2_5'Flank|MUTYH_ENST00000528013.2_5'Flank|MUTYH_ENST00000355498.2_5'Flank|MUTYH_ENST00000354383.6_5'Flank|MUTYH_ENST00000372098.3_5'Flank|MUTYH_ENST00000488731.2_5'Flank|MUTYH_ENST00000450313.1_5'Flank|MUTYH_ENST00000372100.5_5'Flank|TESK2_ENST00000486676.1_5'Flank|MUTYH_ENST00000448481.1_5'Flank|TOE1_ENST00000495703.1_3'UTR|MUTYH_ENST00000372110.3_5'Flank|MUTYH_ENST00000372104.1_5'Flank|MUTYH_ENST00000456914.2_5'Flank|MUTYH_ENST00000531105.1_5'Flank|MUTYH_ENST00000372115.3_5'Flank	NM_025077.3	NP_079353.3	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	65						nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	11	Acute lymphoblastic leukemia(166;0.155)					GCTGTGGACACGGTGAGAGTT	0.547																																					p.T65M		Atlas-SNP	.											.	TOE1	27	.	0			c.C194T						.						114.0	102.0	106.0					1																	45806886		2203	4300	6503	SO:0001630	splice_region_variant	114034	exon2			TGGACACGGTGAG		CCDS521.1	1p33	2011-02-03			ENSG00000132773	ENSG00000132773			15954	protein-coding gene	gene with protein product		613931				12562764	Standard	NM_025077		Approved		uc009vxq.3	Q96GM8	OTTHUMG00000007678	ENST00000372090.5:c.195+1C>T	chr1.hg19:g.45806886C>T		113.0	0.0		118.0	8.0	NM_025077	B4DEM6|Q6IA35|Q8IWN5|Q9H846	Missense_Mutation	SNP	ENST00000372090.5	hg19	CCDS521.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.819469	0.90873	.	.	ENSG00000132773	ENST00000372090	T	0.25579	1.79	5.61	5.61	0.85477	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.52191	0.1719	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.951;0.995	T	0.46148	-0.9212	10	0.52906	T	0.07	-10.9192	20.0018	0.97417	0.0:1.0:0.0:0.0	.	71;65	B4DP23;Q96GM8	.;TOE1_HUMAN	M	65	ENSP00000361162:T65M	ENSP00000361162:T65M	T	+	2	0	TOE1	45579473	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.706000	0.74649	2.793000	0.96121	0.655000	0.94253	ACG	.	.		0.547	TOE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020517.1	NM_025077	Missense_Mutation
MMACHC	25974	hgsc.bcm.edu	37	1	45974679	45974679	+	Missense_Mutation	SNP	G	G	A	rs202189863		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:45974679G>A	ENST00000401061.4	+	4	921	c.641G>A	c.(640-642)cGc>cAc	p.R214H		NM_015506.2	NP_056321.2	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria	214					cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCCCAGGAGCGCTACTCAGAA	0.562																																					p.R214H		Atlas-SNP	.											.	MMACHC	22	.	0			c.G641A						.						102.0	110.0	107.0					1																	45974679		2020	4181	6201	SO:0001583	missense	25974	exon4			AGGAGCGCTACTC		CCDS41324.1	1p34.1	2011-05-12			ENSG00000132763	ENSG00000132763			24525	protein-coding gene	gene with protein product		609831				16311595	Standard	NM_015506		Approved	DKFZP564I122, cblC	uc009vxv.3	Q9Y4U1	OTTHUMG00000007742	ENST00000401061.4:c.641G>A	chr1.hg19:g.45974679G>A	ENSP00000383840:p.Arg214His	112.0	0.0		111.0	45.0	NM_015506	Q5T157|Q9BRQ7	Missense_Mutation	SNP	ENST00000401061.4	hg19	CCDS41324.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040292	0.75732	.	.	ENSG00000132763	ENST00000401061	D	0.97455	-4.39	5.8	5.8	0.92144	.	0.506686	0.21686	N	0.070650	D	0.97932	0.9320	M	0.77820	2.39	0.25042	N	0.991199	D	0.89917	1.0	D	0.69654	0.965	D	0.94221	0.7467	10	0.72032	D	0.01	-19.6562	10.1719	0.42915	0.1479:0.0:0.8521:0.0	.	214	Q9Y4U1	MMAC_HUMAN	H	214	ENSP00000383840:R214H	ENSP00000383840:R214H	R	+	2	0	MMACHC	45747266	0.964000	0.33143	0.998000	0.56505	0.982000	0.71751	2.431000	0.44775	2.758000	0.94735	0.563000	0.77884	CGC	.	G|0.999;A|0.001		0.562	MMACHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020864.2	NM_015506	
SLC5A9	200010	hgsc.bcm.edu	37	1	48696305	48696305	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:48696305A>T	ENST00000438567.2	+	5	590	c.538A>T	c.(538-540)Atg>Ttg	p.M180L	RP5-1024N4.4_ENST00000606809.1_RNA|SLC5A9_ENST00000533824.1_Missense_Mutation_p.M201L|SLC5A9_ENST00000236495.5_Missense_Mutation_p.M205L|SLC5A9_ENST00000420136.2_Intron	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	180					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						CTTCATCCAGATGGCATTGGG	0.577																																					p.M205L		Atlas-SNP	.											.	SLC5A9	82	.	0			c.A613T						.						134.0	104.0	114.0					1																	48696305		2203	4300	6503	SO:0001583	missense	200010	exon6			ATCCAGATGGCAT	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.538A>T	chr1.hg19:g.48696305A>T	ENSP00000401730:p.Met180Leu	81.0	0.0		73.0	32.0	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	hg19	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	A	6.081	0.383290	0.11524	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.86432	-2.12;-2.12;-2.12	5.3	2.89	0.33648	.	0.547984	0.22109	N	0.064514	T	0.48187	0.1486	N	0.00104	-2.125	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.003;0.004;0.004	T	0.56938	-0.7896	10	0.02654	T	1	.	4.2483	0.10682	0.6841:0.0:0.1534:0.1625	.	201;180;205	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	L	201;180;205	ENSP00000431900:M201L;ENSP00000401730:M180L;ENSP00000236495:M205L	ENSP00000236495:M205L	M	+	1	0	SLC5A9	48468892	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.936000	0.40183	0.993000	0.38866	0.533000	0.62120	ATG	.	.		0.577	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
CDKN2C	1031	hgsc.bcm.edu	37	1	51439649	51439649	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:51439649G>A	ENST00000262662.1	+	4	2248	c.214G>A	c.(214-216)Gct>Act	p.A72T	CDKN2C_ENST00000396148.1_Missense_Mutation_p.A72T|CDKN2C_ENST00000371761.3_Missense_Mutation_p.A72T			P42773	CDN2C_HUMAN	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	72			A -> P (in breast cancer; loss of CDK6 interaction). {ECO:0000269|PubMed:8840966, ECO:0000269|PubMed:9636670}.		cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|oligodendrocyte differentiation (GO:0048709)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0?(11)|p.?(1)		central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|thyroid(1)	23				GBM - Glioblastoma multiforme(3;3.61e-13)|all cancers(3;0.00151)		AACTGGTTTCGCTGTCATTCA	0.453			D		"""glioma, MM"""																																p.A72T	Melanoma(47;50 1155 4767 22863 47597)	Atlas-SNP	.		Rec	yes		1	1p32	1031	"""cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)"""		"""O, L"""	CDKN2C,NS,carcinoma,0,1	CDKN2C	24	.	12	Whole gene deletion(11)|Unknown(1)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(5)|thyroid(1)	c.G214A						.						99.0	96.0	97.0					1																	51439649		2203	4300	6503	SO:0001583	missense	1031	exon3			GGTTTCGCTGTCA	BC000598	CCDS555.1	1p32.3	2013-01-10			ENSG00000123080	ENSG00000123080		"""Ankyrin repeat domain containing"""	1789	protein-coding gene	gene with protein product		603369				8001816, 9636670	Standard	NM_001262		Approved	INK4C, p18	uc001csg.3	P42773	OTTHUMG00000008046	ENST00000262662.1:c.214G>A	chr1.hg19:g.51439649G>A	ENSP00000262662:p.Ala72Thr	97.0	0.0		126.0	41.0	NM_001262	Q8TB83	Missense_Mutation	SNP	ENST00000262662.1	hg19	CCDS555.1	.	.	.	.	.	.	.	.	.	.	G	7.071	0.568271	0.13560	.	.	ENSG00000123080	ENST00000262662;ENST00000396148;ENST00000371761	T;T;T	0.57107	0.42;0.42;0.42	5.31	5.31	0.75309	Ankyrin repeat-containing domain (3);	0.052316	0.85682	D	0.000000	T	0.13970	0.0338	N	0.00125	-2.05	0.42527	D	0.993023	B	0.15930	0.015	B	0.11329	0.006	T	0.45086	-0.9285	10	0.02654	T	1	-7.1292	12.8511	0.57858	0.0:0.0:0.7209:0.2791	.	72	P42773	CDN2C_HUMAN	T	72	ENSP00000262662:A72T;ENSP00000379452:A72T;ENSP00000360826:A72T	ENSP00000262662:A72T	A	+	1	0	CDKN2C	51212237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.497000	0.45354	2.770000	0.95276	0.655000	0.94253	GCT	.	.		0.453	CDKN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022058.1	NM_001262	
CPT2	1376	hgsc.bcm.edu	37	1	53679110	53679110	+	Missense_Mutation	SNP	C	C	T	rs201913567		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:53679110C>T	ENST00000371486.3	+	5	2335	c.1820C>T	c.(1819-1821)tCt>tTt	p.S607F	C1orf123_ENST00000470385.1_5'Flank|RP5-1024G6.2_ENST00000452466.1_RNA	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	607					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	CCTGTGGTCTCTGATGGCTTT	0.552																																					p.S607F		Atlas-SNP	.											.	CPT2	34	.	0			c.C1820T						.						173.0	154.0	160.0					1																	53679110		2203	4300	6503	SO:0001583	missense	1376	exon5			TGGTCTCTGATGG	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1820C>T	chr1.hg19:g.53679110C>T	ENSP00000360541:p.Ser607Phe	156.0	0.0		151.0	64.0	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	hg19	CCDS575.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.420844	0.83559	.	.	ENSG00000157184	ENST00000371486	D	0.96745	-4.11	5.9	5.9	0.94986	.	0.272836	0.42964	D	0.000640	D	0.95326	0.8483	L	0.29908	0.895	0.41806	D	0.989945	P	0.40000	0.698	P	0.46419	0.516	D	0.95385	0.8476	10	0.66056	D	0.02	-0.6538	20.2789	0.98501	0.0:1.0:0.0:0.0	.	607	P23786	CPT2_HUMAN	F	607	ENSP00000360541:S607F	ENSP00000360541:S607F	S	+	2	0	CPT2	53451698	0.984000	0.35163	0.998000	0.56505	0.979000	0.70002	5.984000	0.70548	2.788000	0.95919	0.650000	0.86243	TCT	.	C|1.000;G|0.000		0.552	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
DIRAS3	9077	hgsc.bcm.edu	37	1	68512696	68512696	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:68512696G>A	ENST00000370981.1	-	4	921	c.285C>T	c.(283-285)ggC>ggT	p.G95G	GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Silent_p.G95G			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	95					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GGTTGCCGTCGCCACTCTTGC	0.592																																					p.G95G		Atlas-SNP	.											.	DIRAS3	31	.	0			c.C285T						.						111.0	115.0	114.0					1																	68512696		2203	4300	6503	SO:0001819	synonymous_variant	9077	exon2			GCCGTCGCCACTC	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"""ras homolog gene family, member I"""	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.285C>T	chr1.hg19:g.68512696G>A		110.0	0.0		137.0	70.0	NM_004675	B3KMP3	Silent	SNP	ENST00000370981.1	hg19	CCDS641.1																																																																																			.	.		0.592	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675	
RPE65	6121	hgsc.bcm.edu	37	1	68905283	68905283	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:68905283A>G	ENST00000262340.5	-	7	739	c.686T>C	c.(685-687)tTc>tCc	p.F229S		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	229					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						ACTGCAGGGGAATTGTACAAC	0.373																																					p.F229S		Atlas-SNP	.											.	RPE65	87	.	0			c.T686C						.						190.0	182.0	185.0					1																	68905283		2203	4300	6503	SO:0001583	missense	6121	exon7			CAGGGGAATTGTA	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.686T>C	chr1.hg19:g.68905283A>G	ENSP00000262340:p.Phe229Ser	84.0	0.0		75.0	36.0	NM_000329	A8K1L0|Q5T9U3	Missense_Mutation	SNP	ENST00000262340.5	hg19	CCDS643.1	.	.	.	.	.	.	.	.	.	.	a	22.8	4.338621	0.81911	.	.	ENSG00000116745	ENST00000262340	D	0.94613	-3.47	5.56	5.56	0.83823	.	0.043773	0.85682	D	0.000000	D	0.96725	0.8931	M	0.81239	2.535	0.58432	D	0.999999	D	0.89917	1.0	D	0.75020	0.985	D	0.97199	0.9863	10	0.62326	D	0.03	-9.4536	15.7331	0.77822	1.0:0.0:0.0:0.0	.	229	Q16518	RPE65_HUMAN	S	229	ENSP00000262340:F229S	ENSP00000262340:F229S	F	-	2	0	RPE65	68677871	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.771000	0.91751	2.112000	0.64535	0.524000	0.50904	TTC	.	.		0.373	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
LRRC40	55631	hgsc.bcm.edu	37	1	70614318	70614318	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:70614318T>A	ENST00000370952.3	-	14	1634	c.1555A>T	c.(1555-1557)Aca>Tca	p.T519S		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	519						membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						GTTTCAAGTGTGAAGATACGA	0.338																																					p.T519S		Atlas-SNP	.											.	LRRC40	66	.	0			c.A1555T						.						98.0	97.0	97.0					1																	70614318		2203	4300	6503	SO:0001583	missense	55631	exon14			CAAGTGTGAAGAT		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1555A>T	chr1.hg19:g.70614318T>A	ENSP00000359990:p.Thr519Ser	111.0	0.0		86.0	32.0	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	hg19	CCDS646.1	.	.	.	.	.	.	.	.	.	.	T	5.492	0.275784	0.10403	.	.	ENSG00000066557	ENST00000370952	T	0.44482	0.92	5.73	2.14	0.27477	.	0.264710	0.44097	N	0.000500	T	0.03477	0.0100	N	0.02830	-0.485	0.26957	N	0.965892	B	0.09022	0.002	B	0.06405	0.002	T	0.43310	-0.9399	10	0.02654	T	1	.	5.0628	0.14566	0.1259:0.2213:0.0:0.6528	.	519	Q9H9A6	LRC40_HUMAN	S	519	ENSP00000359990:T519S	ENSP00000359990:T519S	T	-	1	0	LRRC40	70386906	0.072000	0.21174	0.487000	0.27428	0.950000	0.60333	0.282000	0.18829	0.108000	0.17862	-0.336000	0.08194	ACA	.	.		0.338	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768	
PTGER3	5733	hgsc.bcm.edu	37	1	71437417	71437417	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:71437417C>T	ENST00000306666.5	-	4	1380		c.e4-1		PTGER3_ENST00000356595.4_Intron|PTGER3_ENST00000354608.5_Intron|PTGER3_ENST00000414819.1_Intron|PTGER3_ENST00000460330.1_Intron|PTGER3_ENST00000370931.3_Intron|PTGER3_ENST00000351052.5_Intron|PTGER3_ENST00000370932.2_Intron	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)						cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	CTTTCATTATCTGTTAGAATA	0.303																																					.		Atlas-SNP	.											.	PTGER3	246	.	0			c.1170-1G>A						.						102.0	110.0	107.0					1																	71437417		2203	4297	6500	SO:0001630	splice_region_variant	5733	exon5			CATTATCTGTTAG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"""GPCR / Class A : Prostanoid receptors"""	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.1170-1G>A	chr1.hg19:g.71437417C>T		606.0	0.0		566.0	213.0	NM_198719	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Splice_Site	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.260033	0.59321	.	.	ENSG00000050628	ENST00000306666	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3246	0.55003	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PTGER3	71210005	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.904000	0.48719	2.605000	0.88082	0.650000	0.86243	.	.	.		0.303	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957	Intron
ST6GALNAC3	256435	hgsc.bcm.edu	37	1	77094388	77094388	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:77094388C>T	ENST00000328299.3	+	5	963	c.815C>T	c.(814-816)gCc>gTc	p.A272V		NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	272					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						CATGAACATGCCCCATATGGG	0.368																																					p.A272V		Atlas-SNP	.											.	ST6GALNAC3	71	.	0			c.C815T						.						116.0	119.0	118.0					1																	77094388		2203	4299	6502	SO:0001583	missense	256435	exon5			AACATGCCCCATA		CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"""Sialyltransferases"""	19343	protein-coding gene	gene with protein product	"""ST6GALNAC III"""	610133	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"""	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.815C>T	chr1.hg19:g.77094388C>T	ENSP00000329214:p.Ala272Val	77.0	0.0		87.0	39.0	NM_152996	Q6PCE0|Q6UX29|Q8N259	Missense_Mutation	SNP	ENST00000328299.3	hg19	CCDS672.1	.	.	.	.	.	.	.	.	.	.	c	20.6	4.015689	0.75161	.	.	ENSG00000184005	ENST00000328299;ENST00000394993;ENST00000415813	T	0.32753	1.44	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.38161	0.1030	L	0.61387	1.9	0.51233	D	0.999916	P;P	0.43701	0.752;0.815	P;P	0.50537	0.459;0.643	T	0.11060	-1.0603	10	0.56958	D	0.05	-9.2724	19.8598	0.96779	0.0:1.0:0.0:0.0	.	171;272	B4DM98;Q8NDV1	.;SIA7C_HUMAN	V	272;271;170	ENSP00000329214:A272V	ENSP00000329214:A272V	A	+	2	0	ST6GALNAC3	76866976	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	5.685000	0.68204	2.761000	0.94854	0.645000	0.84053	GCC	.	.		0.368	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449438	89449438	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:89449438A>G	ENST00000321792.5	-	2	499	c.72T>C	c.(70-72)ctT>ctC	p.L24L	CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000399794.2_Silent_p.L24L|CCBL2_ENST00000446900.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	24	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										ATACTGTTTCAAGAGCTTTCT	0.408											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L24L		Atlas-SNP	.											.	.	.	.	0			c.T72C						.						185.0	184.0	184.0					1																	89449438		2203	4300	6503	SO:0001819	synonymous_variant	494115	exon3			TGTTTCAAGAGCT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.72T>C	chr1.hg19:g.89449438A>G		337.0	0.0	1267	291.0	35.0	NM_001162536		Silent	SNP	ENST00000321792.5	hg19	CCDS716.1																																																																																			.	.		0.408	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
CDC7	8317	hgsc.bcm.edu	37	1	91977470	91977470	+	Missense_Mutation	SNP	C	C	T	rs539320135		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:91977470C>T	ENST00000428239.1	+	6	821	c.562C>T	c.(562-564)Cgc>Tgc	p.R188C	CDC7_ENST00000234626.6_Missense_Mutation_p.R188C|CDC7_ENST00000430031.2_Missense_Mutation_p.R160C	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	188	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		ATATAATAGGCGCCTGAAAAA	0.294																																					p.R188C		Atlas-SNP	.											.	CDC7	74	.	0			c.C562T						.						58.0	60.0	60.0					1																	91977470		2203	4298	6501	SO:0001583	missense	8317	exon6			AATAGGCGCCTGA	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"""CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1"", ""CDC7 cell division cycle 7 (S. cerevisiae)"", ""cell division cycle 7 (S. cerevisiae)"", ""cell division cycle 7 homolog (S. cerevisiae)"""	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.562C>T	chr1.hg19:g.91977470C>T	ENSP00000393139:p.Arg188Cys	391.0	0.0		433.0	24.0	NM_001134419	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	hg19	CCDS734.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.625080	0.46840	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239	T;T;T	0.06933	3.24;3.24;3.24	5.72	3.86	0.44501	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.914960	0.09617	N	0.778113	T	0.14098	0.0341	M	0.81942	2.565	0.19300	N	0.999974	D;D	0.89917	1.0;1.0	D;D	0.69479	0.964;0.939	T	0.19679	-1.0298	10	0.59425	D	0.04	0.0174	6.1234	0.20165	0.1316:0.6623:0.0:0.2061	.	160;188	B7Z5H7;O00311	.;CDC7_HUMAN	C	160;188;188	ENSP00000407477:R160C;ENSP00000234626:R188C;ENSP00000393139:R188C	ENSP00000234626:R188C	R	+	1	0	CDC7	91750058	0.129000	0.22400	0.093000	0.20910	0.893000	0.52053	1.443000	0.35057	0.784000	0.33661	0.467000	0.42956	CGC	.	.		0.294	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503	
SLC30A7	148867	hgsc.bcm.edu	37	1	101379226	101379226	+	Silent	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:101379226A>T	ENST00000370112.4	+	6	706	c.519A>T	c.(517-519)ggA>ggT	p.G173G	SLC30A7_ENST00000357650.4_Silent_p.G173G	NM_001144884.1|NM_133496.4	NP_001138356.1|NP_598003.2	Q8NEW0	ZNT7_HUMAN	solute carrier family 30 (zinc transporter), member 7	173	His-rich loop.				cellular protein metabolic process (GO:0044267)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	cation transmembrane transporter activity (GO:0008324)			endometrium(3)|large_intestine(2)|lung(10)	15		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		TAGGCCACGGACACAGTCATT	0.408																																					p.G173G	NSCLC(91;473 1491 3102 16827 21633)	Atlas-SNP	.											.	SLC30A7	33	.	0			c.A519T						.						152.0	124.0	134.0					1																	101379226		2203	4300	6503	SO:0001819	synonymous_variant	148867	exon6			CCACGGACACAGT	AF233345	CCDS776.1	1p21.1	2013-05-22			ENSG00000162695	ENSG00000162695		"""Solute carriers"""	19306	protein-coding gene	gene with protein product		611149				12446736	Standard	NM_133496		Approved	ZnTL2, ZNT7	uc001dto.2	Q8NEW0	OTTHUMG00000011815	ENST00000370112.4:c.519A>T	chr1.hg19:g.101379226A>T		188.0	0.0		197.0	90.0	NM_133496	B2R949|D3DT61|Q8TCH2	Silent	SNP	ENST00000370112.4	hg19	CCDS776.1																																																																																			.	.		0.408	SLC30A7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032711.1	NM_133496	
NTNG1	22854	hgsc.bcm.edu	37	1	108023282	108023282	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:108023282C>T	ENST00000370068.1	+	8	2286	c.1440C>T	c.(1438-1440)tgC>tgT	p.C480C	NTNG1_ENST00000370061.3_Silent_p.C446C|NTNG1_ENST00000370067.1_Silent_p.C401C|NTNG1_ENST00000370070.2_Silent_p.C401C|NTNG1_ENST00000542803.1_Silent_p.C480C|NTNG1_ENST00000370066.1_Silent_p.C421C|NTNG1_ENST00000370072.3_Silent_p.C435C|NTNG1_ENST00000370073.2_Silent_p.C480C|NTNG1_ENST00000370071.2_Silent_p.C421C|NTNG1_ENST00000370065.1_Silent_p.C435C|NTNG1_ENST00000370074.4_Silent_p.C379C			Q9Y2I2	NTNG1_HUMAN	netrin G1	480					axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		GAGGGACGTGCCACAACAACG	0.667																																					p.C480C		Atlas-SNP	.											.	NTNG1	274	.	0			c.C1440T						.						28.0	31.0	30.0					1																	108023282		2203	4300	6503	SO:0001819	synonymous_variant	22854	exon8			GACGTGCCACAAC	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"""Netrins"""	23319	protein-coding gene	gene with protein product	"""netrin G1f"", ""Netrin-G1"""	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.1440C>T	chr1.hg19:g.108023282C>T		100.0	0.0		99.0	42.0	NM_001113226	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Silent	SNP	ENST00000370068.1	hg19	CCDS44180.1																																																																																			.	.		0.667	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917	
FAM102B	284611	hgsc.bcm.edu	37	1	109171126	109171126	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:109171126T>C	ENST00000370035.3	+	8	1102	c.762T>C	c.(760-762)tgT>tgC	p.C254C	FAM102B_ENST00000405454.1_Silent_p.C254C	NM_001010883.2	NP_001010883.2	Q5T8I3	F102B_HUMAN	family with sequence similarity 102, member B	254										autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		TAGAGCCATGTGATGAAATTG	0.423																																					p.C254C		Atlas-SNP	.											.	FAM102B	49	.	0			c.T762C						.						79.0	87.0	84.0					1																	109171126		2203	4300	6503	SO:0001819	synonymous_variant	284611	exon8			GCCATGTGATGAA	CR749397	CCDS30786.2	1p13.3	2012-11-05			ENSG00000162636	ENSG00000162636			27637	protein-coding gene	gene with protein product	"""sym-3 homolog B (C. elegans)"""						Standard	NM_001010883		Approved	DKFZp779B126, SYM-3B	uc010ouy.2	Q5T8I3	OTTHUMG00000010967	ENST00000370035.3:c.762T>C	chr1.hg19:g.109171126T>C		139.0	0.0		167.0	68.0	NM_001010883	A1L1A1|B0QZ46|B0QZ47|Q68DH7	Silent	SNP	ENST00000370035.3	hg19	CCDS30786.2																																																																																			.	.		0.423	FAM102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030188.3	NM_001010883	
CELSR2	1952	hgsc.bcm.edu	37	1	109801459	109801459	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:109801459A>G	ENST00000271332.3	+	2	3777	c.3716A>G	c.(3715-3717)aAc>aGc	p.N1239S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1239	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		CCCTGCGAGAACTACATGCGC	0.672																																					p.N1239S	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A3716G						.						41.0	35.0	37.0					1																	109801459		2203	4300	6503	SO:0001583	missense	1952	exon2			GCGAGAACTACAT	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.3716A>G	chr1.hg19:g.109801459A>G	ENSP00000271332:p.Asn1239Ser	128.0	0.0		149.0	36.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194416	0.78902	.	.	ENSG00000143126	ENST00000271332	T	0.69561	-0.41	4.54	4.54	0.55810	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.77226	0.4099	M	0.84511	2.7	0.49130	D	0.999754	D	0.76494	0.999	D	0.63703	0.917	T	0.80690	-0.1270	9	0.52906	T	0.07	.	13.991	0.64367	1.0:0.0:0.0:0.0	.	1239	Q9HCU4	CELR2_HUMAN	S	1239	ENSP00000271332:N1239S	ENSP00000271332:N1239S	N	+	2	0	CELSR2	109602982	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.066000	0.76734	2.039000	0.60335	0.379000	0.24179	AAC	.	.		0.672	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
EPS8L3	79574	hgsc.bcm.edu	37	1	110300674	110300674	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:110300674G>A	ENST00000361965.4	-	9	830	c.724C>T	c.(724-726)Ctg>Ttg	p.L242L	EPS8L3_ENST00000494151.1_5'Flank|EPS8L3_ENST00000361852.4_Silent_p.L242L|RP4-735C1.4_ENST00000431955.1_RNA|EPS8L3_ENST00000369805.3_Silent_p.L243L	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	242						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		ACATGGTTCAGCACTTCCTGG	0.572																																					p.L243L		Atlas-SNP	.											.	EPS8L3	73	.	0			c.C727T						.						113.0	118.0	117.0					1																	110300674		2203	4300	6503	SO:0001819	synonymous_variant	79574	exon9			GGTTCAGCACTTC	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.724C>T	chr1.hg19:g.110300674G>A		55.0	0.0		59.0	22.0	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Silent	SNP	ENST00000361965.4	hg19	CCDS814.1																																																																																			.	.		0.572	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526	
VANGL1	81839	hgsc.bcm.edu	37	1	116226598	116226598	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:116226598C>T	ENST00000355485.2	+	6	1251	c.980C>T	c.(979-981)gCc>gTc	p.A327V	VANGL1_ENST00000369510.4_Missense_Mutation_p.A325V|VANGL1_ENST00000474344.1_3'UTR|VANGL1_ENST00000369509.1_Missense_Mutation_p.A327V|VANGL1_ENST00000310260.3_Missense_Mutation_p.A327V	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	327					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		CAGTCCCGGGCCATGATTGCT	0.522																																					p.A327V		Atlas-SNP	.											.	VANGL1	65	.	0			c.C980T						.						61.0	60.0	61.0					1																	116226598		2203	4300	6503	SO:0001583	missense	81839	exon6			CCCGGGCCATGAT	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"""vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)"", ""vang-like 1 (van gogh, Drosophila)"""			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.980C>T	chr1.hg19:g.116226598C>T	ENSP00000347672:p.Ala327Val	501.0	1.0		503.0	219.0	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	hg19	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023933	0.75390	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	4.76	4.76	0.60689	.	0.052282	0.85682	D	0.000000	T	0.81978	0.4937	M	0.87456	2.885	0.80722	D	1	B;B	0.18968	0.026;0.032	B;B	0.20184	0.017;0.028	T	0.82408	-0.0472	10	0.62326	D	0.03	-14.8885	17.9983	0.89191	0.0:1.0:0.0:0.0	.	325;327	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	V	327;325;327;327	ENSP00000347672:A327V;ENSP00000358523:A325V;ENSP00000310800:A327V;ENSP00000358522:A327V	ENSP00000310800:A327V	A	+	2	0	VANGL1	116028121	1.000000	0.71417	0.998000	0.56505	0.798000	0.45092	7.313000	0.78978	2.474000	0.83562	0.551000	0.68910	GCC	.	.		0.522	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1		
ZNF697	90874	hgsc.bcm.edu	37	1	120166363	120166363	+	Silent	SNP	G	G	A	rs587712785	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:120166363G>A	ENST00000421812.2	-	3	722	c.603C>T	c.(601-603)ggC>ggT	p.G201G		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	201					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		GGAAGGCGGCGCCAGGACTGA	0.716													G|||	2	0.000399361	0.0	0.0	5008	,	,		10022	0.0		0.0	False		,,,				2504	0.002				p.G201G		Atlas-SNP	.											.	ZNF697	26	.	0			c.C603T						.						3.0	5.0	4.0					1																	120166363		1736	3553	5289	SO:0001819	synonymous_variant	90874	exon3			GGCGGCGCCAGGA	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"""Zinc fingers, C2H2-type"""	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.603C>T	chr1.hg19:g.120166363G>A		79.0	0.0		59.0	24.0	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	hg19	CCDS44202.1																																																																																			.	.		0.716	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
ZNF697	90874	hgsc.bcm.edu	37	1	120166521	120166521	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:120166521G>T	ENST00000421812.2	-	3	564	c.445C>A	c.(445-447)Ctg>Atg	p.L149M		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		CGACTCCCCAGGGAGAGATGT	0.701																																					p.L149M		Atlas-SNP	.											.	ZNF697	26	.	0			c.C445A						.						13.0	17.0	16.0					1																	120166521		1989	4132	6121	SO:0001583	missense	90874	exon3			TCCCCAGGGAGAG	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"""Zinc fingers, C2H2-type"""	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.445C>A	chr1.hg19:g.120166521G>T	ENSP00000396857:p.Leu149Met	190.0	0.0		193.0	77.0	NM_001080470	Q96IT2	Missense_Mutation	SNP	ENST00000421812.2	hg19	CCDS44202.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.299814	0.23650	.	.	ENSG00000143067	ENST00000421812	T	0.12672	2.66	4.34	2.31	0.28768	.	.	.	.	.	T	0.06690	0.0171	L	0.27053	0.805	0.23320	N	0.997911	D	0.54964	0.969	P	0.53490	0.727	T	0.23404	-1.0189	9	0.46703	T	0.11	.	7.1493	0.25601	0.1036:0.2801:0.6163:0.0	.	149	Q5TEC3	ZN697_HUMAN	M	149	ENSP00000396857:L149M	ENSP00000396857:L149M	L	-	1	2	ZNF697	119968044	0.000000	0.05858	0.983000	0.44433	0.007000	0.05969	-0.080000	0.11339	0.959000	0.37980	0.561000	0.74099	CTG	.	.		0.701	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
NOTCH2	4853	hgsc.bcm.edu	37	1	120468048	120468048	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:120468048G>A	ENST00000256646.2	-	25	4610	c.4391C>T	c.(4390-4392)gCc>gTc	p.A1464V	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1464	Negative regulatory region (NRR).				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAGCAGTTGGCCCAGGGGTT	0.567			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.A1464V		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C4391T						.						95.0	91.0	93.0					1																	120468048		2203	4300	6503	SO:0001583	missense	4853	exon25	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CAGTTGGCCCAGG	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.4391C>T	chr1.hg19:g.120468048G>A	ENSP00000256646:p.Ala1464Val	175.0	0.0		138.0	51.0	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.478314	0.26511	.	.	ENSG00000134250	ENST00000256646	D	0.82344	-1.6	5.86	4.94	0.65067	Notch domain (3);	0.000000	0.37577	U	0.002029	T	0.67942	0.2947	L	0.43923	1.385	0.47819	D	0.999525	B	0.15141	0.012	B	0.14578	0.011	T	0.65063	-0.6259	10	0.36615	T	0.2	.	13.4972	0.61432	0.0742:0.0:0.9258:0.0	.	1464	Q04721	NOTC2_HUMAN	V	1464	ENSP00000256646:A1464V	ENSP00000256646:A1464V	A	-	2	0	NOTCH2	120269571	0.999000	0.42202	1.000000	0.80357	0.343000	0.28985	1.182000	0.32029	2.775000	0.95449	0.655000	0.94253	GCC	.	.		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145075655	145075655	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:145075655C>A	ENST00000530740.1	-	1	246	c.208G>T	c.(208-210)Gct>Tct	p.A70S	PDE4DIP_ENST00000369348.3_Missense_Mutation_p.A70S|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.A70S|PDE4DIP_ENST00000369345.4_Missense_Mutation_p.A70S			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCCGCCGCAGCTGCTTCTTCC	0.716			T	PDGFRB	MPD																																p.A70S		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G208T						.						42.0	52.0	49.0					1																	145075655		2195	4287	6482	SO:0001583	missense	9659	exon1			CCGCAGCTGCTTC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.208G>T	chr1.hg19:g.145075655C>A	ENSP00000435654:p.Ala70Ser	224.0	0.0		184.0	31.0	NM_022359	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000530740.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.59	2.282591	0.40394	.	.	ENSG00000178104	ENST00000530740;ENST00000369359;ENST00000369348;ENST00000369345	T;T;T	0.15017	3.82;3.8;2.46	3.54	3.54	0.40534	.	.	.	.	.	T	0.10809	0.0264	N	0.19112	0.55	0.22693	N	0.998847	D;P	0.60160	0.987;0.598	P;B	0.56398	0.797;0.175	T	0.10847	-1.0612	9	0.87932	D	0	.	10.7869	0.46411	0.0:1.0:0.0:0.0	.	70;70	Q5TB27;E9PJ64	.;.	S	70	ENSP00000435654:A70S;ENSP00000358366:A70S;ENSP00000358354:A70S	ENSP00000358351:A70S	A	-	1	0	PDE4DIP	143787012	0.919000	0.31177	0.482000	0.27366	0.419000	0.31324	1.871000	0.39539	1.960000	0.56953	0.511000	0.50034	GCT	.	.		0.716	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
NUDT17	200035	hgsc.bcm.edu	37	1	145589355	145589355	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:145589355C>G	ENST00000334513.5	-	1	84	c.73G>C	c.(73-75)Ggc>Cgc	p.G25R	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	25							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCCAGGAGGCCACACACACTC	0.692											OREG0013751	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G25R		Atlas-SNP	.											.	NUDT17	25	.	0			c.G73C						.						12.0	12.0	12.0					1																	145589355		2163	4229	6392	SO:0001583	missense	200035	exon1			GGAGGCCACACAC	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"""Nudix motif containing"""	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.73G>C	chr1.hg19:g.145589355C>G	ENSP00000334437:p.Gly25Arg	151.0	0.0	1695	163.0	17.0	NM_001012758		Missense_Mutation	SNP	ENST00000334513.5	hg19	CCDS30830.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.562678	0.45694	.	.	ENSG00000186364	ENST00000334513	.	.	.	4.26	2.33	0.28932	.	0.192024	0.43747	N	0.000529	T	0.16257	0.0391	L	0.43152	1.355	0.36385	D	0.862148	P;B	0.46784	0.884;0.024	B;B	0.35240	0.198;0.013	T	0.02774	-1.1112	9	0.44086	T	0.13	-2.582	6.0627	0.19846	0.0:0.7042:0.1899:0.1059	.	25;25	B4DNV8;P0C025	.;NUD17_HUMAN	R	25	.	ENSP00000334437:G25R	G	-	1	0	NUDT17	144300712	0.018000	0.18449	0.997000	0.53966	0.971000	0.66376	0.604000	0.24164	0.406000	0.25560	0.585000	0.79938	GGC	.	.		0.692	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
GJA5	2702	hgsc.bcm.edu	37	1	147230336	147230336	+	Nonsense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:147230336A>T	ENST00000271348.2	-	2	1172	c.1011T>A	c.(1009-1011)taT>taA	p.Y337*	RP11-433J22.2_ENST00000428911.1_RNA|GJA5_ENST00000369237.1_Nonsense_Mutation_p.Y337*	NM_005266.5	NP_005257.2	P36382	CXA5_HUMAN	gap junction protein, alpha 5, 40kDa	337					angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|atrial cardiac muscle cell action potential (GO:0086014)|atrial septum development (GO:0003283)|AV node cell to bundle of His cell communication by electrical coupling (GO:0086053)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|gap junction assembly (GO:0016264)|mitral valve development (GO:0003174)|outflow tract morphogenesis (GO:0003151)|pulmonary valve formation (GO:0003193)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|transmembrane transport (GO:0055085)|ventricular septum development (GO:0003281)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)	gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling (GO:0086077)|gap junction channel activity involved in cardiac conduction electrical coupling (GO:0086075)|gap junction hemi-channel activity (GO:0055077)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	20	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)			TGTCACTATGATAGCCATGGG	0.552																																					p.Y337X		Atlas-SNP	.											.	GJA5	64	.	0			c.T1011A						.						126.0	116.0	119.0					1																	147230336		2203	4300	6503	SO:0001587	stop_gained	2702	exon2			ACTATGATAGCCA		CCDS929.1	1q21.1	2008-02-05	2007-01-16		ENSG00000143140	ENSG00000265107		"""Ion channels / Gap junction proteins (connexins)"""	4279	protein-coding gene	gene with protein product	"""connexin 40"""	121013	"""gap junction protein, alpha 5, 40kD (connexin 40)"", ""gap junction protein, alpha 5, 40kDa (connexin 40)"""				Standard	NM_005266		Approved	CX40	uc001eps.1	P36382	OTTHUMG00000014020	ENST00000271348.2:c.1011T>A	chr1.hg19:g.147230336A>T	ENSP00000271348:p.Tyr337*	92.0	0.0		112.0	36.0	NM_005266	Q5T3B6|Q5U0N6	Nonsense_Mutation	SNP	ENST00000271348.2	hg19	CCDS929.1	.	.	.	.	.	.	.	.	.	.	A	37	6.130235	0.97310	.	.	ENSG00000143140	ENST00000271348;ENST00000369237	.	.	.	5.38	3.45	0.39498	.	1.050290	0.07374	N	0.886237	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.9372	0.52880	0.1412:0.0:0.8588:0.0	.	.	.	.	X	337	.	ENSP00000271348:Y337X	Y	-	3	2	GJA5	145696960	0.995000	0.38212	0.974000	0.42286	0.878000	0.50629	2.438000	0.44837	0.828000	0.34709	-0.177000	0.13119	TAT	.	.		0.552	GJA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039422.2	NM_181703	
GJA8	2703	hgsc.bcm.edu	37	1	147380385	147380385	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:147380385C>T	ENST00000369235.1	+	1	303	c.303C>T	c.(301-303)cgC>cgT	p.R101R	GJA8_ENST00000240986.4_Silent_p.R101R			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	101					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					ACTACGTCCGCATGGAGGAGA	0.657																																					p.R101R	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											.	GJA8	108	.	0			c.C303T						.						79.0	71.0	73.0					1																	147380385		2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			CGTCCGCATGGAG	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"""Ion channels / Gap junction proteins (connexins)"""	4281	protein-coding gene	gene with protein product	"""connexin 50"""	600897	"""gap junction protein, alpha 8, 50kD (connexin 50)"", ""gap junction protein, alpha 8, 50kDa (connexin 50)"""	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.303C>T	chr1.hg19:g.147380385C>T		47.0	0.0		89.0	39.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	hg19	CCDS30834.1																																																																																			.	.		0.657	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267	
TARS2	80222	hgsc.bcm.edu	37	1	150470091	150470091	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:150470091A>G	ENST00000369064.3	+	10	1140	c.1106A>G	c.(1105-1107)gAg>gGg	p.E369G	TARS2_ENST00000369054.2_Missense_Mutation_p.E239G|TARS2_ENST00000606933.1_Missense_Mutation_p.E287G|TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000438568.2_3'UTR	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	369					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GGGCACTGGGAGCATTATCAG	0.547																																					p.E369G		Atlas-SNP	.											.	TARS2	91	.	0			c.A1106G						.						81.0	72.0	75.0					1																	150470091		2203	4300	6503	SO:0001583	missense	80222	exon10			ACTGGGAGCATTA	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1106A>G	chr1.hg19:g.150470091A>G	ENSP00000358060:p.Glu369Gly	79.0	0.0		78.0	16.0	NM_025150	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	hg19	CCDS952.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.191271	0.58017	.	.	ENSG00000143374	ENST00000369054;ENST00000369064;ENST00000369051;ENST00000369052	T;T;T	0.70045	-0.45;-0.45;-0.45	5.53	4.38	0.52667	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.126361	0.53938	D	0.000057	T	0.43678	0.1258	L	0.43598	1.365	0.80722	D	1	B;B;B	0.27140	0.169;0.07;0.039	B;B;B	0.29524	0.103;0.046;0.032	T	0.42498	-0.9448	10	0.37606	T	0.19	-20.8973	12.4379	0.55610	0.8597:0.1403:0.0:0.0	.	239;94;369	Q9H9V2;E7EVR9;Q9BW92	.;.;SYTM_HUMAN	G	239;369;94;94	ENSP00000358050:E239G;ENSP00000358060:E369G;ENSP00000358047:E94G	ENSP00000358047:E94G	E	+	2	0	TARS2	148736715	1.000000	0.71417	0.995000	0.50966	0.757000	0.42996	5.488000	0.66869	1.071000	0.40834	0.533000	0.62120	GAG	.	.		0.547	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150	
ANXA9	8416	hgsc.bcm.edu	37	1	150958820	150958820	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:150958820G>A	ENST00000368947.4	+	8	957	c.481G>A	c.(481-483)Gtg>Atg	p.V161M		NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	161					single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGATTTCCAGGTGGAGGCTGT	0.562																																					p.V161M		Atlas-SNP	.											.	ANXA9	28	.	0			c.G481A						.						71.0	64.0	66.0					1																	150958820		2203	4300	6503	SO:0001583	missense	8416	exon8			TTCCAGGTGGAGG	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"""Annexins"""	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.481G>A	chr1.hg19:g.150958820G>A	ENSP00000357943:p.Val161Met	102.0	0.0		97.0	32.0	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	hg19	CCDS975.2	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802630	0.31869	.	.	ENSG00000143412	ENST00000368947	T	0.03496	3.91	5.1	3.21	0.36854	.	0.398477	0.25704	N	0.028842	T	0.01523	0.0049	L	0.42245	1.32	0.24730	N	0.993099	B	0.22276	0.067	B	0.30716	0.119	T	0.42865	-0.9426	10	0.72032	D	0.01	.	6.7983	0.23736	0.0914:0.0:0.7347:0.1739	.	161	O76027	ANXA9_HUMAN	M	161	ENSP00000357943:V161M	ENSP00000357943:V161M	V	+	1	0	ANXA9	149225444	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	1.395000	0.34520	0.651000	0.30788	0.462000	0.41574	GTG	.	.		0.562	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	
LCE1A	353131	hgsc.bcm.edu	37	1	152799972	152799972	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:152799972G>A	ENST00000335123.2	+	1	24	c.24G>A	c.(22-24)caG>caA	p.Q8Q		NM_178348.2	NP_848125.1	Q5T7P2	LCE1A_HUMAN	late cornified envelope 1A	8	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	8	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGAGCCAGCAGCAGTGCCAGC	0.612																																					p.Q8Q		Atlas-SNP	.											.	LCE1A	23	.	0			c.G24A						.						51.0	61.0	58.0					1																	152799972		2203	4300	6503	SO:0001819	synonymous_variant	353131	exon1			CCAGCAGCAGTGC		CCDS1028.1	1q21.3	2011-01-28			ENSG00000186844	ENSG00000186844		"""Late cornified envelopes"""	29459	protein-coding gene	gene with protein product		612603				11698679	Standard	NM_178348		Approved	LEP1	uc010pdw.2	Q5T7P2	OTTHUMG00000012447	ENST00000335123.2:c.24G>A	chr1.hg19:g.152799972G>A		352.0	0.0		366.0	20.0	NM_178348		Silent	SNP	ENST00000335123.2	hg19	CCDS1028.1																																																																																			.	.		0.612	LCE1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034660.2	NM_178348	
GATAD2B	57459	hgsc.bcm.edu	37	1	153784289	153784289	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:153784289T>C	ENST00000368655.4	-	10	1809	c.1566A>G	c.(1564-1566)atA>atG	p.I522M		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	522					ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGATGTGGGTATGCCACGCT	0.522																																					p.I522M		Atlas-SNP	.											.	GATAD2B	62	.	0			c.A1566G						.						60.0	59.0	59.0					1																	153784289		2203	4300	6503	SO:0001583	missense	57459	exon10			TGTGGGTATGCCA	AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"""GATA zinc finger domain containing"""	30778	protein-coding gene	gene with protein product	"""transcription repressor p66 beta component of the MeCP1 complex"""	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.1566A>G	chr1.hg19:g.153784289T>C	ENSP00000357644:p.Ile522Met	99.0	0.0		112.0	44.0	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Missense_Mutation	SNP	ENST00000368655.4	hg19	CCDS1054.1	.	.	.	.	.	.	.	.	.	.	t	15.87	2.961229	0.53400	.	.	ENSG00000143614	ENST00000368655	T	0.32515	1.45	5.52	-5.57	0.02521	.	0.172208	0.51477	N	0.000084	T	0.03827	0.0108	N	0.22421	0.69	0.26593	N	0.973165	B	0.18461	0.028	B	0.09377	0.004	T	0.23332	-1.0191	10	0.35671	T	0.21	-16.6883	0.536	0.00636	0.3899:0.1497:0.2224:0.238	.	522	Q8WXI9	P66B_HUMAN	M	522	ENSP00000357644:I522M	ENSP00000357644:I522M	I	-	3	3	GATAD2B	152050913	0.828000	0.29307	0.965000	0.40720	0.994000	0.84299	-0.193000	0.09573	-0.721000	0.04929	-0.359000	0.07587	ATA	.	.		0.522	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699	
DENND4B	9909	hgsc.bcm.edu	37	1	153912225	153912225	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:153912225C>A	ENST00000361217.4	-	12	2077	c.1659G>T	c.(1657-1659)gaG>gaT	p.E553D		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	553					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)			CACACACTGCCTCGTAGTCTG	0.632																																					p.E553D		Atlas-SNP	.											.	DENND4B	210	.	0			c.G1659T						.						50.0	60.0	57.0					1																	153912225		2084	4208	6292	SO:0001583	missense	9909	exon12			CACTGCCTCGTAG	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.1659G>T	chr1.hg19:g.153912225C>A	ENSP00000354597:p.Glu553Asp	94.0	0.0		64.0	26.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	C	3.956	-0.011375	0.07727	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06142	3.34;3.34	5.14	4.21	0.49690	.	0.260438	0.38111	N	0.001816	T	0.00580	0.0019	N	0.01352	-0.895	0.31911	N	0.614708	B	0.06786	0.001	B	0.04013	0.001	T	0.49570	-0.8926	10	0.02654	T	1	-23.6371	7.8022	0.29180	0.0:0.6486:0.2643:0.087	.	553	O75064	DEN4B_HUMAN	D	553;564	ENSP00000354597:E553D;ENSP00000357635:E564D	ENSP00000354597:E553D	E	-	3	2	DENND4B	152178849	0.925000	0.31364	1.000000	0.80357	0.992000	0.81027	0.345000	0.19979	2.689000	0.91719	0.462000	0.41574	GAG	.	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
UBE2Q1	55585	hgsc.bcm.edu	37	1	154527247	154527247	+	Silent	SNP	G	G	A	rs372396696		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:154527247G>A	ENST00000292211.4	-	4	631	c.552C>T	c.(550-552)gaC>gaT	p.D184D	UBE2Q1_ENST00000497453.1_5'UTR|UBE2Q1-AS1_ENST00000441613.1_RNA	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	184					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CTGAAGACACGTCTTCCTGTG	0.557																																					p.D184D		Atlas-SNP	.											UBE2Q1,NS,carcinoma,0,1	UBE2Q1	35	.	0			c.C552T						.	G		0,4406		0,0,2203	67.0	59.0	62.0		552	-8.5	0.7	1		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UBE2Q1	NM_017582.6		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		184/423	154527247	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55585	exon4			AGACACGTCTTCC	AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"""Ubiquitin-conjugating enzymes E2"""	15698	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2Q (putative)"""	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.552C>T	chr1.hg19:g.154527247G>A		268.0	0.0		270.0	98.0	NM_017582	B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Silent	SNP	ENST00000292211.4	hg19	CCDS1069.1																																																																																			.	.		0.557	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1	NM_017582	
CHRNB2	1141	hgsc.bcm.edu	37	1	154542783	154542783	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:154542783T>C	ENST00000368476.3	+	4	569	c.305T>C	c.(304-306)aTg>aCg	p.M102T		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	102					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	TTTGACAACATGAAGAAAGTT	0.542																																					p.M102T		Atlas-SNP	.											.	CHRNB2	74	.	0			c.T305C						.						77.0	65.0	69.0					1																	154542783		2203	4300	6503	SO:0001583	missense	1141	exon4			ACAACATGAAGAA	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1962	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 2 (neuronal)"""	118507	"""cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"""			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.305T>C	chr1.hg19:g.154542783T>C	ENSP00000357461:p.Met102Thr	127.0	0.0		123.0	48.0	NM_000748	Q9UEH9	Missense_Mutation	SNP	ENST00000368476.3	hg19	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.321818	0.60634	.	.	ENSG00000160716	ENST00000368476	T	0.78816	-1.21	5.03	5.03	0.67393	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.54759	0.1878	N	0.17631	0.505	0.58432	D	0.999997	P	0.42161	0.772	B	0.38755	0.281	T	0.67787	-0.5580	10	0.87932	D	0	.	14.6012	0.68443	0.0:0.0:0.0:1.0	.	102	P17787	ACHB2_HUMAN	T	102	ENSP00000357461:M102T	ENSP00000357461:M102T	M	+	2	0	CHRNB2	152809407	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.868000	0.87116	2.114000	0.64651	0.460000	0.39030	ATG	.	.		0.542	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748	
PKLR	5313	hgsc.bcm.edu	37	1	155261612	155261612	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155261612C>T	ENST00000342741.4	-	10	1591	c.1553G>A	c.(1552-1554)cGt>cAt	p.R518H	PKLR_ENST00000392414.3_Missense_Mutation_p.R487H	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	518					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	TGGAGGTTCACGGTAAAGCAA	0.582																																					p.R518H		Atlas-SNP	.											.	PKLR	70	.	0			c.G1553A						.						94.0	92.0	93.0					1																	155261612		2203	4300	6503	SO:0001583	missense	5313	exon10			GGTTCACGGTAAA	BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.1553G>A	chr1.hg19:g.155261612C>T	ENSP00000339933:p.Arg518His	273.0	0.0		267.0	99.0	NM_000298	O75758|P11973	Missense_Mutation	SNP	ENST00000342741.4	hg19	CCDS1109.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.700978	0.48307	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99042	-5.36;-5.36	4.85	2.99	0.34606	Pyruvate kinase, C-terminal (2);Pyruvate kinase, alpha/beta (1);	0.179887	0.46145	N	0.000302	D	0.93890	0.8045	N	0.25957	0.775	0.38695	D	0.952866	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	D	0.91033	0.4865	10	0.45353	T	0.12	-0.5084	9.2448	0.37518	0.0:0.8232:0.0:0.1768	.	518;509	P30613;B1AVT1	KPYR_HUMAN;.	H	543;487;518;432	ENSP00000376214:R487H;ENSP00000339933:R518H	ENSP00000271946:R432H	R	-	2	0	PKLR	153528236	0.924000	0.31332	0.968000	0.41197	0.990000	0.78478	0.758000	0.26447	0.766000	0.33244	0.563000	0.77884	CGT	.	.		0.582	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298	
FDPS	2224	hgsc.bcm.edu	37	1	155282158	155282158	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155282158C>T	ENST00000356657.6	+	4	614	c.452C>T	c.(451-453)gCc>gTc	p.A151V	FDPS_ENST00000487002.1_3'UTR|FDPS_ENST00000368356.4_Missense_Mutation_p.A151V|FDPS_ENST00000447866.1_Missense_Mutation_p.A85V	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	151					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dimethylallyltranstransferase activity (GO:0004161)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	CTCCAGCGGGCCTGGACTGTG	0.572																																					p.A151V		Atlas-SNP	.											.	FDPS	41	.	0			c.C452T						.						61.0	51.0	54.0					1																	155282158		2203	4300	6503	SO:0001583	missense	2224	exon4			AGCGGGCCTGGAC	J05262	CCDS1110.1, CCDS44241.1, CCDS72940.1	1q22	2012-07-13	2010-06-24		ENSG00000160752	ENSG00000160752	2.5.1.1, 2.5.1.10		3631	protein-coding gene	gene with protein product	"""farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase"""	134629				1968462	Standard	NM_002004		Approved		uc001fkc.2	P14324	OTTHUMG00000013909	ENST00000356657.6:c.452C>T	chr1.hg19:g.155282158C>T	ENSP00000349078:p.Ala151Val	61.0	0.0		65.0	6.0	NM_001135821	D3DV91|E9PCI9|Q96G29	Missense_Mutation	SNP	ENST00000356657.6	hg19	CCDS1110.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.959479	0.74016	.	.	ENSG00000160752	ENST00000447866;ENST00000368356;ENST00000356657	T;T;T	0.64803	-0.12;-0.12;-0.12	4.66	4.66	0.58398	Terpenoid synthase (2);	0.136032	0.34088	N	0.004275	T	0.49966	0.1588	M	0.62016	1.91	0.80722	D	1	B	0.30033	0.266	B	0.32342	0.144	T	0.57831	-0.7743	10	0.52906	T	0.07	-17.0909	14.9164	0.70801	0.0:1.0:0.0:0.0	.	151	P14324	FPPS_HUMAN	V	85;151;151	ENSP00000391755:A85V;ENSP00000357340:A151V;ENSP00000349078:A151V	ENSP00000349078:A151V	A	+	2	0	FDPS	153548782	1.000000	0.71417	0.964000	0.40570	0.884000	0.51177	4.480000	0.60243	2.582000	0.87167	0.462000	0.41574	GCC	.	.		0.572	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	NM_002004	
ASH1L	55870	hgsc.bcm.edu	37	1	155450461	155450461	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155450461G>T	ENST00000368346.3	-	3	2839	c.2200C>A	c.(2200-2202)Cta>Ata	p.L734I	ASH1L_ENST00000392403.3_Missense_Mutation_p.L734I			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	734					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCTAATTCTAGCCCTTTTGGA	0.393																																					p.L734I		Atlas-SNP	.											.	ASH1L	279	.	0			c.C2200A						.						68.0	72.0	70.0					1																	155450461		2203	4300	6503	SO:0001583	missense	55870	exon3			ATTCTAGCCCTTT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2200C>A	chr1.hg19:g.155450461G>T	ENSP00000357330:p.Leu734Ile	73.0	0.0		75.0	34.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	G	16.83	3.230756	0.58777	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.91631	-2.88;-2.88	5.38	5.38	0.77491	.	0.000000	0.47852	D	0.000206	D	0.82449	0.5039	N	0.14661	0.345	0.80722	D	1	P;P	0.41784	0.649;0.762	B;B	0.42555	0.219;0.391	T	0.82635	-0.0360	10	0.23302	T	0.38	.	18.916	0.92506	0.0:0.0:1.0:0.0	.	734;734	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	I	734	ENSP00000357330:L734I;ENSP00000376204:L734I	ENSP00000357330:L734I	L	-	1	2	ASH1L	153717085	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.445000	0.44899	2.791000	0.96007	0.650000	0.86243	CTA	.	.		0.393	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
ASH1L	55870	hgsc.bcm.edu	37	1	155452064	155452064	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:155452064G>A	ENST00000368346.3	-	3	1236	c.597C>T	c.(595-597)agC>agT	p.S199S	ASH1L_ENST00000392403.3_Silent_p.S199S|ASH1L_ENST00000548830.1_3'UTR			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	199					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CAGGATCCCGGCTACCAAGAA	0.423																																					p.S199S		Atlas-SNP	.											.	ASH1L	279	.	0			c.C597T						.						131.0	131.0	131.0					1																	155452064		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon3			ATCCCGGCTACCA	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.597C>T	chr1.hg19:g.155452064G>A		117.0	0.0		117.0	5.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.423	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
LMNA	4000	hgsc.bcm.edu	37	1	156106161	156106161	+	Silent	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:156106161G>T	ENST00000368300.4	+	7	1526	c.1314G>T	c.(1312-1314)ggG>ggT	p.G438G	LMNA_ENST00000368297.1_Silent_p.G357G|LMNA_ENST00000368299.3_Silent_p.G438G|LMNA_ENST00000368301.2_Silent_p.G438G|LMNA_ENST00000361308.4_Silent_p.G438G|LMNA_ENST00000473598.2_Silent_p.G339G|LMNA_ENST00000392353.3_Silent_p.G357G|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000347559.2_Silent_p.G438G|LMNA_ENST00000448611.2_Silent_p.G326G	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	438	LTD.|Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					GCACTAGCGGGCGCGTGGCCG	0.612									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.G438G		Atlas-SNP	.											.	LMNA	31	.	0			c.G1314T						.						40.0	45.0	43.0					1																	156106161		2203	4299	6502	SO:0001819	synonymous_variant	4000	exon7	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	TAGCGGGCGCGTG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1314G>T	chr1.hg19:g.156106161G>T		94.0	0.0		77.0	18.0	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	hg19	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	G	7.183	0.589956	0.13812	.	.	ENSG00000160789	ENST00000392355	.	.	.	5.74	-3.71	0.04424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7858	0.40675	0.0683:0.5407:0.2967:0.0943	.	.	.	.	.	-1	.	.	.	+	.	.	LMNA	154372785	0.014000	0.17966	0.989000	0.46669	0.649000	0.38597	-0.910000	0.04054	-0.203000	0.10251	0.655000	0.94253	.	.	.		0.612	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	
INSRR	3645	hgsc.bcm.edu	37	1	156814001	156814001	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:156814001G>T	ENST00000368195.3	-	15	3205	c.2809C>A	c.(2809-2811)Ctt>Att	p.L937I	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	937					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AGGGCAGCAAGAACGATGAGC	0.582																																					p.L937I		Atlas-SNP	.											.	INSRR	309	.	0			c.C2809A						.						90.0	87.0	88.0					1																	156814001		2203	4300	6503	SO:0001583	missense	3645	exon15			CAGCAAGAACGAT	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2809C>A	chr1.hg19:g.156814001G>T	ENSP00000357178:p.Leu937Ile	75.0	0.0		75.0	42.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250541	0.39797	.	.	ENSG00000027644	ENST00000368195	T	0.75477	-0.94	5.18	5.18	0.71444	.	0.000000	0.38058	N	0.001829	T	0.79598	0.4473	.	.	.	0.45791	D	0.998679	D	0.69078	0.997	D	0.72625	0.978	T	0.76479	-0.2944	9	0.25106	T	0.35	.	15.4079	0.74893	0.0:0.0:1.0:0.0	.	937	P14616	INSRR_HUMAN	I	937	ENSP00000357178:L937I	ENSP00000357178:L937I	L	-	1	0	INSRR	155080625	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	4.948000	0.63590	2.398000	0.81561	0.462000	0.41574	CTT	.	.		0.582	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156914894	156914894	+	Missense_Mutation	SNP	G	G	A	rs140673049		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:156914894G>A	ENST00000361409.2	-	29	3530	c.2788C>T	c.(2788-2790)Cgc>Tgc	p.R930C	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.R970C|ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.R346C	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	930					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)					AAACGGTGGCGGTTCTCTGTT	0.597																																					p.R970C		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.C2908T						.	G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	109.0	112.0	111.0		2788,2908	5.3	1.0	1	dbSNP_134	111	0,8600		0,0,4300	no	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	930/1523,970/1563	156914894	1,13005	2203	4300	6503	SO:0001583	missense	9826	exon30			GGTGGCGGTTCTC	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.2788C>T	chr1.hg19:g.156914894G>A	ENSP00000354644:p.Arg930Cys	108.0	0.0		99.0	6.0	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.005245	0.54254	2.27E-4	0.0	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.69435	-0.4;-0.4;-0.4	5.28	5.28	0.74379	Dbl homology (DH) domain (1);	0.242198	0.28853	N	0.013938	T	0.44891	0.1315	L	0.42245	1.32	0.58432	D	0.999999	B;B;B	0.23735	0.08;0.09;0.035	B;B;B	0.19148	0.024;0.016;0.015	T	0.53265	-0.8463	10	0.87932	D	0	-11.8718	10.5742	0.45217	0.0:0.142:0.7113:0.1467	.	346;930;970	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	C	970;930;346	ENSP00000357177:R970C;ENSP00000354644:R930C;ENSP00000313470:R346C	ENSP00000313470:R346C	R	-	1	0	ARHGEF11	155181518	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.412000	0.52679	2.756000	0.94617	0.650000	0.86243	CGC	.	G|1.000;A|0.000		0.597	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
FCRL1	115350	hgsc.bcm.edu	37	1	157772454	157772454	+	Splice_Site	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:157772454C>A	ENST00000368176.3	-	4	387	c.320G>T	c.(319-321)aGg>aTg	p.R107M	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000358292.3_Splice_Site_p.R107M|FCRL1_ENST00000491942.1_Splice_Site_p.R107M	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GACAGGGACCCCTGTGTGGAC	0.532																																					p.R107M	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.G320T						.						32.0	32.0	32.0					1																	157772454		2203	4300	6503	SO:0001630	splice_region_variant	115350	exon4			GGGACCCCTGTGT	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.320-1G>T	chr1.hg19:g.157772454C>A		68.0	0.0		72.0	31.0	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	ENST00000368176.3	hg19	CCDS1170.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.994161	0.35226	.	.	ENSG00000163534	ENST00000358292;ENST00000368176;ENST00000491942	T;T;T	0.46451	0.87;1.03;1.04	5.41	4.48	0.54585	Immunoglobulin-like fold (1);	1.789910	0.03248	N	0.181392	T	0.59770	0.2218	M	0.86420	2.815	0.31474	N	0.667962	D;D;D	0.89917	1.0;1.0;0.994	D;D;P	0.76071	0.976;0.987;0.753	T	0.14896	-1.0456	10	0.34782	T	0.22	.	11.7722	0.51965	0.1762:0.8238:0.0:0.0	.	107;107;107	Q96LA6-3;Q96LA6-2;Q96LA6	.;.;FCRL1_HUMAN	M	107	ENSP00000351039:R107M;ENSP00000357158:R107M;ENSP00000418130:R107M	ENSP00000351039:R107M	R	-	2	0	FCRL1	156039078	0.991000	0.36638	0.800000	0.32199	0.032000	0.12392	3.843000	0.55865	1.398000	0.46701	-0.181000	0.13052	AGG	.	.		0.532	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	Missense_Mutation
OR10R2	343406	hgsc.bcm.edu	37	1	158449993	158449993	+	Missense_Mutation	SNP	C	C	T	rs200874337		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:158449993C>T	ENST00000368152.1	+	1	326	c.326C>T	c.(325-327)gCc>gTc	p.A109V	RP11-144L1.4_ENST00000419738.1_RNA|RP11-144L1.4_ENST00000426251.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A109G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					CTTTCTGTGGCCAGGACAATC	0.443																																					p.A109V		Atlas-SNP	.											OR10R2,NS,NS,0,1	OR10R2	81	.	1	Substitution - Missense(1)	pancreas(1)	c.C326T						.	C	VAL/ALA	0,4406		0,0,2203	360.0	304.0	323.0		326	1.1	1.0	1		323	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR10R2	NM_001004472.1	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	109/336	158449993	1,13005	2203	4300	6503	SO:0001583	missense	343406	exon1			CTGTGGCCAGGAC	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"""GPCR / Class A : Olfactory receptors"""	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.326C>T	chr1.hg19:g.158449993C>T	ENSP00000357134:p.Ala109Val	96.0	0.0		99.0	34.0	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	hg19	CCDS30898.1	.	.	.	.	.	.	.	.	.	.	c	9.721	1.159721	0.21454	0.0	1.16E-4	ENSG00000198965	ENST00000368152	T	0.03035	4.07	4.28	1.11	0.20524	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00724	0.0024	N	0.12637	0.245	0.09310	N	1	B	0.22211	0.066	B	0.19391	0.025	T	0.47736	-0.9094	9	0.45353	T	0.12	.	4.4412	0.11575	0.1614:0.5368:0.0:0.3018	.	109	Q8NGX6	O10R2_HUMAN	V	109	ENSP00000357134:A109V	ENSP00000357134:A109V	A	+	2	0	OR10R2	156716617	0.000000	0.05858	0.985000	0.45067	0.962000	0.63368	-2.129000	0.01313	0.425000	0.26087	0.655000	0.94253	GCC	.	C|0.999;T|0.001		0.443	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472	
IGSF9	57549	hgsc.bcm.edu	37	1	159897228	159897228	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:159897228G>T	ENST00000368094.1	-	21	3644	c.3447C>A	c.(3445-3447)ttC>ttA	p.F1149L	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.F1133L|TAGLN2_ENST00000478033.1_5'Flank|TAGLN2_ENST00000320307.4_5'Flank|TAGLN2_ENST00000368097.4_5'Flank	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	1149					dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GGAAGGCCAGGAATTCCTCCC	0.642																																					p.F1149L		Atlas-SNP	.											.	IGSF9	123	.	0			c.C3447A						.						47.0	52.0	50.0					1																	159897228		2203	4299	6502	SO:0001583	missense	57549	exon21			GGCCAGGAATTCC	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.3447C>A	chr1.hg19:g.159897228G>T	ENSP00000357073:p.Phe1149Leu	332.0	0.0		324.0	111.0	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	G	34	5.372148	0.95923	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.77229	-1.08;-1.02	5.52	5.52	0.82312	.	0.000000	0.43747	D	0.000522	T	0.73697	0.3620	L	0.29908	0.895	0.36065	D	0.841694	P;B	0.49447	0.924;0.064	P;B	0.60682	0.878;0.028	T	0.73833	-0.3858	9	.	.	.	-17.7567	14.9501	0.71067	0.0:0.0:1.0:0.0	.	1149;687	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	1133;1149;687	ENSP00000355049:F1133L;ENSP00000357073:F1149L	.	F	-	3	2	IGSF9	158163852	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.466000	0.53071	2.608000	0.88229	0.563000	0.77884	TTC	.	.		0.642	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
ATP1A2	477	hgsc.bcm.edu	37	1	160109518	160109518	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:160109518A>T	ENST00000361216.3	+	21	3018	c.2929A>T	c.(2929-2931)Atg>Ttg	p.M977L	ATP1A2_ENST00000392233.3_Missense_Mutation_p.M977L	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	977					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			AGCCCTCCGCATGTACCCGCT	0.562																																					p.M977L		Atlas-SNP	.											.	ATP1A2	167	.	0			c.A2929T						.						90.0	80.0	84.0					1																	160109518		2203	4300	6503	SO:0001583	missense	477	exon21			CTCCGCATGTACC	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2929A>T	chr1.hg19:g.160109518A>T	ENSP00000354490:p.Met977Leu	84.0	0.0		88.0	37.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.514058	0.64522	.	.	ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866	D;D	0.95272	-3.66;-3.66	4.37	4.37	0.52481	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93566	0.7946	L	0.52573	1.65	0.58432	D	0.999998	P;P	0.40398	0.521;0.716	P;P	0.55508	0.668;0.777	D	0.93040	0.6456	10	0.40728	T	0.16	.	11.8574	0.52446	1.0:0.0:0.0:0.0	.	877;977	F5GXJ7;P50993	.;AT1A2_HUMAN	L	977;977;680	ENSP00000354490:M977L;ENSP00000376066:M977L	ENSP00000354490:M977L	M	+	1	0	ATP1A2	158376142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.270000	0.78493	1.960000	0.56953	0.533000	0.62120	ATG	.	.		0.562	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
SLAMF1	6504	hgsc.bcm.edu	37	1	160604472	160604472	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:160604472C>T	ENST00000302035.6	-	3	980	c.631G>A	c.(631-633)Gtg>Atg	p.V211M	SLAMF1_ENST00000235739.5_Missense_Mutation_p.V211M|SLAMF1_ENST00000538290.1_Missense_Mutation_p.V211M|SLAMF1_ENST00000355199.3_Missense_Mutation_p.V211M	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	211	Ig-like C2-type.				lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GGGTTGCTCACGGTGCAGATG	0.607																																					p.V211M		Atlas-SNP	.											SLAMF1,NS,carcinoma,0,1	SLAMF1	74	.	0			c.G631A						.						164.0	148.0	154.0					1																	160604472		2203	4300	6503	SO:0001583	missense	6504	exon3			TGCTCACGGTGCA	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10903	protein-coding gene	gene with protein product		603492	"""signaling lymphocytic activation molecule"""	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.631G>A	chr1.hg19:g.160604472C>T	ENSP00000306190:p.Val211Met	168.0	1.0		146.0	73.0	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	hg19	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.585236	0.28268	.	.	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000538290;ENST00000355199	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	4.3	4.3	0.51218	Immunoglobulin-like (1);	0.508912	0.20685	N	0.087577	T	0.57961	0.2089	M	0.88450	2.955	0.09310	N	1	D	0.69078	0.997	P	0.56823	0.807	T	0.53961	-0.8364	10	0.72032	D	0.01	-22.4655	12.5815	0.56393	0.0:1.0:0.0:0.0	.	211	Q13291	SLAF1_HUMAN	M	211	ENSP00000306190:V211M;ENSP00000235739:V211M;ENSP00000438406:V211M;ENSP00000347333:V211M	ENSP00000235739:V211M	V	-	1	0	SLAMF1	158871096	0.008000	0.16893	0.020000	0.16555	0.016000	0.09150	2.513000	0.45494	2.680000	0.91292	0.650000	0.86243	GTG	.	.		0.607	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1		
PRRC2C	23215	hgsc.bcm.edu	37	1	171501935	171501935	+	Missense_Mutation	SNP	G	G	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:171501935G>C	ENST00000338920.4	+	12	1939	c.1702G>C	c.(1702-1704)Gaa>Caa	p.E568Q	PRRC2C_ENST00000426496.2_Missense_Mutation_p.E568Q|PRRC2C_ENST00000367742.3_Missense_Mutation_p.E570Q|PRRC2C_ENST00000392078.3_Missense_Mutation_p.E570Q	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	568	Glu-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										aaaagaactagaacggcagaa	0.373																																					p.E568Q		Atlas-SNP	.											.	.	.	.	0			c.G1702C						.						33.0	36.0	35.0					1																	171501935		2190	4279	6469	SO:0001583	missense	23215	exon12			GAACTAGAACGGC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.1702G>C	chr1.hg19:g.171501935G>C	ENSP00000343629:p.Glu568Gln	286.0	0.0		282.0	104.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	G	12.69	2.013741	0.35511	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000483654	T;T;T;T	0.06449	3.3;3.3;3.3;3.3	6.02	5.11	0.69529	.	0.181808	0.26959	N	0.021630	T	0.04363	0.0120	L	0.47716	1.5	0.30105	N	0.807104	P;P	0.49559	0.925;0.598	P;B	0.47075	0.536;0.188	T	0.24728	-1.0152	9	.	.	.	.	13.0212	0.58789	0.0745:0.0:0.9255:0.0	.	568;570	Q9Y520-4;E7EPN9	.;.	Q	570;568;568;570;568;324;326	ENSP00000375928:E570Q;ENSP00000410219:E568Q;ENSP00000356716:E570Q;ENSP00000343629:E568Q	.	E	+	1	0	PRRC2C	169768559	1.000000	0.71417	0.976000	0.42696	0.847000	0.48162	6.234000	0.72326	1.558000	0.49541	0.650000	0.86243	GAA	.	.		0.373	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
PRRC2C	23215	hgsc.bcm.edu	37	1	171514805	171514805	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:171514805T>C	ENST00000338920.4	+	17	5182	c.4945T>C	c.(4945-4947)Ttt>Ctt	p.F1649L	PRRC2C_ENST00000426496.2_Missense_Mutation_p.F1649L|PRRC2C_ENST00000367742.3_Missense_Mutation_p.F1651L|PRRC2C_ENST00000392078.3_Missense_Mutation_p.F1651L	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1649					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TCTATCACAGTTTGATCTCAA	0.289																																					p.F1649L		Atlas-SNP	.											.	.	.	.	0			c.T4945C						.						68.0	66.0	66.0					1																	171514805		2203	4300	6503	SO:0001583	missense	23215	exon17			TCACAGTTTGATC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4945T>C	chr1.hg19:g.171514805T>C	ENSP00000343629:p.Phe1649Leu	691.0	1.0		727.0	259.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	T	16.26	3.073650	0.55646	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.02446	4.29;4.29;4.29;4.29	5.5	5.5	0.81552	.	0.000000	0.45126	D	0.000382	T	0.09555	0.0235	M	0.75777	2.31	0.58432	D	0.999999	D	0.71674	0.998	D	0.80764	0.994	T	0.01030	-1.1475	10	0.87932	D	0	.	15.6564	0.77140	0.0:0.0:0.0:1.0	.	1649	Q9Y520-4	.	L	1651;1650;1649;1651;1649;1406	ENSP00000375928:F1651L;ENSP00000410219:F1649L;ENSP00000356716:F1651L;ENSP00000343629:F1649L	ENSP00000343629:F1649L	F	+	1	0	PRRC2C	169781429	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.695000	0.84257	2.103000	0.63969	0.524000	0.50904	TTT	.	.		0.289	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
RABGAP1L	9910	hgsc.bcm.edu	37	1	174606551	174606551	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:174606551T>C	ENST00000251507.4	+	14	1923	c.1749T>C	c.(1747-1749)caT>caC	p.H583H		NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	0										NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						GAGATATTCATCGTACATTTC	0.358																																					p.H583H		Atlas-SNP	.											.	RABGAP1L	103	.	0			c.T1749C						.						114.0	103.0	107.0					1																	174606551		2203	4300	6503	SO:0001819	synonymous_variant	9910	exon14			TATTCATCGTACA	AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061			24663	protein-coding gene	gene with protein product		609238				10585558	Standard	NM_014857		Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.1749T>C	chr1.hg19:g.174606551T>C		388.0	1.0		422.0	175.0	NM_014857	B7ZAA4	Silent	SNP	ENST00000251507.4	hg19	CCDS1314.1																																																																																			.	.		0.358	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765	
CACNA1E	777	hgsc.bcm.edu	37	1	181680167	181680167	+	Missense_Mutation	SNP	G	G	A	rs575157426		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:181680167G>A	ENST00000367573.2	+	8	1133	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	CACNA1E_ENST00000358338.5_Missense_Mutation_p.R329H|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R329H|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R378H|CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R378H|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R378H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	378	Binding to the beta subunit. {ECO:0000250}.				calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CAGATTGAGCGTGAGCTGAAT	0.577													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20107	0.0		0.0	False		,,,				2504	0.0				p.R378H		Atlas-SNP	.											CACNA1E_ENST00000367573,colon,carcinoma,0,2	CACNA1E	778	.	0			c.G1133A						.						66.0	72.0	70.0					1																	181680167		1986	4158	6144	SO:0001583	missense	777	exon8			TTGAGCGTGAGCT	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1133G>A	chr1.hg19:g.181680167G>A	ENSP00000356545:p.Arg378His	96.0	0.0		73.0	33.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870022	0.91587	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31;-3.31;-3.31;-3.31	5.29	4.37	0.52481	.	0.109385	0.56097	D	0.000032	D	0.94640	0.8272	M	0.70595	2.14	0.80722	D	1	D;D	0.56287	0.975;0.975	P;P	0.52710	0.707;0.59	D	0.94675	0.7860	10	0.66056	D	0.02	.	14.8817	0.70537	0.0:0.0:0.8551:0.1449	.	378;378	Q15878-2;Q15878-3	.;.	H	378;378;378;329;329;378;378	ENSP00000432038:R378H;ENSP00000356542:R378H;ENSP00000434814:R378H;ENSP00000350183:R329H;ENSP00000351101:R329H;ENSP00000353222:R378H;ENSP00000356545:R378H	ENSP00000350183:R329H	R	+	2	0	CACNA1E	179946790	1.000000	0.71417	0.806000	0.32338	0.911000	0.54048	9.717000	0.98755	1.209000	0.43321	0.655000	0.94253	CGT	.	.		0.577	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
LAMC2	3918	hgsc.bcm.edu	37	1	183204833	183204833	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:183204833G>A	ENST00000264144.4	+	16	2489	c.2424G>A	c.(2422-2424)ccG>ccA	p.P808P	LAMC2_ENST00000493293.1_Silent_p.P808P	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	808	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						GCGGTAGCCCGGACGGTGCTG	0.557											OREG0014042	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P808P		Atlas-SNP	.											.	LAMC2	113	.	0			c.G2424A						.						88.0	82.0	84.0					1																	183204833		2203	4300	6503	SO:0001819	synonymous_variant	3918	exon16			TAGCCCGGACGGT	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2424G>A	chr1.hg19:g.183204833G>A		171.0	0.0	1982	196.0	96.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	hg19	CCDS1352.1																																																																																			.	.		0.557	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
EDEM3	80267	hgsc.bcm.edu	37	1	184688333	184688333	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:184688333A>G	ENST00000318130.8	-	11	1390	c.1124T>C	c.(1123-1125)tTa>tCa	p.L375S	EDEM3_ENST00000367512.3_Missense_Mutation_p.L332S	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	375					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CACCTGATATAACATTTCATG	0.313																																					p.L375S		Atlas-SNP	.											.	EDEM3	63	.	0			c.T1124C						.						85.0	92.0	90.0					1																	184688333		2203	4295	6498	SO:0001583	missense	80267	exon11			TGATATAACATTT	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"""chromosome 1 open reading frame 22"""	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.1124T>C	chr1.hg19:g.184688333A>G	ENSP00000318147:p.Leu375Ser	110.0	0.0		103.0	40.0	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Missense_Mutation	SNP	ENST00000318130.8	hg19	CCDS1363.2	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107954	0.77096	.	.	ENSG00000116406	ENST00000318130;ENST00000367512	T;T	0.72835	-0.69;-0.69	4.83	4.83	0.62350	.	0.000000	0.64402	D	0.000004	D	0.82504	0.5051	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.84659	0.0705	10	0.66056	D	0.02	.	14.421	0.67183	1.0:0.0:0.0:0.0	.	375	Q9BZQ6	EDEM3_HUMAN	S	375;332	ENSP00000318147:L375S;ENSP00000356482:L332S	ENSP00000318147:L375S	L	-	2	0	EDEM3	182954956	1.000000	0.71417	0.893000	0.35052	0.993000	0.82548	9.154000	0.94694	1.816000	0.52996	0.379000	0.24179	TTA	.	.		0.313	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191	
PRG4	10216	hgsc.bcm.edu	37	1	186276994	186276994	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:186276994A>G	ENST00000445192.2	+	7	2188	c.2143A>G	c.(2143-2145)Act>Gct	p.T715A	PRG4_ENST00000367483.4_Missense_Mutation_p.T674A|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Missense_Mutation_p.T672A|PRG4_ENST00000367485.4_Missense_Mutation_p.T622A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	715	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GACTGCTCCAACTACCCTCAA	0.577																																					p.T715A		Atlas-SNP	.											.	PRG4	259	.	0			c.A2143G						.						165.0	177.0	173.0					1																	186276994		2203	4300	6503	SO:0001583	missense	10216	exon7			GCTCCAACTACCC	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2143A>G	chr1.hg19:g.186276994A>G	ENSP00000399679:p.Thr715Ala	99.0	0.0		114.0	8.0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	hg19	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	6.484	0.457467	0.12342	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05258	3.47;3.59;3.48;3.59	2.52	-2.0	0.07433	.	0.170014	0.27577	U	0.018760	T	0.04092	0.0114	L	0.39147	1.195	0.09310	N	1	B;B;B;B	0.18013	0.025;0.025;0.015;0.025	B;B;B;B	0.12837	0.008;0.008;0.003;0.008	T	0.38394	-0.9663	9	.	.	.	.	4.6698	0.12683	0.2507:0.4692:0.2801:0.0	.	581;622;715;674	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	A	672;581;674;622;715	ENSP00000356456:T672A;ENSP00000356453:T674A;ENSP00000356455:T622A;ENSP00000399679:T715A	.	T	+	1	0	PRG4	184543617	0.000000	0.05858	0.001000	0.08648	0.176000	0.22953	-0.805000	0.04530	0.026000	0.15269	0.138000	0.15974	ACT	.	.		0.577	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
F13B	2165	hgsc.bcm.edu	37	1	197026474	197026474	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:197026474A>G	ENST00000367412.1	-	6	970	c.927T>C	c.(925-927)caT>caC	p.H309H		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	309	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						CTGCTGACCCATGGATCTCAA	0.373																																					p.H309H		Atlas-SNP	.											.	F13B	137	.	0			c.T927C						.						204.0	189.0	194.0					1																	197026474		2203	4300	6503	SO:0001819	synonymous_variant	2165	exon6			TGACCCATGGATC	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.927T>C	chr1.hg19:g.197026474A>G		176.0	0.0		196.0	11.0	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	hg19	CCDS1388.1																																																																																			.	.		0.373	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
ASPM	259266	hgsc.bcm.edu	37	1	197113197	197113197	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:197113197T>C	ENST00000367409.4	-	2	587	c.331A>G	c.(331-333)Aca>Gca	p.T111A	ASPM_ENST00000294732.7_Missense_Mutation_p.T111A	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	111					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTGAGTGGTGTCCAGTTAACA	0.299																																					p.T111A		Atlas-SNP	.											.	ASPM	444	.	0			c.A331G						.						63.0	64.0	64.0					1																	197113197		2202	4287	6489	SO:0001583	missense	259266	exon2			GTGGTGTCCAGTT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.331A>G	chr1.hg19:g.197113197T>C	ENSP00000356379:p.Thr111Ala	160.0	0.0		180.0	56.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.218993	0.79464	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367406	T;T	0.72942	-0.7;1.08	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	T	0.82015	0.4945	M	0.61703	1.905	0.58432	D	0.99999	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.83890	0.0284	10	0.72032	D	0.01	.	15.4173	0.74980	0.0:0.0:0.0:1.0	.	111;111	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	A	111	ENSP00000356379:T111A;ENSP00000294732:T111A	ENSP00000294732:T111A	T	-	1	0	ASPM	195379820	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.587000	0.67510	2.180000	0.69256	0.519000	0.50382	ACA	.	.		0.299	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
NAV1	89796	hgsc.bcm.edu	37	1	201752586	201752586	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:201752586G>A	ENST00000367296.4	+	7	2830	c.2410G>A	c.(2410-2412)Gtc>Atc	p.V804I	IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000469130.1_3'UTR|NAV1_ENST00000367300.3_Missense_Mutation_p.V804I|NAV1_ENST00000295624.6_Missense_Mutation_p.V804I|NAV1_ENST00000367302.1_Missense_Mutation_p.V817I|NAV1_ENST00000367295.1_Missense_Mutation_p.V413I|NAV1_ENST00000367297.4_Missense_Mutation_p.V804I	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	804					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						TCTTGACAAGGTCAACTCCAA	0.468																																					p.V804I		Atlas-SNP	.											.	NAV1	143	.	0			c.G2410A						.						288.0	288.0	288.0					1																	201752586		2203	4300	6503	SO:0001583	missense	89796	exon7			GACAAGGTCAACT	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.2410G>A	chr1.hg19:g.201752586G>A	ENSP00000356265:p.Val804Ile	115.0	0.0		108.0	42.0	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.51|17.51	3.408346|3.408346	0.62399|0.62399	.|.	.|.	ENSG00000134369|ENSG00000134369	ENST00000430015|ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000391966;ENST00000367295	.|T;T;T;T;T;T	.|0.08008	.|3.14;3.17;3.17;3.17;3.14;3.17	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.19846|0.19846	0.0477|0.0477	L|L	0.31752|0.31752	0.955|0.955	0.41019|0.41019	D|D	0.985068|0.985068	.|B;B;P;D;B	.|0.53312	.|0.347;0.208;0.488;0.959;0.208	.|B;B;B;D;B	.|0.67103	.|0.146;0.047;0.126;0.949;0.038	T|T	0.00981|0.00981	-1.1492|-1.1492	5|10	.|0.59425	.|D	.|0.04	-37.7154|-37.7154	18.7862|18.7862	0.91955|0.91955	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|804;413;804;312;804	.|Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.|.;.;NAV1_HUMAN;.;.	D|I	361|817;804;804;804;804;312;413	.|ENSP00000356271:V817I;ENSP00000356265:V804I;ENSP00000295624:V804I;ENSP00000356266:V804I;ENSP00000356269:V804I;ENSP00000356264:V413I	.|ENSP00000295624:V804I	G|V	+|+	2|1	0|0	NAV1|NAV1	200019209|200019209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.565000|3.565000	0.53798|0.53798	2.524000|2.524000	0.85096|0.85096	0.585000|0.585000	0.79938|0.79938	GGT|GTC	.	.		0.468	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
CR2	1380	hgsc.bcm.edu	37	1	207648316	207648316	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:207648316A>T	ENST00000367058.3	+	13	2483	c.2294A>T	c.(2293-2295)gAt>gTt	p.D765V	CR2_ENST00000367059.3_Missense_Mutation_p.D765V|CR2_ENST00000458541.2_Missense_Mutation_p.D738V|CR2_ENST00000367057.3_Missense_Mutation_p.D824V	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	765	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TGCAGAAGTGATTCTAAAGGA	0.458																																					p.D824V		Atlas-SNP	.											.	CR2	164	.	0			c.A2471T						.						120.0	127.0	125.0					1																	207648316		2203	4300	6503	SO:0001583	missense	1380	exon14			GAAGTGATTCTAA	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2294A>T	chr1.hg19:g.207648316A>T	ENSP00000356025:p.Asp765Val	97.0	0.0		106.0	47.0	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	13.76	2.332655	0.41297	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.65	4.65	0.58169	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.49440	0.1557	M	0.75150	2.29	0.21697	N	0.999586	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.78314	0.991;0.975;0.984	T	0.36890	-0.9729	9	0.62326	D	0.03	.	11.0163	0.47691	1.0:0.0:0.0:0.0	.	765;765;824	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	V	765;824;765;738	ENSP00000356025:D765V;ENSP00000356024:D824V;ENSP00000356026:D765V;ENSP00000404222:D738V	ENSP00000356024:D824V	D	+	2	0	CR2	205714939	0.844000	0.29557	0.012000	0.15200	0.777000	0.43975	2.659000	0.46741	2.038000	0.60285	0.496000	0.49642	GAT	.	.		0.458	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
ANGEL2	90806	hgsc.bcm.edu	37	1	213178563	213178563	+	Silent	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:213178563T>G	ENST00000366962.3	-	5	1100	c.946A>C	c.(946-948)Agg>Cgg	p.R316R	ANGEL2_ENST00000360506.2_Silent_p.R147R|ANGEL2_ENST00000535388.1_Silent_p.R147R|ANGEL2_ENST00000540642.1_Silent_p.R190R|ANGEL2_ENST00000544555.1_Silent_p.R147R|ANGEL2_ENST00000473303.1_5'Flank	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	316										central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		TCACCTCGCCTTGGATTATAC	0.453																																					p.R316R		Atlas-SNP	.											.	ANGEL2	45	.	0			c.A946C						.						125.0	111.0	116.0					1																	213178563		2203	4300	6503	SO:0001819	synonymous_variant	90806	exon5			CTCGCCTTGGATT	AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.946A>C	chr1.hg19:g.213178563T>G		84.0	0.0		87.0	40.0	NM_144567	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Silent	SNP	ENST00000366962.3	hg19	CCDS1512.1																																																																																			.	.		0.453	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567	
GPATCH2	55105	hgsc.bcm.edu	37	1	217688182	217688182	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:217688182G>A	ENST00000366935.3	-	6	1258	c.1148C>T	c.(1147-1149)cCg>cTg	p.P383L		NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	383					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		ATGAGAATCCGGGGAAAAATG	0.348																																					p.P383L		Atlas-SNP	.											.	GPATCH2	53	.	0			c.C1148T						.						46.0	46.0	46.0					1																	217688182		2203	4300	6503	SO:0001583	missense	55105	exon6			GAATCCGGGGAAA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.1148C>T	chr1.hg19:g.217688182G>A	ENSP00000355902:p.Pro383Leu	399.0	0.0		435.0	177.0	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	hg19	CCDS1518.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964408	0.53507	.	.	ENSG00000092978	ENST00000366935	T	0.31247	1.5	5.95	5.95	0.96441	.	0.106321	0.64402	D	0.000003	T	0.27629	0.0679	L	0.51422	1.61	0.80722	D	1	D	0.52996	0.957	B	0.39068	0.289	T	0.02933	-1.1092	10	0.25106	T	0.35	-25.4565	15.0324	0.71717	0.0:0.0:0.8247:0.1753	.	383	Q9NW75	GPTC2_HUMAN	L	383	ENSP00000355902:P383L	ENSP00000355902:P383L	P	-	2	0	GPATCH2	215754805	1.000000	0.71417	0.992000	0.48379	0.932000	0.56968	3.689000	0.54706	2.827000	0.97445	0.650000	0.86243	CCG	.	.		0.348	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
GPATCH2	55105	hgsc.bcm.edu	37	1	217793392	217793392	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:217793392A>T	ENST00000366935.3	-	2	616	c.506T>A	c.(505-507)gTa>gAa	p.V169E	GPATCH2_ENST00000366934.3_Missense_Mutation_p.V169E	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	169					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TGGGAGATCTACTGCCATGCG	0.483																																					p.V169E		Atlas-SNP	.											.	GPATCH2	53	.	0			c.T506A						.						222.0	200.0	207.0					1																	217793392		2203	4300	6503	SO:0001583	missense	55105	exon2			AGATCTACTGCCA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.506T>A	chr1.hg19:g.217793392A>T	ENSP00000355902:p.Val169Glu	53.0	0.0		56.0	25.0	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Missense_Mutation	SNP	ENST00000366935.3	hg19	CCDS1518.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.325385	0.60743	.	.	ENSG00000092978	ENST00000366935;ENST00000366934	T;T	0.40225	1.04;1.04	5.66	5.66	0.87406	.	0.105548	0.64402	D	0.000006	T	0.51839	0.1698	L	0.42245	1.32	0.47511	D	0.999444	D;D	0.67145	0.976;0.996	P;P	0.56474	0.799;0.719	T	0.54029	-0.8354	10	0.66056	D	0.02	-9.1519	15.8881	0.79269	1.0:0.0:0.0:0.0	.	169;169	Q9NW75-2;Q9NW75	.;GPTC2_HUMAN	E	169	ENSP00000355902:V169E;ENSP00000355901:V169E	ENSP00000355901:V169E	V	-	2	0	GPATCH2	215860015	0.997000	0.39634	0.023000	0.16930	0.256000	0.26092	8.561000	0.90715	2.147000	0.66899	0.482000	0.46254	GTA	.	.		0.483	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
RAB3GAP2	25782	hgsc.bcm.edu	37	1	220387265	220387265	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:220387265A>G	ENST00000358951.2	-	3	353	c.237T>C	c.(235-237)gtT>gtC	p.V79V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	79					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		ATAAGGATAAAACACAATCTT	0.363																																					p.V79V		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.T237C						.						118.0	113.0	115.0					1																	220387265		2203	4300	6503	SO:0001819	synonymous_variant	25782	exon3			GGATAAAACACAA	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.237T>C	chr1.hg19:g.220387265A>G		79.0	0.0		88.0	6.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Silent	SNP	ENST00000358951.2	hg19	CCDS31028.1																																																																																			.	.		0.363	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414	
BROX	148362	hgsc.bcm.edu	37	1	222902172	222902172	+	Splice_Site	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:222902172T>C	ENST00000340934.5	+	9	1162		c.e9+2		BROX_ENST00000537020.1_Splice_Site|BROX_ENST00000539697.1_Splice_Site	NM_144695.2	NP_653296.2	Q5VW32	BROX_HUMAN	BRO1 domain and CAAX motif containing							extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	14						ACAGCTTATGTAAGTATTCAC	0.363																																					.		Atlas-SNP	.											.	BROX	45	.	0			c.756+2T>C						.						75.0	74.0	74.0					1																	222902172		2203	4300	6503	SO:0001630	splice_region_variant	148362	exon9			CTTATGTAAGTAT		CCDS1534.1, CCDS73036.1, CCDS73037.1	1q41	2010-11-30	2010-11-30	2010-11-30	ENSG00000162819	ENSG00000162819			26512	protein-coding gene	gene with protein product	"""BRO1 domain containing protein"""		"""chromosome 1 open reading frame 58"""	C1orf58		18190528	Standard	XM_005273065		Approved	FLJ32421	uc001hnq.1	Q5VW32	OTTHUMG00000037650	ENST00000340934.5:c.756+2T>C	chr1.hg19:g.222902172T>C		57.0	0.0		72.0	34.0	NM_144695	B7Z9G5|Q96MG1	Splice_Site	SNP	ENST00000340934.5	hg19	CCDS1534.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.154572	0.78114	.	.	ENSG00000162819	ENST00000340934;ENST00000537020;ENST00000539697	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9967	0.80256	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	BROX	220968795	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	7.579000	0.82511	2.181000	0.69327	0.477000	0.44152	.	.	.		0.363	BROX-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091815.2	NM_144695	Intron
DNAH14	127602	hgsc.bcm.edu	37	1	225519251	225519251	+	Intron	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:225519251T>C	ENST00000445597.2	+	45	7485				DNAH14_ENST00000430092.1_Missense_Mutation_p.V3186A|DNAH14_ENST00000439375.2_Missense_Mutation_p.V3186A			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TGTGCGTCAGTCTTACTAACT	0.428																																					p.V3186A		Atlas-SNP	.											.	DNAH14	300	.	0			c.T9557C						.						79.0	74.0	76.0					1																	225519251		692	1591	2283	SO:0001627	intron_variant	127602	exon63			CGTCAGTCTTACT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7486-5717T>C	chr1.hg19:g.225519251T>C		287.0	0.0		251.0	98.0	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	hg19		.	.	.	.	.	.	.	.	.	.	T	2.712	-0.268515	0.05716	.	.	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.73789	-0.78;-0.78	5.04	3.83	0.44106	.	1.151520	0.06870	U	0.800602	T	0.64227	0.2579	L	0.29908	0.895	0.23030	N	0.998409	B	0.23650	0.089	B	0.18561	0.022	T	0.49890	-0.8891	10	0.30854	T	0.27	.	10.7624	0.46272	0.1421:0.0:0.0:0.8579	.	3186	Q0VDD8-4	.	A	3186	ENSP00000414402:V3186A;ENSP00000392061:V3186A	ENSP00000414402:V3186A	V	+	2	0	DNAH14	223585874	0.155000	0.22806	0.115000	0.21578	0.361000	0.29550	3.458000	0.53014	2.008000	0.58898	0.438000	0.28831	GTC	.	.		0.428	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PARP1	142	hgsc.bcm.edu	37	1	226556018	226556018	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:226556018A>T	ENST00000366794.5	-	16	2302	c.2159T>A	c.(2158-2160)gTg>gAg	p.V720E	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	720	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|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 envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		GCCCTGAGACACCGCCTGGAG	0.582								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.V720E		Atlas-SNP	.											.	PARP1	100	.	0			c.T2159A						.						51.0	54.0	53.0					1																	226556018		2203	4300	6503	SO:0001583	missense	142	exon16			TGAGACACCGCCT	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2159T>A	chr1.hg19:g.226556018A>T	ENSP00000355759:p.Val720Glu	90.0	0.0		72.0	21.0	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514751	0.85389	.	.	ENSG00000143799	ENST00000366794	T	0.14516	2.5	5.59	5.59	0.84812	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.185224	0.47852	D	0.000218	T	0.29652	0.0740	M	0.72894	2.215	0.80722	D	1	P	0.38565	0.637	P	0.48454	0.578	T	0.02009	-1.1230	10	0.87932	D	0	.	15.7618	0.78087	1.0:0.0:0.0:0.0	.	720	P09874	PARP1_HUMAN	E	720	ENSP00000355759:V720E	ENSP00000355759:V720E	V	-	2	0	PARP1	224622641	1.000000	0.71417	0.910000	0.35882	0.676000	0.39594	8.957000	0.93082	2.123000	0.65237	0.533000	0.62120	GTG	.	.		0.582	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
OBSCN	84033	hgsc.bcm.edu	37	1	228399645	228399645	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:228399645C>T	ENST00000422127.1	+	2	205	c.161C>T	c.(160-162)gCg>gTg	p.A54V	OBSCN_ENST00000570156.2_Missense_Mutation_p.A54V|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A54V|C1orf145_ENST00000295012.5_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	54	Ig-like 1.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCGGCCGGCGCGCGCTTCCGT	0.692																																					p.A54V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C161T						.						7.0	9.0	9.0					1																	228399645		1969	4077	6046	SO:0001583	missense	84033	exon2			CCGGCGCGCGCTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.161C>T	chr1.hg19:g.228399645C>T	ENSP00000409493:p.Ala54Val	176.0	0.0		136.0	60.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.613199	0.46631	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.40476	1.03;1.03	4.66	1.53	0.23141	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.259107	0.29752	N	0.011296	T	0.29620	0.0739	L	0.41906	1.305	0.80722	D	1	B;B	0.25169	0.119;0.098	B;B	0.18561	0.022;0.013	T	0.06679	-1.0813	10	0.33940	T	0.23	.	9.251	0.37555	0.0:0.31:0.588:0.1021	.	54;54	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	V	54	ENSP00000284548:A54V;ENSP00000409493:A54V	ENSP00000284548:A54V	A	+	2	0	OBSCN	226466268	1.000000	0.71417	0.060000	0.19600	0.479000	0.33129	4.036000	0.57304	0.388000	0.25054	0.555000	0.69702	GCG	.	.		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
URB2	9816	hgsc.bcm.edu	37	1	229786983	229786983	+	Splice_Site	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:229786983T>C	ENST00000258243.2	+	8	4287	c.4151T>C	c.(4150-4152)gTa>gCa	p.V1384A		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1384						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						TCATTACAGGTAATGCTGAAA	0.358																																					p.V1384A		Atlas-SNP	.											.	URB2	152	.	0			c.T4151C						.						87.0	82.0	84.0					1																	229786983		2203	4300	6503	SO:0001630	splice_region_variant	9816	exon8			TACAGGTAATGCT	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.4150-1T>C	chr1.hg19:g.229786983T>C		137.0	0.0		140.0	6.0	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	hg19	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.738248	0.69304	.	.	ENSG00000135763	ENST00000258243	T	0.42900	0.96	5.78	5.78	0.91487	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.054294	0.64402	D	0.000001	T	0.49525	0.1562	L	0.56769	1.78	0.50313	D	0.999864	D	0.52996	0.957	P	0.52823	0.71	T	0.48603	-0.9021	9	.	.	.	-15.1399	10.4436	0.44479	0.0:0.0725:0.0:0.9275	.	1384	Q14146	URB2_HUMAN	A	1384	ENSP00000258243:V1384A	.	V	+	2	0	URB2	227853606	1.000000	0.71417	0.968000	0.41197	0.820000	0.46376	4.991000	0.63883	2.199000	0.70637	0.533000	0.62120	GTA	.	.		0.358	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	Missense_Mutation
CAPN9	10753	hgsc.bcm.edu	37	1	230916293	230916293	+	Silent	SNP	C	C	T	rs200514450		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:230916293C>T	ENST00000271971.2	+	11	1433	c.1320C>T	c.(1318-1320)caC>caT	p.H440H	RP11-99J16__A.2_ENST00000452640.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000366666.2_Silent_p.H377H|CAPN9_ENST00000354537.1_Silent_p.H414H	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	440	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				TCAGATACCACGCTTCTCGGG	0.522																																					p.H440H		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1320T						.						102.0	98.0	100.0					1																	230916293		2203	4300	6503	SO:0001819	synonymous_variant	10753	exon11			ATACCACGCTTCT	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1320C>T	chr1.hg19:g.230916293C>T		123.0	0.0		125.0	50.0	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	hg19	CCDS1586.1																																																																																			.	C|0.999;T|0.001		0.522	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
SPRTN	83932	hgsc.bcm.edu	37	1	231488843	231488843	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:231488843T>A	ENST00000295050.7	+	5	1542	c.1206T>A	c.(1204-1206)gaT>gaA	p.D402E	SPRTN_ENST00000391858.4_3'UTR	NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	402					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of protein ubiquitination (GO:0031398)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|ubiquitin binding (GO:0043130)										GGTCTGAAGATACATTCCCAA	0.368																																					p.D402E		Atlas-SNP	.											.	.	.	.	0			c.T1206A						.						72.0	72.0	72.0					1																	231488843		2203	4300	6503	SO:0001583	missense	83932	exon5			TGAAGATACATTC	AL512744	CCDS1594.1, CCDS31054.1, CCDS58066.1	1q42.12-q43	2013-01-30	2012-06-18	2012-06-18	ENSG00000010072	ENSG00000010072			25356	protein-coding gene	gene with protein product	"""SprT-like domain at the N terminus"", ""DNA damage-targeting VCP (p97) adaptor"""		"""chromosome 1 open reading frame 124"""	C1orf124		22681887	Standard	NM_032018		Approved	DKFZP547N043, Spartan, DVC1	uc001hur.4	Q9H040	OTTHUMG00000038022	ENST00000295050.7:c.1206T>A	chr1.hg19:g.231488843T>A	ENSP00000295050:p.Asp402Glu	320.0	1.0		294.0	134.0	NM_032018	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Missense_Mutation	SNP	ENST00000295050.7	hg19	CCDS1594.1	.	.	.	.	.	.	.	.	.	.	T	11.95	1.792729	0.31685	.	.	ENSG00000010072	ENST00000295050	T	0.41758	0.99	5.55	-1.27	0.09347	.	0.689033	0.14116	N	0.340365	T	0.16557	0.0398	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.21965	-1.0230	10	0.08599	T	0.76	-8.3951	2.3029	0.04167	0.1252:0.1668:0.4162:0.2918	.	402	Q9H040	CA124_HUMAN	E	402	ENSP00000295050:D402E	ENSP00000295050:D402E	D	+	3	2	C1orf124	229555466	0.000000	0.05858	0.001000	0.08648	0.080000	0.17528	-0.685000	0.05167	-0.198000	0.10333	0.523000	0.50628	GAT	.	.		0.368	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1	NM_032018	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232600968	232600968	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:232600968G>A	ENST00000366630.1	-	8	2796	c.2438C>T	c.(2437-2439)gCg>gTg	p.A813V	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.A813V|SIPA1L2_ENST00000308942.4_5'Flank			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	813					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AAAGTTCTCCGCCAGATCTTT	0.463																																					p.A813V		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C2438T						.						112.0	110.0	111.0					1																	232600968		1963	4162	6125	SO:0001583	missense	57568	exon7			TTCTCCGCCAGAT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2438C>T	chr1.hg19:g.232600968G>A	ENSP00000355589:p.Ala813Val	135.0	0.0		151.0	62.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.490593	0.64074	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.57752	0.38;0.38	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.51991	0.1707	L	0.41824	1.3	0.80722	D	1	D	0.56035	0.974	P	0.45506	0.483	T	0.49062	-0.8978	10	0.39692	T	0.17	-24.3291	20.053	0.97634	0.0:0.0:1.0:0.0	.	813	Q9P2F8	SI1L2_HUMAN	V	813	ENSP00000355589:A813V;ENSP00000262861:A813V	ENSP00000262861:A813V	A	-	2	0	SIPA1L2	230667591	1.000000	0.71417	0.968000	0.41197	0.959000	0.62525	7.984000	0.88150	2.733000	0.93635	0.650000	0.86243	GCG	.	.		0.463	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
ERO1LB	56605	hgsc.bcm.edu	37	1	236445027	236445027	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:236445027C>G	ENST00000354619.5	-	1	258	c.57G>C	c.(55-57)caG>caC	p.Q19H	ERO1LB_ENST00000327333.8_Missense_Mutation_p.Q19H	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	19					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	TGACCAGCAGCTGCACCGCGG	0.741																																					p.Q19H		Atlas-SNP	.											.	ERO1LB	48	.	0			c.G57C						.						6.0	7.0	7.0					1																	236445027		2042	4045	6087	SO:0001583	missense	56605	exon1			CAGCAGCTGCACC	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.57G>C	chr1.hg19:g.236445027C>G	ENSP00000346635:p.Gln19His	113.0	0.0		108.0	6.0	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	hg19	CCDS31064.1	.	.	.	.	.	.	.	.	.	.	c	3.312	-0.140533	0.06669	.	.	ENSG00000086619	ENST00000354619;ENST00000327333	T;T	0.45276	1.52;0.9	4.17	-0.0922	0.13658	.	0.767685	0.11822	N	0.526099	T	0.21267	0.0512	N	0.22421	0.69	0.21527	N	0.999655	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22521	-1.0214	10	0.15499	T	0.54	-0.059	2.9591	0.05887	0.1952:0.4612:0.0:0.3435	.	19;19	B4DF57;Q86YB8	.;ERO1B_HUMAN	H	19	ENSP00000346635:Q19H;ENSP00000377574:Q19H	ENSP00000377574:Q19H	Q	-	3	2	ERO1LB	234511650	0.999000	0.42202	0.979000	0.43373	0.008000	0.06430	0.710000	0.25748	0.010000	0.14839	-0.679000	0.03777	CAG	.	.		0.741	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
MTR	4548	hgsc.bcm.edu	37	1	236959039	236959039	+	Splice_Site	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:236959039T>C	ENST00000366577.5	+	1	428		c.e1+2		MTR_ENST00000535889.1_Splice_Site|MTR_ENST00000418145.2_Splice_Site	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase						cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	CGCAACCCGGTAACGCTGCGA	0.632																																					.		Atlas-SNP	.											.	MTR	127	.	0			c.34+2T>C						.						98.0	74.0	82.0					1																	236959039		2203	4300	6503	SO:0001630	splice_region_variant	4548	exon1			ACCCGGTAACGCT	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.34+2T>C	chr1.hg19:g.236959039T>C		67.0	0.0		65.0	27.0	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Splice_Site	SNP	ENST00000366577.5	hg19	CCDS1614.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824365	0.90955	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000418145;ENST00000535889	.	.	.	3.79	3.79	0.43588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2732	0.37684	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MTR	235025662	1.000000	0.71417	0.983000	0.44433	0.930000	0.56654	2.736000	0.47385	1.931000	0.55961	0.519000	0.50382	.	.	.		0.632	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	Intron
RYR2	6262	hgsc.bcm.edu	37	1	237951398	237951398	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:237951398T>A	ENST00000366574.2	+	92	13756	c.13439T>A	c.(13438-13440)tTc>tAc	p.F4480Y	RYR2_ENST00000542537.1_Missense_Mutation_p.F4464Y|RYR2_ENST00000360064.6_Missense_Mutation_p.F4486Y	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4480					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAGTCAGCATTCTGGAAGAAA	0.383																																					p.F4480Y		Atlas-SNP	.											.	RYR2	1273	.	0			c.T13439A						.						97.0	106.0	103.0					1																	237951398		2098	4248	6346	SO:0001583	missense	6262	exon92			CAGCATTCTGGAA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13439T>A	chr1.hg19:g.237951398T>A	ENSP00000355533:p.Phe4480Tyr	827.0	1.0		813.0	341.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.786066	0.70337	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.94417	-3.42;-3.42;-3.42	4.55	4.55	0.56014	Ryanodine Receptor TM 4-6 (1);	0.000000	0.64402	U	0.000006	D	0.89795	0.6818	L	0.41492	1.28	0.80722	D	1	D	0.54207	0.965	B	0.39339	0.297	D	0.88248	0.2914	10	0.27082	T	0.32	.	12.7682	0.57403	0.0:0.0:0.0:1.0	.	4480	Q92736	RYR2_HUMAN	Y	4480;4486;4464	ENSP00000355533:F4480Y;ENSP00000353174:F4486Y;ENSP00000443798:F4464Y	ENSP00000353174:F4486Y	F	+	2	0	RYR2	236018021	1.000000	0.71417	0.999000	0.59377	0.519000	0.34347	7.388000	0.79795	1.816000	0.52996	0.477000	0.44152	TTC	.	.		0.383	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
FH	2271	hgsc.bcm.edu	37	1	241680550	241680550	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:241680550A>G	ENST00000366560.3	-	2	237	c.199T>C	c.(199-201)Tat>Cat	p.Y67H	FH_ENST00000493477.1_5'UTR	NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	67					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		GCGCCATAATACTTATCATTT	0.403			"""Mis, N, F"""			"""lieomyomatosis, renal"""			Hereditary Leiomyomatosis and Renal Cell Cancer																												p.Y67H	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"""E, M"""	.	FH	64	.	0			c.T199C						.						137.0	123.0	128.0					1																	241680550		2203	4300	6503	SO:0001583	missense	2271	exon2	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	CATAATACTTATC	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.199T>C	chr1.hg19:g.241680550A>G	ENSP00000355518:p.Tyr67His	102.0	0.0		112.0	45.0	NM_000143	B1ANK7	Missense_Mutation	SNP	ENST00000366560.3	hg19	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.592783	0.66219	.	.	ENSG00000091483	ENST00000366560	D	0.99458	-5.93	5.75	4.63	0.57726	Lyase 1, N-terminal (1);L-Aspartase-like (1);L-Aspartase-like, N-terminal (1);	0.114903	0.64402	D	0.000008	D	0.99677	0.9879	H	0.97896	4.1	0.80722	D	1	D	0.65815	0.995	D	0.76071	0.987	D	0.97864	1.0282	10	0.87932	D	0	-7.926	10.1351	0.42701	0.9209:0.0:0.0791:0.0	.	67	P07954	FUMH_HUMAN	H	67	ENSP00000355518:Y67H	ENSP00000355518:Y67H	Y	-	1	0	FH	239747173	1.000000	0.71417	1.000000	0.80357	0.423000	0.31445	8.852000	0.92215	1.118000	0.41863	0.528000	0.53228	TAT	.	.		0.403	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	
ZNF695	57116	hgsc.bcm.edu	37	1	247150429	247150429	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:247150429G>A	ENST00000339986.7	-	4	1535	c.1388C>T	c.(1387-1389)cCc>cTc	p.P463L	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	463					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACATTTGTAGGGTTTCTCTCC	0.383																																					p.P463L		Atlas-SNP	.											.	ZNF695	55	.	0			c.C1388T						.						67.0	71.0	70.0					1																	247150429		2116	4249	6365	SO:0001583	missense	57116	exon4			TTGTAGGGTTTCT		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.1388C>T	chr1.hg19:g.247150429G>A	ENSP00000341236:p.Pro463Leu	67.0	0.0		80.0	40.0	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	hg19	CCDS44344.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489160	0.44249	.	.	ENSG00000197472	ENST00000339986	T	0.17054	2.3	0.642	-0.87	0.10646	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27629	0.0679	L	0.58101	1.795	0.44247	D	0.997091	D	0.76494	0.999	D	0.63703	0.917	T	0.08932	-1.0698	9	0.62326	D	0.03	.	5.3174	0.15862	0.0:0.0:0.6708:0.3292	.	463	Q8IW36	ZN695_HUMAN	L	463	ENSP00000341236:P463L	ENSP00000341236:P463L	P	-	2	0	ZNF695	245217052	1.000000	0.71417	0.127000	0.21898	0.858000	0.48976	4.808000	0.62583	-0.308000	0.08792	0.205000	0.17691	CCC	.	.		0.383	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
ZNF496	84838	hgsc.bcm.edu	37	1	247464566	247464566	+	Missense_Mutation	SNP	G	G	A	rs551292960		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:247464566G>A	ENST00000294753.4	-	9	1483	c.1019C>T	c.(1018-1020)cCg>cTg	p.P340L	ZNF496_ENST00000462139.1_5'UTR|ZNF496_ENST00000366498.2_Missense_Mutation_p.P376L	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	340					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			TAGAGATCGCGGGTTGCCGCC	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		16776	0.0		0.0	False		,,,				2504	0.001				p.P340L		Atlas-SNP	.											.	ZNF496	80	.	0			c.C1019T						.						60.0	67.0	65.0					1																	247464566		2137	4161	6298	SO:0001583	missense	84838	exon9			GATCGCGGGTTGC	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.1019C>T	chr1.hg19:g.247464566G>A	ENSP00000294753:p.Pro340Leu	34.0	0.0		38.0	13.0	NM_032752	Q8TBS2	Missense_Mutation	SNP	ENST00000294753.4	hg19	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.488895	0.26686	.	.	ENSG00000162714	ENST00000294753;ENST00000366498	T;T	0.07908	3.16;3.15	4.12	2.08	0.27032	.	1.265160	0.05423	N	0.544600	T	0.04092	0.0114	N	0.14661	0.345	0.09310	N	0.999995	P;B	0.38280	0.625;0.016	B;B	0.21917	0.037;0.002	T	0.37009	-0.9724	10	0.30854	T	0.27	-0.8852	4.979	0.14155	0.3226:0.0:0.6774:0.0	.	376;340	Q96IT1-2;Q96IT1	.;ZN496_HUMAN	L	340;376	ENSP00000294753:P340L;ENSP00000355454:P376L	ENSP00000294753:P340L	P	-	2	0	ZNF496	245531189	0.968000	0.33430	0.001000	0.08648	0.032000	0.12392	0.000000	0.12993	0.578000	0.29487	0.655000	0.94253	CCG	.	.		0.602	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
OR2T1	26696	hgsc.bcm.edu	37	1	248569984	248569984	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:248569984A>G	ENST00000366474.1	+	1	689	c.689A>G	c.(688-690)gAg>gGg	p.E230G		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTCTTCTGTGAGGCACCAGCA	0.512																																					p.E230G		Atlas-SNP	.											.	OR2T1	89	.	0			c.A689G						.						165.0	147.0	153.0					1																	248569984		2203	4300	6503	SO:0001583	missense	26696	exon1			TCTGTGAGGCACC	U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"""GPCR / Class A : Olfactory receptors"""	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.689A>G	chr1.hg19:g.248569984A>G	ENSP00000355430:p.Glu230Gly	93.0	0.0		109.0	32.0	NM_030904	Q6IEZ9	Missense_Mutation	SNP	ENST00000366474.1	hg19	CCDS31115.1	.	.	.	.	.	.	.	.	.	.	a	18.27	3.587845	0.66105	.	.	ENSG00000175143	ENST00000366474	T	0.00227	8.5	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37012	U	0.002281	T	0.00815	0.0027	M	0.93375	3.41	0.39267	D	0.964328	D	0.89917	1.0	D	0.97110	1.0	T	0.57808	-0.7747	10	0.87932	D	0	.	13.3845	0.60789	1.0:0.0:0.0:0.0	.	230	O43869	OR2T1_HUMAN	G	230	ENSP00000355430:E230G	ENSP00000355430:E230G	E	+	2	0	OR2T1	246636607	1.000000	0.71417	0.993000	0.49108	0.704000	0.40688	4.920000	0.63390	1.993000	0.58246	0.528000	0.53228	GAG	.	.		0.512	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2		
OR2T2	401992	hgsc.bcm.edu	37	1	248616797	248616797	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:248616797G>T	ENST00000342927.3	+	1	721	c.699G>T	c.(697-699)gaG>gaT	p.E233D		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	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)			ACTCTGCTGAGGGCCGGCGCA	0.557																																					p.E233D		Atlas-SNP	.											.	OR2T2	73	.	0			c.G699T						.						65.0	48.0	54.0					1																	248616797		2187	4262	6449	SO:0001583	missense	401992	exon1			TGCTGAGGGCCGG	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.699G>T	chr1.hg19:g.248616797G>T	ENSP00000343062:p.Glu233Asp	248.0	0.0		245.0	11.0	NM_001004136	B2RNM1|B9EH01	Missense_Mutation	SNP	ENST00000342927.3	hg19	CCDS31116.1	.	.	.	.	.	.	.	.	.	.	g	5.467	0.271212	0.10349	.	.	ENSG00000196240	ENST00000342927	T	0.00193	8.58	3.61	1.47	0.22746	GPCR, rhodopsin-like superfamily (1);	0.283792	0.24876	N	0.034884	T	0.00210	0.0006	M	0.73962	2.25	0.09310	N	1	B	0.16603	0.018	B	0.22152	0.038	T	0.43605	-0.9381	10	0.72032	D	0.01	.	4.4295	0.11520	0.5104:0.0:0.4896:0.0	.	233	Q6IF00	OR2T2_HUMAN	D	233	ENSP00000343062:E233D	ENSP00000343062:E233D	E	+	3	2	OR2T2	246683420	0.000000	0.05858	0.145000	0.22337	0.010000	0.07245	-0.302000	0.08221	0.711000	0.32018	0.449000	0.29647	GAG	.	.		0.557	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
ZNF672	79894	hgsc.bcm.edu	37	1	249142190	249142190	+	Silent	SNP	C	C	T	rs373331980		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:249142190C>T	ENST00000306562.3	+	4	1463	c.717C>T	c.(715-717)agC>agT	p.S239S		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	239					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(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TCCTGGAGAGCGCCACGCTGG	0.652																																					p.S239S		Atlas-SNP	.											.	ZNF672	32	.	0			c.C717T						.	C		1,4363		0,1,2181	9.0	9.0	9.0		717	-7.9	0.6	1		9	0,8506		0,0,4253	no	coding-synonymous	ZNF672	NM_024836.1		0,1,6434	TT,TC,CC		0.0,0.0229,0.0078		239/453	249142190	1,12869	2182	4253	6435	SO:0001819	synonymous_variant	79894	exon4			GGAGAGCGCCACG	AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"""Zinc fingers, C2H2-type"""	26179	protein-coding gene	gene with protein product	"""hypothetical protein FLJ22301"""					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.717C>T	chr1.hg19:g.249142190C>T		81.0	0.0		61.0	25.0	NM_024836	Q96H65|Q96IM3|Q9H6G5	Silent	SNP	ENST00000306562.3	hg19	CCDS1638.1																																																																																			.	.		0.652	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836	
PXDN	7837	hgsc.bcm.edu	37	2	1670259	1670259	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:1670259C>T	ENST00000252804.4	-	10	1069		c.e10-1		PXDN_ENST00000483018.1_Splice_Site	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)						extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GTGGGTCGAGCTGTCACAATT	0.483																																					.		Atlas-SNP	.											.	PXDN	255	.	0			c.1019-1G>A						.						24.0	25.0	25.0					2																	1670259		1947	4139	6086	SO:0001630	splice_region_variant	7837	exon11			GTCGAGCTGTCAC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1019-1G>A	chr2.hg19:g.1670259C>T		190.0	0.0		167.0	73.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Splice_Site	SNP	ENST00000252804.4	hg19	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.450884	0.84209	.	.	ENSG00000130508	ENST00000252804;ENST00000433670	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6763	0.85280	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PXDN	1649266	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.744000	0.85034	2.369000	0.80426	0.655000	0.94253	.	.	.		0.483	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	Intron
TRAPPC12	51112	hgsc.bcm.edu	37	2	3469411	3469411	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:3469411A>G	ENST00000324266.5	+	9	1916	c.1721A>G	c.(1720-1722)tAt>tGt	p.Y574C	TRAPPC12_ENST00000469147.1_3'UTR|TRAPPC12_ENST00000382110.2_Missense_Mutation_p.Y574C	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	574					vesicle-mediated transport (GO:0016192)												GTTATCAAGTATTACCCAGAG	0.527																																					p.Y574C		Atlas-SNP	.											.	.	.	.	0			c.A1721G						.						121.0	117.0	119.0					2																	3469411		2203	4300	6503	SO:0001583	missense	51112	exon9			TCAAGTATTACCC	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1721A>G	chr2.hg19:g.3469411A>G	ENSP00000324318:p.Tyr574Cys	101.0	0.0		82.0	15.0	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	hg19	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.389474	0.25118	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266;ENST00000415624	T;T;T	0.62941	-0.01;-0.01;-0.01	5.65	-3.1	0.05315	.	0.311783	0.36101	N	0.002794	T	0.45175	0.1329	L	0.47716	1.5	0.34164	D	0.669015	B;B	0.24675	0.109;0.035	B;B	0.26693	0.072;0.023	T	0.11842	-1.0571	10	0.40728	T	0.16	.	4.1305	0.10148	0.4903:0.0:0.2797:0.23	.	563;574	E7ENL7;Q8WVT3	.;TPC12_HUMAN	C	574;563;574;72	ENSP00000371544:Y574C;ENSP00000324318:Y574C;ENSP00000396592:Y72C	ENSP00000303612:Y563C	Y	+	2	0	TTC15	3448418	0.978000	0.34361	0.000000	0.03702	0.001000	0.01503	2.607000	0.46300	-0.842000	0.04195	-0.290000	0.09829	TAT	.	.		0.527	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
NBAS	51594	hgsc.bcm.edu	37	2	15359052	15359052	+	Missense_Mutation	SNP	G	G	A	rs200331420		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:15359052G>A	ENST00000281513.5	-	48	6302	c.6277C>T	c.(6277-6279)Cgg>Tgg	p.R2093W	NBAS_ENST00000441750.1_Missense_Mutation_p.R1973W	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2093					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CAGAAAGGCCGCAGCCACTCC	0.557																																					p.R2093W		Atlas-SNP	.											.	NBAS	246	.	0			c.C6277T						.						37.0	41.0	40.0					2																	15359052		2203	4300	6503	SO:0001583	missense	51594	exon48			AAGGCCGCAGCCA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6277C>T	chr2.hg19:g.15359052G>A	ENSP00000281513:p.Arg2093Trp	293.0	0.0		291.0	113.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.295724	0.60086	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.32515	1.45;1.45	5.57	4.69	0.59074	.	0.056518	0.64402	D	0.000002	T	0.34716	0.0907	M	0.63843	1.955	0.53688	D	0.999979	P;P	0.51791	0.948;0.498	B;B	0.43728	0.429;0.064	T	0.27938	-1.0059	10	0.87932	D	0	.	12.4462	0.55651	0.0:0.0:0.5767:0.4233	.	1973;2093	A2RRP1-2;A2RRP1	.;NBAS_HUMAN	W	1973;2093	ENSP00000413201:R1973W;ENSP00000281513:R2093W	ENSP00000281513:R2093W	R	-	1	2	NBAS	15276503	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.600000	0.46240	1.334000	0.45468	0.591000	0.81541	CGG	.	G|0.999;C|0.001		0.557	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
NBAS	51594	hgsc.bcm.edu	37	2	15607895	15607895	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:15607895A>G	ENST00000281513.5	-	18	1936	c.1911T>C	c.(1909-1911)agT>agC	p.S637S	NBAS_ENST00000441750.1_Silent_p.S637S	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	637					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CATAGGAGATACTGTCAATGT	0.338																																					p.S637S		Atlas-SNP	.											.	NBAS	246	.	0			c.T1911C						.						100.0	94.0	96.0					2																	15607895		2202	4300	6502	SO:0001819	synonymous_variant	51594	exon18			GGAGATACTGTCA	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.1911T>C	chr2.hg19:g.15607895A>G		322.0	0.0		338.0	127.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	hg19	CCDS1685.1																																																																																			.	.		0.338	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
DDX1	1653	hgsc.bcm.edu	37	2	15768807	15768807	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:15768807G>A	ENST00000381341.2	+	23	2194	c.1805G>A	c.(1804-1806)cGa>cAa	p.R602Q	DDX1_ENST00000233084.3_Missense_Mutation_p.R602Q			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	602	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Necessary for interaction with HNRNPK.|Necessary for interaction with replicase polyprotein 1ab nsp14 of IBV.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		TACGTACATCGAATTGGCAGA	0.323																																					p.R602Q		Atlas-SNP	.											.	DDX1	70	.	0			c.G1805A						.						62.0	63.0	63.0					2																	15768807		2203	4300	6503	SO:0001583	missense	1653	exon22			TACATCGAATTGG	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"""DEAD-boxes"""	2734	protein-coding gene	gene with protein product		601257	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"""			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.1805G>A	chr2.hg19:g.15768807G>A	ENSP00000370745:p.Arg602Gln	166.0	0.0		147.0	61.0	NM_004939	B4DME8|B4DPN6	Missense_Mutation	SNP	ENST00000381341.2	hg19	CCDS1686.1	.	.	.	.	.	.	.	.	.	.	G	37	6.066328	0.97251	.	.	ENSG00000079785	ENST00000381341;ENST00000233084;ENST00000543614	D;D	0.82344	-1.6;-1.6	6.17	6.17	0.99709	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.93174	0.7826	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93112	0.6517	10	0.87932	D	0	-14.4893	20.8794	0.99867	0.0:0.0:1.0:0.0	.	602	Q92499	DDX1_HUMAN	Q	602;602;586	ENSP00000370745:R602Q;ENSP00000233084:R602Q	ENSP00000233084:R602Q	R	+	2	0	DDX1	15686258	1.000000	0.71417	0.870000	0.34147	0.987000	0.75469	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGA	.	.		0.323	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939	
MYCN	4613	hgsc.bcm.edu	37	2	16082705	16082705	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:16082705C>T	ENST00000281043.3	+	2	816	c.519C>T	c.(517-519)gcC>gcT	p.A173A	MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000453400.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000420452.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	173					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			gcgccggggccgccctgcccg	0.811			A		neuroblastoma																																p.A173A		Atlas-SNP	.		Dom	yes		2	2p24.1	4613	"""v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"""		O	.	MYCN	63	.	0			c.C519T						.						1.0	2.0	1.0					2																	16082705		736	1843	2579	SO:0001819	synonymous_variant	4613	exon2			CGGGGCCGCCCTG	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"""Basic helix-loop-helix proteins"""	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.519C>T	chr2.hg19:g.16082705C>T		102.0	0.0		92.0	35.0	NM_005378	Q53XS5|Q6LDT9	Silent	SNP	ENST00000281043.3	hg19	CCDS1687.1																																																																																			.	.		0.811	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378	
APOB	338	hgsc.bcm.edu	37	2	21265319	21265319	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:21265319T>C	ENST00000233242.1	-	3	278	c.151A>G	c.(151-153)Aag>Gag	p.K51E	APOB_ENST00000399256.4_Missense_Mutation_p.K51E	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	51	Heparin-binding.|Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATGTGTACTTCCGGAGGTGC	0.512																																					p.K51E		Atlas-SNP	.											.	APOB	761	.	0			c.A151G						.						159.0	142.0	148.0					2																	21265319		2203	4300	6503	SO:0001583	missense	338	exon3			TGTACTTCCGGAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.151A>G	chr2.hg19:g.21265319T>C	ENSP00000233242:p.Lys51Glu	159.0	0.0		139.0	59.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	17.76	3.469715	0.63625	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.36520	1.25;1.25	5.58	5.58	0.84498	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.000000	0.64402	D	0.000008	T	0.62514	0.2434	M	0.80183	2.485	0.39872	D	0.973521	D	0.89917	1.0	D	0.79784	0.993	T	0.69187	-0.5211	10	0.72032	D	0.01	.	15.055	0.71908	0.0:0.0:0.0:1.0	.	51	P04114	APOB_HUMAN	E	51	ENSP00000233242:K51E;ENSP00000382200:K51E	ENSP00000233242:K51E	K	-	1	0	APOB	21118824	1.000000	0.71417	0.991000	0.47740	0.360000	0.29518	3.325000	0.52030	2.254000	0.74563	0.533000	0.62120	AAG	.	.		0.512	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
DRC1	92749	hgsc.bcm.edu	37	2	26676396	26676396	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:26676396T>C	ENST00000288710.2	+	14	1972	c.1898T>C	c.(1897-1899)gTc>gCc	p.V633A		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	633			V -> F (in dbSNP:rs12623642).		axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											GAGGCCTTCGTCATGGGTCTG	0.617																																					p.V633A		Atlas-SNP	.											.	CCDC164	84	.	0			c.T1898C						.						52.0	55.0	54.0					2																	26676396		2203	4300	6503	SO:0001583	missense	92749	exon14			CCTTCGTCATGGG	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.1898T>C	chr2.hg19:g.26676396T>C	ENSP00000288710:p.Val633Ala	156.0	0.0		143.0	57.0	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	hg19	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.054675	0.75960	.	.	ENSG00000157856	ENST00000288710	T	0.20069	2.1	5.03	5.03	0.67393	.	0.302633	0.31747	N	0.007127	T	0.27697	0.0681	M	0.67953	2.075	0.36542	D	0.871378	P	0.40534	0.72	B	0.40506	0.331	T	0.39742	-0.9599	10	0.72032	D	0.01	-28.8909	14.0395	0.64665	0.0:0.0:0.0:1.0	.	633	Q96MC2	CC164_HUMAN	A	633	ENSP00000288710:V633A	ENSP00000288710:V633A	V	+	2	0	CCDC164	26529900	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.595000	0.54016	2.028000	0.59812	0.496000	0.49642	GTC	.	.		0.617	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
BIRC6	57448	hgsc.bcm.edu	37	2	32696085	32696085	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:32696085T>C	ENST00000421745.2	+	32	6619	c.6485T>C	c.(6484-6486)gTa>gCa	p.V2162A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2162					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TCTCCAGGAGTACTAGATATT	0.393																																					p.V2162A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T6485C						.						139.0	112.0	121.0					2																	32696085		2202	4299	6501	SO:0001583	missense	57448	exon32			CAGGAGTACTAGA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.6485T>C	chr2.hg19:g.32696085T>C	ENSP00000393596:p.Val2162Ala	121.0	0.0		126.0	55.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	18.72	3.684730	0.68157	.	.	ENSG00000115760	ENST00000421745	T	0.73789	-0.78	5.3	5.3	0.74995	.	0.070053	0.56097	D	0.000029	T	0.80336	0.4604	L	0.44542	1.39	0.58432	D	0.999996	D	0.58970	0.984	D	0.65443	0.935	T	0.78785	-0.2068	10	0.33940	T	0.23	.	15.2916	0.73870	0.0:0.0:0.0:1.0	.	2162	Q9NR09	BIRC6_HUMAN	A	2162	ENSP00000393596:V2162A	ENSP00000393596:V2162A	V	+	2	0	BIRC6	32549589	1.000000	0.71417	0.999000	0.59377	0.678000	0.39670	8.036000	0.88901	1.999000	0.58509	0.524000	0.50904	GTA	.	.		0.393	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
BIRC6	57448	hgsc.bcm.edu	37	2	32696135	32696135	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:32696135C>T	ENST00000421745.2	+	32	6669	c.6535C>T	c.(6535-6537)Ctg>Ttg	p.L2179L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2179					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GTCCAGGTTGCTGGATTATGT	0.428																																					p.L2179L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C6535T						.						148.0	119.0	129.0					2																	32696135		2202	4299	6501	SO:0001819	synonymous_variant	57448	exon32			AGGTTGCTGGATT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.6535C>T	chr2.hg19:g.32696135C>T		134.0	0.0		165.0	75.0	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.		0.428	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LTBP1	4052	hgsc.bcm.edu	37	2	33500964	33500964	+	Missense_Mutation	SNP	G	G	A	rs142262862		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:33500964G>A	ENST00000404816.2	+	18	3319	c.2966G>A	c.(2965-2967)cGc>cAc	p.R989H	LTBP1_ENST00000354476.3_Missense_Mutation_p.R990H|LTBP1_ENST00000407925.1_Missense_Mutation_p.R663H|LTBP1_ENST00000402934.1_Missense_Mutation_p.R610H|LTBP1_ENST00000390003.4_Missense_Mutation_p.R664H|LTBP1_ENST00000418533.2_Missense_Mutation_p.R663H|LTBP1_ENST00000404525.1_Missense_Mutation_p.R610H			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	989	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AGCGGGTACCGCATGACTCAG	0.572																																					p.R989H		Atlas-SNP	.											.	LTBP1	317	.	0			c.G2966A						.						119.0	107.0	111.0					2																	33500964		2203	4300	6503	SO:0001583	missense	4052	exon18			GGTACCGCATGAC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.2966G>A	chr2.hg19:g.33500964G>A	ENSP00000386043:p.Arg989His	85.0	0.0		65.0	17.0	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	G	10.12	1.261759	0.23051	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.92299	-2.26;-2.26;-2.26;-2.26;-3.01;-2.26;-2.26	4.73	2.8	0.32819	EGF-like calcium-binding (2);	.	.	.	.	D	0.85358	0.5678	L	0.33792	1.035	0.80722	D	1	B;B;B;B;B;B	0.12630	0.006;0.005;0.003;0.005;0.005;0.005	B;B;B;B;B;B	0.14578	0.011;0.004;0.003;0.006;0.01;0.006	T	0.80013	-0.1560	9	0.44086	T	0.13	.	7.1534	0.25624	0.1695:0.0:0.6905:0.1399	.	989;663;610;663;664;990	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	H	989;990;664;663;610;610;663	ENSP00000386043:R989H;ENSP00000346467:R990H;ENSP00000374653:R664H;ENSP00000393057:R663H;ENSP00000384373:R610H;ENSP00000385359:R610H;ENSP00000384091:R663H	ENSP00000346467:R990H	R	+	2	0	LTBP1	33354468	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.344000	0.52174	1.134000	0.42165	0.655000	0.94253	CGC	.	G|1.000;T|0.000		0.572	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
FAM98A	25940	hgsc.bcm.edu	37	2	33810066	33810066	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:33810066T>C	ENST00000238823.8	-	8	1474	c.1334A>G	c.(1333-1335)gAc>gGc	p.D445G	FAM98A_ENST00000441530.2_Missense_Mutation_p.D250G|FAM98A_ENST00000498340.1_5'Flank|FAM98A_ENST00000403368.1_3'UTR			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	446	Gly-rich.						poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					GTATCTATTGTCCTGCTGGTA	0.587																																					p.D445G		Atlas-SNP	.											.	FAM98A	42	.	0			c.A1334G						.						153.0	133.0	140.0					2																	33810066		2203	4300	6503	SO:0001583	missense	25940	exon8			CTATTGTCCTGCT		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.1334A>G	chr2.hg19:g.33810066T>C	ENSP00000238823:p.Asp445Gly	76.0	0.0		102.0	34.0	NM_015475	B2RNA2|Q9Y3Y6	Missense_Mutation	SNP	ENST00000238823.8	hg19	CCDS33179.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434634	0.43224	.	.	ENSG00000119812	ENST00000238823;ENST00000395190;ENST00000441530	T;T	0.48522	0.81;0.84	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.30978	0.0782	N	0.08118	0	0.50171	D	0.999859	B;B;B;B	0.17852	0.024;0.024;0.015;0.024	B;B;B;B	0.15052	0.012;0.012;0.011;0.007	T	0.08086	-1.0739	10	0.39692	T	0.17	-12.4697	16.1354	0.81481	0.0:0.0:0.0:1.0	.	446;276;445;283	Q8NCA5;B4DY25;Q8NCA5-2;B3KTW4	FA98A_HUMAN;.;.;.	G	445;446;250	ENSP00000238823:D445G;ENSP00000408716:D250G	ENSP00000238823:D445G	D	-	2	0	FAM98A	33663570	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.125000	0.77193	2.207000	0.71202	0.533000	0.62120	GAC	.	.		0.587	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475	
SOCS5	9655	hgsc.bcm.edu	37	2	46986966	46986966	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:46986966T>C	ENST00000306503.5	+	2	1469	c.1297T>C	c.(1297-1299)Tgg>Cgg	p.W433R	SOCS5_ENST00000394861.2_Missense_Mutation_p.W433R	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	433	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			AATTGAGCAGTGGAATCACAA	0.493																																					p.W433R		Atlas-SNP	.											.	SOCS5	62	.	0			c.T1297C						.						112.0	110.0	111.0					2																	46986966		2203	4300	6503	SO:0001583	missense	9655	exon2			GAGCAGTGGAATC	AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1297T>C	chr2.hg19:g.46986966T>C	ENSP00000305133:p.Trp433Arg	173.0	0.0		83.0	4.0	NM_144949	Q53SD4|Q8IYZ4	Missense_Mutation	SNP	ENST00000306503.5	hg19	CCDS1830.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.538077	0.65085	.	.	ENSG00000171150	ENST00000306503;ENST00000394861	D;D	0.87571	-2.27;-2.27	5.43	5.43	0.79202	SH2 motif (4);	0.131240	0.64402	D	0.000014	D	0.87645	0.6229	N	0.17674	0.51	0.80722	D	1	D	0.55172	0.97	P	0.62885	0.908	D	0.89211	0.3564	10	0.59425	D	0.04	-15.4853	15.3001	0.73940	0.0:0.0:0.0:1.0	.	433	O75159	SOCS5_HUMAN	R	433	ENSP00000305133:W433R;ENSP00000378330:W433R	ENSP00000305133:W433R	W	+	1	0	SOCS5	46840470	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.121000	0.71602	2.279000	0.76181	0.533000	0.62120	TGG	.	.		0.493	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2		
USP34	9736	hgsc.bcm.edu	37	2	61633160	61633160	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:61633160C>A	ENST00000398571.2	-	3	311	c.235G>T	c.(235-237)Gac>Tac	p.D79Y		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	79					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CAAAGCTGGTCCCGGAGCACT	0.378																																					p.D79Y		Atlas-SNP	.											.	USP34	334	.	0			c.G235T						.						139.0	124.0	129.0					2																	61633160		1870	4110	5980	SO:0001583	missense	9736	exon3			GCTGGTCCCGGAG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.235G>T	chr2.hg19:g.61633160C>A	ENSP00000381577:p.Asp79Tyr	146.0	0.0		65.0	46.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.967301	0.74131	.	.	ENSG00000115464	ENST00000398571	T	0.14144	2.53	6.07	6.07	0.98685	.	.	.	.	.	T	0.34687	0.0906	L	0.47716	1.5	0.54753	D	0.999987	D	0.76494	0.999	D	0.80764	0.994	T	0.00406	-1.1759	9	0.62326	D	0.03	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	79	Q70CQ2	UBP34_HUMAN	Y	79	ENSP00000381577:D79Y	ENSP00000381577:D79Y	D	-	1	0	USP34	61486664	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.591000	0.67536	2.885000	0.99019	0.655000	0.94253	GAC	.	.		0.378	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
TMEM17	200728	hgsc.bcm.edu	37	2	62733210	62733210	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:62733210A>G	ENST00000335390.5	-	1	266	c.55T>C	c.(55-57)Ttc>Ctc	p.F19L		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	19					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GAATCACTGAACACGGCCCGG	0.667																																					p.F19L		Atlas-SNP	.											.	TMEM17	19	.	0			c.T55C						.						31.0	33.0	32.0					2																	62733210		2203	4300	6503	SO:0001583	missense	200728	exon1			CACTGAACACGGC		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.55T>C	chr2.hg19:g.62733210A>G	ENSP00000335094:p.Phe19Leu	195.0	0.0		113.0	74.0	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	hg19	CCDS1871.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.643489	0.47258	.	.	ENSG00000186889	ENST00000335390	T	0.51817	0.69	4.82	4.82	0.62117	.	0.093568	0.64402	D	0.000002	T	0.37517	0.1006	L	0.32530	0.975	0.45899	D	0.998746	B	0.20780	0.048	B	0.18263	0.021	T	0.29119	-1.0022	10	0.66056	D	0.02	-15.613	11.9159	0.52765	1.0:0.0:0.0:0.0	.	19	Q86X19	TMM17_HUMAN	L	19	ENSP00000335094:F19L	ENSP00000335094:F19L	F	-	1	0	TMEM17	62586714	1.000000	0.71417	1.000000	0.80357	0.323000	0.28346	4.391000	0.59652	2.043000	0.60533	0.374000	0.22700	TTC	.	.		0.667	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
ADD2	119	hgsc.bcm.edu	37	2	70900405	70900405	+	Intron	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:70900405T>A	ENST00000264436.4	-	15	2186				ADD2_ENST00000355733.3_Missense_Mutation_p.S599C|ADD2_ENST00000407644.2_Intron	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)						actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						AGGGCAACGCTGAAGAACTCG	0.542																																					p.S599C		Atlas-SNP	.											.	ADD2	261	.	0			c.A1795T						.						86.0	81.0	82.0					2																	70900405		2203	4300	6503	SO:0001627	intron_variant	119	exon15			CAACGCTGAAGAA	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1742-267A>T	chr2.hg19:g.70900405T>A		151.0	0.0		77.0	60.0	NM_017488	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	hg19	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.455236	0.43634	.	.	ENSG00000075340	ENST00000355733	T	0.08370	3.1	3.21	-2.93	0.05598	.	.	.	.	.	T	0.04952	0.0133	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.42766	-0.9432	8	0.87932	D	0	.	0.6394	0.00808	0.2385:0.1292:0.3475:0.2848	.	599	P35612-3	.	C	599	ENSP00000347972:S599C	ENSP00000347972:S599C	S	-	1	0	ADD2	70753913	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.777000	0.04669	-0.689000	0.05149	0.377000	0.23210	AGC	.	.		0.542	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
ZNF638	27332	hgsc.bcm.edu	37	2	71650049	71650049	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71650049T>G	ENST00000409544.1	+	22	4035	c.3405T>G	c.(3403-3405)atT>atG	p.I1135M	ZNF638_ENST00000409407.1_Missense_Mutation_p.I75M|ZNF638_ENST00000264447.4_Missense_Mutation_p.I1135M|ZNF638_ENST00000355812.3_Intron	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1135	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						CTCCCAGCATTCAAACAGAAA	0.408																																					p.I1135M		Atlas-SNP	.											.	ZNF638	179	.	0			c.T3405G						.						96.0	94.0	95.0					2																	71650049		2203	4300	6503	SO:0001583	missense	27332	exon22			CAGCATTCAAACA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3405T>G	chr2.hg19:g.71650049T>G	ENSP00000386433:p.Ile1135Met	210.0	0.0		122.0	89.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	T	4.379	0.069935	0.08436	.	.	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.34667	1.35;1.35;1.49	5.54	-0.259	0.12971	.	0.665977	0.14043	N	0.345301	T	0.16854	0.0405	N	0.17082	0.46	0.40676	D	0.982268	B;B;B	0.10296	0.003;0.001;0.0	B;B;B	0.09377	0.004;0.004;0.002	T	0.12426	-1.0548	10	0.45353	T	0.12	-0.7711	1.1287	0.01740	0.1947:0.1154:0.3386:0.3513	.	1135;1135;1135	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	M	714;1135;1135;75;75	ENSP00000264447:I1135M;ENSP00000386433:I1135M;ENSP00000386813:I75M	ENSP00000264447:I1135M	I	+	3	3	ZNF638	71503557	0.254000	0.23992	0.197000	0.23402	0.329000	0.28539	0.712000	0.25779	0.090000	0.17273	-1.333000	0.01266	ATT	.	.		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
DYSF	8291	hgsc.bcm.edu	37	2	71740432	71740432	+	Intron	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71740432T>C	ENST00000258104.3	+	6	734				DYSF_ENST00000413539.2_Missense_Mutation_p.Y174H|DYSF_ENST00000429174.2_Intron|DYSF_ENST00000410020.3_Missense_Mutation_p.Y175H|DYSF_ENST00000409582.3_Missense_Mutation_p.Y174H|DYSF_ENST00000409762.1_Missense_Mutation_p.Y174H|DYSF_ENST00000409366.1_Intron|DYSF_ENST00000409651.1_Missense_Mutation_p.Y175H|DYSF_ENST00000410041.1_Missense_Mutation_p.Y175H|DYSF_ENST00000394120.2_Intron|DYSF_ENST00000409744.1_Intron	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin						plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGACACGAGATACTCTGGAAA	0.637																																					p.Y175H		Atlas-SNP	.											.	DYSF	536	.	0			c.T523C						.						31.0	39.0	37.0					2																	71740432		692	1591	2283	SO:0001627	intron_variant	8291	exon6			ACGAGATACTCTG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.458-414T>C	chr2.hg19:g.71740432T>C		249.0	0.0		131.0	94.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	T	13.85	2.361528	0.41801	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000409651;ENST00000410020;ENST00000410041	D;D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59;-1.59	5.31	2.93	0.34026	.	.	.	.	.	T	0.76535	0.4001	.	.	.	0.21802	N	0.999536	D;D;P;P;D;D	0.59357	0.985;0.985;0.814;0.814;0.985;0.967	P;P;P;B;P;P	0.49085	0.563;0.563;0.532;0.408;0.563;0.6	T	0.62714	-0.6796	8	0.15499	T	0.54	-8.3227	6.9853	0.24725	0.0:0.182:0.0:0.818	.	175;175;175;174;174;174	O75923-8;O75923-13;O75923-11;O75923-5;O75923-2;O75923-7	.;.;.;.;.;.	H	174;174;174;175;175;175	ENSP00000407046:Y174H;ENSP00000387137:Y174H;ENSP00000386547:Y174H;ENSP00000386683:Y175H;ENSP00000386881:Y175H;ENSP00000386617:Y175H	ENSP00000386547:Y174H	Y	+	1	0	DYSF	71593940	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.843000	0.27640	0.344000	0.23847	0.443000	0.29094	TAC	.	.		0.637	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
DYSF	8291	hgsc.bcm.edu	37	2	71755509	71755509	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71755509A>C	ENST00000258104.3	+	13	1539	c.1262A>C	c.(1261-1263)gAg>gCg	p.E421A	DYSF_ENST00000413539.2_Missense_Mutation_p.E452A|DYSF_ENST00000429174.2_Missense_Mutation_p.E421A|DYSF_ENST00000410020.3_Missense_Mutation_p.E453A|DYSF_ENST00000409582.3_Missense_Mutation_p.E452A|DYSF_ENST00000409762.1_Missense_Mutation_p.E452A|DYSF_ENST00000409366.1_Missense_Mutation_p.E422A|DYSF_ENST00000409651.1_Missense_Mutation_p.E453A|DYSF_ENST00000410041.1_Missense_Mutation_p.E453A|DYSF_ENST00000394120.2_Missense_Mutation_p.E422A|DYSF_ENST00000409744.1_Missense_Mutation_p.E422A	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	421	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CCCTTTGTGGAGGTCAGCTTT	0.557																																					p.E453A		Atlas-SNP	.											.	DYSF	536	.	0			c.A1358C						.						95.0	82.0	86.0					2																	71755509		2203	4300	6503	SO:0001583	missense	8291	exon14			TTGTGGAGGTCAG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1262A>C	chr2.hg19:g.71755509A>C	ENSP00000258104:p.Glu421Ala	122.0	0.0		71.0	49.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.525293	0.85600	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	4.82	4.82	0.62117	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.81322	0.4798	M	0.79926	2.475	0.54753	D	0.999986	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.998;1.0;0.998;1.0;0.999;0.999;0.968;0.992;0.998;0.999;0.999	D;D;D;D;D;D;D;D;D;P;D;D;D;D	0.97110	0.998;0.998;0.998;0.998;1.0;0.987;1.0;0.987;0.998;0.852;0.932;0.998;0.998;0.999	D	0.83610	0.0133	10	0.62326	D	0.03	-23.5455	12.6301	0.56653	1.0:0.0:0.0:0.0	.	453;453;422;422;453;422;452;421;452;452;421;421;422;421	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	A	452;452;452;421;421;453;422;422;422;453;453	ENSP00000407046:E452A;ENSP00000387137:E452A;ENSP00000386547:E452A;ENSP00000398305:E421A;ENSP00000258104:E421A;ENSP00000386683:E453A;ENSP00000377678:E422A;ENSP00000386285:E422A;ENSP00000386512:E422A;ENSP00000386881:E453A;ENSP00000386617:E453A	ENSP00000258104:E421A	E	+	2	0	DYSF	71609017	1.000000	0.71417	0.972000	0.41901	0.953000	0.61014	8.945000	0.92985	1.948000	0.56530	0.379000	0.24179	GAG	.	.		0.557	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
DYSF	8291	hgsc.bcm.edu	37	2	71766312	71766312	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:71766312G>A	ENST00000258104.3	+	16	1700	c.1423G>A	c.(1423-1425)Gtg>Atg	p.V475M	DYSF_ENST00000413539.2_Missense_Mutation_p.V506M|DYSF_ENST00000429174.2_Missense_Mutation_p.V475M|DYSF_ENST00000410020.3_Missense_Mutation_p.V507M|DYSF_ENST00000409582.3_Missense_Mutation_p.V506M|DYSF_ENST00000409762.1_Missense_Mutation_p.V506M|DYSF_ENST00000409366.1_Missense_Mutation_p.V476M|DYSF_ENST00000409651.1_Missense_Mutation_p.V507M|DYSF_ENST00000410041.1_Missense_Mutation_p.V507M|DYSF_ENST00000394120.2_Missense_Mutation_p.V476M|DYSF_ENST00000409744.1_Missense_Mutation_p.V476M	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	475	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CAATGACATCGTGGCTACCAC	0.557																																					p.V507M		Atlas-SNP	.											DYSF_ENST00000410020,bladder,carcinoma,0,2	DYSF	536	.	0			c.G1519A						.						164.0	137.0	146.0					2																	71766312		2203	4300	6503	SO:0001583	missense	8291	exon17			GACATCGTGGCTA	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1423G>A	chr2.hg19:g.71766312G>A	ENSP00000258104:p.Val475Met	63.0	0.0		47.0	33.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968347	0.53614	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	5.05	5.05	0.67936	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.072041	0.64402	D	0.000016	T	0.75932	0.3917	L	0.43598	1.365	0.35605	D	0.808191	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.76494	0.999;0.999;0.998;0.996;0.999;0.999;0.999;0.995;0.999;0.999;0.997;0.996;0.998;0.997	D;D;D;P;D;D;D;D;D;D;P;D;D;D	0.71414	0.918;0.918;0.918;0.9;0.973;0.958;0.973;0.924;0.918;0.952;0.9;0.918;0.918;0.951	T	0.80446	-0.1379	10	0.59425	D	0.04	-28.6766	9.6381	0.39822	0.0927:0.0:0.9073:0.0	.	507;507;476;476;507;476;506;475;506;506;475;475;476;475	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	M	506;506;506;475;475;507;476;476;476;507;507	ENSP00000407046:V506M;ENSP00000387137:V506M;ENSP00000386547:V506M;ENSP00000398305:V475M;ENSP00000258104:V475M;ENSP00000386683:V507M;ENSP00000377678:V476M;ENSP00000386285:V476M;ENSP00000386512:V476M;ENSP00000386881:V507M;ENSP00000386617:V507M	ENSP00000258104:V475M	V	+	1	0	DYSF	71619820	0.997000	0.39634	0.994000	0.49952	0.472000	0.32918	2.236000	0.43052	2.786000	0.95864	0.563000	0.77884	GTG	.	.		0.557	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
DCTN1	1639	hgsc.bcm.edu	37	2	74593128	74593128	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:74593128C>T	ENST00000361874.3	-	24	3095	c.2778G>A	c.(2776-2778)ctG>ctA	p.L926L	DCTN1_ENST00000495643.1_5'UTR|DCTN1_ENST00000394003.3_Silent_p.L919L|DCTN1_ENST00000409868.1_Silent_p.L909L|DCTN1_ENST00000409567.3_Silent_p.L906L|DCTN1_ENST00000409240.1_Silent_p.L889L|DCTN1_ENST00000409438.1_Silent_p.L792L|DCTN1_ENST00000407639.2_Silent_p.L792L|RP11-287D1.3_ENST00000451608.2_5'Flank	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	926					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CAGCAGCCCGCAGTTCAACCG	0.512																																					p.L926L		Atlas-SNP	.											DCTN1,right_upper_lobe,carcinoma,-2,1	DCTN1	110	.	0			c.G2778A						.						69.0	72.0	71.0					2																	74593128		2203	4300	6503	SO:0001819	synonymous_variant	1639	exon24			AGCCCGCAGTTCA		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.2778G>A	chr2.hg19:g.74593128C>T		60.0	0.0		81.0	37.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	hg19	CCDS1939.1																																																																																			.	.		0.512	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
M1AP	130951	hgsc.bcm.edu	37	2	74789369	74789369	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:74789369T>C	ENST00000290536.5	-	8	1372	c.1256A>G	c.(1255-1257)cAt>cGt	p.H419R	M1AP_ENST00000536235.1_Missense_Mutation_p.H419R|M1AP_ENST00000358434.2_Intron|M1AP_ENST00000409585.1_Missense_Mutation_p.H419R|M1AP_ENST00000464686.1_5'UTR	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	419					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GCTATCATCATGTGGGTCCTC	0.557																																					p.H419R		Atlas-SNP	.											.	.	.	.	0			c.A1256G						.						139.0	126.0	130.0					2																	74789369		2203	4300	6503	SO:0001583	missense	130951	exon8			TCATCATGTGGGT		CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"""meiosis 1 arresting protein"", ""spermatogenesis associated 37"""		"""chromosome 2 open reading frame 65"""	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.1256A>G	chr2.hg19:g.74789369T>C	ENSP00000290536:p.His419Arg	112.0	0.0		121.0	21.0	NM_138804	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Missense_Mutation	SNP	ENST00000290536.5	hg19	CCDS33229.1	.	.	.	.	.	.	.	.	.	.	T	2.905	-0.226739	0.06022	.	.	ENSG00000159374	ENST00000290536;ENST00000409585;ENST00000536235	T;T;T	0.40476	1.03;1.03;1.03	5.28	2.29	0.28610	.	0.335776	0.32473	N	0.006041	T	0.19604	0.0471	N	0.08118	0	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.14783	-1.0460	10	0.30078	T	0.28	-15.8409	7.4257	0.27098	0.0:0.1686:0.4955:0.3358	.	419;419;175	E9PGG8;Q8TC57;B3KX03	.;CB065_HUMAN;.	R	419	ENSP00000290536:H419R;ENSP00000386793:H419R;ENSP00000445662:H419R	ENSP00000290536:H419R	H	-	2	0	C2orf65	74642877	0.345000	0.24835	0.557000	0.28306	0.397000	0.30659	1.621000	0.36986	0.617000	0.30160	-1.228000	0.01579	CAT	.	.		0.557	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804	
LRRTM4	80059	hgsc.bcm.edu	37	2	77746553	77746553	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:77746553A>G	ENST00000409093.1	-	3	778	c.442T>C	c.(442-444)Ttg>Ctg	p.L148L	LRRTM4_ENST00000409884.1_Silent_p.L148L|LRRTM4_ENST00000409911.1_Silent_p.L149L|LRRTM4_ENST00000409088.3_Silent_p.L148L|LRRTM4_ENST00000409282.1_Silent_p.L149L			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	148					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		TCAGATTGCAATGTCTGAAGC	0.388																																					p.L148L		Atlas-SNP	.											.	LRRTM4	334	.	0			c.T442C						.						90.0	81.0	84.0					2																	77746553		1844	4082	5926	SO:0001819	synonymous_variant	80059	exon3			ATTGCAATGTCTG	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.442T>C	chr2.hg19:g.77746553A>G		180.0	0.0		162.0	71.0	NM_024993	Q4FZ98|Q6UXJ7	Silent	SNP	ENST00000409093.1	hg19	CCDS46346.1																																																																																			.	.		0.388	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993	
GGCX	2677	hgsc.bcm.edu	37	2	85788544	85788544	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:85788544A>G	ENST00000233838.4	-	1	88	c.8T>C	c.(7-9)gTg>gCg	p.V3A	GGCX_ENST00000430215.3_Missense_Mutation_p.V3A|VAMP8_ENST00000432071.1_5'Flank	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	3					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	CCCGGCAGACACCGCCATTGC	0.701																																					p.V3A		Atlas-SNP	.											.	GGCX	44	.	0			c.T8C						.						6.0	8.0	7.0					2																	85788544		2109	4194	6303	SO:0001583	missense	2677	exon1			GCAGACACCGCCA		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.8T>C	chr2.hg19:g.85788544A>G	ENSP00000233838:p.Val3Ala	217.0	0.0		194.0	77.0	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	hg19	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.049881	0.36181	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.94280	-3.39;-3.22	2.56	-4.86	0.03132	.	1.066580	0.07375	N	0.886497	D	0.85522	0.5716	L	0.33485	1.01	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.70073	-0.4972	10	0.30854	T	0.27	0.012	4.497	0.11842	0.3193:0.0:0.4938:0.187	.	3;3	E9PEE1;P38435	.;VKGC_HUMAN	A	3	ENSP00000233838:V3A;ENSP00000408045:V3A	ENSP00000233838:V3A	V	-	2	0	GGCX	85642055	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-1.571000	0.02138	-1.174000	0.02754	0.454000	0.30748	GTG	.	.		0.701	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
STARD7	56910	hgsc.bcm.edu	37	2	96852600	96852600	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:96852600A>T	ENST00000337288.5	-	8	1364	c.981T>A	c.(979-981)aaT>aaA	p.N327K	STARD7_ENST00000462501.1_5'UTR	NM_020151.3	NP_064536.2	Q9NQZ5	STAR7_HUMAN	StAR-related lipid transfer (START) domain containing 7	327	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.					mitochondrion (GO:0005739)	lipid binding (GO:0008289)			endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2)	14						TAATCTCCATATTCTTGGCTT	0.483																																					p.N327K		Atlas-SNP	.											.	STARD7	49	.	0			c.T981A						.						78.0	75.0	76.0					2																	96852600		2203	4300	6503	SO:0001583	missense	56910	exon8			CTCCATATTCTTG	AF270647	CCDS2017.2	2p11.1	2011-09-12	2007-08-16		ENSG00000084090	ENSG00000084090		"""StAR-related lipid transfer (START) domain containing"""	18063	protein-coding gene	gene with protein product			"""START domain containing 7"""				Standard	NM_020151		Approved	GTT1	uc002svm.4	Q9NQZ5	OTTHUMG00000130457	ENST00000337288.5:c.981T>A	chr2.hg19:g.96852600A>T	ENSP00000338030:p.Asn327Lys	152.0	0.0		161.0	74.0	NM_020151	D3DXG9|Q53T44|Q6GU43|Q969M6	Missense_Mutation	SNP	ENST00000337288.5	hg19	CCDS2017.2	.	.	.	.	.	.	.	.	.	.	A	22.7	4.319266	0.81469	.	.	ENSG00000084090	ENST00000337288	T	0.44482	0.92	5.84	3.08	0.35506	Lipid-binding START (2);	0.000000	0.85682	D	0.000000	T	0.35189	0.0923	L	0.51422	1.61	0.58432	D	0.999997	P	0.48589	0.912	B	0.43478	0.421	T	0.06552	-1.0820	10	0.19147	T	0.46	-30.1027	9.2388	0.37484	0.2406:0.0:0.7594:0.0	.	327	Q9NQZ5	STAR7_HUMAN	K	327	ENSP00000338030:N327K	ENSP00000338030:N327K	N	-	3	2	STARD7	96216327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.239000	0.51360	0.375000	0.24679	-0.242000	0.12053	AAT	.	.		0.483	STARD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252848.2		
TMEM131	23505	hgsc.bcm.edu	37	2	98382614	98382614	+	Silent	SNP	C	C	T	rs376329900		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:98382614C>T	ENST00000186436.5	-	35	4914	c.4686G>A	c.(4684-4686)ccG>ccA	p.P1562P		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1562						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						AATCCCACTCCGGTGGAGGAG	0.498																																					p.P1562P		Atlas-SNP	.											.	TMEM131	258	.	0			c.G4686A						.	C		0,3728		0,0,1864	87.0	87.0	87.0		4686	-11.6	0.3	2		87	1,8193		0,1,4096	no	coding-synonymous	TMEM131	NM_015348.1		0,1,5960	TT,TC,CC		0.0122,0.0,0.0084		1562/1884	98382614	1,11921	1864	4097	5961	SO:0001819	synonymous_variant	23505	exon35			CCACTCCGGTGGA	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.4686G>A	chr2.hg19:g.98382614C>T		238.0	0.0		213.0	86.0	NM_015348		Silent	SNP	ENST00000186436.5	hg19	CCDS46368.1																																																																																			.	.		0.498	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
MGAT4A	11320	hgsc.bcm.edu	37	2	99294779	99294779	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:99294779T>A	ENST00000264968.3	-	2	613	c.250A>T	c.(250-252)Aat>Tat	p.N84Y	MGAT4A_ENST00000409391.1_Missense_Mutation_p.N84Y|MGAT4A_ENST00000393487.1_Missense_Mutation_p.N84Y			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	84					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						GAAAACTTATTCAACGCATCC	0.294																																					p.N84Y		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A250T						.						86.0	83.0	84.0					2																	99294779		2202	4300	6502	SO:0001583	missense	11320	exon3			ACTTATTCAACGC	AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7047	protein-coding gene	gene with protein product		604623	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"""			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.250A>T	chr2.hg19:g.99294779T>A	ENSP00000264968:p.Asn84Tyr	72.0	0.0		63.0	21.0	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	hg19	CCDS2036.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.768726	0.31320	.	.	ENSG00000071073	ENST00000393487;ENST00000264968;ENST00000409391	T;T;T	0.44482	0.92;0.92;0.92	5.44	4.29	0.51040	.	0.819623	0.11745	N	0.533589	T	0.38427	0.1040	L	0.40543	1.245	0.09310	N	1	B	0.26041	0.14	B	0.31547	0.132	T	0.37502	-0.9703	10	0.66056	D	0.02	.	10.3625	0.44003	0.0:0.0769:0.0:0.9231	.	84	Q9UM21	MGT4A_HUMAN	Y	84	ENSP00000377127:N84Y;ENSP00000264968:N84Y;ENSP00000386841:N84Y	ENSP00000264968:N84Y	N	-	1	0	MGAT4A	98661211	0.996000	0.38824	0.407000	0.26434	0.365000	0.29674	2.347000	0.44036	0.906000	0.36621	0.454000	0.30748	AAT	.	.		0.294	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214	
SLC9A2	6549	hgsc.bcm.edu	37	2	103311560	103311560	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:103311560T>G	ENST00000233969.2	+	7	1716	c.1574T>G	c.(1573-1575)tTt>tGt	p.F525C	SLC9A2_ENST00000469286.1_3'UTR	NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	525					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						GGTCACAACTTTTGGAGAGAC	0.378																																					p.F525C		Atlas-SNP	.											.	SLC9A2	112	.	0			c.T1574G						.						212.0	211.0	211.0					2																	103311560		2203	4300	6503	SO:0001583	missense	6549	exon7			ACAACTTTTGGAG		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"""Solute carriers"""	11072	protein-coding gene	gene with protein product		600530	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 2"""	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.1574T>G	chr2.hg19:g.103311560T>G	ENSP00000233969:p.Phe525Cys	116.0	0.0		109.0	40.0	NM_003048	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	hg19	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663705	0.67700	.	.	ENSG00000115616	ENST00000233969	T	0.56275	0.47	5.91	5.91	0.95273	.	0.165493	0.56097	D	0.000031	T	0.54046	0.1834	L	0.40543	1.245	0.43756	D	0.996263	D	0.61080	0.989	P	0.52514	0.701	T	0.56763	-0.7925	10	0.56958	D	0.05	.	11.4321	0.50047	0.1345:0.0:0.0:0.8655	.	525	Q9UBY0	SL9A2_HUMAN	C	525	ENSP00000233969:F525C	ENSP00000233969:F525C	F	+	2	0	SLC9A2	102677992	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.403000	0.59729	2.254000	0.74563	0.533000	0.62120	TTT	.	.		0.378	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2		
BUB1	699	hgsc.bcm.edu	37	2	111416240	111416240	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:111416240C>T	ENST00000302759.6	-	12	1474	c.1356G>A	c.(1354-1356)acG>acA	p.T452T	BUB1_ENST00000535254.1_Silent_p.T432T|BUB1_ENST00000409311.1_Silent_p.T452T	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	452					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.T452T(1)		breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		CTTTGGATGGCGTTGCCTGAA	0.433																																					p.T452T		Atlas-SNP	.											BUB1,colon,NS,0,1	BUB1	91	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1356A						.						226.0	192.0	204.0					2																	111416240		2203	4300	6503	SO:0001819	synonymous_variant	699	exon12			GGATGGCGTTGCC	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"""budding uninhibited by benzimidazoles 1 (yeast homolog)"", ""budding uninhibited by benzimidazoles 1 homolog (yeast)"""	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.1356G>A	chr2.hg19:g.111416240C>T		114.0	0.0		114.0	45.0	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Silent	SNP	ENST00000302759.6	hg19	CCDS33273.1																																																																																			.	.		0.433	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336	
RALB	5899	hgsc.bcm.edu	37	2	121036312	121036312	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:121036312C>T	ENST00000272519.5	+	2	342	c.72C>T	c.(70-72)ggC>ggT	p.G24G	RALB_ENST00000470417.1_Intron|RALB_ENST00000404963.3_Silent_p.G24G|RALB_ENST00000420510.1_Silent_p.G24G|RALB_ENST00000474855.2_Silent_p.G46G	NM_002881.2	NP_002872.1	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	24					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of exocyst assembly (GO:0001928)|regulation of exocyst localization (GO:0060178)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(154;0.122)				GCAGCGGAGGCGTTGGCAAGT	0.577																																					p.G24G		Atlas-SNP	.											.	RALB	27	.	0			c.C72T						.						108.0	83.0	92.0					2																	121036312		2203	4300	6503	SO:0001819	synonymous_variant	5899	exon2			CGGAGGCGTTGGC		CCDS2131.1	2q14.2	2014-05-09	2013-07-09		ENSG00000144118	ENSG00000144118			9840	protein-coding gene	gene with protein product	"""ras related GTP binding protein B"""	179551					Standard	NM_002881		Approved		uc002tmk.3	P11234	OTTHUMG00000131435	ENST00000272519.5:c.72C>T	chr2.hg19:g.121036312C>T		97.0	0.0		68.0	25.0	NM_002881	B4E040|Q53T32|Q6ZS74	Silent	SNP	ENST00000272519.5	hg19	CCDS2131.1																																																																																			.	.		0.577	RALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254232.3	NM_002881	
GLI2	2736	hgsc.bcm.edu	37	2	121746146	121746146	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:121746146C>T	ENST00000452319.1	+	14	2716	c.2656C>T	c.(2656-2658)Cag>Tag	p.Q886*	GLI2_ENST00000361492.4_Nonsense_Mutation_p.Q886*|GLI2_ENST00000314490.11_Nonsense_Mutation_p.Q558*					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GCCGGCGCAGCAGTACAGCCT	0.741																																					p.Q886X		Atlas-SNP	.											.	GLI2	187	.	0			c.C2656T						.						2.0	2.0	2.0					2																	121746146		1550	3232	4782	SO:0001587	stop_gained	2736	exon13			GCGCAGCAGTACA		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.2656C>T	chr2.hg19:g.121746146C>T	ENSP00000390436:p.Gln886*	138.0	0.0		158.0	67.0	NM_005270		Nonsense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	C	39	7.347207	0.98228	.	.	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	.	.	.	4.94	4.94	0.65067	.	0.231838	0.45126	D	0.000395	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.3616	0.90376	0.0:1.0:0.0:0.0	.	.	.	.	X	886;886;558	.	ENSP00000312694:Q558X	Q	+	1	0	GLI2	121462616	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	7.361000	0.79497	2.563000	0.86464	0.561000	0.74099	CAG	.	.		0.741	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
WDR33	55339	hgsc.bcm.edu	37	2	128471170	128471170	+	Missense_Mutation	SNP	G	G	A	rs373594035		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:128471170G>A	ENST00000322313.4	-	18	3453	c.3295C>T	c.(3295-3297)Cgc>Tgc	p.R1099C		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1099					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TCTTCTCTGCGCCCTCGAAAA	0.582																																					p.R1099C		Atlas-SNP	.											WDR33,NS,carcinoma,0,1	WDR33	136	.	0			c.C3295T						.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	124.0	129.0	128.0		3295	4.9	1.0	2		128	0,8600		0,0,4300	no	missense	WDR33	NM_018383.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1099/1337	128471170	1,13005	2203	4300	6503	SO:0001583	missense	55339	exon18			CTCTGCGCCCTCG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3295C>T	chr2.hg19:g.128471170G>A	ENSP00000325377:p.Arg1099Cys	132.0	1.0		81.0	25.0	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.810035	0.70797	2.27E-4	0.0	ENSG00000136709	ENST00000322313	D	0.91068	-2.78	5.81	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83936	0.5362	N	0.08118	0	0.80722	D	1	D	0.69078	0.997	P	0.47603	0.551	D	0.86199	0.1617	10	0.49607	T	0.09	-8.0567	14.9159	0.70798	0.0:0.0:0.7541:0.2459	.	1099	Q9C0J8	WDR33_HUMAN	C	1099	ENSP00000325377:R1099C	ENSP00000325377:R1099C	R	-	1	0	WDR33	128187640	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.889000	0.48601	2.738000	0.93877	0.655000	0.94253	CGC	.	.		0.582	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
CCDC74B	91409	hgsc.bcm.edu	37	2	130897479	130897479	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:130897479C>T	ENST00000310463.6	-	7	1129	c.992G>A	c.(991-993)aGc>aAc	p.S331N	MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000409943.3_Missense_Mutation_p.S265N|CCDC74B_ENST00000392984.3_Missense_Mutation_p.S433N	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	331										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					CTTGGAGAGGCTCTTGGTGGA	0.642																																					p.S331N		Atlas-SNP	.											.	CCDC74B	27	.	0			c.G992A						.						23.0	26.0	25.0					2																	130897479		2199	4275	6474	SO:0001583	missense	91409	exon7			GAGAGGCTCTTGG		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.992G>A	chr2.hg19:g.130897479C>T	ENSP00000308873:p.Ser331Asn	125.0	0.0		124.0	39.0	NM_207310	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	hg19	CCDS2155.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.006|0.006	-2.084878|-2.084878	0.00371|0.00371	.|.	.|.	ENSG00000152076|ENSG00000152076	ENST00000409488|ENST00000409943;ENST00000310463;ENST00000392984	.|T;T;T	.|0.30981	.|1.51;1.51;1.51	3.92|3.92	2.09|2.09	0.27110|0.27110	.|.	.|0.684728	.|0.11076	.|U	.|0.602420	T|T	0.12263|0.12263	0.0298|0.0298	N|N	0.05078|0.05078	-0.115|-0.115	0.09310|0.09310	N|N	1|1	.|B;B;P	.|0.50528	.|0.003;0.0;0.936	.|B;B;B	.|0.41236	.|0.004;0.001;0.351	T|T	0.04400|0.04400	-1.0954|-1.0954	6|10	0.31617|0.12430	T|T	0.26|0.62	.|.	5.6153|5.6153	0.17428|0.17428	0.0:0.7517:0.0:0.2483|0.0:0.7517:0.0:0.2483	.|.	.|433;265;331	.|E7ESC5;Q96LY2-2;Q96LY2	.|.;.;CC74B_HUMAN	T|N	229|265;331;433	.|ENSP00000386294:S265N;ENSP00000308873:S331N;ENSP00000376710:S433N	ENSP00000386250:A229T|ENSP00000308873:S331N	A|S	-|-	1|2	0|0	CCDC74B|CCDC74B	130613949|130613949	0.016000|0.016000	0.18221|0.18221	0.004000|0.004000	0.12327|0.12327	0.003000|0.003000	0.03518|0.03518	0.190000|0.190000	0.17057|0.17057	1.005000|1.005000	0.39183|0.39183	-0.401000|-0.401000	0.06369|0.06369	GCC|AGC	.	.		0.642	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310	
CCNT2	905	hgsc.bcm.edu	37	2	135711218	135711218	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:135711218A>T	ENST00000264157.5	+	9	1223	c.1193A>T	c.(1192-1194)gAc>gTc	p.D398V	CCNT2_ENST00000537343.1_Missense_Mutation_p.D223V|CCNT2_ENST00000295238.6_Missense_Mutation_p.D398V	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	398					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CACAGACCTGACAAAATTTCA	0.413																																					p.D398V		Atlas-SNP	.											.	CCNT2	98	.	0			c.A1193T						.						80.0	81.0	81.0					2																	135711218		2203	4300	6503	SO:0001583	missense	905	exon9			GACCTGACAAAAT	AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1193A>T	chr2.hg19:g.135711218A>T	ENSP00000264157:p.Asp398Val	286.0	0.0		154.0	107.0	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Missense_Mutation	SNP	ENST00000264157.5	hg19	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.456750	0.43634	.	.	ENSG00000082258	ENST00000537343;ENST00000295238;ENST00000264157	T;T	0.28255	1.75;1.62	5.71	5.71	0.89125	.	0.175765	0.64402	D	0.000010	T	0.44008	0.1273	L	0.54323	1.7	0.80722	D	1	P;B;D	0.57571	0.665;0.036;0.98	P;B;P	0.53649	0.607;0.005;0.731	T	0.32851	-0.9891	10	0.52906	T	0.07	.	16.0044	0.80349	1.0:0.0:0.0:0.0	.	223;398;398	B4DH21;O60583;O60583-2	.;CCNT2_HUMAN;.	V	223;398;398	ENSP00000295238:D398V;ENSP00000264157:D398V	ENSP00000264157:D398V	D	+	2	0	CCNT2	135427688	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.602000	0.90868	2.191000	0.70037	0.528000	0.53228	GAC	.	.		0.413	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241	
ZRANB3	84083	hgsc.bcm.edu	37	2	136029454	136029454	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:136029454G>A	ENST00000264159.6	-	10	1206	c.1090C>T	c.(1090-1092)Cgt>Tgt	p.R364C	ZRANB3_ENST00000536680.1_Missense_Mutation_p.R364C|ZRANB3_ENST00000401392.1_Missense_Mutation_p.R364C	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	364	DNA annealing helicase activity.|Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		CTAATGTAACGAGTCTAGCAT	0.368																																					p.R364C		Atlas-SNP	.											.	ZRANB3	109	.	0			c.C1090T						.						68.0	65.0	66.0					2																	136029454		1870	4112	5982	SO:0001583	missense	84083	exon10			TGTAACGAGTCTA	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1090C>T	chr2.hg19:g.136029454G>A	ENSP00000264159:p.Arg364Cys	65.0	0.0		39.0	29.0	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.218594	0.79464	.	.	ENSG00000121988	ENST00000401392;ENST00000264159;ENST00000536680;ENST00000397448	T;T;T	0.77358	-1.09;-1.09;-1.09	5.94	5.94	0.96194	Helicase, C-terminal (3);	0.153021	0.64402	D	0.000008	D	0.87398	0.6167	M	0.63208	1.945	0.58432	D	0.999999	D;D;D	0.89917	0.997;1.0;1.0	P;D;D	0.73380	0.613;0.98;0.962	D	0.87035	0.2137	10	0.66056	D	0.02	-10.0918	20.3593	0.98849	0.0:0.0:1.0:0.0	.	304;364;364	E9PBP0;Q5FWF4;Q5FWF4-3	.;ZRAB3_HUMAN;.	C	364;364;364;304	ENSP00000383979:R364C;ENSP00000264159:R364C;ENSP00000441320:R364C	ENSP00000264159:R364C	R	-	1	0	ZRANB3	135745924	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.377000	0.52425	2.807000	0.96579	0.591000	0.81541	CGT	.	.		0.368	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
LRP1B	53353	hgsc.bcm.edu	37	2	141232790	141232790	+	Missense_Mutation	SNP	A	A	T	rs377526659		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:141232790A>T	ENST00000389484.3	-	60	10513	c.9542T>A	c.(9541-9543)aTa>aAa	p.I3181K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3181					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AACATAATCTATTGTTAGTGC	0.408										TSP Lung(27;0.18)																											p.I3181K	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T9542A						.						114.0	104.0	107.0					2																	141232790		2203	4300	6503	SO:0001583	missense	53353	exon60			TAATCTATTGTTA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.9542T>A	chr2.hg19:g.141232790A>T	ENSP00000374135:p.Ile3181Lys	190.0	0.0		131.0	99.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.209552	0.79240	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.94138	-3.36	5.63	5.63	0.86233	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.97526	0.9190	M	0.93283	3.4	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.98597	1.0657	10	0.87932	D	0	.	15.8229	0.78673	1.0:0.0:0.0:0.0	.	3181	Q9NZR2	LRP1B_HUMAN	K	3181;3119	ENSP00000374135:I3181K	ENSP00000374135:I3181K	I	-	2	0	LRP1B	140949260	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.282000	0.95840	2.142000	0.66516	0.528000	0.53228	ATA	.	.		0.408	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
ARHGAP15	55843	hgsc.bcm.edu	37	2	144313999	144313999	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:144313999T>C	ENST00000295095.6	+	11	1115	c.948T>C	c.(946-948)taT>taC	p.Y316Y	RP11-570L15.2_ENST00000546678.1_RNA|RP11-570L15.1_ENST00000553076.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	316	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)			endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		ATGGAATATATCGAGTTAGTG	0.318																																					p.Y316Y		Atlas-SNP	.											.	ARHGAP15	99	.	0			c.T948C						.						193.0	201.0	198.0					2																	144313999		2203	4298	6501	SO:0001819	synonymous_variant	55843	exon11			AATATATCGAGTT	AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.948T>C	chr2.hg19:g.144313999T>C		131.0	0.0		93.0	72.0	NM_018460	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Silent	SNP	ENST00000295095.6	hg19	CCDS2184.1																																																																																			.	.		0.318	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460	
ACVR2A	92	hgsc.bcm.edu	37	2	148674907	148674907	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:148674907A>T	ENST00000241416.7	+	6	1364	c.728A>T	c.(727-729)cAt>cTt	p.H243L	ACVR2A_ENST00000404590.1_Missense_Mutation_p.H243L|ACVR2A_ENST00000535787.1_Missense_Mutation_p.H135L	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	243	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GGAATGAAGCATGAGAACATA	0.383																																					p.H243L		Atlas-SNP	.											.	ACVR2A	125	.	0			c.A728T						.						110.0	91.0	98.0					2																	148674907		2203	4300	6503	SO:0001583	missense	92	exon6			TGAAGCATGAGAA		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.728A>T	chr2.hg19:g.148674907A>T	ENSP00000241416:p.His243Leu	244.0	0.0		125.0	91.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	A	32	5.137092	0.94517	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	T;T;T	0.78481	-1.18;-1.18;-1.18	5.68	5.68	0.88126	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92678	0.7673	H	0.97783	4.075	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95288	0.8392	10	0.87932	D	0	.	15.9354	0.79698	1.0:0.0:0.0:0.0	.	243	P27037	AVR2A_HUMAN	L	243;135;243	ENSP00000241416:H243L;ENSP00000439988:H135L;ENSP00000384338:H243L	ENSP00000241416:H243L	H	+	2	0	ACVR2A	148391377	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.313000	0.96297	2.182000	0.69389	0.533000	0.62120	CAT	.	.		0.383	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
PKP4	8502	hgsc.bcm.edu	37	2	159526240	159526240	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:159526240G>A	ENST00000389759.3	+	17	2849	c.2737G>A	c.(2737-2739)Gcc>Acc	p.A913T	AC005042.4_ENST00000342892.4_RNA|PKP4_ENST00000389757.3_Missense_Mutation_p.A913T	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	913					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						AGGCAAATACGCCATGCGAGA	0.507										HNSCC(62;0.18)																											p.A913T		Atlas-SNP	.											.	PKP4	133	.	0			c.G2737A						.						49.0	52.0	51.0					2																	159526240		2203	4300	6503	SO:0001583	missense	8502	exon17			AAATACGCCATGC	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.2737G>A	chr2.hg19:g.159526240G>A	ENSP00000374409:p.Ala913Thr	270.0	0.0		114.0	73.0	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.959642	0.92791	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.51071	0.72;0.72	5.82	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.052613	0.85682	D	0.000000	T	0.67646	0.2915	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.985;1.0;1.0	P;D;D	0.91635	0.806;0.999;0.983	T	0.72067	-0.4402	10	0.87932	D	0	-12.3708	16.2419	0.82418	0.0:0.0:0.8661:0.1339	.	868;913;913	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	T	913	ENSP00000374407:A913T;ENSP00000374409:A913T	ENSP00000374407:A913T	A	+	1	0	PKP4	159234486	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	9.756000	0.98918	1.450000	0.47717	0.650000	0.86243	GCC	.	.		0.507	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
COBLL1	22837	hgsc.bcm.edu	37	2	165556006	165556006	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:165556006T>G	ENST00000392717.2	-	12	1699	c.1695A>C	c.(1693-1695)gaA>gaC	p.E565D	COBLL1_ENST00000491126.2_5'Flank|COBLL1_ENST00000342193.4_Missense_Mutation_p.E527D|COBLL1_ENST00000194871.6_Missense_Mutation_p.E593D|COBLL1_ENST00000375458.2_Missense_Mutation_p.E488D|COBLL1_ENST00000409184.3_Missense_Mutation_p.E526D			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	565						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						CACTGTGTGGTTCTCTGGAAG	0.388																																					p.E527D		Atlas-SNP	.											.	COBLL1	122	.	0			c.A1581C						.						174.0	165.0	168.0					2																	165556006		2203	4298	6501	SO:0001583	missense	22837	exon11			GTGTGGTTCTCTG	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1695A>C	chr2.hg19:g.165556006T>G	ENSP00000376478:p.Glu565Asp	75.0	0.0		39.0	34.0	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.120	1.008719	0.19199	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	4.83	-1.74	0.08056	.	1.239710	0.05541	N	0.565694	T	0.20210	0.0486	N	0.08118	0	0.09310	N	1	P;B;B	0.34815	0.47;0.41;0.43	B;B;B	0.38296	0.139;0.071;0.27	T	0.23904	-1.0175	9	0.16896	T	0.51	-0.1507	8.9301	0.35666	0.0:0.419:0.0:0.581	.	565;593;526	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	D	488;527;526;565;593	.	ENSP00000194871:E593D	E	-	3	2	COBLL1	165264252	0.000000	0.05858	0.001000	0.08648	0.061000	0.15899	-0.120000	0.10660	-0.513000	0.06496	-0.250000	0.11733	GAA	.	.		0.388	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
TTC21B	79809	hgsc.bcm.edu	37	2	166747435	166747435	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:166747435A>G	ENST00000243344.7	-	23	3151	c.3014T>C	c.(3013-3015)gTc>gCc	p.V1005A	TTC21B_ENST00000536175.1_5'Flank	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	1005					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						AAATCTTGGGACATCCTCGAG	0.343																																					p.V1005A		Atlas-SNP	.											.	TTC21B	130	.	0			c.T3014C						.						63.0	68.0	66.0					2																	166747435		2203	4300	6503	SO:0001583	missense	79809	exon23			CTTGGGACATCCT	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.3014T>C	chr2.hg19:g.166747435A>G	ENSP00000243344:p.Val1005Ala	250.0	0.0		142.0	6.0	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	hg19	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.240432	0.22711	.	.	ENSG00000123607	ENST00000243344	T	0.24350	1.86	5.57	5.57	0.84162	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.168969	0.51477	D	0.000088	T	0.13157	0.0319	N	0.11106	0.095	0.80722	D	1	B	0.15141	0.012	B	0.09377	0.004	T	0.07693	-1.0759	10	0.02654	T	1	-25.0127	15.7265	0.77763	1.0:0.0:0.0:0.0	.	1005	Q7Z4L5	TT21B_HUMAN	A	1005	ENSP00000243344:V1005A	ENSP00000243344:V1005A	V	-	2	0	TTC21B	166455681	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.423000	0.66458	2.106000	0.64143	0.445000	0.29226	GTC	.	.		0.343	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
SCN1A	6323	hgsc.bcm.edu	37	2	166850833	166850833	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:166850833T>G	ENST00000303395.4	-	25	4674	c.4675A>C	c.(4675-4677)Atg>Ctg	p.M1559L	SCN1A_ENST00000375405.3_Missense_Mutation_p.M1548L|SCN1A_ENST00000423058.2_Missense_Mutation_p.M1559L|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.M1531L|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1559			Missing (in EIEE6). {ECO:0000269|PubMed:14738421}.		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)	GTTTCCACCATCATTGTGACC	0.383																																					p.M1559L		Atlas-SNP	.											.	SCN1A	641	.	0			c.A4675C						.						145.0	120.0	128.0					2																	166850833		2203	4300	6503	SO:0001583	missense	6323	exon25			CCACCATCATTGT	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.4675A>C	chr2.hg19:g.166850833T>G	ENSP00000303540:p.Met1559Leu	225.0	0.0		125.0	12.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.915134	0.92178	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97303	-4.33;-4.33;-4.33;-4.33	5.9	5.9	0.94986	.	0.047303	0.85682	D	0.000000	D	0.98931	0.9637	H	0.95365	3.66	0.58432	D	0.999999	D	0.58268	0.982	D	0.72338	0.977	D	0.99486	1.0949	10	0.66056	D	0.02	.	16.3322	0.83039	0.0:0.0:0.0:1.0	.	1548	P35498-2	.	L	1559;1559;1548;1531	ENSP00000407030:M1559L;ENSP00000303540:M1559L;ENSP00000364554:M1548L;ENSP00000386312:M1531L	ENSP00000303540:M1559L	M	-	1	0	SCN1A	166559079	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.907000	0.87430	2.251000	0.74343	0.528000	0.53228	ATG	.	.		0.383	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
SCN1A	6323	hgsc.bcm.edu	37	2	166850895	166850895	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:166850895A>G	ENST00000303395.4	-	25	4612	c.4613T>C	c.(4612-4614)gTa>gCa	p.V1538A	SCN1A_ENST00000375405.3_Missense_Mutation_p.V1527A|SCN1A_ENST00000423058.2_Missense_Mutation_p.V1538A|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.V1510A|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1538					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)	TTGTCTGGTTACGAAGTCAAA	0.358																																					p.V1538A		Atlas-SNP	.											.	SCN1A	641	.	0			c.T4613C						.						111.0	100.0	104.0					2																	166850895		2203	4300	6503	SO:0001583	missense	6323	exon25			CTGGTTACGAAGT	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.4613T>C	chr2.hg19:g.166850895A>G	ENSP00000303540:p.Val1538Ala	190.0	0.0		93.0	34.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182172	0.57800	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97279	-4.32;-4.32;-4.27;-4.25	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000002	D	0.96981	0.9014	M	0.77486	2.375	0.38301	D	0.942982	P	0.39181	0.663	B	0.42692	0.395	D	0.98718	1.0707	10	0.59425	D	0.04	.	16.0863	0.81056	1.0:0.0:0.0:0.0	.	1527	P35498-2	.	A	1538;1538;1527;1510	ENSP00000407030:V1538A;ENSP00000303540:V1538A;ENSP00000364554:V1527A;ENSP00000386312:V1510A	ENSP00000303540:V1538A	V	-	2	0	SCN1A	166559141	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.710000	0.68392	2.197000	0.70478	0.454000	0.30748	GTA	.	.		0.358	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
XIRP2	129446	hgsc.bcm.edu	37	2	168103817	168103817	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:168103817A>G	ENST00000409195.1	+	9	6004	c.5915A>G	c.(5914-5916)aAc>aGc	p.N1972S	XIRP2_ENST00000295237.9_Missense_Mutation_p.N1972S|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.N1750S|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1797					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GTCCAGAGGAACAAAAATAGT	0.458																																					p.N1972S		Atlas-SNP	.											.	XIRP2	914	.	0			c.A5915G						.						42.0	41.0	41.0					2																	168103817		1913	4129	6042	SO:0001583	missense	129446	exon9			AGAGGAACAAAAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5915A>G	chr2.hg19:g.168103817A>G	ENSP00000386840:p.Asn1972Ser	245.0	0.0		167.0	67.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	2.136	-0.397954	0.04865	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02579	4.24;4.24;4.24	5.73	2.04	0.26737	.	0.562741	0.19002	N	0.125325	T	0.02156	0.0067	N	0.22421	0.69	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.0	B;B;B	0.10450	0.002;0.005;0.001	T	0.44742	-0.9308	10	0.37606	T	0.19	0.0057	6.1322	0.20211	0.7154:0.1378:0.1467:0.0	.	1797;1797;1750	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	1972;1972;1750	ENSP00000386840:N1972S;ENSP00000295237:N1972S;ENSP00000387255:N1750S	ENSP00000295237:N1972S	N	+	2	0	XIRP2	167812063	0.963000	0.33076	0.003000	0.11579	0.005000	0.04900	2.154000	0.42291	0.424000	0.26061	-0.274000	0.10170	AAC	.	.		0.458	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
FASTKD1	79675	hgsc.bcm.edu	37	2	170396679	170396679	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:170396679A>T	ENST00000453153.2	-	10	2173	c.1827T>A	c.(1825-1827)gaT>gaA	p.D609E	FASTKD1_ENST00000495505.1_5'Flank|FASTKD1_ENST00000453929.2_Missense_Mutation_p.D609E	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	609					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						ATATAAAAGGATCCAATATAC	0.289																																					p.D609E		Atlas-SNP	.											.	FASTKD1	86	.	0			c.T1827A						.						24.0	25.0	24.0					2																	170396679		2189	4273	6462	SO:0001583	missense	79675	exon10			AAAAGGATCCAAT	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1827T>A	chr2.hg19:g.170396679A>T	ENSP00000400513:p.Asp609Glu	532.0	2.0		342.0	243.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	hg19	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	A	6.793	0.515346	0.12944	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.40225	1.04;1.04	4.94	0.905	0.19307	FAST kinase leucine-rich (1);	0.145914	0.64402	N	0.000011	T	0.26557	0.0649	L	0.42632	1.34	0.49130	D	0.999751	B;B	0.23128	0.025;0.08	B;B	0.31337	0.05;0.128	T	0.05451	-1.0884	10	0.08179	T	0.78	-16.837	2.4517	0.04519	0.6038:0.1226:0.0889:0.1846	.	609;609	Q53R41-2;Q53R41	.;FAKD1_HUMAN	E	609	ENSP00000400513:D609E;ENSP00000403229:D609E	ENSP00000400513:D609E	D	-	3	2	FASTKD1	170104925	1.000000	0.71417	0.997000	0.53966	0.306000	0.27790	0.983000	0.29552	0.355000	0.24131	0.533000	0.62120	GAT	.	.		0.289	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
FASTKD1	79675	hgsc.bcm.edu	37	2	170403008	170403008	+	Missense_Mutation	SNP	G	G	A	rs540349050		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:170403008G>A	ENST00000453153.2	-	8	1767	c.1421C>T	c.(1420-1422)gCg>gTg	p.A474V	FASTKD1_ENST00000453929.2_Missense_Mutation_p.A474V	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	474					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						CAGTTGTTTCGCAGTCATATT	0.383													G|||	1	0.000199681	0.0	0.0	5008	,	,		19733	0.001		0.0	False		,,,				2504	0.0				p.A474V		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1421T						.						124.0	108.0	114.0					2																	170403008		2203	4300	6503	SO:0001583	missense	79675	exon8			TGTTTCGCAGTCA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1421C>T	chr2.hg19:g.170403008G>A	ENSP00000400513:p.Ala474Val	265.0	1.0		148.0	111.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	hg19	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	G	7.034	0.561239	0.13498	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.17854	2.25;2.25	4.57	-0.413	0.12363	.	0.445361	0.27591	N	0.018695	T	0.06416	0.0165	N	0.22421	0.69	0.09310	N	0.999998	P;P	0.41643	0.566;0.758	B;B	0.31101	0.124;0.058	T	0.34079	-0.9843	10	0.29301	T	0.29	-0.5854	3.6131	0.08067	0.2361:0.4323:0.2342:0.0973	.	474;474	Q53R41-2;Q53R41	.;FAKD1_HUMAN	V	474	ENSP00000400513:A474V;ENSP00000403229:A474V	ENSP00000400513:A474V	A	-	2	0	FASTKD1	170111254	0.014000	0.17966	0.323000	0.25347	0.068000	0.16541	1.393000	0.34497	0.016000	0.14998	-1.826000	0.00596	GCG	.	.		0.383	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
KIAA1715	80856	hgsc.bcm.edu	37	2	176802232	176802232	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:176802232A>G	ENST00000272748.4	-	12	1141	c.894T>C	c.(892-894)tgT>tgC	p.C298C	KIAA1715_ENST00000535310.1_Silent_p.C223C|KIAA1715_ENST00000544803.1_Silent_p.C329C	NM_030650.1	NP_085153.1	Q9C0E8	LNP_HUMAN	KIAA1715	298					blood coagulation (GO:0007596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|limb development (GO:0060173)|regulation of chondrocyte differentiation (GO:0032330)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)	20			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			AACAGTAGGCACATCGAAAAG	0.388																																					p.C298C		Atlas-SNP	.											.	KIAA1715	61	.	0			c.T894C						.						38.0	38.0	38.0					2																	176802232		2203	4299	6502	SO:0001819	synonymous_variant	80856	exon12			GTAGGCACATCGA	AB051502	CCDS33332.1	2q31	2014-06-27			ENSG00000144320	ENSG00000144320			21610	protein-coding gene	gene with protein product	"""lunapark"", ""limb and neural patterns"""	610236				11214970, 22729086	Standard	NM_030650		Approved	ulnaless, Ul, LNP1, LNP	uc002ukc.1	Q9C0E8	OTTHUMG00000154112	ENST00000272748.4:c.894T>C	chr2.hg19:g.176802232A>G		97.0	0.0		56.0	5.0	NM_030650	B7ZLA8|Q2M2V8|Q2YD99|Q658W8|Q8N5V9|Q96MS5	Silent	SNP	ENST00000272748.4	hg19	CCDS33332.1																																																																																			.	.		0.388	KIAA1715-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333949.3	XM_042834	
TTN	7273	hgsc.bcm.edu	37	2	179411087	179411087	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:179411087A>T	ENST00000591111.1	-	292	90272	c.90048T>A	c.(90046-90048)gaT>gaA	p.D30016E	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D29089E|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D22592E|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D22784E|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D31657E|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D22717E|TTN-AS1_ENST00000590040.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30016	Ig-like 136.				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)			TTTCACAGAGATCTAGCTCCT	0.438																																					p.D31657E		Atlas-SNP	.											.	TTN	18412	.	0			c.T94971A						.						142.0	140.0	140.0					2																	179411087		1954	4150	6104	SO:0001583	missense	7273	exon342			ACAGAGATCTAGC	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.90048T>A	chr2.hg19:g.179411087A>T	ENSP00000465570:p.Asp30016Glu	74.0	0.0		39.0	27.0	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		.	.	.	.	.	.	.	.	.	.	A	15.52	2.856810	0.51376	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.81	-2.51	0.06365	Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.34745	0.0908	N	0.11560	0.145	0.80722	D	1	B;B;B;B	0.12630	0.006;0.006;0.006;0.006	B;B;B;B	0.15484	0.013;0.013;0.013;0.013	T	0.04723	-1.0931	9	0.87932	D	0	.	3.4064	0.07343	0.346:0.1985:0.359:0.0965	.	22592;22717;22784;30016	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	29089;22592;22784;22717;22589	ENSP00000343764:D29089E;ENSP00000434586:D22592E;ENSP00000340554:D22784E;ENSP00000352154:D22717E	ENSP00000340554:D22784E	D	-	3	2	TTN	179119333	0.581000	0.26741	0.618000	0.29105	0.921000	0.55340	-0.067000	0.11579	-0.362000	0.08113	-0.290000	0.09829	GAT	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ITGA4	3676	hgsc.bcm.edu	37	2	182399041	182399041	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:182399041T>C	ENST00000397033.2	+	26	3257	c.2827T>C	c.(2827-2829)Ttt>Ctt	p.F943L		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	943					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	AGCAACAGGTTTTCCAGAGCC	0.338																																					p.F943L		Atlas-SNP	.											.	ITGA4	142	.	0			c.T2827C						.						76.0	69.0	71.0					2																	182399041		1835	4094	5929	SO:0001583	missense	3676	exon26			ACAGGTTTTCCAG		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2827T>C	chr2.hg19:g.182399041T>C	ENSP00000380227:p.Phe943Leu	537.0	2.0		283.0	191.0	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	hg19	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	T	9.786	1.176685	0.21704	.	.	ENSG00000115232	ENST00000397033	T	0.42513	0.97	5.96	4.74	0.60224	.	0.516425	0.22981	N	0.053303	T	0.25644	0.0624	N	0.14661	0.345	0.32806	D	0.500731	B	0.06786	0.001	B	0.04013	0.001	T	0.22800	-1.0206	10	0.28530	T	0.3	.	11.6696	0.51393	0.0:0.0:0.1476:0.8523	.	943	P13612	ITA4_HUMAN	L	943	ENSP00000380227:F943L	ENSP00000380227:F943L	F	+	1	0	ITGA4	182107286	0.998000	0.40836	1.000000	0.80357	0.320000	0.28249	3.266000	0.51569	2.279000	0.76181	0.533000	0.62120	TTT	.	.		0.338	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
FAM171B	165215	hgsc.bcm.edu	37	2	187626496	187626496	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:187626496A>G	ENST00000304698.5	+	8	1630	c.1427A>G	c.(1426-1428)aAt>aGt	p.N476S		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	476						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						AATCAAAATAATTACTCAAGA	0.353																																					p.N476S		Atlas-SNP	.											.	FAM171B	146	.	0			c.A1427G						.						48.0	52.0	50.0					2																	187626496		2201	4299	6500	SO:0001583	missense	165215	exon8			AAAATAATTACTC	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1427A>G	chr2.hg19:g.187626496A>G	ENSP00000304108:p.Asn476Ser	126.0	0.0		122.0	10.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	2.286	-0.363666	0.05103	.	.	ENSG00000144369	ENST00000304698	T	0.29655	1.56	5.7	0.0857	0.14443	.	0.638975	0.17586	N	0.168938	T	0.08758	0.0217	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33675	-0.9859	10	0.14252	T	0.57	-11.4546	5.0192	0.14352	0.4206:0.2829:0.2965:0.0	.	476;477	Q6P995;A8K122	F171B_HUMAN;.	S	476	ENSP00000304108:N476S	ENSP00000304108:N476S	N	+	2	0	FAM171B	187334741	0.939000	0.31865	0.983000	0.44433	0.973000	0.67179	0.509000	0.22707	0.087000	0.17167	0.533000	0.62120	AAT	.	.		0.353	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
SLC40A1	30061	hgsc.bcm.edu	37	2	190426694	190426694	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:190426694G>A	ENST00000261024.2	-	8	2052	c.1626C>T	c.(1624-1626)gcC>gcT	p.A542A		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	542					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)			GAGTATTTTGGGCAAATCGGA	0.418																																					p.A542A		Atlas-SNP	.											.	SLC40A1	51	.	0			c.C1626T						.						80.0	76.0	78.0					2																	190426694		2203	4300	6503	SO:0001819	synonymous_variant	30061	exon8			ATTTTGGGCAAAT	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.1626C>T	chr2.hg19:g.190426694G>A		224.0	0.0		248.0	100.0	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Silent	SNP	ENST00000261024.2	hg19	CCDS2299.1																																																																																			.	.		0.418	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2		
ANKAR	150709	hgsc.bcm.edu	37	2	190585420	190585420	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:190585420C>T	ENST00000520309.1	+	12	2630	c.2542C>T	c.(2542-2544)Cgg>Tgg	p.R848W	ANKAR_ENST00000281412.6_Missense_Mutation_p.R612W|ANKAR_ENST00000438402.2_Missense_Mutation_p.R848W|ANKAR_ENST00000431575.2_Missense_Mutation_p.R777W|ANKAR_ENST00000313581.4_Missense_Mutation_p.R848W	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	848						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			GAACTGTATACGGGTATTGTG	0.323																																					p.R848W		Atlas-SNP	.											.	ANKAR	184	.	0			c.C2542T						.						171.0	192.0	185.0					2																	190585420		2203	4300	6503	SO:0001583	missense	150709	exon12			TGTATACGGGTAT	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"""Ankyrin repeat domain containing"", ""Armadillo repeat containing"""	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.2542C>T	chr2.hg19:g.190585420C>T	ENSP00000427882:p.Arg848Trp	121.0	0.0		113.0	5.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	hg19	CCDS33351.2	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467624	0.43839	.	.	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.84	3.92	0.45320	.	0.091025	0.41396	D	0.000896	T	0.42607	0.1210	M	0.64997	1.995	0.32027	N	0.600043	.	.	.	.	.	.	T	0.54497	-0.8285	8	0.72032	D	0.01	-8.4049	11.6577	0.51328	0.3035:0.6965:0.0:0.0	.	.	.	.	W	848;848;848;777;612	ENSP00000427882:R848W;ENSP00000313513:R848W;ENSP00000397243:R848W;ENSP00000393043:R777W;ENSP00000281412:R612W	ENSP00000281412:R612W	R	+	1	2	ANKAR	190293665	0.950000	0.32346	0.060000	0.19600	0.215000	0.24574	0.857000	0.27831	2.539000	0.85634	0.655000	0.94253	CGG	.	.		0.323	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708	
C2orf88	84281	hgsc.bcm.edu	37	2	191064799	191064799	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:191064799T>C	ENST00000340623.4	+	2	624	c.213T>C	c.(211-213)tgT>tgC	p.C71C	C2orf88_ENST00000409870.1_Silent_p.C71C|C2orf88_ENST00000443551.2_Silent_p.C71C|C2orf88_ENST00000396974.2_Silent_p.C71C	NM_001042519.1|NM_001042520.1|NM_001042521.1|NM_032321.2	NP_001035984.1|NP_001035985.1|NP_001035986.1|NP_115697.2	Q9BSF0	SMAKA_HUMAN	chromosome 2 open reading frame 88	71	PKA-RI-binding.					plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(1)	3						ATATCTTGTGTGATGCCTTGC	0.468																																					p.C71C		Atlas-SNP	.											.	C2orf88	7	.	0			c.T213C						.						195.0	192.0	193.0					2																	191064799		2019	4184	6203	SO:0001819	synonymous_variant	84281	exon2			CTTGTGTGATGCC	BC005083	CCDS42792.1	2q32.2	2014-02-12	2009-04-08		ENSG00000187699	ENSG00000187699			28191	protein-coding gene	gene with protein product	"""small membrane AKAP"""	615117				23996002	Standard	NM_032321		Approved	MGC13057, smAKAP	uc002urt.3	Q9BSF0	OTTHUMG00000154361	ENST00000340623.4:c.213T>C	chr2.hg19:g.191064799T>C		114.0	0.0		111.0	42.0	NM_001042519	D3DPI3|P0C876|Q53TC7	Silent	SNP	ENST00000340623.4	hg19	CCDS42792.1																																																																																			.	.		0.468	C2orf88-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334954.1	NM_032321	
NAB1	4664	hgsc.bcm.edu	37	2	191524471	191524471	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:191524471C>T	ENST00000337386.5	+	4	1030	c.569C>T	c.(568-570)gCg>gTg	p.A190V	NAB1_ENST00000357215.5_Missense_Mutation_p.A190V|NAB1_ENST00000409581.1_Missense_Mutation_p.A190V|NAB1_ENST00000409641.1_Missense_Mutation_p.A190V|NAB1_ENST00000545490.1_5'Flank	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	190					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)			AGCAGTGAGGCGCTGGATGCT	0.602																																					p.A190V		Atlas-SNP	.											.	NAB1	31	.	0			c.C569T						.						31.0	33.0	32.0					2																	191524471		2203	4300	6503	SO:0001583	missense	4664	exon4			GTGAGGCGCTGGA		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.569C>T	chr2.hg19:g.191524471C>T	ENSP00000336894:p.Ala190Val	211.0	0.0		243.0	93.0	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	hg19	CCDS2307.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088721	0.36855	.	.	ENSG00000138386	ENST00000409581;ENST00000337386;ENST00000357215;ENST00000409641	.	.	.	5.51	3.68	0.42216	NAB co-repressor, domain (1);	0.256387	0.45606	N	0.000346	T	0.31327	0.0793	N	0.16368	0.405	0.80722	D	1	B;B;B	0.29716	0.255;0.039;0.039	B;B;B	0.19946	0.027;0.012;0.012	T	0.06588	-1.0818	9	0.21540	T	0.41	-6.8587	10.6712	0.45760	0.0:0.8419:0.0:0.1581	.	190;190;190	F8W8J7;B8ZZS2;Q13506	.;.;NAB1_HUMAN	V	190	.	ENSP00000336894:A190V	A	+	2	0	NAB1	191232716	0.999000	0.42202	0.912000	0.35992	0.986000	0.74619	3.711000	0.54868	0.847000	0.35167	0.561000	0.74099	GCG	.	.		0.602	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966	
GTF3C3	9330	hgsc.bcm.edu	37	2	197653948	197653948	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:197653948C>T	ENST00000263956.3	-	6	962	c.873G>A	c.(871-873)caG>caA	p.Q291Q	GTF3C3_ENST00000470386.1_5'UTR|GTF3C3_ENST00000409364.3_Silent_p.Q291Q	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	291					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)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTCTAGCCAGCTGCATAAAAC	0.378																																					p.Q291Q		Atlas-SNP	.											.	GTF3C3	96	.	0			c.G873A						.						113.0	105.0	108.0					2																	197653948		2203	4300	6503	SO:0001819	synonymous_variant	9330	exon6			AGCCAGCTGCATA	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"""General transcription factors"", ""Tetratricopeptide (TTC) repeat domain containing"""	4666	protein-coding gene	gene with protein product		604888	"""general transcription factor IIIC, polypeptide 3 (102kD)"""			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.873G>A	chr2.hg19:g.197653948C>T		158.0	0.0		139.0	49.0	NM_001206774	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Silent	SNP	ENST00000263956.3	hg19	CCDS2316.1																																																																																			.	.		0.378	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1		
KCTD18	130535	hgsc.bcm.edu	37	2	201355178	201355178	+	Missense_Mutation	SNP	G	G	A	rs543025211		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:201355178G>A	ENST00000359878.3	-	7	1436	c.926C>T	c.(925-927)gCg>gTg	p.A309V	KCTD18_ENST00000409157.1_Missense_Mutation_p.A309V|KCTD18_ENST00000468413.1_5'Flank	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	309					protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GTTTGCTGTCGCCCCAGCCGA	0.592													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17936	0.0		0.0	False		,,,				2504	0.0				p.A309V		Atlas-SNP	.											.	KCTD18	44	.	0			c.C926T						.						39.0	43.0	42.0					2																	201355178		2203	4300	6503	SO:0001583	missense	130535	exon7			GCTGTCGCCCCAG	AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 18"""				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.926C>T	chr2.hg19:g.201355178G>A	ENSP00000352941:p.Ala309Val	72.0	0.0		50.0	27.0	NM_152387	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	hg19	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	G	0.780	-0.762574	0.02996	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.34275	1.37;1.37	4.14	-3.75	0.04372	.	1.124140	0.06730	N	0.776490	T	0.13927	0.0337	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26677	-1.0096	10	0.02654	T	1	-0.034	2.4717	0.04566	0.5529:0.1392:0.1681:0.1398	.	309	Q6PI47	KCD18_HUMAN	V	309	ENSP00000352941:A309V;ENSP00000386751:A309V	ENSP00000352941:A309V	A	-	2	0	KCTD18	201063423	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.303000	0.08210	-0.883000	0.03982	-1.619000	0.00793	GCG	.	.		0.592	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387	
CARF	79800	hgsc.bcm.edu	37	2	203846349	203846349	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:203846349C>T	ENST00000402905.3	+	14	1951	c.1630C>T	c.(1630-1632)Cca>Tca	p.P544S	WDR12_ENST00000477723.1_Intron|CARF_ENST00000545253.1_Missense_Mutation_p.P456S|CARF_ENST00000545262.1_Missense_Mutation_p.P468S|CARF_ENST00000438828.2_Missense_Mutation_p.P544S|CARF_ENST00000414439.1_Missense_Mutation_p.P442S|CARF_ENST00000428585.1_Missense_Mutation_p.P468S|CARF_ENST00000320443.8_Missense_Mutation_p.P544S	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	544					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GTCTCCTGAGCCAACCCACTT	0.378																																					p.P544S		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.C1630T						.						100.0	98.0	99.0					2																	203846349		1834	4079	5913	SO:0001583	missense	79800	exon15			CCTGAGCCAACCC	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"""calcium-response factor"""	607586	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"""	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1630C>T	chr2.hg19:g.203846349C>T	ENSP00000384006:p.Pro544Ser	703.0	2.0		603.0	222.0	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	hg19	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.161441	0.38119	.	.	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.7	2.64	0.31445	.	0.385237	0.25701	N	0.028870	T	0.34600	0.0903	L	0.44542	1.39	0.29329	N	0.866849	B;B;B	0.12630	0.006;0.002;0.006	B;B;B	0.12156	0.007;0.005;0.007	T	0.26395	-1.0104	9	0.51188	T	0.08	-5.3304	4.7953	0.13269	0.3186:0.4957:0.0:0.1857	.	456;468;544	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	S	544;442;468;456;468;544;544	.	ENSP00000316224:P544S	P	+	1	0	ALS2CR8	203554594	0.968000	0.33430	0.565000	0.28409	0.921000	0.55340	0.947000	0.29082	0.756000	0.33013	0.313000	0.20887	CCA	.	.		0.378	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586	
ABI2	10152	hgsc.bcm.edu	37	2	204281668	204281668	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:204281668A>G	ENST00000422511.2	+	10	1162	c.1131A>G	c.(1129-1131)gaA>gaG	p.E377E	ABI2_ENST00000424558.1_Silent_p.E404E|ABI2_ENST00000261018.7_Silent_p.E196E|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000261017.5_Silent_p.E372E|ABI2_ENST00000430418.1_Silent_p.E355E|ABI2_ENST00000261016.6_Silent_p.E298E|ABI2_ENST00000295851.5_Silent_p.E410E|RAPH1_ENST00000457812.1_Intron			Q9NYB9	ABI2_HUMAN	abl-interactor 2	410	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						CTGTGGAAGAACCAGTCTTTG	0.463																																					p.E372E		Atlas-SNP	.											.	ABI2	44	.	0			c.A1116G						.						115.0	109.0	111.0					2																	204281668		2203	4300	6503	SO:0001819	synonymous_variant	10152	exon9			GGAAGAACCAGTC	AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1131A>G	chr2.hg19:g.204281668A>G		69.0	0.0		78.0	23.0	NM_005759	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Silent	SNP	ENST00000422511.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.15	1.269860	0.23221	.	.	ENSG00000138443	ENST00000454023	.	.	.	6.03	-0.969	0.10310	.	.	.	.	.	T	0.63977	0.2557	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61113	-0.7128	4	.	.	.	-4.0586	13.0833	0.59125	0.3874:0.0:0.6126:0.0	.	.	.	.	S	190	.	.	N	+	2	0	ABI2	203989913	0.999000	0.42202	0.995000	0.50966	0.982000	0.71751	1.695000	0.37763	-0.138000	0.11434	-0.290000	0.09829	AAC	.	.		0.463	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759	
ZDBF2	57683	hgsc.bcm.edu	37	2	207171520	207171520	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:207171520G>A	ENST00000374423.3	+	5	2654	c.2268G>A	c.(2266-2268)ccG>ccA	p.P756P		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	756							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ATTCTGACCCGCCTCTTCTGT	0.418																																					p.P756P		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G2268A						.						185.0	188.0	187.0					2																	207171520		1899	4092	5991	SO:0001819	synonymous_variant	57683	exon5			TGACCCGCCTCTT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.2268G>A	chr2.hg19:g.207171520G>A		74.0	0.0		73.0	26.0	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.418	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
PLEKHM3	389072	hgsc.bcm.edu	37	2	208725985	208725985	+	Splice_Site	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:208725985A>G	ENST00000427836.2	-	7	2441	c.1952T>C	c.(1951-1953)gTa>gCa	p.V651A	PLEKHM3_ENST00000389247.4_Splice_Site_p.V651A	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	651					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TCCCTCTATTACCTGCAGAAA	0.448																																					p.V651A		Atlas-SNP	.											.	PLEKHM3	101	.	0			c.T1952C						.						79.0	75.0	77.0					2																	208725985		1914	4139	6053	SO:0001630	splice_region_variant	389072	exon7			TCTATTACCTGCA	AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"""Pleckstrin homology (PH) domain containing"""	34006	protein-coding gene	gene with protein product	"""differentiation associated protein"""		"""pleckstrin homology domain containing, family M, member 1-like"""	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.1951-1T>C	chr2.hg19:g.208725985A>G		108.0	0.0		112.0	57.0	NM_001080475	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	hg19	CCDS42808.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.475136	0.84640	.	.	ENSG00000178385	ENST00000427836;ENST00000389247	D;D	0.87103	-2.18;-2.21	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.91962	0.7454	M	0.79805	2.47	0.80722	D	1	D	0.63880	0.993	P	0.57204	0.815	D	0.92903	0.6341	10	0.62326	D	0.03	.	15.3549	0.74421	1.0:0.0:0.0:0.0	.	651	Q6ZWE6	PKHM3_HUMAN	A	651	ENSP00000417003:V651A;ENSP00000373899:V651A	ENSP00000373899:V651A	V	-	2	0	PLEKHM3	208434230	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.087000	0.94110	2.265000	0.75225	0.533000	0.62120	GTA	.	.		0.448	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475	Missense_Mutation
CRYGC	1420	hgsc.bcm.edu	37	2	208992994	208992994	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:208992994C>T	ENST00000282141.3	-	3	495	c.458G>A	c.(457-459)cGg>cAg	p.R153Q		NM_020989.3	NP_066269.1	P07315	CRGC_HUMAN	crystallin, gamma C	153	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(1)|large_intestine(2)|lung(5)	9				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		GTCCTGGCACCGCCTGTACTC	0.567																																					p.R153Q		Atlas-SNP	.											.	CRYGC	28	.	0			c.G458A						.						62.0	69.0	67.0					2																	208992994		2203	4300	6503	SO:0001583	missense	1420	exon3			TGGCACCGCCTGT		CCDS2379.1	2q33.3	2013-02-14			ENSG00000163254	ENSG00000163254			2410	protein-coding gene	gene with protein product		123680		CRYG3			Standard	NM_020989		Approved		uc002vco.4	P07315	OTTHUMG00000132942	ENST00000282141.3:c.458G>A	chr2.hg19:g.208992994C>T	ENSP00000282141:p.Arg153Gln	128.0	0.0		139.0	45.0	NM_020989	Q53R50	Missense_Mutation	SNP	ENST00000282141.3	hg19	CCDS2379.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484512	0.44147	.	.	ENSG00000163254	ENST00000282141	T	0.75154	-0.91	4.98	1.12	0.20585	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.190513	0.43260	N	0.000585	T	0.72277	0.3440	M	0.80746	2.51	0.09310	N	1	B	0.30634	0.288	B	0.33295	0.161	T	0.66504	-0.5907	10	0.72032	D	0.01	.	8.0289	0.30453	0.0:0.6458:0.0:0.3542	.	153	P07315	CRGC_HUMAN	Q	153	ENSP00000282141:R153Q	ENSP00000282141:R153Q	R	-	2	0	CRYGC	208701239	0.000000	0.05858	0.244000	0.24202	0.972000	0.66771	0.427000	0.21379	0.245000	0.21373	0.557000	0.71058	CGG	.	.		0.567	CRYGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256474.1	NM_020989	
ABCA12	26154	hgsc.bcm.edu	37	2	215852484	215852484	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:215852484G>A	ENST00000272895.7	-	27	4082	c.3863C>T	c.(3862-3864)cCa>cTa	p.P1288L	ABCA12_ENST00000389661.4_Missense_Mutation_p.P970L	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1288					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)		AGGAAGAATTGGAAAATACCA	0.413																																					p.P1288L	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C3863T						.						55.0	50.0	52.0					2																	215852484		2203	4300	6503	SO:0001583	missense	26154	exon27			AGAATTGGAAAAT	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.3863C>T	chr2.hg19:g.215852484G>A	ENSP00000272895:p.Pro1288Leu	262.0	0.0		236.0	95.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.578037	0.65878	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	T;T	0.62941	-0.01;-0.01	5.26	5.26	0.73747	.	0.000000	0.64402	D	0.000004	T	0.61527	0.2354	L	0.52364	1.645	0.80722	D	1	B;B	0.33299	0.348;0.407	B;B	0.35727	0.08;0.209	T	0.62680	-0.6803	10	0.48119	T	0.1	.	18.8492	0.92220	0.0:0.0:1.0:0.0	.	1288;970	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	L	1288;970	ENSP00000272895:P1288L;ENSP00000374312:P970L	ENSP00000272895:P1288L	P	-	2	0	ABCA12	215560729	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	5.664000	0.68045	2.464000	0.83262	0.561000	0.74099	CCA	.	.		0.413	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
ATIC	471	hgsc.bcm.edu	37	2	216197219	216197219	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:216197219T>C	ENST00000236959.9	+	8	1129	c.803T>C	c.(802-804)gTc>gCc	p.V268A	ATIC_ENST00000435675.1_Missense_Mutation_p.V267A|ATIC_ENST00000540518.1_Missense_Mutation_p.V209A	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	268					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)		ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	TTCAAACATGTCAGCCCAGCA	0.428			T	ALK	ALCL																																p.V268A		Atlas-SNP	.		Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	.	ATIC	84	.	0			c.T803C						.						41.0	45.0	43.0					2																	216197219		2203	4300	6503	SO:0001583	missense	471	exon8			AACATGTCAGCCC		CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"""phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"""	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.803T>C	chr2.hg19:g.216197219T>C	ENSP00000236959:p.Val268Ala	88.0	0.0		65.0	22.0	NM_004044	A8K202|E9PBU3|Q13856|Q53S28	Missense_Mutation	SNP	ENST00000236959.9	hg19	CCDS2398.1	.	.	.	.	.	.	.	.	.	.	T	19.25	3.792392	0.70452	.	.	ENSG00000138363	ENST00000236959;ENST00000540518;ENST00000435675	T;T;T	0.76186	-1.0;-1.0;-1.0	5.94	4.78	0.61160	AICAR transformylase domain (1);Cytidine deaminase-like (1);	0.000000	0.85682	D	0.000000	D	0.83954	0.5366	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81581	-0.0867	10	0.21014	T	0.42	-7.778	11.8202	0.52235	0.0:0.0691:0.0:0.9309	.	267;268	E9PBU3;P31939	.;PUR9_HUMAN	A	268;209;267	ENSP00000236959:V268A;ENSP00000440523:V209A;ENSP00000415935:V267A	ENSP00000236959:V268A	V	+	2	0	ATIC	215905464	1.000000	0.71417	0.998000	0.56505	0.595000	0.36748	7.894000	0.87336	1.067000	0.40740	-0.297000	0.09499	GTC	.	.		0.428	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044	
FN1	2335	hgsc.bcm.edu	37	2	216259426	216259426	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:216259426T>A	ENST00000359671.1	-	24	3886	c.3621A>T	c.(3619-3621)agA>agT	p.R1207S	FN1_ENST00000432072.2_Missense_Mutation_p.R1207S|FN1_ENST00000357867.4_Missense_Mutation_p.R1207S|FN1_ENST00000354785.4_Missense_Mutation_p.R1207S|FN1_ENST00000323926.6_Missense_Mutation_p.R1207S|FN1_ENST00000356005.4_Missense_Mutation_p.R1207S|FN1_ENST00000443816.1_Missense_Mutation_p.R1207S|FN1_ENST00000346544.3_Missense_Mutation_p.R1207S|FN1_ENST00000446046.1_Missense_Mutation_p.R1207S|FN1_ENST00000357009.2_Missense_Mutation_p.R1207S|FN1_ENST00000336916.4_Missense_Mutation_p.R1207S|FN1_ENST00000345488.5_Missense_Mutation_p.R1207S|FN1_ENST00000421182.1_Missense_Mutation_p.R1207S			P02751	FINC_HUMAN	fibronectin 1	1207	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TTGTGGTAATTCTATAACCAG	0.448																																					p.R1207S		Atlas-SNP	.											.	FN1	521	.	0			c.A3621T						.						89.0	98.0	95.0					2																	216259426		2203	4300	6503	SO:0001583	missense	2335	exon24			GGTAATTCTATAA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3621A>T	chr2.hg19:g.216259426T>A	ENSP00000352696:p.Arg1207Ser	56.0	0.0		73.0	30.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.4	3.977855	0.74360	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000002	T	0.72423	0.3458	M	0.79926	2.475	0.58432	D	0.999999	D;P;D;D;D;D;D;D;D;P	0.89917	0.995;0.542;1.0;1.0;0.996;0.996;1.0;0.999;0.999;0.923	D;B;D;D;D;D;D;D;D;P	0.91635	0.991;0.279;0.998;0.999;0.958;0.973;0.999;0.996;0.996;0.79	T	0.75750	-0.3208	10	0.59425	D	0.04	.	12.1309	0.53942	0.1281:0.0:0.0:0.8719	.	1207;1207;1207;1207;1207;1207;1207;1207;1207;1207	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	S	1207	ENSP00000394423:R1207S;ENSP00000323534:R1207S;ENSP00000338200:R1207S;ENSP00000350534:R1207S;ENSP00000346839:R1207S;ENSP00000352696:R1207S;ENSP00000265312:R1207S;ENSP00000273049:R1207S;ENSP00000349509:R1207S;ENSP00000410422:R1207S;ENSP00000415018:R1207S;ENSP00000399538:R1207S;ENSP00000348285:R1207S	ENSP00000265313:R1207S	R	-	3	2	FN1	215967671	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.449000	0.44935	2.145000	0.66743	0.533000	0.62120	AGA	.	.		0.448	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
CATIP	375307	hgsc.bcm.edu	37	2	219222348	219222348	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:219222348G>A	ENST00000289388.3	+	3	239	c.210G>A	c.(208-210)gtG>gtA	p.V70V	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		70					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCATTGAGGTGCAGAGAGGGA	0.542																																					p.V70V		Atlas-SNP	.											.	C2orf62	28	.	0			c.G210A						.						61.0	54.0	56.0					2																	219222348		2203	4300	6503	SO:0001819	synonymous_variant	375307	exon3			TGAGGTGCAGAGA																												ENST00000289388.3:c.210G>A	chr2.hg19:g.219222348G>A		76.0	0.0		58.0	24.0	NM_198559		Silent	SNP	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.		0.542	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1		
STK36	27148	hgsc.bcm.edu	37	2	219563382	219563382	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:219563382C>T	ENST00000295709.3	+	26	3394	c.3115C>T	c.(3115-3117)Cgc>Tgc	p.R1039C	STK36_ENST00000440309.1_Missense_Mutation_p.R1039C|STK36_ENST00000392106.2_Missense_Mutation_p.R1018C|STK36_ENST00000392105.3_Missense_Mutation_p.R1018C	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CCTTCTCACACGCCTGGCCCT	0.537																																					p.R1039C		Atlas-SNP	.											.	STK36	111	.	0			c.C3115T						.						212.0	186.0	194.0					2																	219563382		2203	4300	6503	SO:0001583	missense	27148	exon26			CTCACACGCCTGG	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3115C>T	chr2.hg19:g.219563382C>T	ENSP00000295709:p.Arg1039Cys	108.0	0.0		119.0	49.0	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	hg19	CCDS2421.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960700	0.74016	.	.	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.75367	-0.93;-0.93;-0.17;-0.93	6.06	6.06	0.98353	.	0.691003	0.12632	N	0.452119	T	0.79764	0.4502	L	0.32530	0.975	0.58432	D	0.999993	D;D;D	0.76494	0.995;0.999;0.999	P;P;P	0.58077	0.661;0.832;0.802	T	0.79254	-0.1879	10	0.87932	D	0	-3.789	18.8014	0.92018	0.0:1.0:0.0:0.0	.	1018;1018;1039	A8MU99;Q9NRP7-2;Q9NRP7	.;.;STK36_HUMAN	C	1039;1018;1018;1039	ENSP00000295709:R1039C;ENSP00000375955:R1018C;ENSP00000375954:R1018C;ENSP00000394095:R1039C	ENSP00000295709:R1039C	R	+	1	0	STK36	219271626	0.999000	0.42202	0.927000	0.36925	0.349000	0.29174	5.327000	0.65881	2.882000	0.98803	0.655000	0.94253	CGC	.	.		0.537	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
CNPPD1	27013	hgsc.bcm.edu	37	2	220037323	220037323	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220037323G>A	ENST00000409789.1	-	9	1645	c.1218C>T	c.(1216-1218)ttC>ttT	p.F406F	SLC23A3_ENST00000409878.3_5'Flank|SLC23A3_ENST00000396775.3_5'Flank|CNPPD1_ENST00000360507.5_Silent_p.F406F|SLC23A3_ENST00000295738.7_5'Flank|SLC23A3_ENST00000455516.2_5'Flank			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	406					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						CTGGGAAAACGAAAGACTTGA	0.542																																					p.F406F		Atlas-SNP	.											.	CNPPD1	22	.	0			c.C1218T						.						112.0	113.0	113.0					2																	220037323		2203	4300	6503	SO:0001819	synonymous_variant	27013	exon8			GAAAACGAAAGAC	AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 24"""	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.1218C>T	chr2.hg19:g.220037323G>A		82.0	0.0		76.0	24.0	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Silent	SNP	ENST00000409789.1	hg19	CCDS2433.1																																																																																			.	.		0.542	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680	
ZFAND2B	130617	hgsc.bcm.edu	37	2	220073041	220073041	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220073041A>G	ENST00000289528.5	+	5	693	c.498A>G	c.(496-498)caA>caG	p.Q166Q	ZFAND2B_ENST00000444522.2_Silent_p.Q166Q|ZFAND2B_ENST00000409206.1_Silent_p.Q166Q|ZFAND2B_ENST00000409097.1_Silent_p.Q166Q|ZFAND2B_ENST00000409594.1_Silent_p.Q166Q|ZFAND2B_ENST00000409336.1_Silent_p.Q166Q|ZFAND2B_ENST00000409217.1_Silent_p.Q166Q	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	166						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCAAGTCAAACCATGCCTT	0.542																																					p.Q166Q		Atlas-SNP	.											.	ZFAND2B	28	.	0			c.A498G						.						111.0	88.0	96.0					2																	220073041		2203	4300	6503	SO:0001819	synonymous_variant	130617	exon5			AAGTCAAACCATG	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"""Zinc fingers, AN1-type domain containing"""	25206	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein-like"""	613474	"""zinc finger, AN1-type 2B"""			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.498A>G	chr2.hg19:g.220073041A>G		190.0	0.0		147.0	45.0	NM_138802	Q8NB98	Silent	SNP	ENST00000289528.5	hg19	CCDS2435.1																																																																																			.	.		0.542	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802	
TUBA4A	7277	hgsc.bcm.edu	37	2	220115838	220115838	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220115838G>T	ENST00000248437.4	-	4	756	c.583C>A	c.(583-585)Ctg>Atg	p.L195M	TUBA4A_ENST00000392088.2_Missense_Mutation_p.L180M|TUBA4A_ENST00000498660.1_5'UTR|TUBA4B_ENST00000490341.1_RNA	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	195					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	GAGTGCTCCAGGGTGGTGTGG	0.557																																					p.L195M		Atlas-SNP	.											.	TUBA4A	96	.	0			c.C583A						.						103.0	105.0	104.0					2																	220115838		2203	4300	6503	SO:0001583	missense	7277	exon4			GCTCCAGGGTGGT	AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"""Tubulins"""	12407	protein-coding gene	gene with protein product		191110	"""tubulin, alpha 1 (testis specific)"", ""tubulin, alpha 1"""	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.583C>A	chr2.hg19:g.220115838G>T	ENSP00000248437:p.Leu195Met	89.0	0.0		88.0	9.0	NM_006000	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	hg19	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.613424	0.46631	.	.	ENSG00000127824	ENST00000248437;ENST00000392088;ENST00000398989;ENST00000427737	T;T;T;T	0.70869	-0.48;-0.48;-0.48;-0.52	5.28	5.28	0.74379	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	D	0.000011	D	0.84822	0.5557	M	0.88906	2.99	0.80722	D	1	P	0.49559	0.925	P	0.61592	0.891	D	0.87145	0.2205	10	0.87932	D	0	.	14.3324	0.66566	0.0729:0.0:0.9271:0.0	.	195	P68366	TBA4A_HUMAN	M	195;180;42;180	ENSP00000248437:L195M;ENSP00000375938:L180M;ENSP00000396212:L42M;ENSP00000408194:L180M	ENSP00000248437:L195M	L	-	1	2	TUBA4A	219824082	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.374000	0.59543	2.755000	0.94549	0.655000	0.94253	CTG	.	.		0.557	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000	
OBSL1	23363	hgsc.bcm.edu	37	2	220427202	220427202	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:220427202C>T	ENST00000404537.1	-	8	2931	c.2875G>A	c.(2875-2877)Gct>Act	p.A959T	OBSL1_ENST00000373876.1_Missense_Mutation_p.A959T|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000603926.1_Missense_Mutation_p.A959T|OBSL1_ENST00000289656.3_Missense_Mutation_p.A546T|OBSL1_ENST00000265318.4_Missense_Mutation_p.A959T|OBSL1_ENST00000373873.4_Missense_Mutation_p.A959T	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	959	Ig-like 7.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		AGCTGGACAGCGGGCAGCACC	0.647																																					p.A959T		Atlas-SNP	.											.	OBSL1	120	.	0			c.G2875A						.						65.0	77.0	73.0					2																	220427202		2203	4300	6503	SO:0001583	missense	23363	exon8			GGACAGCGGGCAG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2875G>A	chr2.hg19:g.220427202C>T	ENSP00000385636:p.Ala959Thr	113.0	0.0		116.0	5.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	C	4.564	0.104704	0.08731	.	.	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000373873;ENST00000289656	T;T;T;T;T	0.04809	3.55;3.55;3.55;3.55;3.55	4.72	1.72	0.24424	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.05593	0.0147	L	0.35644	1.08	0.09310	N	1	P;P;P;B	0.38473	0.633;0.633;0.528;0.056	B;B;B;B	0.42522	0.39;0.39;0.145;0.027	T	0.40403	-0.9565	9	0.14252	T	0.57	.	10.5828	0.45265	0.5146:0.419:0.0:0.0664	.	960;959;546;959	A4KVA4;O75147;A8MSZ8;O75147-2	.;OBSL1_HUMAN;.;.	T	959;959;959;959;546	ENSP00000265318:A959T;ENSP00000385636:A959T;ENSP00000362983:A959T;ENSP00000362980:A959T;ENSP00000289656:A546T	ENSP00000265318:A959T	A	-	1	0	OBSL1	220135446	0.000000	0.05858	0.001000	0.08648	0.199000	0.23934	-0.249000	0.08842	-0.109000	0.12044	-0.808000	0.03180	GCT	.	.		0.647	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
TRIP12	9320	hgsc.bcm.edu	37	2	230652245	230652245	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:230652245A>G	ENST00000283943.5	-	32	4924	c.4746T>C	c.(4744-4746)gtT>gtC	p.V1582V	TRIP12_ENST00000389044.4_Silent_p.V1630V|TRIP12_ENST00000389045.3_Silent_p.V1312V	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1582					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ATCTAGGTGCAACTCTGCTAT	0.343																																					p.V1582V		Atlas-SNP	.											.	TRIP12	207	.	0			c.T4746C						.						145.0	143.0	144.0					2																	230652245		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon32			AGGTGCAACTCTG	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4746T>C	chr2.hg19:g.230652245A>G		131.0	0.0		167.0	71.0	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.		0.343	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	
NMUR1	10316	hgsc.bcm.edu	37	2	232393179	232393179	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:232393179C>T	ENST00000305141.4	-	2	686	c.553G>A	c.(553-555)Gtc>Atc	p.V185I		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	185					activation of phospholipase C activity (GO:0007202)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|chloride transport (GO:0006821)|G-protein coupled receptor signaling pathway (GO:0007186)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|smooth muscle contraction (GO:0006939)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuromedin U receptor activity (GO:0001607)|neuropeptide receptor activity (GO:0008188)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(12)|pancreas(1)|skin(1)	24		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		AGACCCCAGACGGCCCCAAGC	0.687																																					p.V185I		Atlas-SNP	.											NMUR1,NS,carcinoma,0,1	NMUR1	46	.	0			c.G553A						.						36.0	33.0	34.0					2																	232393179		2203	4298	6501	SO:0001583	missense	10316	exon2			CCCAGACGGCCCC	AF044600	CCDS2486.1	2q37.1	2012-08-08	2004-05-27	2004-05-28	ENSG00000171596	ENSG00000171596		"""GPCR / Class A : Neuromedin U receptors"""	4518	protein-coding gene	gene with protein product		604153	"""G protein-coupled receptor 66"""	GPR66		9782091	Standard	NM_006056		Approved	GPC-R, FM-3, NMU1R	uc002vry.4	Q9HB89	OTTHUMG00000133225	ENST00000305141.4:c.553G>A	chr2.hg19:g.232393179C>T	ENSP00000305877:p.Val185Ile	94.0	0.0		99.0	58.0	NM_006056	O43664|Q7LDP6|Q8NE20	Missense_Mutation	SNP	ENST00000305141.4	hg19	CCDS2486.1	.	.	.	.	.	.	.	.	.	.	.	0.019	-1.459859	0.01062	.	.	ENSG00000171596	ENST00000305141	T	0.73152	-0.72	5.08	-7.44	0.01379	GPCR, rhodopsin-like superfamily (1);	0.529642	0.20465	N	0.091804	T	0.36690	0.0976	N	0.12443	0.215	0.09310	N	0.999995	B	0.21147	0.052	B	0.23150	0.044	T	0.50659	-0.8802	10	0.02654	T	1	-17.9982	7.5504	0.27793	0.0:0.3762:0.3266:0.2971	.	185	Q9HB89	NMUR1_HUMAN	I	185	ENSP00000305877:V185I	ENSP00000305877:V185I	V	-	1	0	NMUR1	232101423	0.000000	0.05858	0.011000	0.14972	0.018000	0.09664	-0.300000	0.08243	-0.760000	0.04677	0.456000	0.33151	GTC	.	.		0.687	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056	
GIGYF2	26058	hgsc.bcm.edu	37	2	233612329	233612329	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:233612329C>T	ENST00000409547.1	+	6	357	c.46C>T	c.(46-48)Cga>Tga	p.R16*	GIGYF2_ENST00000409480.1_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000373566.3_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000409451.3_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000373563.4_Nonsense_Mutation_p.R16*|GIGYF2_ENST00000409196.3_Nonsense_Mutation_p.R16*	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	16					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		TTCTAGGCTCCGAGCTCTGTC	0.378																																					p.R16X		Atlas-SNP	.											.	GIGYF2	288	.	0			c.C46T						.						129.0	129.0	129.0					2																	233612329		2203	4300	6503	SO:0001587	stop_gained	26058	exon4			AGGCTCCGAGCTC	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.46C>T	chr2.hg19:g.233612329C>T	ENSP00000386537:p.Arg16*	82.0	0.0		95.0	4.0	NM_001103146	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Nonsense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	36	5.973652	0.97162	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000428883;ENST00000456491;ENST00000409480;ENST00000421433;ENST00000425040;ENST00000430720;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000429187;ENST00000440945	.	.	.	5.55	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.288	9.291	0.37786	0.1437:0.7835:0.0:0.0728	.	.	.	.	X	16	.	ENSP00000362664:R16X	R	+	1	2	GIGYF2	233320573	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.757000	0.62213	1.365000	0.46057	0.561000	0.74099	CGA	.	.		0.378	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
NEU2	4759	hgsc.bcm.edu	37	2	233899090	233899090	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:233899090A>G	ENST00000233840.3	+	2	466	c.466A>G	c.(466-468)Acc>Gcc	p.T156A		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	156					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	GGAGTGGTCCACCTTTGCAGT	0.657																																					p.T156A		Atlas-SNP	.											.	NEU2	42	.	0			c.A466G						.						46.0	51.0	49.0					2																	233899090		2203	4300	6503	SO:0001583	missense	4759	exon2			TGGTCCACCTTTG	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"""N-acetyl-alpha-neuraminidase 2"""	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.466A>G	chr2.hg19:g.233899090A>G	ENSP00000233840:p.Thr156Ala	69.0	0.0		60.0	6.0	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	hg19	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	A	19.10	3.761504	0.69763	.	.	ENSG00000115488	ENST00000233840	D	0.84873	-1.91	4.88	4.88	0.63580	Neuraminidase (2);	0.000000	0.64402	D	0.000005	D	0.90556	0.7040	M	0.89601	3.045	0.53005	D	0.999967	P	0.50369	0.934	P	0.54759	0.76	D	0.89720	0.3918	10	0.12103	T	0.63	-29.9195	13.6972	0.62587	1.0:0.0:0.0:0.0	.	156	Q9Y3R4	NEUR2_HUMAN	A	156	ENSP00000233840:T156A	ENSP00000233840:T156A	T	+	1	0	NEU2	233607334	1.000000	0.71417	0.999000	0.59377	0.202000	0.24057	9.035000	0.93752	1.821000	0.53095	0.459000	0.35465	ACC	.	.		0.657	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383	
HDAC4	9759	hgsc.bcm.edu	37	2	240029867	240029867	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:240029867T>C	ENST00000345617.3	-	15	2767	c.1976A>G	c.(1975-1977)gAc>gGc	p.D659G	HDAC4_ENST00000543185.1_Missense_Mutation_p.D243G|HDAC4_ENST00000541256.1_Missense_Mutation_p.D633G	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	659	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|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)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|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 transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CATCAGCGTGTCATACACGAG	0.692																																					p.D659G		Atlas-SNP	.											.	HDAC4	127	.	0			c.A1976G						.						22.0	21.0	21.0					2																	240029867		2192	4291	6483	SO:0001583	missense	9759	exon15			AGCGTGTCATACA	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1976A>G	chr2.hg19:g.240029867T>C	ENSP00000264606:p.Asp659Gly	208.0	0.0		158.0	57.0	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869275	0.72065	.	.	ENSG00000068024	ENST00000345617;ENST00000456922;ENST00000543185;ENST00000541256;ENST00000393621	T;T;T	0.78924	-0.91;-1.22;0.13	4.01	4.01	0.46588	Histone deacetylase domain (1);	0.000000	0.85682	D	0.000000	D	0.87390	0.6165	M	0.80616	2.505	0.80722	D	1	P;D;D;D;B;B	0.76494	0.549;0.998;0.999;0.998;0.262;0.134	B;D;D;D;B;B	0.79108	0.099;0.955;0.992;0.912;0.257;0.134	D	0.89202	0.3558	10	0.87932	D	0	.	13.2665	0.60137	0.0:0.0:0.0:1.0	.	659;542;633;633;627;659	B7Z8G5;F5H0Q9;F5H5W4;B7Z8I2;Q53SM2;P56524	.;.;.;.;.;HDAC4_HUMAN	G	659;547;243;633;542	ENSP00000264606:D659G;ENSP00000440481:D243G;ENSP00000443057:D633G	ENSP00000264606:D659G	D	-	2	0	HDAC4	239694804	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.623000	0.83113	1.598000	0.50083	0.460000	0.39030	GAC	.	.		0.692	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
HDLBP	3069	hgsc.bcm.edu	37	2	242174657	242174657	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:242174657A>G	ENST00000391975.1	-	23	3250	c.3023T>C	c.(3022-3024)gTc>gCc	p.V1008A	HDLBP_ENST00000427183.2_Missense_Mutation_p.V975A|HDLBP_ENST00000310931.4_Missense_Mutation_p.V1008A|HDLBP_ENST00000391976.2_Missense_Mutation_p.V1008A	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1008	KH 12. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		AGGTGCCGGGACATGTATGTT	0.582																																					p.V1008A		Atlas-SNP	.											.	HDLBP	118	.	0			c.T3023C						.						77.0	74.0	75.0					2																	242174657		2203	4300	6503	SO:0001583	missense	3069	exon23			GCCGGGACATGTA		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3023T>C	chr2.hg19:g.242174657A>G	ENSP00000375836:p.Val1008Ala	52.0	0.0		47.0	20.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.992974	0.74703	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.79	4.62	0.57501	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	M	0.86178	2.8	0.80722	D	1	D;D	0.64830	0.987;0.994	D;P	0.67231	0.95;0.9	T	0.69351	-0.5168	10	0.59425	D	0.04	-29.4794	12.215	0.54402	0.8721:0.0:0.0:0.1279	.	975;1008	E7EM71;Q00341	.;VIGLN_HUMAN	A	1008;1008;1008;975	ENSP00000375836:V1008A;ENSP00000375837:V1008A;ENSP00000312042:V1008A;ENSP00000399139:V975A	ENSP00000312042:V1008A	V	-	2	0	HDLBP	241823330	1.000000	0.71417	0.022000	0.16811	0.677000	0.39632	9.220000	0.95180	0.995000	0.38917	0.455000	0.32223	GTC	.	.		0.582	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
SSUH2	51066	hgsc.bcm.edu	37	3	8671370	8671370	+	Missense_Mutation	SNP	C	C	T	rs532787180		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:8671370C>T	ENST00000317371.4	-	14	1727	c.502G>A	c.(502-504)Ggc>Agc	p.G168S	SSUH2_ENST00000544814.1_Missense_Mutation_p.G190S|SSUH2_ENST00000415132.1_Missense_Mutation_p.G168S|SSUH2_ENST00000341795.3_Missense_Mutation_p.G168S			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	168	Cys-rich.					cytoplasm (GO:0005737)											CCGTGGCAGCCGCTGCACTTG	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		17694	0.0		0.001	False		,,,				2504	0.0				p.G190S		Atlas-SNP	.											.	.	.	.	0			c.G568A						.						82.0	86.0	85.0					3																	8671370		2203	4300	6503	SO:0001583	missense	51066	exon7			GGCAGCCGCTGCA	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.502G>A	chr3.hg19:g.8671370C>T	ENSP00000324551:p.Gly168Ser	86.0	0.0		59.0	23.0	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	hg19	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.176932	0.57692	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814	T;T;T;T	0.40756	1.02;1.02;1.02;1.04	4.75	2.91	0.33838	.	0.301641	0.37857	N	0.001909	T	0.41971	0.1182	L	0.46157	1.445	0.30122	N	0.805604	D;D	0.67145	0.996;0.99	P;P	0.56823	0.807;0.651	T	0.35549	-0.9784	10	0.12103	T	0.63	-25.2349	6.0251	0.19650	0.1849:0.7162:0.0:0.0989	.	190;168	F5H2S5;Q9Y2M2	.;CC032_HUMAN	S	168;168;168;190	ENSP00000339150:G168S;ENSP00000324551:G168S;ENSP00000410757:G168S;ENSP00000439378:G190S	ENSP00000324551:G168S	G	-	1	0	C3orf32	8646370	0.542000	0.26426	0.611000	0.29010	0.837000	0.47467	0.867000	0.27968	0.404000	0.25506	0.467000	0.42956	GGC	.	.		0.627	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	
TMEM40	55287	hgsc.bcm.edu	37	3	12790175	12790175	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:12790175A>G	ENST00000314124.7	-	3	546	c.190T>C	c.(190-192)Tct>Cct	p.S64P	TMEM40_ENST00000431022.2_Missense_Mutation_p.S80P|TMEM40_ENST00000435218.2_Missense_Mutation_p.S64P|TMEM40_ENST00000435575.1_Intron|TMEM40_ENST00000264728.8_Missense_Mutation_p.S64P	NM_001284406.1|NM_018306.2	NP_001271335.1|NP_060776.2	Q8WWA1	TMM40_HUMAN	transmembrane protein 40	64	Ser-rich.					integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(5)|urinary_tract(1)	10						gaggatgaagaagatgaggag	0.413																																					p.S64P		Atlas-SNP	.											.	TMEM40	22	.	0			c.T190C						.						156.0	149.0	151.0					3																	12790175		2203	4300	6503	SO:0001583	missense	55287	exon3			ATGAAGAAGATGA	BC020658	CCDS2613.1, CCDS68347.1, CCDS68348.1	3p25.2	2005-01-10			ENSG00000088726	ENSG00000088726			25620	protein-coding gene	gene with protein product						12477932	Standard	NM_018306		Approved	FLJ11036	uc003bxg.1	Q8WWA1	OTTHUMG00000129801	ENST00000314124.7:c.190T>C	chr3.hg19:g.12790175A>G	ENSP00000322837:p.Ser64Pro	27.0	0.0		32.0	18.0	NM_018306	C9JID5|Q8NAL4|Q9NUZ4	Missense_Mutation	SNP	ENST00000314124.7	hg19	CCDS2613.1	.	.	.	.	.	.	.	.	.	.	A	9.564	1.119136	0.20877	.	.	ENSG00000088726	ENST00000314124;ENST00000435218;ENST00000264728;ENST00000431022	.	.	.	3.29	3.29	0.37713	.	0.156430	0.30347	N	0.009840	T	0.48370	0.1496	L	0.31926	0.97	0.09310	N	1	D;B;D	0.76494	0.999;0.002;0.999	D;B;D	0.80764	0.994;0.004;0.994	T	0.20840	-1.0263	9	0.87932	D	0	.	8.3511	0.32303	1.0:0.0:0.0:0.0	.	80;64;64	B4DXI0;Q8WWA1-2;Q8WWA1	.;.;TMM40_HUMAN	P	64;64;64;80	.	ENSP00000264728:S64P	S	-	1	0	TMEM40	12765175	0.164000	0.22935	0.052000	0.19188	0.229000	0.25112	2.986000	0.49370	1.750000	0.51863	0.454000	0.30748	TCT	.	.		0.413	TMEM40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252029.2	NM_018306	
NUP210	23225	hgsc.bcm.edu	37	3	13368741	13368741	+	Missense_Mutation	SNP	C	C	T	rs199638243		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:13368741C>T	ENST00000254508.5	-	32	4565	c.4483G>A	c.(4483-4485)Gcc>Acc	p.A1495T		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1495					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)					AGAACAGTGGCCAGACAGAGC	0.627																																					p.A1495T		Atlas-SNP	.											.	NUP210	182	.	0			c.G4483A						.						34.0	37.0	36.0					3																	13368741		2202	4300	6502	SO:0001583	missense	23225	exon32			CAGTGGCCAGACA	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.4483G>A	chr3.hg19:g.13368741C>T	ENSP00000254508:p.Ala1495Thr	67.0	0.0		48.0	8.0	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.667449	0.29604	.	.	ENSG00000132182	ENST00000254508	T	0.04758	3.56	5.88	1.3	0.21679	.	0.747393	0.12860	N	0.433231	T	0.03520	0.0101	L	0.34521	1.04	0.09310	N	0.999999	B	0.09022	0.002	B	0.09377	0.004	T	0.43621	-0.9380	10	0.33141	T	0.24	.	2.5038	0.04640	0.4424:0.2249:0.0:0.3326	.	1495	Q8TEM1	PO210_HUMAN	T	1495	ENSP00000254508:A1495T	ENSP00000254508:A1495T	A	-	1	0	NUP210	13343741	0.000000	0.05858	0.448000	0.26945	0.601000	0.36947	-0.434000	0.06939	0.317000	0.23160	0.655000	0.94253	GCC	.	.		0.627	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
C3orf20	84077	hgsc.bcm.edu	37	3	14724484	14724484	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:14724484C>T	ENST00000253697.3	+	3	716	c.264C>T	c.(262-264)gtC>gtT	p.V88V	C3orf20_ENST00000435614.1_5'UTR|C3orf20_ENST00000412910.1_5'UTR	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	88						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						TTGTGCAGGTCCCCACACTGA	0.627																																					p.V88V		Atlas-SNP	.											.	C3orf20	109	.	0			c.C264T						.						60.0	55.0	56.0					3																	14724484		2203	4300	6503	SO:0001819	synonymous_variant	84077	exon3			GCAGGTCCCCACA	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.264C>T	chr3.hg19:g.14724484C>T		127.0	0.0		139.0	57.0	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	hg19	CCDS33706.1																																																																																			.	.		0.627	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
NR2C2	7182	hgsc.bcm.edu	37	3	15057748	15057748	+	Silent	SNP	C	C	T	rs369008989		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:15057748C>T	ENST00000425241.1	+	4	725	c.363C>T	c.(361-363)ggC>ggT	p.G121G	NR2C2_ENST00000406272.2_Silent_p.G121G|NR2C2_ENST00000323373.6_Silent_p.G140G|NR2C2_ENST00000393102.3_Silent_p.G121G			P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	121					cell differentiation (GO:0030154)|gene expression (GO:0010467)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TGGTCTGTGGCGACAAAGCCT	0.507																																					p.G140G		Atlas-SNP	.											.	NR2C2	44	.	0			c.C420T						.	C		1,4405	2.1+/-5.4	0,1,2202	181.0	158.0	166.0		420	-6.4	0.6	3		166	0,8600		0,0,4300	no	coding-synonymous	NR2C2	NM_003298.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		140/616	15057748	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7182	exon5			CTGTGGCGACAAA	L27586	CCDS2621.1, CCDS74905.1	3p25	2013-01-16			ENSG00000177463	ENSG00000177463		"""Nuclear hormone receptors"""	7972	protein-coding gene	gene with protein product		601426		TR4		8661150, 8016112	Standard	XM_005265428		Approved	TAK1, TR2R1, hTAK1	uc003bzi.3	P49116	OTTHUMG00000129839	ENST00000425241.1:c.363C>T	chr3.hg19:g.15057748C>T		160.0	0.0		113.0	39.0	NM_003298	A8K3H5|B6ZGT8|P55092	Silent	SNP	ENST00000425241.1	hg19																																																																																				.	.		0.507	NR2C2-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000340729.1	NM_003298	
ZFYVE20	64145	hgsc.bcm.edu	37	3	15116270	15116270	+	Silent	SNP	C	C	T	rs551879008	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:15116270C>T	ENST00000253699.3	-	14	1987	c.1374G>A	c.(1372-1374)ccG>ccA	p.P458P	ZFYVE20_ENST00000476527.2_Silent_p.P458P	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	458	Necessary for the interaction with EHD1.|Necessary for the interaction with RAB4A.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						GCTGGAGGAGCGGGTCTGAGT	0.642													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18852	0.0		0.001	False		,,,				2504	0.0				p.P458P		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G1374A						.						61.0	54.0	56.0					3																	15116270		2203	4300	6503	SO:0001819	synonymous_variant	64145	exon14			GAGGAGCGGGTCT	AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381		"""Zinc fingers, FYVE domain containing"""	20759	protein-coding gene	gene with protein product		609511				11062261	Standard	XR_427283		Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.1374G>A	chr3.hg19:g.15116270C>T		99.0	0.0		100.0	41.0	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Silent	SNP	ENST00000253699.3	hg19	CCDS2623.1																																																																																			.	.		0.642	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340	
DAZL	1618	hgsc.bcm.edu	37	3	16639957	16639957	+	Splice_Site	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:16639957A>G	ENST00000399444.2	-	2	444		c.e2+1		DAZL_ENST00000250863.8_Splice_Site	NM_001351.3	NP_001342.2	Q92904	DAZL_HUMAN	deleted in azoospermia-like						female meiosis II (GO:0007147)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|oocyte maturation (GO:0001556)|positive regulation of meiosis (GO:0045836)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)		RAF1/DAZL(2)	endometrium(1)|large_intestine(3)|lung(4)|prostate(3)	11						TGAATACAATACCCTAACATC	0.383																																					.		Atlas-SNP	.											.	DAZL	23	.	0			c.150+2T>C						.						155.0	150.0	152.0					3																	16639957		2203	4300	6503	SO:0001630	splice_region_variant	1618	exon3			TACAATACCCTAA	BC027595	CCDS43059.1, CCDS54556.1	3p24	2013-02-12			ENSG00000092345	ENSG00000092345		"""RNA binding motif (RRM) containing"""	2685	protein-coding gene	gene with protein product		601486		DAZLA		8896558	Standard	NM_001351		Approved	DAZH, SPGYLA, MGC26406, DAZL1	uc003cbb.3	Q92904	OTTHUMG00000157050	ENST00000399444.2:c.150+1T>C	chr3.hg19:g.16639957A>G		56.0	0.0		41.0	20.0	NM_001351	O15396|Q5HYB4|Q92909	Splice_Site	SNP	ENST00000399444.2	hg19	CCDS43059.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.521904	0.64747	.	.	ENSG00000092345	ENST00000250863;ENST00000399444;ENST00000454457	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5349	0.75996	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DAZL	16614961	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	7.320000	0.79064	2.142000	0.66516	0.482000	0.46254	.	.	.		0.383	DAZL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347261.2	NM_001351	Intron
UBE2E2	7325	hgsc.bcm.edu	37	3	23631290	23631290	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:23631290G>A	ENST00000396703.1	+	6	754	c.574G>A	c.(574-576)Gcc>Acc	p.A192T	UBE2E2_ENST00000425792.1_Missense_Mutation_p.A192T	NM_152653.3	NP_689866.1	Q96LR5	UB2E2_HUMAN	ubiquitin-conjugating enzyme E2E 2	192					ISG15-protein conjugation (GO:0032020)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)		ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(2)	10						TGACCGGATGGCCAGACAGTG	0.602																																					p.A192T	GBM(85;1941 2083 9456)	Atlas-SNP	.											.	UBE2E2	24	.	0			c.G574A						.						97.0	82.0	87.0					3																	23631290		2203	4300	6503	SO:0001583	missense	7325	exon6			CGGATGGCCAGAC	AK057886	CCDS2637.1	3p24.2	2011-05-19	2011-05-19		ENSG00000182247	ENSG00000182247		"""Ubiquitin-conjugating enzymes E2"""	12478	protein-coding gene	gene with protein product		602163	"""ubiquitin-conjugating enzyme E2E 2 (homologous to yeast UBC4/5)"", ""ubiquitin-conjugating enzyme E2E 2 (UBC4/5 homolog, yeast)"""			9371400	Standard	NM_152653		Approved	UbcH8, FLJ25157	uc003ccg.2	Q96LR5	OTTHUMG00000130482	ENST00000396703.1:c.574G>A	chr3.hg19:g.23631290G>A	ENSP00000379931:p.Ala192Thr	364.0	0.0		347.0	141.0	NM_152653		Missense_Mutation	SNP	ENST00000396703.1	hg19	CCDS2637.1	.	.	.	.	.	.	.	.	.	.	G	33	5.267165	0.95399	.	.	ENSG00000182247	ENST00000425792;ENST00000396703	T;T	0.75154	-0.91;-0.91	5.45	5.45	0.79879	Ubiquitin-conjugating enzyme, E2 (1);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000007	D	0.91935	0.7446	H	0.98314	4.2	0.80722	D	1	D	0.69078	0.997	D	0.68192	0.956	D	0.94903	0.8058	10	0.87932	D	0	.	19.2915	0.94102	0.0:0.0:1.0:0.0	.	192	Q96LR5	UB2E2_HUMAN	T	192	ENSP00000401053:A192T;ENSP00000379931:A192T	ENSP00000379931:A192T	A	+	1	0	UBE2E2	23606294	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.970000	0.88000	2.562000	0.86427	0.655000	0.94253	GCC	.	.		0.602	UBE2E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252881.2	NM_152653	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33885697	33885697	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:33885697T>C	ENST00000307296.3	+	11	1830	c.1453T>C	c.(1453-1455)Tat>Cat	p.Y485H	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.Y490H			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	485	Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CAATGAACTGTATAAGCCTTT	0.343																																					p.Y490H		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.T1468C						.						69.0	69.0	69.0					3																	33885697		2203	4298	6501	SO:0001583	missense	10015	exon11			GAACTGTATAAGC	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1453T>C	chr3.hg19:g.33885697T>C	ENSP00000307387:p.Tyr485His	641.0	0.0		573.0	205.0	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	hg19	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.177281	0.78564	.	.	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.30448	1.53;1.53	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.49762	0.1576	L	0.57536	1.79	0.80722	D	1	D;D;D	0.63880	0.976;0.993;0.987	D;D;D	0.70016	0.947;0.967;0.967	T	0.39272	-0.9622	10	0.27082	T	0.32	-10.0324	15.205	0.73173	0.0:0.0:0.0:1.0	.	266;490;485	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	H	485;490	ENSP00000307387:Y485H;ENSP00000411825:Y490H	ENSP00000307387:Y485H	Y	+	1	0	PDCD6IP	33860701	1.000000	0.71417	0.915000	0.36163	0.984000	0.73092	6.716000	0.74702	2.002000	0.58637	0.455000	0.32223	TAT	.	.		0.343	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
TRANK1	9881	hgsc.bcm.edu	37	3	36872532	36872532	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:36872532C>T	ENST00000429976.2	-	21	8657	c.8410G>A	c.(8410-8412)Gcc>Acc	p.A2804T	TRANK1_ENST00000428977.2_Missense_Mutation_p.A2254T|TRANK1_ENST00000301807.6_Missense_Mutation_p.A2254T	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2804							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TCATCAATGGCCGGGTCCACC	0.532																																					p.A2804T		Atlas-SNP	.											.	TRANK1	398	.	0			c.G8410A						.						242.0	239.0	240.0					3																	36872532		2085	4203	6288	SO:0001583	missense	9881	exon21			CAATGGCCGGGTC	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.8410G>A	chr3.hg19:g.36872532C>T	ENSP00000416168:p.Ala2804Thr	116.0	0.0		102.0	7.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077639	0.36662	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.32272	1.46;1.88;1.46	5.48	3.61	0.41365	.	0.594227	0.16066	N	0.231255	T	0.15739	0.0379	L	0.27053	0.805	0.18873	N	0.999986	P	0.35433	0.501	B	0.27608	0.081	T	0.14671	-1.0464	10	0.37606	T	0.19	.	3.2309	0.06747	0.1427:0.5553:0.1386:0.1634	.	2804	O15050	TRNK1_HUMAN	T	2254;2804;2254	ENSP00000416826:A2254T;ENSP00000416168:A2804T;ENSP00000301807:A2254T	ENSP00000301807:A2254T	A	-	1	0	TRANK1	36847536	0.563000	0.26594	0.783000	0.31826	0.745000	0.42441	0.886000	0.28241	0.735000	0.32537	0.555000	0.69702	GCC	.	.		0.532	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
TRANK1	9881	hgsc.bcm.edu	37	3	36875360	36875360	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:36875360T>C	ENST00000429976.2	-	21	5829	c.5582A>G	c.(5581-5583)tAt>tGt	p.Y1861C	TRANK1_ENST00000428977.2_Missense_Mutation_p.Y1311C|TRANK1_ENST00000301807.6_Missense_Mutation_p.Y1311C	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1861							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						ACTGGCAGAATAGGAGAGCTT	0.418																																					p.Y1861C		Atlas-SNP	.											.	TRANK1	398	.	0			c.A5582G						.						73.0	70.0	71.0					3																	36875360		1873	4099	5972	SO:0001583	missense	9881	exon21			GCAGAATAGGAGA	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5582A>G	chr3.hg19:g.36875360T>C	ENSP00000416168:p.Tyr1861Cys	61.0	0.0		54.0	23.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	8.238	0.806179	0.16467	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.33865	1.39;1.81;1.39	5.27	4.1	0.47936	.	0.126578	0.36409	N	0.002616	T	0.21761	0.0524	N	0.19112	0.55	0.36433	D	0.865001	B	0.10296	0.003	B	0.06405	0.002	T	0.10776	-1.0615	10	0.34782	T	0.22	.	8.0264	0.30440	0.0:0.1749:0.0:0.8251	.	1861	O15050	TRNK1_HUMAN	C	1311;1861;1311	ENSP00000416826:Y1311C;ENSP00000416168:Y1861C;ENSP00000301807:Y1311C	ENSP00000301807:Y1311C	Y	-	2	0	TRANK1	36850364	0.996000	0.38824	0.998000	0.56505	0.985000	0.73830	1.717000	0.37991	0.940000	0.37473	0.448000	0.29417	TAT	.	.		0.418	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
EPM2AIP1	9852	hgsc.bcm.edu	37	3	37032816	37032816	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:37032816G>A	ENST00000322716.5	-	1	1979	c.1753C>T	c.(1753-1755)Cgg>Tgg	p.R585W	MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000455445.2_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	585					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						GTGGCAACCCGAAACAGGGCT	0.408																																					p.R585W		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.C1753T						.						83.0	82.0	82.0					3																	37032816		1864	4103	5967	SO:0001583	missense	9852	exon1			CAACCCGAAACAG	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1753C>T	chr3.hg19:g.37032816G>A	ENSP00000406027:p.Arg585Trp	182.0	0.0		166.0	9.0	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	hg19	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023385	0.54683	.	.	ENSG00000178567	ENST00000322716	T	0.22945	1.93	4.66	2.67	0.31697	.	.	.	.	.	T	0.48786	0.1519	M	0.73217	2.22	0.34659	D	0.722517	D	0.89917	1.0	D	0.97110	1.0	T	0.63229	-0.6684	9	0.87932	D	0	4.3078	13.3326	0.60497	0.0:0.0:0.8101:0.1899	.	585	Q7L775	EPMIP_HUMAN	W	585	ENSP00000406027:R585W	ENSP00000406027:R585W	R	-	1	2	EPM2AIP1	37007820	0.267000	0.24122	0.997000	0.53966	0.957000	0.61999	0.503000	0.22610	0.394000	0.25230	0.655000	0.94253	CGG	.	.		0.408	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805	
ITGA9	3680	hgsc.bcm.edu	37	3	37821428	37821428	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:37821428A>G	ENST00000264741.5	+	25	2959	c.2703A>G	c.(2701-2703)gcA>gcG	p.A901A	AC093415.2_ENST00000438136.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	901					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GCCTAACAGCACACTGTAACT	0.353																																					p.A901A		Atlas-SNP	.											.	ITGA9	98	.	0			c.A2703G						.						124.0	123.0	123.0					3																	37821428		2203	4300	6503	SO:0001819	synonymous_variant	3680	exon25			AACAGCACACTGT	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2703A>G	chr3.hg19:g.37821428A>G		109.0	0.0		78.0	25.0	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	hg19	CCDS2669.1																																																																																			.	.		0.353	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
WDR48	57599	hgsc.bcm.edu	37	3	39125659	39125659	+	Missense_Mutation	SNP	A	A	T	rs112491258		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:39125659A>T	ENST00000302313.5	+	12	1215	c.1187A>T	c.(1186-1188)gAa>gTa	p.E396V	WDR48_ENST00000396258.3_Missense_Mutation_p.E314V|WDR48_ENST00000544962.1_Missense_Mutation_p.E121V|WDR48_ENST00000418020.1_De_novo_Start_OutOfFrame	NM_020839.2	NP_065890.1	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	396					double-strand break repair via homologous recombination (GO:0000724)|embryonic organ development (GO:0048568)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|positive regulation of epithelial cell proliferation (GO:0050679)|protein deubiquitination (GO:0016579)|regulation of protein monoubiquitination (GO:1902525)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TGTAAAGTTGAAGATCTGGGC	0.299																																					p.E396V		Atlas-SNP	.											.	WDR48	41	.	0			c.A1187T						.						89.0	96.0	93.0					3																	39125659		2203	4297	6500	SO:0001583	missense	57599	exon12			AAGTTGAAGATCT	AF468833	CCDS33738.1	3p21.33	2014-06-16			ENSG00000114742	ENSG00000114742		"""WD repeat domain containing"""	30914	protein-coding gene	gene with protein product		612167				10819331, 12196293, 24482476	Standard	NM_020839		Approved	KIAA1449, P80, SPG60	uc003cit.3	Q8TAF3	OTTHUMG00000155972	ENST00000302313.5:c.1187A>T	chr3.hg19:g.39125659A>T	ENSP00000307491:p.Glu396Val	104.0	0.0		104.0	33.0	NM_020839	B4DM86|B4DQI2|B4DY84|Q63HJ2|Q658Y1|Q8N3Z1|Q9NSK8|Q9P279	Missense_Mutation	SNP	ENST00000302313.5	hg19	CCDS33738.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928055	0.92389	.	.	ENSG00000114742	ENST00000302313;ENST00000544962;ENST00000396258	T;D;T	0.90133	1.01;-2.62;0.72	5.91	5.91	0.95273	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.94974	0.8374	M	0.75447	2.3	0.80722	D	1	D;P;D;D	0.61080	0.989;0.946;0.969;0.975	D;P;P;P	0.72625	0.978;0.754;0.754;0.841	D	0.95251	0.8360	10	0.66056	D	0.02	-1.8365	16.3483	0.83171	1.0:0.0:0.0:0.0	.	121;314;387;396	Q8TAF3-5;Q8TAF3-4;Q8TAF3-3;Q8TAF3	.;.;.;WDR48_HUMAN	V	396;121;314	ENSP00000307491:E396V;ENSP00000445187:E121V;ENSP00000379557:E314V	ENSP00000307491:E396V	E	+	2	0	WDR48	39100663	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.254000	0.74563	0.533000	0.62120	GAA	.	A|0.500;G|0.500		0.299	WDR48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342529.1	NM_020839	
CCR8	1237	hgsc.bcm.edu	37	3	39374347	39374347	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:39374347C>A	ENST00000326306.4	+	2	663	c.525C>A	c.(523-525)gcC>gcA	p.A175A	CCR8_ENST00000545843.1_Silent_p.A92A|CCR8_ENST00000414803.1_Missense_Mutation_p.L118I	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	175					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		ACCAAGTGGCCTCTGAAGATG	0.433																																					p.A175A		Atlas-SNP	.											.	CCR8	34	.	0			c.C525A						.						207.0	185.0	192.0					3																	39374347		2203	4300	6503	SO:0001819	synonymous_variant	1237	exon2			AGTGGCCTCTGAA	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.525C>A	chr3.hg19:g.39374347C>A		86.0	0.0		94.0	24.0	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Silent	SNP	ENST00000326306.4	hg19	CCDS2684.1	.	.	.	.	.	.	.	.	.	.	C	7.971	0.749096	0.15710	.	.	ENSG00000179934	ENST00000414803	T	0.54279	0.58	4.76	3.8	0.43715	.	.	.	.	.	T	0.54631	0.1870	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59568	-0.7430	6	0.87932	D	0	.	4.2069	0.10493	0.0:0.6097:0.2377:0.1525	.	.	.	.	I	118	ENSP00000390104:L118I	ENSP00000390104:L118I	L	+	1	0	CCR8	39349351	.	.	0.998000	0.56505	0.559000	0.35586	.	.	2.476000	0.83614	0.655000	0.94253	CTC	.	.		0.433	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266137	41266137	+	Missense_Mutation	SNP	C	C	T	rs121913409		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:41266137C>T	ENST00000349496.5	+	3	414	c.134C>T	c.(133-135)tCt>tTt	p.S45F	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45F|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer). {ECO:0000269|PubMed:9065402}.|S -> F (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> P (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S45F(384)|p.S45del(53)|p.A5_A80del(53)|p.S45C(19)|p.S45Y(17)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.S45_S47>C(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.S45fs*2(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ACAGCTCCTTCTCTGAGTGGT	0.498	S45F(HCC15_LUNG)|S45F(LS180_LARGE_INTESTINE)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.S45F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,NS,carcinoma,+1,2	CTNNB1	4904	.	601	Substitution - Missense(421)|Deletion - In frame(152)|Complex - deletion inframe(20)|Unknown(7)|Deletion - Frameshift(1)	soft_tissue(233)|liver(141)|large_intestine(85)|kidney(74)|endometrium(16)|skin(11)|adrenal_gland(9)|stomach(7)|biliary_tract(5)|ovary(4)|lung(3)|central_nervous_system(2)|cervix(2)|small_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(1)|pituitary(1)|prostate(1)|bone(1)|pancreas(1)	c.C134T						.						84.0	74.0	77.0					3																	41266137		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTCCTTCTCTGAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.134C>T	chr3.hg19:g.41266137C>T	ENSP00000344456:p.Ser45Phe	157.0	0.0		182.0	67.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569754	0.86439	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.68165	0.2971	M	0.65677	2.01	0.80722	D	1	D	0.67145	0.996	D	0.64687	0.928	T	0.68895	-0.5288	10	0.87932	D	0	-13.6823	20.2983	0.98569	0.0:1.0:0.0:0.0	.	45	P35222	CTNB1_HUMAN	F	38;45;45;45;45;38;45;45;45	ENSP00000400508:S38F;ENSP00000385604:S45F;ENSP00000412219:S45F;ENSP00000379486:S45F;ENSP00000344456:S45F;ENSP00000411226:S38F;ENSP00000379488:S45F;ENSP00000409302:S45F;ENSP00000401599:S45F	ENSP00000344456:S45F	S	+	2	0	CTNNB1	41241141	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.802000	0.96397	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
FYCO1	79443	hgsc.bcm.edu	37	3	46008574	46008574	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:46008574T>C	ENST00000296137.2	-	8	2457	c.2252A>G	c.(2251-2253)aAa>aGa	p.K751R	FYCO1_ENST00000535325.1_Missense_Mutation_p.K751R	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	751					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CTGTTGGCCTTTCTCTGCTGT	0.622																																					p.K751R		Atlas-SNP	.											.,1	FYCO1	115	.	0			c.A2252G						.						92.0	91.0	91.0					3																	46008574		2203	4300	6503	SO:0001583	missense	79443	exon8			TGGCCTTTCTCTG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2252A>G	chr3.hg19:g.46008574T>C	ENSP00000296137:p.Lys751Arg	55.0	0.0		39.0	11.0	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	T	1.695	-0.503001	0.04261	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.25749	1.78;1.79	5.66	3.33	0.38152	.	0.329778	0.34959	N	0.003547	T	0.21387	0.0515	L	0.50333	1.59	0.09310	N	0.999996	B;B	0.16166	0.016;0.016	B;B	0.15484	0.013;0.007	T	0.14671	-1.0464	10	0.34782	T	0.22	-4.5521	8.2555	0.31754	0.0:0.154:0.0:0.846	.	751;751	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	R	751	ENSP00000296137:K751R;ENSP00000441178:K751R	ENSP00000296137:K751R	K	-	2	0	FYCO1	45983578	0.868000	0.29978	0.120000	0.21714	0.124000	0.20399	2.758000	0.47565	0.992000	0.38840	0.533000	0.62120	AAA	.	.		0.622	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
CCR3	1232	hgsc.bcm.edu	37	3	46307586	46307586	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:46307586C>T	ENST00000357422.2	+	4	1480	c.937C>T	c.(937-939)Cgc>Tgc	p.R313C	CCR3_ENST00000545097.1_Missense_Mutation_p.R334C|CCR3_ENST00000541018.1_Missense_Mutation_p.R313C|CCR3_ENST00000395940.2_Missense_Mutation_p.R313C|CCR3_ENST00000395942.2_Missense_Mutation_p.R313C			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	313					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		GAAGTACCTGCGCCACTTCTT	0.552																																					p.R334C		Atlas-SNP	.											.	CCR3	52	.	0			c.C1000T						.						106.0	88.0	94.0					3																	46307586		2203	4300	6503	SO:0001583	missense	1232	exon3			TACCTGCGCCACT	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.937C>T	chr3.hg19:g.46307586C>T	ENSP00000350003:p.Arg313Cys	58.0	0.0		77.0	37.0	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	hg19	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	C	8.150	0.787200	0.16189	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.42	-0.218	0.13142	.	0.811875	0.10866	N	0.625524	T	0.26846	0.0657	L	0.31371	0.925	0.09310	N	0.999997	B;B	0.20550	0.046;0.027	B;B	0.20577	0.03;0.009	T	0.22103	-1.0226	10	0.30854	T	0.27	.	6.2461	0.20818	0.1228:0.4921:0.0:0.3851	.	334;313	F5GWL6;P51677	.;CCR3_HUMAN	C	313;334;313;313;313	ENSP00000350003:R313C;ENSP00000441600:R334C;ENSP00000440097:R313C;ENSP00000379271:R313C;ENSP00000379273:R313C	ENSP00000350003:R313C	R	+	1	0	CCR3	46282590	0.000000	0.05858	0.439000	0.26833	0.641000	0.38312	-0.349000	0.07731	0.016000	0.14998	-0.254000	0.11334	CGC	.	.		0.552	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2		
TDGF1	6997	hgsc.bcm.edu	37	3	46619474	46619474	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:46619474G>T	ENST00000296145.5	+	1	748	c.15G>T	c.(13-15)aaG>aaT	p.K5N	LRRC2_ENST00000296144.3_Intron|TDGF1_ENST00000542931.1_Intron	NM_003212.3	NP_003203.1	P13385	TDGF1_HUMAN	teratocarcinoma-derived growth factor 1	5					activation of MAPK activity (GO:0000187)|anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle cell differentiation (GO:0055007)|cell differentiation (GO:0030154)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-6 (GO:0071354)|cellular response to tumor necrosis factor (GO:0071356)|embryo development (GO:0009790)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of signal transduction (GO:0009966)|vasculogenesis (GO:0001570)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	growth factor activity (GO:0008083)|receptor binding (GO:0005102)			cervix(2)|endometrium(1)|kidney(1)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)		ACTGCAGGAAGATGGCCCGCT	0.408																																					p.K5N		Atlas-SNP	.											.	TDGF1	17	.	0			c.G15T						.						205.0	197.0	200.0					3																	46619474		2203	4300	6503	SO:0001583	missense	6997	exon1			CAGGAAGATGGCC	M96955	CCDS2742.1, CCDS54575.1	3p21.31	2012-10-03			ENSG00000241186	ENSG00000241186			11701	protein-coding gene	gene with protein product		187395				1882841, 10393436	Standard	NM_003212		Approved	CRIPTO, CR, Cripto-1	uc021wxd.1	P13385	OTTHUMG00000133482	ENST00000296145.5:c.15G>T	chr3.hg19:g.46619474G>T	ENSP00000296145:p.Lys5Asn	69.0	0.0		66.0	25.0	NM_003212	Q8TCC1	Missense_Mutation	SNP	ENST00000296145.5	hg19	CCDS2742.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100438	0.56183	.	.	ENSG00000241186	ENST00000296145	T	0.67345	-0.26	4.16	2.31	0.28768	.	0.650011	0.13736	N	0.366333	T	0.53206	0.1782	L	0.44542	1.39	0.54753	D	0.999982	P	0.44877	0.845	B	0.38428	0.273	T	0.42666	-0.9438	10	0.18276	T	0.48	.	10.5559	0.45117	0.0:0.3817:0.6183:0.0	.	5	P13385	TDGF1_HUMAN	N	5	ENSP00000296145:K5N	ENSP00000296145:K5N	K	+	3	2	AC104304.1	46594478	0.984000	0.35163	0.631000	0.29282	0.509000	0.34042	0.957000	0.29215	0.675000	0.31264	0.655000	0.94253	AAG	.	.		0.408	TDGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257378.2	NM_003212	
NBEAL2	23218	hgsc.bcm.edu	37	3	47047032	47047032	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47047032G>T	ENST00000450053.3	+	41	6793	c.6614G>T	c.(6613-6615)cGc>cTc	p.R2205L	NBEAL2_ENST00000383740.2_Missense_Mutation_p.R484L|NBEAL2_ENST00000292309.5_Missense_Mutation_p.R2021L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2205	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGGCAGGCACGCCTGGAGAGC	0.617																																					p.R2205L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G6614T						.						17.0	19.0	18.0					3																	47047032		1932	4137	6069	SO:0001583	missense	23218	exon41			AGGCACGCCTGGA	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6614G>T	chr3.hg19:g.47047032G>T	ENSP00000415034:p.Arg2205Leu	150.0	0.0		141.0	7.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.453|8.453	0.853450|0.853450	0.17106|0.17106	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000383740;ENST00000450053;ENST00000445550;ENST00000423436	.|T;T;T;T	.|0.78816	.|-1.21;-1.21;-1.21;-1.21	4.9|4.9	4.9|4.9	0.64082|0.64082	.|BEACH domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.43831|0.43831	0.1265|0.1265	N|N	0.00608|0.00608	-1.33|-1.33	0.58432|0.58432	D|D	0.999999|0.999999	.|P;B	.|0.40211	.|0.707;0.001	.|B;B	.|0.35550	.|0.205;0.013	T|T	0.63839|0.63839	-0.6546|-0.6546	5|10	.|0.02654	.|T	.|1	.|.	16.8148|16.8148	0.85730|0.85730	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2021;2205	.|Q6ZNJ1-2;Q6ZNJ1	.|.;NBEL2_HUMAN	S|L	1493|2021;484;2205;148;32	.|ENSP00000292309:R2021L;ENSP00000373246:R484L;ENSP00000415034:R2205L;ENSP00000415063:R32L	.|ENSP00000292309:R2021L	A|R	+|+	1|2	0|0	NBEAL2|NBEAL2	47022036|47022036	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.929000|0.929000	0.56500|0.56500	4.466000|4.466000	0.60148|0.60148	2.544000|2.544000	0.85801|0.85801	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.		0.617	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
CELSR3	1951	hgsc.bcm.edu	37	3	48689914	48689914	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:48689914C>T	ENST00000164024.4	-	11	5987	c.5707G>A	c.(5707-5709)Ggc>Agc	p.G1903S	CELSR3_ENST00000544264.1_Missense_Mutation_p.G1903S	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1903	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCTGCACTGCCGGGGGGCAGG	0.627																																					p.G1903S		Atlas-SNP	.											.,1	CELSR3	237	.	0			c.G5707A						.						56.0	56.0	56.0					3																	48689914		2203	4300	6503	SO:0001583	missense	1951	exon11			CACTGCCGGGGGG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.5707G>A	chr3.hg19:g.48689914C>T	ENSP00000164024:p.Gly1903Ser	109.0	0.0		93.0	42.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	4.631	0.117388	0.08881	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.79352	-1.26;-1.26	3.71	-3.02	0.05446	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.48750	0.1517	N	0.03608	-0.345	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.15870	0.001;0.014	T	0.40440	-0.9563	9	0.09084	T	0.74	.	9.3689	0.38241	0.0:0.5703:0.0:0.4297	.	1903;1973	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	S	1903	ENSP00000164024:G1903S;ENSP00000445694:G1903S	ENSP00000164024:G1903S	G	-	1	0	CELSR3	48664918	0.004000	0.15560	0.147000	0.22382	0.315000	0.28087	-0.320000	0.08028	-0.589000	0.05874	-0.367000	0.07326	GGC	.	.		0.627	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
RNF123	63891	hgsc.bcm.edu	37	3	49751388	49751388	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:49751388G>A	ENST00000327697.6	+	30	3027	c.2883G>A	c.(2881-2883)cgG>cgA	p.R961R	RNF123_ENST00000433785.1_Silent_p.R73R	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	961					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)		ATGAGCAGCGGCCCTGGGCCC	0.667																																					p.R961R		Atlas-SNP	.											.	RNF123	100	.	0			c.G2883A						.						63.0	67.0	66.0					3																	49751388		2203	4300	6503	SO:0001819	synonymous_variant	63891	exon30			GCAGCGGCCCTGG	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.2883G>A	chr3.hg19:g.49751388G>A		120.0	0.0		113.0	47.0	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.		0.667	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
RBM5	10181	hgsc.bcm.edu	37	3	50145541	50145541	+	Nonsense_Mutation	SNP	T	T	A	rs148691467		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:50145541T>A	ENST00000347869.3	+	13	1255	c.1080T>A	c.(1078-1080)taT>taA	p.Y360*	RBM5_ENST00000441812.2_3'UTR	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	360	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)		ACTACAGTTATCTGCAACCAG	0.408																																					p.Y360X		Atlas-SNP	.											.	RBM5	76	.	0			c.T1080A						.						212.0	181.0	192.0					3																	50145541		2203	4300	6503	SO:0001587	stop_gained	10181	exon13			CAGTTATCTGCAA	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.1080T>A	chr3.hg19:g.50145541T>A	ENSP00000343054:p.Tyr360*	120.0	0.0		111.0	30.0	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Nonsense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	T	35	5.538428	0.96460	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	.	.	.	5.88	-1.3	0.09259	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.5536	12.0826	0.53680	0.0:0.4905:0.0:0.5095	.	.	.	.	X	360;359;50	.	ENSP00000343054:Y360X	Y	+	3	2	RBM5	50120545	0.562000	0.26586	0.965000	0.40720	0.927000	0.56198	-0.387000	0.07361	-0.328000	0.08539	-0.366000	0.07423	TAT	.	T|1.000;C|0.000		0.408	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
DNAH1	25981	hgsc.bcm.edu	37	3	52382985	52382985	+	Missense_Mutation	SNP	C	C	T	rs371359758		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:52382985C>T	ENST00000420323.2	+	13	2449	c.2188C>T	c.(2188-2190)Cgg>Tgg	p.R730W		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	730	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R730W(2)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGAAGAGCTACGGGCCACCAT	0.582																																					p.R730W		Atlas-SNP	.											DNAH1_ENST00000420323,NS,carcinoma,0,2	DNAH1	534	.	2	Substitution - Missense(2)	endometrium(2)	c.C2188T						.	C	TRP/ARG	1,4323		0,1,2161	112.0	119.0	117.0		2188	2.4	0.4	3		117	0,8534		0,0,4267	no	missense	DNAH1	NM_015512.4	101	0,1,6428	TT,TC,CC		0.0,0.0231,0.0078	possibly-damaging	730/4266	52382985	1,12857	2162	4267	6429	SO:0001583	missense	25981	exon13			GAGCTACGGGCCA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.2188C>T	chr3.hg19:g.52382985C>T	ENSP00000401514:p.Arg730Trp	57.0	0.0		39.0	15.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799648	0.50208	2.31E-4	0.0	ENSG00000114841	ENST00000420323	T	0.25579	1.79	5.24	2.39	0.29439	.	0.000000	0.47852	D	0.000220	T	0.50411	0.1614	M	0.87180	2.865	0.49915	D	0.999837	P;D	0.63880	0.871;0.993	B;P	0.60789	0.353;0.879	T	0.55211	-0.8176	10	0.41790	T	0.15	.	14.2149	0.65786	0.3916:0.6084:0.0:0.0	.	730;730	C9JXH6;Q9P2D7-3	.;.	W	730	ENSP00000401514:R730W	ENSP00000401514:R730W	R	+	1	2	DNAH1	52358025	0.994000	0.37717	0.358000	0.25811	0.142000	0.21351	1.415000	0.34748	0.188000	0.20168	0.655000	0.94253	CGG	.	.		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
DNAH1	25981	hgsc.bcm.edu	37	3	52428572	52428572	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:52428572A>T	ENST00000420323.2	+	67	10979	c.10718A>T	c.(10717-10719)gAc>gTc	p.D3573V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3638					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCTTGGCGAGACATCCTAGCA	0.582																																					p.D3573V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A10718T						.						100.0	109.0	106.0					3																	52428572		2049	4202	6251	SO:0001583	missense	25981	exon67			GGCGAGACATCCT	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.10718A>T	chr3.hg19:g.52428572A>T	ENSP00000401514:p.Asp3573Val	122.0	0.0		116.0	55.0	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.649719	0.87958	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.08720	3.06	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.31451	0.0797	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	0.985;1.0	P;D	0.87578	0.9;0.998	T	0.08827	-1.0703	10	0.87932	D	0	.	15.0069	0.71519	1.0:0.0:0.0:0.0	.	3573;3638	C9JXH6;Q9P2D7-2	.;.	V	3573;326	ENSP00000401514:D3573V	ENSP00000273600:D326V	D	+	2	0	DNAH1	52403612	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.305000	0.89960	1.957000	0.56846	0.533000	0.62120	GAC	.	.		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
ITIH3	3699	hgsc.bcm.edu	37	3	52840398	52840398	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:52840398C>T	ENST00000449956.2	+	18	2038	c.2032C>T	c.(2032-2034)Cgc>Tgc	p.R678C	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	678					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		CACAGTGCTGCGCCTTATTCA	0.612																																					p.R678C		Atlas-SNP	.											ITIH3_ENST00000449956,NS,carcinoma,-1,1	ITIH3	132	.	0			c.C2032T						.						45.0	45.0	45.0					3																	52840398		1966	4141	6107	SO:0001583	missense	3699	exon18			GTGCTGCGCCTTA		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"""pre-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha-trypsin inhibitor heavy chain H3"""	146650	"""inter-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha (globulin) inhibitor H3"""			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.2032C>T	chr3.hg19:g.52840398C>T	ENSP00000415769:p.Arg678Cys	48.0	1.0		65.0	27.0	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	hg19	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	15.08	2.727264	0.48833	.	.	ENSG00000162267	ENST00000273291;ENST00000449956	T	0.01745	4.66	5.38	2.05	0.26809	.	0.337826	0.33496	N	0.004854	T	0.04907	0.0132	M	0.74881	2.28	0.40856	D	0.983796	D	0.54397	0.966	P	0.48677	0.586	T	0.38972	-0.9636	10	0.66056	D	0.02	-10.1344	12.7828	0.57487	0.6466:0.3534:0.0:0.0	.	678	Q06033	ITIH3_HUMAN	C	673;678	ENSP00000415769:R678C	ENSP00000273291:R673C	R	+	1	0	ITIH3	52815438	0.797000	0.28877	1.000000	0.80357	0.093000	0.18481	0.444000	0.21661	0.724000	0.32296	0.561000	0.74099	CGC	.	.		0.612	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217	
LRTM1	57408	hgsc.bcm.edu	37	3	54958759	54958759	+	Missense_Mutation	SNP	G	G	A	rs372086680		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:54958759G>A	ENST00000273286.5	-	2	653	c.491C>T	c.(490-492)gCg>gTg	p.A164V	CACNA2D3_ENST00000490478.1_Intron|LRTM1_ENST00000493075.1_Missense_Mutation_p.A88V|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000474759.1_Intron|CACNA2D3_ENST00000288197.5_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	164						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		TTCCAGGAGCGCTCGATCAAG	0.483																																					p.A164V		Atlas-SNP	.											.	LRTM1	52	.	0			c.C491T						.						98.0	99.0	99.0					3																	54958759		2203	4300	6503	SO:0001583	missense	57408	exon2			AGGAGCGCTCGAT	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.491C>T	chr3.hg19:g.54958759G>A	ENSP00000273286:p.Ala164Val	136.0	0.0		100.0	46.0	NM_020678	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	hg19	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.645678	0.00792	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;D	0.90133	4.29;-2.62	5.95	-3.18	0.05186	.	1.058120	0.07165	N	0.851454	T	0.78091	0.4229	N	0.20807	0.61	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.60900	-0.7171	10	0.29301	T	0.29	.	0.3837	0.00399	0.3326:0.1849:0.1341:0.3483	.	164	Q9HBL6	LRTM1_HUMAN	V	164;88	ENSP00000273286:A164V;ENSP00000419772:A88V	ENSP00000273286:A164V	A	-	2	0	LRTM1	54933799	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.609000	0.24238	-0.737000	0.04824	0.650000	0.86243	GCG	.	.		0.483	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678	
WNT5A	7474	hgsc.bcm.edu	37	3	55508545	55508545	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:55508545C>T	ENST00000474267.1	-	5	1025	c.504G>A	c.(502-504)gcG>gcA	p.A168A	WNT5A_ENST00000497027.1_Silent_p.A153A|WNT5A_ENST00000264634.4_Silent_p.A168A			P41221	WNT5A_HUMAN	wingless-type MMTV integration site family, member 5A	168					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|ameboidal cell migration (GO:0001667)|anterior/posterior axis specification, embryo (GO:0008595)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular protein localization (GO:0034613)|cellular response to calcium ion (GO:0071277)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cervix development (GO:0060067)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|dopaminergic neuron differentiation (GO:0071542)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system development (GO:0048706)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity (GO:0001736)|face development (GO:0060324)|genitalia development (GO:0048806)|heart looping (GO:0001947)|hematopoietic stem cell proliferation (GO:0071425)|hindgut morphogenesis (GO:0007442)|hypophysis morphogenesis (GO:0048850)|keratinocyte differentiation (GO:0030216)|lateral sprouting involved in mammary gland duct morphogenesis (GO:0060599)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|male gonad development (GO:0008584)|mammary gland branching involved in thelarche (GO:0060744)|mesenchymal-epithelial cell signaling (GO:0060638)|midgut development (GO:0007494)|negative chemotaxis (GO:0050919)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of synapse assembly (GO:0051964)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|olfactory bulb interneuron development (GO:0021891)|optic cup formation involved in camera-type eye development (GO:0003408)|palate development (GO:0060021)|planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:0061350)|planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:0061349)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar cell polarity pathway involved in outflow tract morphogenesis (GO:0061347)|planar cell polarity pathway involved in pericardium morphogenesis (GO:0061354)|planar cell polarity pathway involved in ventricular septum morphogenesis (GO:0061348)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of meiosis (GO:0045836)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ossification (GO:0045778)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of response to cytokine stimulus (GO:0060760)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|protein phosphorylation (GO:0006468)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|response to organic substance (GO:0010033)|somitogenesis (GO:0001756)|type B pancreatic cell development (GO:0003323)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vagina development (GO:0060068)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|wound healing (GO:0042060)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor tyrosine kinase-like orphan receptor binding (GO:0005115)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(1)|large_intestine(4)|lung(3)|prostate(2)|urinary_tract(1)	13				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)		CCTTGGGGCGCGCGGCGCGGC	0.716																																					p.A168A		Atlas-SNP	.											.	WNT5A	43	.	0			c.G504A						.						4.0	6.0	6.0					3																	55508545		1752	3806	5558	SO:0001819	synonymous_variant	7474	exon4			GGGGCGCGCGGCG	L20861	CCDS46850.1, CCDS58835.1	3p21-p14	2013-02-28			ENSG00000114251	ENSG00000114251		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12784	protein-coding gene	gene with protein product	"""WNT-5A protein"""	164975				8288227	Standard	NM_001256105		Approved	hWNT5A	uc010hmw.4	P41221	OTTHUMG00000158361	ENST00000474267.1:c.504G>A	chr3.hg19:g.55508545C>T		56.0	0.0		78.0	28.0	NM_003392	A8K4A4|Q6P278	Silent	SNP	ENST00000474267.1	hg19	CCDS46850.1																																																																																			.	.		0.716	WNT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350793.3	NM_003392	
LRIG1	26018	hgsc.bcm.edu	37	3	66449417	66449417	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:66449417C>T	ENST00000273261.3	-	10	1733	c.1209G>A	c.(1207-1209)tcG>tcA	p.S403S	LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.S427S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	403					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		CTTCCAGCCCCGAGAATGCTC	0.522																																					p.S403S		Atlas-SNP	.											.	LRIG1	138	.	0			c.G1209A						.						69.0	59.0	62.0					3																	66449417		2203	4300	6503	SO:0001819	synonymous_variant	26018	exon10			CAGCCCCGAGAAT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1209G>A	chr3.hg19:g.66449417C>T		96.0	0.0		70.0	22.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	hg19	CCDS33783.1																																																																																			.	.		0.522	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
CADM2	253559	hgsc.bcm.edu	37	3	85961549	85961549	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:85961549G>A	ENST00000407528.2	+	5	591	c.529G>A	c.(529-531)Gca>Aca	p.A177T	CADM2_ENST00000383699.3_Missense_Mutation_p.A186T|CADM2_ENST00000405615.2_Missense_Mutation_p.A179T	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	177	Ig-like C2-type 1.				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)		AGAAGAGGATGCAAATCGCAA	0.383																																					p.A186T		Atlas-SNP	.											.	CADM2	195	.	0			c.G556A						.						69.0	57.0	61.0					3																	85961549		2203	4300	6503	SO:0001583	missense	253559	exon6			GAGGATGCAAATC	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.529G>A	chr3.hg19:g.85961549G>A	ENSP00000384575:p.Ala177Thr	465.0	1.0		464.0	176.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519087	0.64634	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.75704	-0.96;-0.96;-0.96	5.6	5.6	0.85130	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.098719	0.64402	D	0.000001	T	0.68769	0.3037	L	0.27053	0.805	0.58432	D	0.999993	P;P;P	0.50528	0.581;0.702;0.936	B;B;P	0.51945	0.287;0.321;0.685	T	0.63175	-0.6696	10	0.12766	T	0.61	.	12.8969	0.58104	0.0743:0.0:0.9257:0.0	.	179;186;177	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	T	186;177;179	ENSP00000373200:A186T;ENSP00000384575:A177T;ENSP00000384193:A179T	ENSP00000373200:A186T	A	+	1	0	CADM2	86044239	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	5.309000	0.65774	2.640000	0.89533	0.591000	0.81541	GCA	.	.		0.383	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
EPHA3	2042	hgsc.bcm.edu	37	3	89462400	89462400	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:89462400T>A	ENST00000336596.2	+	10	2097	c.1872T>A	c.(1870-1872)gaT>gaA	p.D624E	EPHA3_ENST00000494014.1_Missense_Mutation_p.D624E	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	624	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TATCCATTGATAAAGTTGTTG	0.423										TSP Lung(6;0.00050)																											p.D624E		Atlas-SNP	.											.	EPHA3	501	.	0			c.T1872A						.						167.0	147.0	154.0					3																	89462400		2203	4299	6502	SO:0001583	missense	2042	exon10			CATTGATAAAGTT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1872T>A	chr3.hg19:g.89462400T>A	ENSP00000337451:p.Asp624Glu	164.0	0.0		160.0	60.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	T	3.342	-0.134471	0.06711	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.61510	0.1;0.1	5.95	2.59	0.31030	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.52677	0.1749	N	0.11927	0.2	0.54753	D	0.999986	P	0.46952	0.887	D	0.65773	0.938	T	0.43734	-0.9373	9	.	.	.	.	8.3296	0.32178	0.0:0.4283:0.0:0.5717	.	624	P29320	EPHA3_HUMAN	E	624	ENSP00000337451:D624E;ENSP00000419190:D624E	.	D	+	3	2	EPHA3	89545090	0.986000	0.35501	1.000000	0.80357	0.991000	0.79684	0.182000	0.16900	0.176000	0.19873	-0.417000	0.06048	GAT	.	.		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
ZBTB11	27107	hgsc.bcm.edu	37	3	101383437	101383437	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:101383437T>C	ENST00000312938.4	-	5	2325	c.1745A>G	c.(1744-1746)tAc>tGc	p.Y582C	Y_RNA_ENST00000364251.1_RNA	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	582					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TATAAGGGCGTATCGTCTCTG	0.353																																					p.Y582C		Atlas-SNP	.											.	ZBTB11	77	.	0			c.A1745G						.						248.0	234.0	239.0					3																	101383437		2202	4300	6502	SO:0001583	missense	27107	exon5			AGGGCGTATCGTC	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.1745A>G	chr3.hg19:g.101383437T>C	ENSP00000326200:p.Tyr582Cys	138.0	0.0		121.0	43.0	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.394587	0.62066	.	.	ENSG00000066422	ENST00000312938	T	0.53640	0.61	5.69	5.69	0.88448	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.063950	0.64402	D	0.000004	T	0.63343	0.2503	L	0.49126	1.545	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.62450	-0.6852	10	0.44086	T	0.13	-20.1595	15.9526	0.79855	0.0:0.0:0.0:1.0	.	582	O95625	ZBT11_HUMAN	C	582	ENSP00000326200:Y582C	ENSP00000326200:Y582C	Y	-	2	0	ZBTB11	102866127	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	4.617000	0.61204	2.168000	0.68352	0.533000	0.62120	TAC	.	.		0.353	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415	
CD47	961	hgsc.bcm.edu	37	3	107798890	107798890	+	Silent	SNP	T	T	G	rs560443707		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:107798890T>G	ENST00000361309.5	-	2	453	c.348A>C	c.(346-348)gtA>gtC	p.V116V	CD47_ENST00000355354.7_Silent_p.V116V	NM_001777.3	NP_001768.1	Q08722	CD47_HUMAN	CD47 molecule	116	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|opsonization (GO:0008228)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of inflammatory response (GO:0050729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T cell activation (GO:0050870)|response to bacterium (GO:0009617)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(3;0.0191)|Epithelial(53;0.118)			TTAATTCTGTTACTTCACAAG	0.378																																					p.V116V		Atlas-SNP	.											.	CD47	37	.	0			c.A348C						.						237.0	210.0	218.0					3																	107798890		1879	4122	6001	SO:0001819	synonymous_variant	961	exon2			TTCTGTTACTTCA		CCDS43125.1, CCDS43126.1	3q13.1-q13.2	2013-01-11	2006-03-28		ENSG00000196776	ENSG00000196776		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1682	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibody 1D8"", ""antigenic surface determinant protein OA3"", ""integrin associated protein"", ""Rh-related antigen"", ""leukocyte surface antigen CD47"", ""CD47 glycoprotein"""	601028	"""CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"""	MER6		8294396, 2277087	Standard	XM_005247908		Approved	IAP, OA3	uc003dwt.1	Q08722	OTTHUMG00000044216	ENST00000361309.5:c.348A>C	chr3.hg19:g.107798890T>G		146.0	0.0		161.0	65.0	NM_198793	A8K198|D3DN59|Q53Y71|Q96A60	Silent	SNP	ENST00000361309.5	hg19	CCDS43126.1																																																																																			.	.		0.378	CD47-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000102793.1	NM_001777	
SLC9C1	285335	hgsc.bcm.edu	37	3	111898494	111898494	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:111898494T>C	ENST00000305815.5	-	23	3055	c.2803A>G	c.(2803-2805)Aaa>Gaa	p.K935E	SLC9C1_ENST00000487372.1_Missense_Mutation_p.K887E	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	935					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										GGAAAATCTTTCTCCTTTGAC	0.358																																					p.K935E		Atlas-SNP	.											.	.	.	.	0			c.A2803G						.						84.0	84.0	84.0					3																	111898494		2203	4299	6502	SO:0001583	missense	285335	exon23			AATCTTTCTCCTT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2803A>G	chr3.hg19:g.111898494T>C	ENSP00000306627:p.Lys935Glu	62.0	0.0		85.0	38.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483357	0.26598	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.77098	-1.07;-1.07	5.98	4.83	0.62350	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.215834	0.32503	N	0.006011	T	0.75170	0.3813	L	0.37750	1.13	0.21386	N	0.999705	B;D	0.56746	0.24;0.977	B;P	0.55011	0.096;0.766	T	0.65911	-0.6053	10	0.34782	T	0.22	-23.3858	8.0269	0.30442	0.0:0.0882:0.0:0.9118	.	887;935	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	E	935;887	ENSP00000306627:K935E;ENSP00000420688:K887E	ENSP00000306627:K935E	K	-	1	0	SLC9A10	113381184	0.933000	0.31639	0.355000	0.25773	0.023000	0.10783	4.037000	0.57311	2.289000	0.77006	0.421000	0.28195	AAA	.	.		0.358	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
CCDC80	151887	hgsc.bcm.edu	37	3	112358126	112358126	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:112358126G>A	ENST00000206423.3	-	2	1580	c.627C>T	c.(625-627)atC>atT	p.I209I	CCDC80_ENST00000439685.2_Silent_p.I209I|CCDC80_ENST00000475181.1_5'Flank	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	209					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						GCTGCTCCAGGATCTGGCCCT	0.582																																					p.I209I		Atlas-SNP	.											.	CCDC80	100	.	0			c.C627T						.						101.0	90.0	94.0					3																	112358126		2203	4300	6503	SO:0001819	synonymous_variant	151887	exon2			CTCCAGGATCTGG	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"""steroid sensitive gene 1"""	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.627C>T	chr3.hg19:g.112358126G>A		85.0	0.0		99.0	31.0	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Silent	SNP	ENST00000206423.3	hg19	CCDS2968.1																																																																																			.	.		0.582	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511	
SPICE1	152185	hgsc.bcm.edu	37	3	113188014	113188014	+	Missense_Mutation	SNP	A	A	G	rs558422433		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:113188014A>G	ENST00000295872.4	-	8	942	c.683T>C	c.(682-684)aTa>aCa	p.I228T		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	228					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CTGGGTTGCTATTTTCTGCTG	0.393													A|||	1	0.000199681	0.0008	0.0	5008	,	,		11173	0.0		0.0	False		,,,				2504	0.0				p.I228T		Atlas-SNP	.											.	SPICE1	130	.	0			c.T683C						.						119.0	112.0	114.0					3																	113188014		2203	4300	6503	SO:0001583	missense	152185	exon8			GTTGCTATTTTCT	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.683T>C	chr3.hg19:g.113188014A>G	ENSP00000295872:p.Ile228Thr	118.0	0.0		151.0	31.0	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	hg19	CCDS2973.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	1.024|1.024	-0.684008|-0.684008	0.03353|0.03353	.|.	.|.	ENSG00000163611|ENSG00000163611	ENST00000295872|ENST00000467618	T|.	0.32023|.	1.47|.	4.91|4.91	2.3|2.3	0.28687|0.28687	.|.	0.838498|.	0.10836|.	N|.	0.628823|.	T|.	0.39306|.	0.1073|.	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	B;B|.	0.33238|.	0.403;0.275|.	B;B|.	0.31337|.	0.128;0.087|.	T|.	0.29366|.	-1.0014|.	10|.	0.45353|.	T|.	0.12|.	-2.906|-2.906	4.1692|4.1692	0.10322|0.10322	0.6525:0.0:0.0966:0.2509|0.6525:0.0:0.0966:0.2509	.|.	124;228|.	B3KX77;Q8N0Z3|.	.;SPICE_HUMAN|.	T|Q	228|40	ENSP00000295872:I228T|.	ENSP00000295872:I228T|.	I|X	-|-	2|1	0|0	SPICE1|SPICE1	114670704|114670704	0.513000|0.513000	0.26194|0.26194	0.336000|0.336000	0.25522|0.25522	0.408000|0.408000	0.30992|0.30992	0.646000|0.646000	0.24797|0.24797	0.806000|0.806000	0.34183|0.34183	0.482000|0.482000	0.46254|0.46254	ATA|TAG	.	.		0.393	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
ZBTB20	26137	hgsc.bcm.edu	37	3	114070331	114070331	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:114070331G>A	ENST00000474710.1	-	4	772	c.594C>T	c.(592-594)ggC>ggT	p.G198G	ZBTB20_ENST00000357258.3_Silent_p.G125G|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20_ENST00000462705.1_Silent_p.G125G|ZBTB20_ENST00000464560.1_Silent_p.G125G|ZBTB20_ENST00000471418.1_Silent_p.G125G|ZBTB20_ENST00000481632.1_Silent_p.G125G|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000393785.2_Silent_p.G125G	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	198						nucleus (GO:0005634)	DNA binding (GO:0003677)|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)	p.G125G(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		GGAACACATCGCCCACGTTCT	0.647																																					p.G198G	NSCLC(69;748 1344 9802 11203 30933)	Atlas-SNP	.											ZBTB20,colon,carcinoma,0,1	ZBTB20	157	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C594T						.						74.0	62.0	66.0					3																	114070331		2203	4300	6503	SO:0001819	synonymous_variant	26137	exon4			CACATCGCCCACG	AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13503	protein-coding gene	gene with protein product		606025	"""zinc finger protein 288"""	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.594C>T	chr3.hg19:g.114070331G>A		89.0	0.0		76.0	9.0	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	hg19	CCDS54626.1																																																																																			.	.		0.647	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642	
HCLS1	3059	hgsc.bcm.edu	37	3	121353148	121353148	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:121353148G>A	ENST00000314583.3	-	10	900	c.809C>T	c.(808-810)gCt>gTt	p.A270V	HCLS1_ENST00000428394.2_Missense_Mutation_p.A233V|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	270					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		CTTTGTCACAGCCTTTCGCTC	0.577																																					p.A270V		Atlas-SNP	.											.	HCLS1	78	.	0			c.C809T						.						87.0	81.0	83.0					3																	121353148		2203	4300	6503	SO:0001583	missense	3059	exon10			GTCACAGCCTTTC		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.809C>T	chr3.hg19:g.121353148G>A	ENSP00000320176:p.Ala270Val	57.0	0.0		68.0	26.0	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	hg19	CCDS3003.1	.	.	.	.	.	.	.	.	.	.	G	7.714	0.695824	0.15106	.	.	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.21191	2.04;2.02	5.38	3.46	0.39613	.	0.631964	0.17207	N	0.182890	T	0.17916	0.0430	L	0.50333	1.59	0.09310	N	1	B;B	0.23442	0.017;0.085	B;B	0.17098	0.01;0.017	T	0.13602	-1.0503	10	0.52906	T	0.07	-0.7608	6.6477	0.22945	0.212:0.0:0.788:0.0	.	233;270	E7EVW7;P14317	.;HCLS1_HUMAN	V	270;233	ENSP00000320176:A270V;ENSP00000387645:A233V	ENSP00000320176:A270V	A	-	2	0	HCLS1	122835838	0.726000	0.28059	0.616000	0.29078	0.075000	0.17131	3.059000	0.49947	1.506000	0.48736	-0.142000	0.14014	GCT	.	.		0.577	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	
CSTA	1475	hgsc.bcm.edu	37	3	122060396	122060396	+	Silent	SNP	C	C	T	rs569377469		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:122060396C>T	ENST00000264474.3	+	3	328	c.279C>T	c.(277-279)gaC>gaT	p.D93D		NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	93					keratinocyte differentiation (GO:0030216)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|peptide cross-linking (GO:0018149)|single organismal cell-cell adhesion (GO:0016337)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			large_intestine(2)|lung(2)	4				GBM - Glioblastoma multiforme(114;0.155)		ACAAGGATGACGAGCTGACGG	0.393																																					p.D93D	Pancreas(26;157 1503 12440)	Atlas-SNP	.											CSTA,NS,carcinoma,0,1	CSTA	11	.	0			c.C279T						.						122.0	120.0	120.0					3																	122060396		2203	4300	6503	SO:0001819	synonymous_variant	1475	exon3			GGATGACGAGCTG		CCDS3011.1	3q21	2008-04-15			ENSG00000121552	ENSG00000121552			2481	protein-coding gene	gene with protein product		184600		STF1, STFA		1674139	Standard	NM_005213		Approved		uc003eex.3	P01040	OTTHUMG00000159488	ENST00000264474.3:c.279C>T	chr3.hg19:g.122060396C>T		163.0	0.0		174.0	29.0	NM_005213	Q6IB90	Silent	SNP	ENST00000264474.3	hg19	CCDS3011.1																																																																																			.	.		0.393	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213	
EFCAB12	90288	hgsc.bcm.edu	37	3	129137245	129137245	+	Missense_Mutation	SNP	T	T	C	rs116798859	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:129137245T>C	ENST00000505956.1	-	3	695	c.533A>G	c.(532-534)cAg>cGg	p.Q178R	EFCAB12_ENST00000326085.3_Missense_Mutation_p.Q178R	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	178							calcium ion binding (GO:0005509)										CAGCTGGAGCTGGGGCACCAT	0.607																																					p.Q178R		Atlas-SNP	.											.	.	.	.	0			c.A533G						.						31.0	30.0	30.0					3																	129137245		1904	4113	6017	SO:0001583	missense	90288	exon3			TGGAGCTGGGGCA	AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.533A>G	chr3.hg19:g.129137245T>C	ENSP00000420854:p.Gln178Arg	91.0	0.0		88.0	28.0	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	hg19	CCDS54638.1	.	.	.	.	.	.	.	.	.	.	T	13.11	2.138343	0.37728	.	.	ENSG00000172771	ENST00000505956;ENST00000326085;ENST00000503957	T;T;T	0.33216	2.47;2.47;1.42	4.82	-2.68	0.06041	.	0.623436	0.14251	N	0.331422	T	0.22742	0.0549	L	0.34521	1.04	0.20873	N	0.999831	P	0.52061	0.95	P	0.50708	0.648	T	0.11155	-1.0599	10	0.41790	T	0.15	-17.8429	1.6546	0.02779	0.4769:0.0911:0.1374:0.2946	.	178	Q6NXP0	CC025_HUMAN	R	178;178;28	ENSP00000420854:Q178R;ENSP00000324241:Q178R;ENSP00000421462:Q28R	ENSP00000324241:Q178R	Q	-	2	0	C3orf25	130619935	0.954000	0.32549	0.988000	0.46212	0.232000	0.25224	-0.068000	0.11561	-0.177000	0.10690	0.459000	0.35465	CAG	.	T|0.975;G|0.025		0.607	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
PLXND1	23129	hgsc.bcm.edu	37	3	129284250	129284250	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:129284250C>T	ENST00000324093.4	-	25	4632	c.4454G>A	c.(4453-4455)cGc>cAc	p.R1485H	PLXND1_ENST00000393239.1_Missense_Mutation_p.R1485H	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1485					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.R1485H(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						AGACTCTGTGCGCCGCAGCAT	0.602																																					p.R1485H	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											PLXND1,colon,carcinoma,0,1	PLXND1	149	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4454A						.						115.0	102.0	106.0					3																	129284250		2203	4300	6503	SO:0001583	missense	23129	exon25			TCTGTGCGCCGCA	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4454G>A	chr3.hg19:g.129284250C>T	ENSP00000317128:p.Arg1485His	115.0	1.0		103.0	40.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.537357	0.65085	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.17213	2.29;2.29	4.96	4.09	0.47781	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.300750	0.30620	N	0.009222	T	0.44582	0.1300	M	0.82823	2.61	0.58432	D	0.999996	D;D	0.89917	0.999;1.0	D;D	0.91635	0.987;0.999	T	0.50608	-0.8808	10	0.87932	D	0	.	13.4503	0.61167	0.0:0.9239:0.0:0.0761	.	80;1485	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	H	1485	ENSP00000317128:R1485H;ENSP00000376931:R1485H	ENSP00000317128:R1485H	R	-	2	0	PLXND1	130766940	0.999000	0.42202	1.000000	0.80357	0.257000	0.26127	7.800000	0.85949	1.083000	0.41159	-0.291000	0.09656	CGC	.	.		0.602	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
DNAJC13	23317	hgsc.bcm.edu	37	3	132169658	132169658	+	Silent	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:132169658A>T	ENST00000260818.6	+	6	752	c.504A>T	c.(502-504)ggA>ggT	p.G168G	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	168					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						ATCAAGGAGGATTTTGTATAC	0.328																																					p.G168G		Atlas-SNP	.											.	DNAJC13	253	.	0			c.A504T						.						52.0	57.0	55.0					3																	132169658		2203	4300	6503	SO:0001819	synonymous_variant	23317	exon6			AGGAGGATTTTGT	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.504A>T	chr3.hg19:g.132169658A>T		230.0	0.0		194.0	83.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	hg19	CCDS33857.1																																																																																			.	.		0.328	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135825069	135825069	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:135825069C>T	ENST00000264977.3	+	13	3851	c.3234C>T	c.(3232-3234)aaC>aaT	p.N1078N	PPP2R3A_ENST00000490467.1_Silent_p.N342N|PPP2R3A_ENST00000334546.2_Silent_p.N457N|PPP2R3A_ENST00000469270.1_3'UTR	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	1078					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATGTTGAGAACGATGGGCCTG	0.463																																					p.N1078N		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.C3234T						.						65.0	66.0	66.0					3																	135825069		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon13			TGAGAACGATGGG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.3234C>T	chr3.hg19:g.135825069C>T		107.0	0.0		111.0	9.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.		0.463	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
STAG1	10274	hgsc.bcm.edu	37	3	136141653	136141653	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:136141653T>G	ENST00000383202.2	-	18	2046	c.1790A>C	c.(1789-1791)cAg>cCg	p.Q597P	STAG1_ENST00000236698.5_Missense_Mutation_p.Q597P|STAG1_ENST00000536929.1_Missense_Mutation_p.Q181P|STAG1_ENST00000434713.2_Missense_Mutation_p.Q371P	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	597					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						ATCAAAATACTGTGGGATTTG	0.308																																					p.Q597P		Atlas-SNP	.											.	STAG1	135	.	0			c.A1790C						.						67.0	67.0	67.0					3																	136141653		2202	4299	6501	SO:0001583	missense	10274	exon18			AAATACTGTGGGA	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.1790A>C	chr3.hg19:g.136141653T>G	ENSP00000372689:p.Gln597Pro	187.0	0.0		164.0	7.0	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.217523	0.79352	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.66	5.66	0.87406	Armadillo-type fold (1);	0.055974	0.64402	D	0.000001	T	0.26195	0.0639	L	0.60957	1.885	0.80722	D	1	P;P;P	0.52692	0.819;0.955;0.91	P;P;P	0.52793	0.707;0.709;0.707	T	0.00651	-1.1626	10	0.35671	T	0.21	.	15.9375	0.79723	0.0:0.0:0.0:1.0	.	614;597;597	Q4LE48;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	P	597;597;371;181	ENSP00000372689:Q597P;ENSP00000236698:Q597P;ENSP00000404396:Q371P;ENSP00000445787:Q181P	ENSP00000236698:Q597P	Q	-	2	0	STAG1	137624343	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.159000	0.67721	0.529000	0.55759	CAG	.	.		0.308	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
ZBTB38	253461	hgsc.bcm.edu	37	3	141162007	141162007	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:141162007A>G	ENST00000514251.1	+	4	1056	c.777A>G	c.(775-777)aaA>aaG	p.K259K	ZBTB38_ENST00000441582.2_Silent_p.K259K|ZBTB38_ENST00000321464.5_Silent_p.K260K					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						TTGCAGCGAAACCGAAAACAT	0.473																																					p.K259K		Atlas-SNP	.											.	ZBTB38	92	.	0			c.A777G						.						64.0	65.0	65.0					3																	141162007		1979	4177	6156	SO:0001819	synonymous_variant	253461	exon8			AGCGAAACCGAAA	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.777A>G	chr3.hg19:g.141162007A>G		109.0	0.0		112.0	39.0	NM_001080412		Silent	SNP	ENST00000514251.1	hg19	CCDS43157.1																																																																																			.	.		0.473	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
GK5	256356	hgsc.bcm.edu	37	3	141901813	141901813	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:141901813T>A	ENST00000392993.2	-	10	1046	c.895A>T	c.(895-897)Aca>Tca	p.T299S		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	299					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						TCCAAAAATGTCCCAGTTCCC	0.373																																					p.T299S		Atlas-SNP	.											.	GK5	45	.	0			c.A895T						.						93.0	88.0	90.0					3																	141901813		2203	4300	6503	SO:0001583	missense	256356	exon10			AAAATGTCCCAGT	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"""Glycerol kinases"""	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.895A>T	chr3.hg19:g.141901813T>A	ENSP00000418001:p.Thr299Ser	128.0	0.0		119.0	43.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	hg19	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.643855	0.29246	.	.	ENSG00000175066	ENST00000392993	D	0.84146	-1.81	5.69	5.69	0.88448	Carbohydrate kinase, FGGY, C-terminal (1);	0.157389	0.56097	D	0.000027	T	0.70500	0.3231	N	0.04063	-0.285	0.80722	D	1	B	0.15930	0.015	B	0.26517	0.07	T	0.68119	-0.5493	10	0.66056	D	0.02	-14.7751	8.9817	0.35970	0.2637:0.0:0.0:0.7362	.	299	Q6ZS86	GLPK5_HUMAN	S	299	ENSP00000418001:T299S	ENSP00000418001:T299S	T	-	1	0	GK5	143384503	0.995000	0.38212	0.932000	0.37286	0.690000	0.40134	2.543000	0.45752	2.162000	0.67917	0.533000	0.62120	ACA	.	.		0.373	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547	
ZIC1	7545	hgsc.bcm.edu	37	3	147128096	147128096	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:147128096C>T	ENST00000282928.4	+	1	926	c.197C>T	c.(196-198)tCg>tTg	p.S66L		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	66					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|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)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						GCCTTCACGTCGCAGGCGCCA	0.697																																					p.S66L		Atlas-SNP	.											.	ZIC1	141	.	0			c.C197T						.						17.0	20.0	19.0					3																	147128096		2186	4293	6479	SO:0001583	missense	7545	exon1			TCACGTCGCAGGC	D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"""Zinc fingers, C2H2-type"""	12872	protein-coding gene	gene with protein product		600470	"""Zic family member 1 (odd-paired Drosophila homolog)"", ""Zic family member 1 (odd-paired homolog, Drosophila)"""			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.197C>T	chr3.hg19:g.147128096C>T	ENSP00000282928:p.Ser66Leu	90.0	0.0		92.0	34.0	NM_003412	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	hg19	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.467258	0.63625	.	.	ENSG00000152977	ENST00000282928	D	0.85861	-2.04	4.04	3.08	0.35506	.	0.000000	0.85682	D	0.000000	D	0.85605	0.5735	L	0.59436	1.845	0.58432	D	0.999998	D	0.57257	0.979	P	0.50378	0.639	D	0.87053	0.2148	10	0.59425	D	0.04	.	12.9438	0.58362	0.0:0.8358:0.1642:0.0	.	66	Q15915	ZIC1_HUMAN	L	66	ENSP00000282928:S66L	ENSP00000282928:S66L	S	+	2	0	ZIC1	148610786	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	5.412000	0.66392	1.806000	0.52798	0.442000	0.29010	TCG	.	.		0.697	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412	
CPA3	1359	hgsc.bcm.edu	37	3	148599317	148599317	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:148599317A>C	ENST00000296046.3	+	7	637	c.585A>C	c.(583-585)aaA>aaC	p.K195N	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	195					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			AGGCAACCAAAACTTATGGGA	0.338																																					p.K195N		Atlas-SNP	.											.	CPA3	75	.	0			c.A585C						.						96.0	95.0	96.0					3																	148599317		2203	4300	6503	SO:0001583	missense	1359	exon7			AACCAAAACTTAT		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"""mast cell carboxypeptidase A"", ""tissue carboxypeptidase A"""	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.585A>C	chr3.hg19:g.148599317A>C	ENSP00000296046:p.Lys195Asn	100.0	0.0		111.0	43.0	NM_001870	Q96E94	Missense_Mutation	SNP	ENST00000296046.3	hg19	CCDS3138.1	.	.	.	.	.	.	.	.	.	.	A	8.576	0.881211	0.17467	.	.	ENSG00000163751	ENST00000296046	T	0.10382	2.88	5.06	3.92	0.45320	Peptidase M14, carboxypeptidase A (2);	0.354238	0.29579	N	0.011756	T	0.04588	0.0125	N	0.05177	-0.1	0.27807	N	0.942289	B	0.24576	0.106	B	0.24155	0.051	T	0.39981	-0.9587	10	0.15499	T	0.54	.	7.315	0.26495	0.8166:0.0:0.1834:0.0	.	195	P15088	CBPA3_HUMAN	N	195	ENSP00000296046:K195N	ENSP00000296046:K195N	K	+	3	2	CPA3	150082007	0.651000	0.27340	1.000000	0.80357	0.986000	0.74619	0.491000	0.22419	0.952000	0.37798	0.533000	0.62120	AAA	.	.		0.338	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870	
GPR87	53836	hgsc.bcm.edu	37	3	151012803	151012803	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:151012803T>C	ENST00000260843.4	-	3	695	c.231A>G	c.(229-231)atA>atG	p.I77M	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	77					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGAGATAGAATATGAAGCTGG	0.398																																					p.I77M		Atlas-SNP	.											.	GPR87	52	.	0			c.A231G						.						105.0	106.0	106.0					3																	151012803		2203	4300	6503	SO:0001583	missense	53836	exon3			ATAGAATATGAAG	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"""GPCR / Class A : Orphans"""	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.231A>G	chr3.hg19:g.151012803T>C	ENSP00000260843:p.Ile77Met	129.0	0.0		93.0	35.0	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	hg19	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.968712	0.53614	.	.	ENSG00000138271	ENST00000260843	T	0.23348	1.91	5.31	1.22	0.21188	GPCR, rhodopsin-like superfamily (1);	0.061473	0.64402	D	0.000002	T	0.49133	0.1539	M	0.85197	2.74	0.42393	D	0.992534	D	0.76494	0.999	D	0.72338	0.977	T	0.46190	-0.9209	10	0.46703	T	0.11	-11.5763	9.9589	0.41684	0.1125:0.0:0.4646:0.4229	.	77	Q9BY21	GPR87_HUMAN	M	77	ENSP00000260843:I77M	ENSP00000260843:I77M	I	-	3	3	GPR87	152495493	0.000000	0.05858	0.999000	0.59377	0.994000	0.84299	-1.539000	0.02202	0.028000	0.15324	0.533000	0.62120	ATA	.	.		0.398	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		
P2RY13	53829	hgsc.bcm.edu	37	3	151046419	151046419	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:151046419A>G	ENST00000325602.5	-	2	444	c.425T>C	c.(424-426)tTc>tCc	p.F142S	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_176894.2	NP_795713.2	Q9BPV8	P2Y13_HUMAN	purinergic receptor P2Y, G-protein coupled, 13	142					negative regulation of adenylate cyclase activity (GO:0007194)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(72;0.0189)|Lung(72;0.0278)			GATCTTGAGGAATCTGTCAAA	0.393																																					p.F142S		Atlas-SNP	.											.	P2RY13	80	.	0			c.T425C						.						51.0	51.0	51.0					3																	151046419		2203	4300	6503	SO:0001583	missense	53829	exon2			TTGAGGAATCTGT	AF295368	CCDS3158.2	3q24	2012-08-08	2004-07-12	2004-07-14	ENSG00000181631	ENSG00000181631		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	4537	protein-coding gene	gene with protein product		606380	"""G protein-coupled receptor 86"""	GPR94, GPR86		11273702, 11574155	Standard	NM_176894		Approved	FKSG77, P2Y13	uc003eyv.2	Q9BPV8	OTTHUMG00000155745	ENST00000325602.5:c.425T>C	chr3.hg19:g.151046419A>G	ENSP00000320376:p.Phe142Ser	246.0	0.0		285.0	89.0	NM_176894	B2R827|Q05C50|Q6DKN4|Q8IUT5|Q8TDU7|Q9BY61	Missense_Mutation	SNP	ENST00000325602.5	hg19	CCDS3158.2	.	.	.	.	.	.	.	.	.	.	A	17.47	3.397711	0.62177	.	.	ENSG00000181631	ENST00000325602	T	0.73681	-0.77	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.112777	0.64402	D	0.000008	D	0.82300	0.5007	L	0.59436	1.845	0.32849	D	0.506394	P	0.52316	0.952	P	0.60236	0.871	D	0.87620	0.2509	10	0.87932	D	0	-23.9887	15.5586	0.76219	1.0:0.0:0.0:0.0	.	142	Q9BPV8	P2Y13_HUMAN	S	142	ENSP00000320376:F142S	ENSP00000320376:F142S	F	-	2	0	P2RY13	152529109	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	0.936000	0.28938	2.075000	0.62263	0.455000	0.32223	TTC	.	.		0.393	P2RY13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341468.1	NM_023914	
P2RY1	5028	hgsc.bcm.edu	37	3	152554282	152554282	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:152554282C>T	ENST00000305097.3	+	1	1547	c.711C>T	c.(709-711)taC>taT	p.Y237Y	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	237					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TGGGCTGTTACGGATTAATTG	0.453																																					p.Y237Y		Atlas-SNP	.											.	P2RY1	49	.	0			c.C711T						.						121.0	110.0	114.0					3																	152554282		2203	4300	6503	SO:0001819	synonymous_variant	5028	exon1			CTGTTACGGATTA	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.711C>T	chr3.hg19:g.152554282C>T		93.0	0.0		110.0	48.0	NM_002563		Silent	SNP	ENST00000305097.3	hg19	CCDS3169.1																																																																																			.	.		0.453	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563	
ARHGEF26	26084	hgsc.bcm.edu	37	3	153912436	153912436	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:153912436A>G	ENST00000356448.4	+	9	2058	c.1774A>G	c.(1774-1776)Atc>Gtc	p.I592V	ARHGEF26_ENST00000465817.1_Intron|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.I592V	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	592	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						ATTACAGACTATCTGTCAAAA	0.328																																					p.I592V	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.A1774G						.						57.0	54.0	55.0					3																	153912436		1816	4073	5889	SO:0001583	missense	26084	exon9			CAGACTATCTGTC	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24490	protein-coding gene	gene with protein product	"""Src homology 3 domain-containing guanine nucleotide exchange factor"""					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.1774A>G	chr3.hg19:g.153912436A>G	ENSP00000348828:p.Ile592Val	181.0	0.0		189.0	69.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	a	18.00	3.525082	0.64747	.	.	ENSG00000114790	ENST00000356448;ENST00000465093	T;T	0.35789	1.29;1.29	5.7	5.7	0.88788	Dbl homology (DH) domain (5);	0.051159	0.85682	D	0.000000	T	0.52306	0.1726	L	0.42686	1.345	0.80722	D	1	D;D	0.69078	0.98;0.997	D;D	0.80764	0.961;0.994	T	0.46884	-0.9159	10	0.38643	T	0.18	-18.9384	16.0468	0.80725	1.0:0.0:0.0:0.0	.	592;592	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	V	592	ENSP00000348828:I592V;ENSP00000423418:I592V	ENSP00000348828:I592V	I	+	1	0	ARHGEF26	155395126	1.000000	0.71417	0.973000	0.42090	0.918000	0.54935	8.253000	0.89842	2.176000	0.68965	0.520000	0.50463	ATC	.	.		0.328	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
GPR149	344758	hgsc.bcm.edu	37	3	154146778	154146778	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:154146778T>C	ENST00000389740.2	-	1	726	c.627A>G	c.(625-627)tcA>tcG	p.S209S		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	209					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TGAGTGGGACTGAGAGGCCCA	0.597																																					p.S209S		Atlas-SNP	.											.	GPR149	134	.	0			c.A627G						.						54.0	61.0	59.0					3																	154146778		1976	4152	6128	SO:0001819	synonymous_variant	344758	exon1			TGGGACTGAGAGG	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.627A>G	chr3.hg19:g.154146778T>C		262.0	0.0		219.0	88.0	NM_001038705		Silent	SNP	ENST00000389740.2	hg19	CCDS43162.1																																																																																			.	.		0.597	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
KCNAB1	7881	hgsc.bcm.edu	37	3	155861202	155861202	+	Intron	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:155861202G>A	ENST00000490337.1	+	1	339				KCNAB1_ENST00000389636.5_Intron|KCNAB1_ENST00000471742.1_Missense_Mutation_p.A79T	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GACGGGCATGGCATACAGGTA	0.453																																					p.A79T		Atlas-SNP	.											.	KCNAB1	176	.	0			c.G235A						.						110.0	108.0	108.0					3																	155861202		2203	4300	6503	SO:0001627	intron_variant	7881	exon1			GGCATGGCATACA	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.275+22527G>A	chr3.hg19:g.155861202G>A		126.0	0.0		85.0	43.0	NM_003471	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	hg19	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.095788	0.36952	.	.	ENSG00000169282	ENST00000471742	T	0.41758	0.99	5.29	0.157	0.14915	.	.	.	.	.	T	0.24774	0.0601	.	.	.	0.80722	D	1	B	0.15719	0.014	B	0.18871	0.023	T	0.06862	-1.0803	8	0.28530	T	0.3	.	4.1948	0.10438	0.3404:0.3191:0.3405:0.0	.	79	Q14722-3	.	T	79	ENSP00000418956:A79T	ENSP00000418956:A79T	A	+	1	0	KCNAB1	157343896	0.378000	0.25114	0.973000	0.42090	0.993000	0.82548	0.373000	0.20484	0.313000	0.23062	0.561000	0.74099	GCA	.	.		0.453	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
PLD1	5337	hgsc.bcm.edu	37	3	171453412	171453412	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:171453412G>A	ENST00000351298.4	-	4	430	c.304C>T	c.(304-306)Ctt>Ttt	p.L102F	PLD1_ENST00000356327.5_Missense_Mutation_p.L102F|PLD1_ENST00000340989.4_Missense_Mutation_p.L102F|PLD1_ENST00000342215.6_Missense_Mutation_p.L102F	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	102	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ATAGTGTAAAGATTAATACTT	0.299																																					p.L102F	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.C304T						.						71.0	68.0	69.0					3																	171453412		2203	4300	6503	SO:0001583	missense	5337	exon4			TGTAAAGATTAAT	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.304C>T	chr3.hg19:g.171453412G>A	ENSP00000342793:p.Leu102Phe	135.0	0.0		153.0	77.0	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177229	0.57692	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989;ENST00000418087	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.18	4.31	0.51392	Phox homologous domain (5);	0.199342	0.43416	D	0.000577	T	0.54319	0.1851	L	0.60067	1.865	0.32291	N	0.566369	P;B	0.45126	0.851;0.154	P;B	0.58820	0.846;0.261	T	0.64153	-0.6474	10	0.54805	T	0.06	-8.9613	9.7833	0.40662	0.0:0.3446:0.52:0.1354	.	125;102	Q59EA4;Q13393	.;PLD1_HUMAN	F	102	ENSP00000348681:L102F;ENSP00000342793:L102F;ENSP00000339936:L102F;ENSP00000340326:L102F;ENSP00000400639:L102F	ENSP00000340326:L102F	L	-	1	0	PLD1	172936106	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.787000	0.26858	1.158000	0.42547	0.563000	0.77884	CTT	.	.		0.299	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
KCNMB2	10242	hgsc.bcm.edu	37	3	178525220	178525220	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:178525220G>A	ENST00000432997.1	+	2	375	c.23G>A	c.(22-24)cGg>cAg	p.R8Q	KCNMB2_ENST00000470361.2_3'UTR|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000452583.1_Missense_Mutation_p.R8Q|RP11-385J1.2_ENST00000425330.1_RNA|RP11-385J1.2_ENST00000451742.1_RNA|KCNMB2_ENST00000358316.3_Missense_Mutation_p.R8Q|KCNMB2_ENST00000420517.2_Missense_Mutation_p.R8Q|RP11-385J1.2_ENST00000432385.1_RNA	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	0					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	ACCAGTGGCCGGACCTCTTCA	0.438																																					p.R8Q		Atlas-SNP	.											.	KCNMB2	35	.	0			c.G23A						.						99.0	95.0	97.0					3																	178525220		2203	4300	6503	SO:0001583	missense	10242	exon3			GTGGCCGGACCTC	AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"""Potassium channels"""	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.23G>A	chr3.hg19:g.178525220G>A	ENSP00000407592:p.Arg8Gln	106.0	0.0		91.0	27.0	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000432997.1	hg19	CCDS3223.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766730	0.69878	.	.	ENSG00000197584	ENST00000437510;ENST00000420517;ENST00000452583;ENST00000432997;ENST00000455865;ENST00000358316;ENST00000457763	T;T;T;T;T;T	0.24538	2.17;3.04;3.04;3.04;1.85;3.04	5.41	5.41	0.78517	KCNMB2, ball/chain domain (2);	0.482489	0.23235	N	0.050420	T	0.36441	0.0967	N	0.14661	0.345	0.46701	D	0.999163	D;B	0.71674	0.998;0.039	D;B	0.79108	0.992;0.01	T	0.34477	-0.9827	10	0.62326	D	0.03	-19.7358	18.3237	0.90246	0.0:0.0:1.0:0.0	.	8;8	B5BNW9;Q9Y691	.;KCMB2_HUMAN	Q	8	ENSP00000395807:R8Q;ENSP00000408252:R8Q;ENSP00000397483:R8Q;ENSP00000407592:R8Q;ENSP00000399100:R8Q;ENSP00000351068:R8Q	ENSP00000351068:R8Q	R	+	2	0	KCNMB2	180007914	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.946000	0.70234	2.697000	0.92050	0.563000	0.77884	CGG	.	.		0.438	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361	
USP13	8975	hgsc.bcm.edu	37	3	179448452	179448452	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:179448452G>A	ENST00000263966.3	+	10	1680	c.1209G>A	c.(1207-1209)ccG>ccA	p.P403P	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_Silent_p.P338P	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	403	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CAAAGCCTCCGGTGAAATCTG	0.458																																					p.P403P		Atlas-SNP	.											.	USP13	117	.	0			c.G1209A						.						56.0	54.0	55.0					3																	179448452		2203	4300	6503	SO:0001819	synonymous_variant	8975	exon10			GCCTCCGGTGAAA	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.1209G>A	chr3.hg19:g.179448452G>A		156.0	0.0		146.0	59.0	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Silent	SNP	ENST00000263966.3	hg19	CCDS3235.1																																																																																			.	.		0.458	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1		
CCDC39	339829	hgsc.bcm.edu	37	3	180378451	180378451	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:180378451T>G	ENST00000442201.2	-	4	542	c.423A>C	c.(421-423)caA>caC	p.Q141H	CCDC39_ENST00000273654.4_Missense_Mutation_p.Q225H	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	141					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CCTCCAATGCTTGCTGGTCCC	0.388																																					p.Q141H		Atlas-SNP	.											.	CCDC39	242	.	0			c.A423C						.						91.0	82.0	85.0					3																	180378451		1838	4087	5925	SO:0001583	missense	339829	exon4			CAATGCTTGCTGG	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.423A>C	chr3.hg19:g.180378451T>G	ENSP00000405708:p.Gln141His	86.0	0.0		93.0	39.0	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.376177	0.61735	.	.	ENSG00000145075	ENST00000273654;ENST00000442201	.	.	.	5.5	1.72	0.24424	.	0.107759	0.64402	D	0.000005	T	0.52948	0.1766	M	0.64997	1.995	0.39424	D	0.966967	D	0.53151	0.958	P	0.49140	0.601	T	0.54423	-0.8296	9	0.51188	T	0.08	-17.4904	8.7163	0.34414	0.0:0.4245:0.0:0.5755	.	141	Q9UFE4	CCD39_HUMAN	H	225;141	.	ENSP00000273654:Q225H	Q	-	3	2	CCDC39	181861145	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.357000	0.20199	0.388000	0.25054	0.477000	0.44152	CAA	.	.		0.388	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
B3GNT5	84002	hgsc.bcm.edu	37	3	182988028	182988028	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:182988028T>C	ENST00000326505.3	+	2	972	c.442T>C	c.(442-444)Tgg>Cgg	p.W148R	B3GNT5_ENST00000460419.1_Missense_Mutation_p.W148R|MCF2L2_ENST00000473233.1_Intron|MCF2L2_ENST00000447025.2_Intron|MCF2L2_ENST00000328913.3_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.W148R	NM_032047.4	NP_114436.1	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	148					cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycolipid biosynthetic process (GO:0009247)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity (GO:0008457)|galactosyltransferase activity (GO:0008378)|lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase activity (GO:0047256)|lipopolysaccharide N-acetylglucosaminyltransferase activity (GO:0008917)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	all_cancers(143;8.52e-13)|Ovarian(172;0.0355)		all cancers(12;4.52e-44)|Epithelial(37;8.82e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			AAAACTGGCTTGGGAAGATCA	0.378																																					p.W148R		Atlas-SNP	.											.	B3GNT5	26	.	0			c.T442C						.						55.0	54.0	54.0					3																	182988028		2203	4300	6503	SO:0001583	missense	84002	exon2			CTGGCTTGGGAAG	AB045278	CCDS3244.1	3q28	2013-02-21			ENSG00000176597	ENSG00000176597	2.4.1.206	"""Beta 3-glycosyltransferases"""	15684	protein-coding gene	gene with protein product	"""lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase"""	615333				11283017	Standard	XM_005247824		Approved	B3GN-T5, beta3Gn-T5	uc003flk.3	Q9BYG0	OTTHUMG00000158436	ENST00000326505.3:c.442T>C	chr3.hg19:g.182988028T>C	ENSP00000316173:p.Trp148Arg	157.0	0.0		154.0	61.0	NM_032047	D3DNS5|Q59FE3|Q7L9Z5|Q8WWP9	Missense_Mutation	SNP	ENST00000326505.3	hg19	CCDS3244.1	.	.	.	.	.	.	.	.	.	.	T	0.489	-0.876211	0.02550	.	.	ENSG00000176597	ENST00000326505;ENST00000460419;ENST00000465010	T;T;T	0.39056	1.1;1.1;1.1	5.91	-1.56	0.08532	.	0.822726	0.10930	N	0.618469	T	0.16981	0.0408	N	0.11364	0.135	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18587	-1.0332	10	0.24483	T	0.36	.	1.5143	0.02503	0.1981:0.1386:0.3664:0.297	.	148	Q9BYG0	B3GN5_HUMAN	R	148	ENSP00000316173:W148R;ENSP00000420778:W148R;ENSP00000417868:W148R	ENSP00000316173:W148R	W	+	1	0	B3GNT5	184470722	0.000000	0.05858	0.127000	0.21898	0.006000	0.05464	-0.593000	0.05740	0.114000	0.18032	-0.309000	0.09137	TGG	.	.		0.378	B3GNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351009.1	NM_032047	
VWA5B2	90113	hgsc.bcm.edu	37	3	183955189	183955189	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:183955189G>A	ENST00000426955.2	+	11	1809	c.1709G>A	c.(1708-1710)cGc>cAc	p.R570H	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Missense_Mutation_p.R351H	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	581										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						TTCCGGTCCCGCCCACCAGGG	0.647																																					p.R570H		Atlas-SNP	.											VWA5B2,caecum,carcinoma,0,1	VWA5B2	47	.	0			c.G1709A						.						16.0	16.0	16.0					3																	183955189		692	1591	2283	SO:0001583	missense	90113	exon11			GGTCCCGCCCACC		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.1709G>A	chr3.hg19:g.183955189G>A	ENSP00000398688:p.Arg570His	79.0	0.0		66.0	23.0	NM_138345	B9EGN7	Missense_Mutation	SNP	ENST00000426955.2	hg19	CCDS54686.1	.	.	.	.	.	.	.	.	.	.	G	3.247	-0.154005	0.06585	.	.	ENSG00000145198	ENST00000426955;ENST00000273794	T;T	0.18338	2.89;2.22	5.2	-0.877	0.10621	.	0.758874	0.11768	N	0.531431	T	0.11580	0.0282	L	0.36672	1.1	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.04013	0.001;0.0;0.001	T	0.41627	-0.9498	10	0.12430	T	0.62	-0.4901	10.1679	0.42890	0.5298:0.0:0.4702:0.0	.	351;570;581	E9PF42;B9EGN7;Q8N398	.;.;VW5B2_HUMAN	H	570;351	ENSP00000398688:R570H;ENSP00000273794:R351H	ENSP00000273794:R351H	R	+	2	0	VWA5B2	185437883	0.000000	0.05858	0.003000	0.11579	0.025000	0.11179	-0.224000	0.09164	-0.424000	0.07382	-1.069000	0.02264	CGC	.	.		0.647	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
DGKG	1608	hgsc.bcm.edu	37	3	185975727	185975727	+	Splice_Site	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:185975727A>C	ENST00000265022.3	-	17	1965	c.1426T>G	c.(1426-1428)Ttg>Gtg	p.L476V	DGKG_ENST00000344484.4_Splice_Site_p.L451V|DGKG_ENST00000382164.4_Splice_Site_p.L437V|DGKG_ENST00000544847.1_Splice_Site_p.L417V	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	476	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	AAAAAGTTCAACCTGGGAAGA	0.483																																					p.L476V		Atlas-SNP	.											.	DGKG	98	.	0			c.T1426G						.						91.0	83.0	86.0					3																	185975727		2203	4300	6503	SO:0001630	splice_region_variant	1608	exon17			AGTTCAACCTGGG	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"""EF-hand domain containing"""	2853	protein-coding gene	gene with protein product		601854	"""diacylglycerol kinase, gamma (90kD)"""	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1425-1T>G	chr3.hg19:g.185975727A>C		105.0	0.0		98.0	6.0	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	hg19	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.509616	0.64522	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.33	0.017	0.14110	Diacylglycerol kinase, catalytic domain (3);	0.000000	0.64402	D	0.000009	T	0.54431	0.1858	M	0.87682	2.9	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.997;0.997	D;D;D;D	0.79108	0.992;0.992;0.979;0.988	T	0.56420	-0.7982	10	0.87932	D	0	.	9.6746	0.40032	0.7424:0.0:0.2576:0.0	.	417;451;437;476	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	V	476;451;437;417;440	ENSP00000265022:L476V;ENSP00000339777:L451V;ENSP00000371599:L437V;ENSP00000440507:L417V	ENSP00000265022:L476V	L	-	1	2	DGKG	187458421	0.160000	0.22878	0.917000	0.36280	0.785000	0.44390	0.513000	0.22770	-0.134000	0.11516	0.533000	0.62120	TTG	.	.		0.483	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		Missense_Mutation
IL1RAP	3556	hgsc.bcm.edu	37	3	190338162	190338162	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:190338162T>C	ENST00000412504.2	+	5	888	c.636T>C	c.(634-636)tgT>tgC	p.C212C	IL1RAP_ENST00000072516.3_Silent_p.C212C|IL1RAP_ENST00000422940.1_Silent_p.C212C|IL1RAP_ENST00000447382.1_Silent_p.C212C|IL1RAP_ENST00000422485.1_Silent_p.C212C|IL1RAP_ENST00000434491.1_Silent_p.C71C|IL1RAP_ENST00000443369.2_Silent_p.C212C|IL1RAP_ENST00000317757.3_Silent_p.C212C|IL1RAP_ENST00000439062.1_Silent_p.C212C			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	212	Ig-like C2-type 2.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		ATTACACATGTGTTGTTACAT	0.353																																					p.C212C		Atlas-SNP	.											.	IL1RAP	96	.	0			c.T636C						.						124.0	114.0	117.0					3																	190338162		2203	4300	6503	SO:0001819	synonymous_variant	3556	exon5			CACATGTGTTGTT	AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.636T>C	chr3.hg19:g.190338162T>C		135.0	0.0		95.0	20.0	NM_001167929	B1NLD0|D3DNW0|O14915|Q86WJ7	Silent	SNP	ENST00000412504.2	hg19	CCDS3298.1	.	.	.	.	.	.	.	.	.	.	T	10.55	1.381719	0.24944	.	.	ENSG00000196083	ENST00000412080	.	.	.	5.22	1.57	0.23409	.	.	.	.	.	T	0.53883	0.1824	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43845	-0.9366	4	.	.	.	.	6.4536	0.21918	0.0:0.2862:0.0:0.7138	.	.	.	.	A	49	.	.	V	+	2	0	IL1RAP	191820856	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	0.421000	0.21280	0.396000	0.25283	0.528000	0.53228	GTG	.	.		0.353	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1		
MUC4	4585	hgsc.bcm.edu	37	3	195475922	195475922	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:195475922C>T	ENST00000346145.4	-	23	3216	c.3177G>A	c.(3175-3177)acG>acA	p.T1059T	MUC4_ENST00000463781.3_Silent_p.T5295T|MUC4_ENST00000349607.4_Silent_p.T1008T|MUC4_ENST00000475231.1_Silent_p.T5243T	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2052					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)		AAGCCTTCAGCGTGCTCACGT	0.532																																					p.T5295T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G15885A						.						72.0	64.0	67.0					3																	195475922		2203	4300	6503	SO:0001819	synonymous_variant	4585	exon24			CTTCAGCGTGCTC	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	ENST00000346145.4:c.3177G>A	chr3.hg19:g.195475922C>T		57.0	0.0		49.0	6.0	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	ENST00000346145.4	hg19	CCDS3310.1																																																																																			.	.		0.532	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
UVSSA	57654	hgsc.bcm.edu	37	4	1343357	1343357	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:1343357A>G	ENST00000389851.4	+	3	591	c.144A>G	c.(142-144)gcA>gcG	p.A48A	UVSSA_ENST00000511216.1_Silent_p.A48A|UVSSA_ENST00000507531.1_Silent_p.A48A	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	48	VHS-like.				protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										TGCTGATAGCACAGCTGACCC	0.622																																					p.A48A		Atlas-SNP	.											.	.	.	.	0			c.A144G						.						74.0	66.0	69.0					4																	1343357		2203	4300	6503	SO:0001819	synonymous_variant	57654	exon3			GATAGCACAGCTG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.144A>G	chr4.hg19:g.1343357A>G		87.0	0.0		78.0	32.0	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	hg19	CCDS33938.1																																																																																			.	.		0.622	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
HTT	3064	hgsc.bcm.edu	37	4	3241599	3241599	+	Missense_Mutation	SNP	G	G	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:3241599G>C	ENST00000355072.5	+	67	9387	c.9242G>C	c.(9241-9243)gGc>gCc	p.G3081A		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3081					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGCAGGATGGGCAAGCTGGAG	0.577																																					p.G3081A		Atlas-SNP	.											.	HTT	221	.	0			c.G9242C						.						27.0	28.0	28.0					4																	3241599		2141	4233	6374	SO:0001583	missense	3064	exon67			GGATGGGCAAGCT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.9242G>C	chr4.hg19:g.3241599G>C	ENSP00000347184:p.Gly3081Ala	79.0	0.0		77.0	33.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875073	0.91664	.	.	ENSG00000197386	ENST00000355072	T	0.68025	-0.3	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.81336	0.4801	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.83690	0.0176	10	0.72032	D	0.01	.	17.272	0.87104	0.0:0.0:1.0:0.0	.	3081	P42858	HD_HUMAN	A	3081	ENSP00000347184:G3081A	ENSP00000347184:G3081A	G	+	2	0	HTT	3211397	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.848000	0.99507	2.284000	0.76573	0.655000	0.94253	GGC	.	.		0.577	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
AFAP1	60312	hgsc.bcm.edu	37	4	7783227	7783227	+	Intron	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:7783227T>A	ENST00000360265.4	-	12	1765				AFAP1_ENST00000420658.1_Missense_Mutation_p.D553V|AFAP1_ENST00000358461.2_Intron|AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000382543.3_Missense_Mutation_p.D553V|AFAP1-AS1_ENST00000608442.1_RNA			Q8N556	AFAP1_HUMAN	actin filament associated protein 1							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						GGCCTTTCTGTCAGCAGGAGA	0.537																																					p.D553V		Atlas-SNP	.											.	AFAP1	93	.	0			c.A1658T						.						125.0	119.0	120.0					4																	7783227		692	1591	2283	SO:0001627	intron_variant	60312	exon13			TTTCTGTCAGCAG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1531-2624A>T	chr4.hg19:g.7783227T>A		202.0	0.0		179.0	81.0	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	hg19	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.135403	0.37728	.	.	ENSG00000196526	ENST00000420658;ENST00000382543	T;T	0.15017	2.46;2.46	5.8	3.36	0.38483	.	.	.	.	.	T	0.11324	0.0276	N	0.22421	0.69	0.80722	D	1	B	0.27559	0.181	B	0.29440	0.102	T	0.15925	-1.0420	9	0.31617	T	0.26	.	8.7406	0.34556	0.0:0.0661:0.1291:0.8048	.	553	E9PDT7	.	V	553	ENSP00000410689:D553V;ENSP00000371983:D553V	ENSP00000371983:D553V	D	-	2	0	AFAP1	7834127	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.517000	0.45529	0.458000	0.26988	0.533000	0.62120	GAC	.	.		0.537	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
LAP3	51056	hgsc.bcm.edu	37	4	17590466	17590466	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:17590466G>T	ENST00000226299.4	+	7	1003	c.729G>T	c.(727-729)caG>caT	p.Q243H	LAP3_ENST00000503467.1_3'UTR|LAP3_ENST00000606142.1_Missense_Mutation_p.Q212H|AC006160.5_ENST00000511010.1_RNA	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	243					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						TTGAGGAACAGGCAATGGGAT	0.438																																					p.Q243H		Atlas-SNP	.											.	LAP3	50	.	0			c.G729T						.						102.0	103.0	103.0					4																	17590466		2203	4300	6503	SO:0001583	missense	51056	exon7			GGAACAGGCAATG	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"""peptidase S"""	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.729G>T	chr4.hg19:g.17590466G>T	ENSP00000226299:p.Gln243His	339.0	0.0		337.0	137.0	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	hg19	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836790	0.50951	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.45668	0.89;0.89	5.12	1.13	0.20643	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.155036	0.64402	D	0.000017	T	0.53738	0.1815	M	0.64567	1.98	0.43047	D	0.994641	D	0.57899	0.981	D	0.63703	0.917	T	0.50849	-0.8779	10	0.45353	T	0.12	-18.0423	10.1037	0.42519	0.5372:0.0:0.4628:0.0	.	243	P28838	AMPL_HUMAN	H	243;77	ENSP00000226299:Q243H;ENSP00000424724:Q77H	ENSP00000226299:Q243H	Q	+	3	2	LAP3	17199564	0.998000	0.40836	0.520000	0.27837	0.926000	0.56050	0.483000	0.22292	0.200000	0.20447	0.557000	0.71058	CAG	.	.		0.438	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1		
FAM184B	27146	hgsc.bcm.edu	37	4	17649411	17649411	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:17649411G>A	ENST00000265018.3	-	12	2407	c.2195C>T	c.(2194-2196)tCg>tTg	p.S732L		NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	732										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						CTGTCTGAGCGACTCTGGAAA	0.602																																					p.S732L		Atlas-SNP	.											.	FAM184B	38	.	0			c.C2195T						.						27.0	27.0	27.0					4																	17649411		692	1591	2283	SO:0001583	missense	27146	exon12			CTGAGCGACTCTG		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.2195C>T	chr4.hg19:g.17649411G>A	ENSP00000265018:p.Ser732Leu	24.0	0.0		23.0	5.0	NM_015688		Missense_Mutation	SNP	ENST00000265018.3	hg19	CCDS47033.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.470162	0.63625	.	.	ENSG00000047662	ENST00000265018	T	0.39406	1.08	4.76	4.76	0.60689	.	0.330187	0.30260	N	0.010023	T	0.41534	0.1163	L	0.52905	1.665	0.47407	D	0.999417	P	0.46512	0.879	B	0.41619	0.361	T	0.43829	-0.9367	10	0.54805	T	0.06	-10.1553	15.1538	0.72723	0.0:0.0:1.0:0.0	.	732	Q9ULE4	F184B_HUMAN	L	732	ENSP00000265018:S732L	ENSP00000265018:S732L	S	-	2	0	FAM184B	17258509	1.000000	0.71417	1.000000	0.80357	0.192000	0.23643	4.919000	0.63383	2.642000	0.89623	0.561000	0.74099	TCG	.	.		0.602	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
GPR125	166647	hgsc.bcm.edu	37	4	22389385	22389385	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:22389385A>G	ENST00000334304.5	-	19	4178	c.3909T>C	c.(3907-3909)ggT>ggC	p.G1303G	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	1303					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				TGCTATCGGTACCGAGCAAGG	0.433																																					p.G1303G		Atlas-SNP	.											.	GPR125	118	.	0			c.T3909C						.						113.0	106.0	108.0					4																	22389385		2203	4300	6503	SO:0001819	synonymous_variant	166647	exon19			ATCGGTACCGAGC	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.3909T>C	chr4.hg19:g.22389385A>G		236.0	1.0		265.0	113.0	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	hg19	CCDS33964.1																																																																																			.	.		0.433	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3		
PPARGC1A	10891	hgsc.bcm.edu	37	4	23833257	23833257	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:23833257T>C	ENST00000264867.2	-	3	471	c.352A>G	c.(352-354)Acc>Gcc	p.T118A	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	118					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				TTGTCAGTGGTCACGTCTCCA	0.537																																					p.T118A	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.A352G						.						415.0	325.0	355.0					4																	23833257		2203	4300	6503	SO:0001583	missense	10891	exon3			CAGTGGTCACGTC	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.352A>G	chr4.hg19:g.23833257T>C	ENSP00000264867:p.Thr118Ala	129.0	0.0		110.0	5.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307209	0.40795	.	.	ENSG00000109819	ENST00000264867	T	0.23552	1.9	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.47414	0.1444	L	0.56769	1.78	0.80722	D	1	D	0.64830	0.994	D	0.70716	0.97	T	0.26258	-1.0108	10	0.36615	T	0.2	-6.5014	16.5582	0.84512	0.0:0.0:0.0:1.0	.	118	Q9UBK2	PRGC1_HUMAN	A	118	ENSP00000264867:T118A	ENSP00000264867:T118A	T	-	1	0	PPARGC1A	23442355	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.308000	0.77769	0.533000	0.62120	ACC	.	.		0.537	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
LGI2	55203	hgsc.bcm.edu	37	4	25005399	25005399	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:25005399G>A	ENST00000382114.4	-	8	1497	c.1312C>T	c.(1312-1314)Cgc>Tgc	p.R438C		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	438						extracellular region (GO:0005576)		p.R438S(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				CCGATGAAGCGGGTAAGGGAA	0.547																																					p.R438C		Atlas-SNP	.											.	LGI2	62	.	1	Substitution - Missense(1)	lung(1)	c.C1312T						.						178.0	190.0	186.0					4																	25005399		2203	4300	6503	SO:0001583	missense	55203	exon8			TGAAGCGGGTAAG	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.1312C>T	chr4.hg19:g.25005399G>A	ENSP00000371548:p.Arg438Cys	163.0	0.0		207.0	96.0	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	hg19	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255992	0.59321	.	.	ENSG00000153012	ENST00000382114;ENST00000282970	T	0.81163	-1.46	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.79015	0.4375	L	0.54323	1.7	0.80722	D	1	P	0.51791	0.948	P	0.45310	0.476	T	0.80986	-0.1137	10	0.59425	D	0.04	-24.2404	12.6604	0.56811	0.0:0.0:0.7238:0.2762	.	438	Q8N0V4	LGI2_HUMAN	C	438;86	ENSP00000371548:R438C	ENSP00000282970:R86C	R	-	1	0	LGI2	24614497	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.233000	0.58651	2.618000	0.88619	0.557000	0.71058	CGC	.	.		0.547	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		
NWD2	57495	hgsc.bcm.edu	37	4	37446811	37446811	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:37446811C>T	ENST00000309447.5	+	7	4049	c.3201C>T	c.(3199-3201)tcC>tcT	p.S1067S		NM_001144990.1	NP_001138462.1	Q9ULI1	NWD2_HUMAN		1067										breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(2)|skin(2)	16						TTACACTGTCCGCCAACCACG	0.498																																					p.S1067S		Atlas-SNP	.											.	KIAA1239	79	.	0			c.C3201T						.						143.0	115.0	124.0					4																	37446811		692	1591	2283	SO:0001819	synonymous_variant	57495	exon7			ACTGTCCGCCAAC																												ENST00000309447.5:c.3201C>T	chr4.hg19:g.37446811C>T		111.0	0.0		148.0	60.0	NM_001144990	A8MRU1	Silent	SNP	ENST00000309447.5	hg19	CCDS47040.1																																																																																			.	.		0.498	KIAA1239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347551.2		
RPL9	6133	hgsc.bcm.edu	37	4	39458043	39458043	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:39458043C>A	ENST00000449470.2	-	4	822	c.374G>T	c.(373-375)aGg>aTg	p.R125M	LIAS_ENST00000340169.2_5'Flank|LIAS_ENST00000513731.1_5'Flank|RPL9_ENST00000295955.9_Missense_Mutation_p.R125M|LIAS_ENST00000261434.3_5'Flank|LIAS_ENST00000381846.1_5'Flank	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9	125					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						CATCCGAACCCTGCGGATATA	0.408																																					p.R125M		Atlas-SNP	.											.	RPL9	16	.	0			c.G374T						.						48.0	50.0	50.0					4																	39458043		2203	4300	6503	SO:0001583	missense	6133	exon5			CGAACCCTGCGGA	D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"""L ribosomal proteins"""	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367	ENST00000449470.2:c.374G>T	chr4.hg19:g.39458043C>A	ENSP00000400467:p.Arg125Met	690.0	0.0		608.0	247.0	NM_000661		Missense_Mutation	SNP	ENST00000449470.2	hg19	CCDS3452.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.69|18.69	3.678088|3.678088	0.68042|0.68042	.|.	.|.	ENSG00000163682|ENSG00000163682	ENST00000508595|ENST00000295955;ENST00000449470;ENST00000394452;ENST00000503040;ENST00000504470	.|.	.|.	.|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|Ribosomal protein L6, alpha-beta domain (3);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.70116|0.70116	0.3187|0.3187	M|M	0.73753|0.73753	2.245|2.245	0.80722|0.80722	D|D	1|1	.|P;P	.|0.48764	.|0.915;0.567	.|P;P	.|0.46253	.|0.474;0.509	T|T	0.74990|0.74990	-0.3475|-0.3475	5|9	.|0.72032	.|D	.|0.01	.|.	18.7279|18.7279	0.91722|0.91722	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|125;125	.|B4DLV8;P32969	.|.;RL9_HUMAN	H|M	121|125	.|.	.|ENSP00000346022:R125M	Q|R	-|-	3|2	2|0	RPL9|RPL9	39134438|39134438	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.262000|0.262000	0.26303|0.26303	7.741000|7.741000	0.84997|0.84997	2.665000|2.665000	0.90641|0.90641	0.561000|0.561000	0.74099|0.74099	CAG|AGG	.	.		0.408	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1		
PDS5A	23244	hgsc.bcm.edu	37	4	39891910	39891910	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:39891910C>A	ENST00000303538.8	-	17	2384	c.1845G>T	c.(1843-1845)ttG>ttT	p.L615F		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						CGATTCTTTCCAACAGAAATT	0.363																																					p.L615F		Atlas-SNP	.											.	PDS5A	114	.	0			c.G1845T						.						79.0	75.0	76.0					4																	39891910		1819	4086	5905	SO:0001583	missense	23244	exon17			TCTTTCCAACAGA	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.1845G>T	chr4.hg19:g.39891910C>A	ENSP00000303427:p.Leu615Phe	74.0	0.0		78.0	27.0	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058098	0.76074	.	.	ENSG00000121892	ENST00000303538	.	.	.	5.46	3.73	0.42828	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69691	0.3139	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.67848	-0.5564	8	.	.	.	-6.2637	10.3707	0.44053	0.0:0.7874:0.0:0.2126	.	615	Q29RF7	PDS5A_HUMAN	F	615	.	.	L	-	3	2	PDS5A	39568305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.278000	0.51662	0.786000	0.33708	-0.140000	0.14226	TTG	.	.		0.363	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
LIMCH1	22998	hgsc.bcm.edu	37	4	41621359	41621359	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:41621359C>T	ENST00000313860.7	+	8	891	c.837C>T	c.(835-837)taC>taT	p.Y279Y	LIMCH1_ENST00000381753.4_Silent_p.Y125Y|LIMCH1_ENST00000509454.1_Silent_p.Y127Y|LIMCH1_ENST00000509638.1_Silent_p.Y120Y|LIMCH1_ENST00000503057.1_Silent_p.Y120Y|LIMCH1_ENST00000512632.1_Silent_p.Y279Y|LIMCH1_ENST00000512820.1_Silent_p.Y279Y|LIMCH1_ENST00000511496.1_Silent_p.Y120Y|LIMCH1_ENST00000513024.1_Silent_p.Y120Y|LIMCH1_ENST00000512946.1_Silent_p.Y279Y|LIMCH1_ENST00000509277.1_Silent_p.Y125Y|LIMCH1_ENST00000396595.3_Silent_p.Y125Y|LIMCH1_ENST00000514096.1_Silent_p.Y132Y|LIMCH1_ENST00000508501.1_Silent_p.Y279Y	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	279					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						AGACGGCCTACGTCCCCGCGC	0.572																																					p.Y279Y		Atlas-SNP	.											.	LIMCH1	233	.	0			c.C837T						.						89.0	90.0	89.0					4																	41621359		2203	4300	6503	SO:0001819	synonymous_variant	22998	exon8			GGCCTACGTCCCC	AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.837C>T	chr4.hg19:g.41621359C>T		95.0	0.0		111.0	54.0	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Silent	SNP	ENST00000313860.7	hg19	CCDS33977.1	.	.	.	.	.	.	.	.	.	.	C	3.110	-0.182780	0.06340	.	.	ENSG00000064042	ENST00000508466	.	.	.	5.74	-5.27	0.02763	.	.	.	.	.	T	0.65481	0.2695	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65553	-0.6140	4	.	.	.	-15.6245	16.7172	0.85399	0.0:0.3074:0.0:0.6926	.	.	.	.	M	114	.	.	T	+	2	0	LIMCH1	41316116	0.002000	0.14202	0.488000	0.27440	0.379000	0.30106	-1.427000	0.02441	-1.497000	0.01826	-1.008000	0.02478	ACG	.	.		0.572	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988	
KIAA1211	57482	hgsc.bcm.edu	37	4	57181271	57181271	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:57181271C>T	ENST00000504228.1	+	6	1708	c.1603C>T	c.(1603-1605)Cgg>Tgg	p.R535W	KIAA1211_ENST00000541073.1_Missense_Mutation_p.R528W|KIAA1211_ENST00000264229.6_Missense_Mutation_p.R535W			Q6ZU35	K1211_HUMAN	KIAA1211	535										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GACCATGCCCCGGCCCTACAC	0.647																																					p.R535W		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C1603T						.						15.0	21.0	19.0					4																	57181271		2064	4194	6258	SO:0001583	missense	57482	exon8			ATGCCCCGGCCCT	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1603C>T	chr4.hg19:g.57181271C>T	ENSP00000423366:p.Arg535Trp	266.0	1.0		305.0	124.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823247	0.71143	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.02395	4.31;4.31;4.31	4.86	-1.26	0.09376	.	.	.	.	.	T	0.12347	0.0300	M	0.71581	2.175	0.49483	D	0.99979	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.01093	-1.1454	9	0.87932	D	0	-11.4339	14.7464	0.69492	0.386:0.614:0.0:0.0	.	528;528;535	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	W	535;535;528;445	ENSP00000264229:R535W;ENSP00000423366:R535W;ENSP00000444006:R528W	ENSP00000264229:R535W	R	+	1	2	KIAA1211	56876028	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	3.137000	0.50562	-0.121000	0.11787	-0.397000	0.06425	CGG	.	.		0.647	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
REST	5978	hgsc.bcm.edu	37	4	57777460	57777460	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:57777460A>G	ENST00000309042.7	+	2	970	c.656A>G	c.(655-657)gAc>gGc	p.D219G	REST_ENST00000514063.1_3'UTR	NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	219					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					ATTCGCTGTGACCGCTGCGGC	0.488																																					p.D219G		Atlas-SNP	.											.	REST	104	.	0			c.A656G						.						54.0	51.0	52.0					4																	57777460		2203	4300	6503	SO:0001583	missense	5978	exon2			GCTGTGACCGCTG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.656A>G	chr4.hg19:g.57777460A>G	ENSP00000311816:p.Asp219Gly	199.0	0.0		152.0	61.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	hg19	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306562	0.81247	.	.	ENSG00000084093	ENST00000456010;ENST00000309042;ENST00000358605	T	0.29142	1.58	5.25	5.25	0.73442	Zinc finger, C2H2-like (1);	0.077335	0.52532	D	0.000072	T	0.40862	0.1134	N	0.21545	0.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.981;1.0	T	0.18777	-1.0326	10	0.32370	T	0.25	-35.5772	14.9902	0.71381	1.0:0.0:0.0:0.0	.	219;219	Q13127-2;Q13127	.;REST_HUMAN	G	219	ENSP00000311816:D219G	ENSP00000311816:D219G	D	+	2	0	REST	57472217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.107000	0.94261	2.220000	0.72140	0.533000	0.62120	GAC	.	.		0.488	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
LPHN3	23284	hgsc.bcm.edu	37	4	62849207	62849207	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:62849207T>C	ENST00000514591.1	+	18	3247	c.2918T>C	c.(2917-2919)tTt>tCt	p.F973S	LPHN3_ENST00000545650.1_Missense_Mutation_p.F973S|LPHN3_ENST00000506720.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000506746.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000511324.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000507164.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000508693.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000506700.1_Missense_Mutation_p.F973S|LPHN3_ENST00000514157.1_Missense_Mutation_p.F973S|LPHN3_ENST00000507625.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000509896.1_Missense_Mutation_p.F1041S|LPHN3_ENST00000514996.1_Missense_Mutation_p.F973S|LPHN3_ENST00000512091.2_Missense_Mutation_p.F973S|LPHN3_ENST00000508946.1_Missense_Mutation_p.F973S|LPHN3_ENST00000504896.1_Missense_Mutation_p.F973S			Q9HAR2	LPHN3_HUMAN	latrophilin 3	960					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GTGGAGGTTTTTGAGAGTGAA	0.478																																					p.F973S		Atlas-SNP	.											.	LPHN3	800	.	0			c.T2918C						.						201.0	191.0	195.0					4																	62849207		1950	4158	6108	SO:0001583	missense	23284	exon16			AGGTTTTTGAGAG	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2918T>C	chr4.hg19:g.62849207T>C	ENSP00000422533:p.Phe973Ser	155.0	0.0		163.0	12.0	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816145	0.90790	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17	5.72	5.72	0.89469	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.67859	0.2938	M	0.89785	3.06	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.996;0.994	T	0.75651	-0.3244	10	0.87932	D	0	.	16.0129	0.80417	0.0:0.0:0.0:1.0	.	973;960;973	E9PE04;Q9HAR2;Q9HAR2-2	.;LPHN3_HUMAN;.	S	973;973;1041;1041;973;973;960;973;1041;1041;1041;973;973;973;1041;1041;973	ENSP00000423388:F973S;ENSP00000422533:F973S;ENSP00000423787:F1041S;ENSP00000425033:F1041S;ENSP00000424120:F973S;ENSP00000439831:F973S;ENSP00000421476:F1041S;ENSP00000424030:F1041S;ENSP00000421372:F1041S;ENSP00000425201:F973S;ENSP00000423434:F973S;ENSP00000421627:F973S;ENSP00000420931:F1041S;ENSP00000425884:F1041S;ENSP00000424258:F973S	ENSP00000280009:F973S	F	+	2	0	LPHN3	62531802	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.184000	0.69523	0.482000	0.46254	TTT	.	.		0.478	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
AMTN	401138	hgsc.bcm.edu	37	4	71394475	71394475	+	Splice_Site	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:71394475G>A	ENST00000339336.4	+	6	460	c.330G>A	c.(328-330)caG>caA	p.Q110Q	AMTN_ENST00000504451.1_Splice_Site_p.Q109Q	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	110					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			TTGGAGCCCAGGTAAAAATTA	0.333																																					p.Q110Q		Atlas-SNP	.											.	AMTN	28	.	0			c.G330A						.						86.0	90.0	89.0					4																	71394475		2202	4299	6501	SO:0001630	splice_region_variant	401138	exon6			AGCCCAGGTAAAA	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.330+1G>A	chr4.hg19:g.71394475G>A		211.0	0.0		256.0	93.0	NM_212557	Q0P503|Q0P506	Silent	SNP	ENST00000339336.4	hg19	CCDS3542.1																																																																																			.	.		0.333	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557	Silent
IGJ	3512	hgsc.bcm.edu	37	4	71532164	71532164	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:71532164A>T	ENST00000254801.4	-	1	213	c.44T>A	c.(43-45)aTt>aAt	p.I15N	ENAM_ENST00000472903.1_Intron|IGJ_ENST00000543780.1_Missense_Mutation_p.I15N	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	15					adaptive immune response (GO:0002250)|antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|dimeric IgA immunoglobulin complex (GO:0071750)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|pentameric IgM immunoglobulin complex (GO:0071756)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7			Lung(101;0.235)			AACAGCCTTAATAAAAACCGC	0.363																																					p.I15N		Atlas-SNP	.											.	IGJ	13	.	0			c.T44A						.						72.0	72.0	72.0					4																	71532164		2203	4300	6503	SO:0001583	missense	3512	exon1			GCCTTAATAAAAA	M12759	CCDS3545.1	4q21	2012-10-02			ENSG00000132465	ENSG00000132465		"""Immunoglobulins / IGJ linker"""	5713	protein-coding gene	gene with protein product	"""immunoglobulin J chain"", ""IgJ chain"""	147790				3016707, 2984306	Standard	NM_144646		Approved	IGCJ, JCH	uc003hfn.4	P01591	OTTHUMG00000129909	ENST00000254801.4:c.44T>A	chr4.hg19:g.71532164A>T	ENSP00000254801:p.Ile15Asn	209.0	0.0		223.0	11.0	NM_144646		Missense_Mutation	SNP	ENST00000254801.4	hg19	CCDS3545.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.387407	0.25031	.	.	ENSG00000132465	ENST00000254801;ENST00000510437;ENST00000543780;ENST00000510614;ENST00000391614;ENST00000470866	.	.	.	5.78	3.49	0.39957	.	0.722701	0.12334	N	0.478077	T	0.19046	0.0457	N	0.08118	0	0.19945	N	0.999941	B;B	0.23735	0.027;0.09	B;B	0.24394	0.029;0.053	T	0.16453	-1.0402	9	0.72032	D	0.01	.	5.7415	0.18096	0.6285:0.275:0.0965:0.0	.	15;15	D6RHJ6;P01591	.;IGJ_HUMAN	N	15	.	ENSP00000254801:I15N	I	-	2	0	IGJ	71751028	0.922000	0.31269	0.998000	0.56505	0.304000	0.27724	1.634000	0.37123	1.024000	0.39682	0.533000	0.62120	ATT	.	.		0.363	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646	
ADAMTS3	9508	hgsc.bcm.edu	37	4	73149372	73149372	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:73149372C>T	ENST00000286657.4	-	22	3135	c.3099G>A	c.(3097-3099)ttG>ttA	p.L1033L		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	1033	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.				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)			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)			AGTATCGTGCCAACACTTCCA	0.408																																					p.L1033L	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.G3099A						.						99.0	92.0	94.0					4																	73149372		2203	4300	6503	SO:0001819	synonymous_variant	9508	exon22			TCGTGCCAACACT	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.3099G>A	chr4.hg19:g.73149372C>T		58.0	0.0		55.0	23.0	NM_014243	A1L3U9|Q9BXZ8	Silent	SNP	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.408	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
PF4V1	5197	hgsc.bcm.edu	37	4	74719172	74719172	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:74719172C>T	ENST00000226524.3	+	1	267	c.93C>T	c.(91-93)ttC>ttT	p.F31F		NM_002620.2	NP_002611.1	P10720	PF4V_HUMAN	platelet factor 4 variant 1	31					cell chemotaxis (GO:0060326)|immune response (GO:0006955)	extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|liver(2)	3	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			TGGTCGCCTTCGCCAGAGGTG	0.662																																					p.F31F		Atlas-SNP	.											.	PF4V1	8	.	0			c.C93T						.						20.0	21.0	21.0					4																	74719172		2203	4300	6503	SO:0001819	synonymous_variant	5197	exon1			CGCCTTCGCCAGA	M26167	CCDS3561.1	4q12-q21	2008-08-15			ENSG00000109272	ENSG00000109272			8862	protein-coding gene	gene with protein product		173461				2725510	Standard	NM_002620		Approved	SCYB4V1, CXCL4V1, CXCL4L1	uc003hhg.1	P10720	OTTHUMG00000130177	ENST00000226524.3:c.93C>T	chr4.hg19:g.74719172C>T		230.0	0.0		227.0	86.0	NM_002620	A1L4S0	Silent	SNP	ENST00000226524.3	hg19	CCDS3561.1																																																																																			.	.		0.662	PF4V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252495.1		
PPEF2	5470	hgsc.bcm.edu	37	4	76811198	76811198	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:76811198A>G	ENST00000286719.7	-	5	685	c.329T>C	c.(328-330)gTa>gCa	p.V110A	PPEF2_ENST00000510607.1_5'Flank	NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	110					detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ACTGTCGGGTACCTCTATGGA	0.527																																					p.V110A	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.T329C						.						250.0	218.0	229.0					4																	76811198		2203	4300	6503	SO:0001583	missense	5470	exon5			TCGGGTACCTCTA	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9244	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, beta isozyme"""	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.329T>C	chr4.hg19:g.76811198A>G	ENSP00000286719:p.Val110Ala	168.0	0.0		178.0	31.0	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	hg19	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962355	0.74016	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.55760	0.5	4.8	4.8	0.61643	Serine/threonine phosphatase, PPP5 (1);	0.064498	0.64402	D	0.000008	T	0.76047	0.3933	M	0.89904	3.07	0.48696	D	0.99969	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.81331	-0.0981	10	0.87932	D	0	-4.9812	12.3127	0.54938	1.0:0.0:0.0:0.0	.	110;110	O14830-2;O14830	.;PPE2_HUMAN	A	110	ENSP00000286719:V110A	ENSP00000286719:V110A	V	-	2	0	PPEF2	77030222	1.000000	0.71417	0.929000	0.37066	0.586000	0.36452	6.939000	0.75911	1.808000	0.52836	0.260000	0.18958	GTA	.	.		0.527	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
CCDC158	339965	hgsc.bcm.edu	37	4	77300543	77300543	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:77300543T>A	ENST00000388914.3	-	8	1081	c.929A>T	c.(928-930)aAc>aTc	p.N310I	CCDC158_ENST00000434846.2_Missense_Mutation_p.N310I	NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	310										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						AGAGTTTTGGTTTCTTGCTTG	0.388																																					p.N310I		Atlas-SNP	.											.	CCDC158	114	.	0			c.A929T						.						124.0	113.0	117.0					4																	77300543		1857	4099	5956	SO:0001583	missense	339965	exon8			TTTTGGTTTCTTG	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.929A>T	chr4.hg19:g.77300543T>A	ENSP00000373566:p.Asn310Ile	79.0	0.0		83.0	39.0	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	hg19	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.678121	0.47886	.	.	ENSG00000163749	ENST00000388914;ENST00000318586;ENST00000434846	T;T	0.78924	-1.22;1.19	5.35	5.35	0.76521	.	0.000000	0.56097	D	0.000024	T	0.79251	0.4414	N	0.19112	0.55	0.39836	D	0.973033	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.80989	-0.1136	10	0.44086	T	0.13	.	12.876	0.57989	0.0:0.0:0.0:1.0	.	310;310	Q5M9N0-3;Q5M9N0	.;CD158_HUMAN	I	310	ENSP00000373566:N310I;ENSP00000401742:N310I	ENSP00000316815:N310I	N	-	2	0	CCDC158	77519567	1.000000	0.71417	1.000000	0.80357	0.160000	0.22226	2.785000	0.47782	2.024000	0.59613	0.528000	0.53228	AAC	.	.		0.388	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
HELQ	113510	hgsc.bcm.edu	37	4	84358187	84358187	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:84358187G>A	ENST00000295488.3	-	9	2034	c.1872C>T	c.(1870-1872)ggC>ggT	p.G624G	HELQ_ENST00000510985.1_Silent_p.G557G	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	624	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						GGTTGCCATTGCCAATATTCT	0.393								Other identified genes with known or suspected DNA repair function																													p.G624G		Atlas-SNP	.											.	HELQ	95	.	0			c.C1872T						.						152.0	147.0	149.0					4																	84358187		2203	4300	6503	SO:0001819	synonymous_variant	113510	exon9			GCCATTGCCAATA	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1872C>T	chr4.hg19:g.84358187G>A		137.0	0.0		179.0	76.0	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	hg19	CCDS3603.1																																																																																			.	.		0.393	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
PTPN13	5783	hgsc.bcm.edu	37	4	87622823	87622823	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:87622823G>A	ENST00000411767.2	+	7	1127	c.1064G>A	c.(1063-1065)gGc>gAc	p.G355D	PTPN13_ENST00000427191.2_Missense_Mutation_p.G355D|PTPN13_ENST00000511467.1_Missense_Mutation_p.G355D|PTPN13_ENST00000316707.6_Missense_Mutation_p.G355D|PTPN13_ENST00000436978.1_Missense_Mutation_p.G355D			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	355					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GATATCTTTGGCCCTCAGAAA	0.453																																					p.G355D		Atlas-SNP	.											.	PTPN13	203	.	0			c.G1064A						.						86.0	83.0	84.0					4																	87622823		1909	4122	6031	SO:0001583	missense	5783	exon7			TCTTTGGCCCTCA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1064G>A	chr4.hg19:g.87622823G>A	ENSP00000407249:p.Gly355Asp	216.0	0.0		194.0	83.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290675	0.59976	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	6.03	5.19	0.71726	.	0.000000	0.52532	D	0.000072	T	0.32194	0.0821	M	0.72894	2.215	0.51233	D	0.999917	B;B;B;B	0.32753	0.383;0.278;0.182;0.278	B;B;B;B	0.34093	0.175;0.126;0.059;0.126	T	0.08534	-1.0717	10	0.44086	T	0.13	.	15.1117	0.72362	0.0673:0.0:0.9327:0.0	.	355;355;355;355	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	D	355;355;355;355;355;323	ENSP00000408368:G355D;ENSP00000394794:G355D;ENSP00000322675:G355D;ENSP00000407249:G355D;ENSP00000426626:G355D	ENSP00000322675:G355D	G	+	2	0	PTPN13	87841847	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.109000	0.64615	1.561000	0.49584	0.655000	0.94253	GGC	.	.		0.453	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
HSD17B13	345275	hgsc.bcm.edu	37	4	88239575	88239575	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:88239575T>C	ENST00000328546.4	-	2	288	c.224A>G	c.(223-225)gAa>gGa	p.E75G	RP11-529H2.2_ENST00000508163.1_RNA|HSD17B13_ENST00000302219.6_Intron	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	75						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)		AGCTGCAGTTTCCTCCACACC	0.443																																					p.E75G		Atlas-SNP	.											.	HSD17B13	27	.	0			c.A224G						.						107.0	92.0	98.0					4																	88239575		2203	4300	6503	SO:0001583	missense	345275	exon2			GCAGTTTCCTCCA		CCDS3618.1, CCDS47097.1	4q22.1	2011-09-20			ENSG00000170509	ENSG00000170509	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18685	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 3"""	612127				19027726	Standard	NM_178135		Approved	SCDR9, SDR16C3	uc003hqo.2	Q7Z5P4	OTTHUMG00000130602	ENST00000328546.4:c.224A>G	chr4.hg19:g.88239575T>C	ENSP00000333300:p.Glu75Gly	86.0	0.0		118.0	5.0	NM_178135	A8K9R9|Q2M1L5|Q86W22|Q86W23	Missense_Mutation	SNP	ENST00000328546.4	hg19	CCDS3618.1	.	.	.	.	.	.	.	.	.	.	T	15.52	2.857451	0.51376	.	.	ENSG00000170509	ENST00000328546	D	0.89415	-2.51	4.84	4.84	0.62591	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000005	D	0.93086	0.7799	M	0.73753	2.245	0.50171	D	0.999852	D	0.65815	0.995	P	0.62184	0.899	D	0.93873	0.7164	10	0.72032	D	0.01	.	14.2534	0.66035	0.0:0.0:0.0:1.0	.	75	Q7Z5P4	DHB13_HUMAN	G	75	ENSP00000333300:E75G	ENSP00000333300:E75G	E	-	2	0	HSD17B13	88458599	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	3.694000	0.54742	2.016000	0.59253	0.482000	0.46254	GAA	.	.		0.443	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	NM_178135	
SPP1	6696	hgsc.bcm.edu	37	4	88903791	88903791	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:88903791C>T	ENST00000395080.3	+	7	815	c.688C>T	c.(688-690)Ctg>Ttg	p.L230L	SPP1_ENST00000237623.7_Silent_p.L216L|SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000360804.4_Silent_p.L203L	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	230					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		AACGAGTCAGCTGGATGACCA	0.512																																					p.L243L		Atlas-SNP	.											.	SPP1	35	.	0			c.C727T						.						149.0	137.0	141.0					4																	88903791		2203	4300	6503	SO:0001819	synonymous_variant	6696	exon8			AGTCAGCTGGATG		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.688C>T	chr4.hg19:g.88903791C>T		171.0	0.0		202.0	85.0	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	hg19	CCDS43250.1																																																																																			.	.		0.512	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
FAM13A	10144	hgsc.bcm.edu	37	4	89689146	89689146	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:89689146A>G	ENST00000264344.5	-	12	1730	c.1523T>C	c.(1522-1524)aTg>aCg	p.M508T	FAM13A_ENST00000508369.1_Missense_Mutation_p.M182T|FAM13A_ENST00000503556.1_Missense_Mutation_p.M168T|FAM13A_ENST00000395002.2_Missense_Mutation_p.M182T|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000511976.1_Missense_Mutation_p.M94T|FAM13A_ENST00000513837.1_Missense_Mutation_p.M154T	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	508					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TTCATCAGACATCCATTCAAA	0.338																																					p.M508T		Atlas-SNP	.											.	FAM13A	181	.	0			c.T1523C						.						98.0	92.0	94.0					4																	89689146		2203	4300	6503	SO:0001583	missense	10144	exon12			TCAGACATCCATT	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.1523T>C	chr4.hg19:g.89689146A>G	ENSP00000264344:p.Met508Thr	244.0	0.0		227.0	65.0	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	hg19	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	A	3.400	-0.122379	0.06795	.	.	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.62498	0.02;0.02;1.5;1.53;0.02;1.5	5.13	-0.215	0.13157	.	0.803358	0.12096	N	0.499947	T	0.45776	0.1359	L	0.50333	1.59	0.09310	N	1	B;B;B;B;B;B	0.30664	0.009;0.039;0.289;0.022;0.022;0.009	B;B;B;B;B;B	0.23275	0.014;0.023;0.045;0.014;0.014;0.014	T	0.22487	-1.0215	10	0.17832	T	0.49	.	5.306	0.15803	0.6421:0.1377:0.2201:0.0	.	154;94;508;182;168;182	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	T	182;508;168;94;182;154	ENSP00000378450:M182T;ENSP00000264344:M508T;ENSP00000427189:M168T;ENSP00000421914:M94T;ENSP00000421562:M182T;ENSP00000423252:M154T	ENSP00000264344:M508T	M	-	2	0	FAM13A	89908169	0.038000	0.19896	0.003000	0.11579	0.016000	0.09150	1.139000	0.31504	-0.141000	0.11374	-0.263000	0.10527	ATG	.	.		0.338	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
CCSER1	401145	hgsc.bcm.edu	37	4	92519977	92519977	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:92519977C>T	ENST00000509176.1	+	11	2760	c.2472C>T	c.(2470-2472)acC>acT	p.T824T	CCSER1_ENST00000333691.8_Silent_p.T824T	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	824																	TACGGGCCACCGTTGGGCAGA	0.478																																					p.T824T		Atlas-SNP	.											.	.	.	.	0			c.C2472T						.						88.0	77.0	81.0					4																	92519977		692	1591	2283	SO:0001819	synonymous_variant	401145	exon11			GGCCACCGTTGGG		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.2472C>T	chr4.hg19:g.92519977C>T		153.0	0.0		168.0	54.0	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	hg19	CCDS47099.1																																																																																			.	.		0.478	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
NFKB1	4790	hgsc.bcm.edu	37	4	103498147	103498147	+	Silent	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:103498147T>G	ENST00000505458.1	+	7	796	c.519T>G	c.(517-519)ccT>ccG	p.P173P	NFKB1_ENST00000226574.4_Silent_p.P174P|NFKB1_ENST00000394820.4_Silent_p.P173P|NFKB1_ENST00000510638.1_3'UTR|NFKB1_ENST00000600343.1_5'Flank			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	173	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	TGGTGCACCCTGACCTTGCCT	0.493																																					p.P174P		Atlas-SNP	.											.	NFKB1	78	.	0			c.T522G						.						129.0	128.0	128.0					4																	103498147		2203	4300	6503	SO:0001819	synonymous_variant	4790	exon7			GCACCCTGACCTT	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.519T>G	chr4.hg19:g.103498147T>G		113.0	0.0		110.0	7.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	hg19	CCDS54783.1																																																																																			.	.		0.493	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
NFKB1	4790	hgsc.bcm.edu	37	4	103528382	103528382	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:103528382A>G	ENST00000505458.1	+	18	2304	c.2027A>G	c.(2026-2028)gAc>gGc	p.D676G	NFKB1_ENST00000226574.4_Missense_Mutation_p.D677G|NFKB1_ENST00000394820.4_Missense_Mutation_p.D676G|NFKB1_ENST00000600343.1_Missense_Mutation_p.D496G			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	676	Essential for interaction with HIF1AN.|Interaction with CFLAR.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	GCTGGGGCTGACGTCAATGCT	0.577																																					p.D677G		Atlas-SNP	.											.	NFKB1	78	.	0			c.A2030G						.						94.0	92.0	93.0					4																	103528382		2203	4300	6503	SO:0001583	missense	4790	exon18			GGGCTGACGTCAA	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.2027A>G	chr4.hg19:g.103528382A>G	ENSP00000424790:p.Asp676Gly	190.0	0.0		173.0	63.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	hg19	CCDS54783.1	.	.	.	.	.	.	.	.	.	.	A	14.76	2.632558	0.47049	.	.	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.43688	0.94;0.94;0.94	4.71	4.71	0.59529	Ankyrin repeat-containing domain (3);	0.124476	0.52532	D	0.000067	T	0.51261	0.1664	M	0.86097	2.795	0.36931	D	0.891897	P;P;P	0.41232	0.623;0.623;0.743	B;B;B	0.40825	0.341;0.223;0.281	T	0.67601	-0.5629	10	0.59425	D	0.04	.	14.4996	0.67711	1.0:0.0:0.0:0.0	.	496;676;677	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	G	677;676;676	ENSP00000226574:D677G;ENSP00000378297:D676G;ENSP00000424790:D676G	ENSP00000226574:D677G	D	+	2	0	NFKB1	103747420	0.739000	0.28196	0.869000	0.34112	0.577000	0.36160	4.877000	0.63086	1.872000	0.54250	0.533000	0.62120	GAC	.	.		0.577	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
TBCK	93627	hgsc.bcm.edu	37	4	107173107	107173107	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:107173107A>T	ENST00000273980.5	-	7	960	c.513T>A	c.(511-513)gaT>gaA	p.D171E	TBCK_ENST00000361687.4_Missense_Mutation_p.D108E|TBCK_ENST00000394706.3_Intron|TBCK_ENST00000432496.2_Missense_Mutation_p.D171E|TBCK_ENST00000394708.2_Missense_Mutation_p.D171E					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						TTGGCATGTGATCAGTGGTTT	0.368																																					p.D171E		Atlas-SNP	.											.	TBCK	89	.	0			c.T513A						.						106.0	105.0	105.0					4																	107173107		2203	4300	6503	SO:0001583	missense	93627	exon6			CATGTGATCAGTG		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.513T>A	chr4.hg19:g.107173107A>T	ENSP00000273980:p.Asp171Glu	108.0	0.0		115.0	36.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.915315	0.52546	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394708	T;T;T;T	0.62498	0.02;0.02;3.81;0.02	5.74	3.02	0.34903	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043220	0.85682	D	0.000000	T	0.42200	0.1192	L	0.28649	0.875	0.38524	D	0.948791	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.002	T	0.22521	-1.0214	10	0.19590	T	0.45	.	5.0969	0.14739	0.6474:0.0:0.2206:0.1321	.	171;108	Q8TEA7;Q8TEA7-3	TBCK_HUMAN;.	E	171;171;108;171	ENSP00000273980:D171E;ENSP00000405847:D171E;ENSP00000355338:D108E;ENSP00000378198:D171E	ENSP00000273980:D171E	D	-	3	2	TBCK	107392556	0.996000	0.38824	0.998000	0.56505	0.977000	0.68977	0.578000	0.23773	1.023000	0.39654	0.533000	0.62120	GAT	.	.		0.368	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
LRIT3	345193	hgsc.bcm.edu	37	4	110791477	110791477	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:110791477G>A	ENST00000594814.1	+	4	1572	c.1572G>A	c.(1570-1572)ggG>ggA	p.G524G	LRIT3_ENST00000327908.3_Silent_p.G341G|LRIT3_ENST00000409621.2_Silent_p.G341G|LRIT3_ENST00000379920.3_Silent_p.G479G	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	524	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		AGTATGGTGGGAAGGACCTGC	0.483																																					p.G524G		Atlas-SNP	.											.	LRIT3	107	.	0			c.G1572A						.						137.0	126.0	129.0					4																	110791477		2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			TGGTGGGAAGGAC	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1572G>A	chr4.hg19:g.110791477G>A		135.0	0.0		179.0	75.0	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	hg19	CCDS3688.3																																																																																			.	.		0.483	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
FAT4	79633	hgsc.bcm.edu	37	4	126241913	126241913	+	Silent	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:126241913A>C	ENST00000394329.3	+	1	4360	c.4347A>C	c.(4345-4347)gcA>gcC	p.A1449A		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1449	Cadherin 14. {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						ACCCTGATGCAGACATTAATG	0.408																																					p.A1449A		Atlas-SNP	.											.	FAT4	1752	.	0			c.A4347C						.						142.0	130.0	134.0					4																	126241913		1910	4136	6046	SO:0001819	synonymous_variant	79633	exon1			TGATGCAGACATT	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.4347A>C	chr4.hg19:g.126241913A>C		278.0	0.0		253.0	104.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.		0.408	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	hgsc.bcm.edu	37	4	126412250	126412250	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:126412250C>T	ENST00000394329.3	+	17	14286	c.14273C>T	c.(14272-14274)gCc>gTc	p.A4758V	FAT4_ENST00000335110.5_Missense_Mutation_p.A2999V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4758	Necessary and sufficient for interaction with MPDZ. {ECO:0000250}.				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						AGTCCTCAGGCCATGGCATCA	0.493																																					p.A4758V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C14273T						.						55.0	54.0	54.0					4																	126412250		2203	4300	6503	SO:0001583	missense	79633	exon17			CTCAGGCCATGGC	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.14273C>T	chr4.hg19:g.126412250C>T	ENSP00000377862:p.Ala4758Val	103.0	0.0		101.0	52.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	8.573	0.880562	0.17467	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.74106	-0.65;-0.81	4.87	4.02	0.46733	.	0.222293	0.22053	U	0.065298	T	0.57607	0.2065	N	0.14661	0.345	0.35823	D	0.824722	B;B;B	0.30634	0.288;0.19;0.288	B;B;B	0.29942	0.109;0.051;0.109	T	0.60110	-0.7327	10	0.23302	T	0.38	.	14.2568	0.66058	0.0:0.8501:0.1499:0.0	.	2999;4758;4757	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	V	4758;2999	ENSP00000377862:A4758V;ENSP00000335169:A2999V	ENSP00000335169:A2999V	A	+	2	0	FAT4	126631700	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	4.629000	0.61290	1.025000	0.39708	0.561000	0.74099	GCC	.	.		0.493	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
GATB	5188	hgsc.bcm.edu	37	4	152622627	152622627	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:152622627C>T	ENST00000515812.1	-	8	944	c.928G>A	c.(928-930)Gcc>Acc	p.A310T	PET112_ENST00000263985.6_Missense_Mutation_p.A351T														p.A351T(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						AGAGATGTGGCGTCGTAGAGC	0.562																																					p.A351T		Atlas-SNP	.											PET112,NS,carcinoma,0,1	PET112	43	.	1	Substitution - Missense(1)	endometrium(1)	c.G1051A						.						59.0	57.0	58.0					4																	152622627		2203	4300	6503	SO:0001583	missense	5188	exon9			ATGTGGCGTCGTA																												ENST00000515812.1:c.928G>A	chr4.hg19:g.152622627C>T	ENSP00000426859:p.Ala310Thr	106.0	0.0		88.0	35.0	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.751	0.703241	0.15172	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.45668	0.91;0.89	5.7	-11.4	0.00090	.	0.993958	0.08184	N	0.984946	T	0.16854	0.0405	N	0.08118	0	0.33990	D	0.649014	B	0.09022	0.002	B	0.08055	0.003	T	0.15206	-1.0445	10	0.29301	T	0.29	-24.3714	10.0843	0.42408	0.4981:0.3826:0.0:0.1193	.	351	O75879	GATB_HUMAN	T	351;310	ENSP00000263985:A351T;ENSP00000426859:A310T	ENSP00000263985:A351T	A	-	1	0	PET112	152842077	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-3.449000	0.00467	-3.065000	0.00255	-0.911000	0.02809	GCC	.	.		0.562	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
FBXW7	55294	hgsc.bcm.edu	37	4	153244121	153244121	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:153244121T>C	ENST00000281708.4	-	12	3265	c.2036A>G	c.(2035-2037)aAc>aGc	p.N679S	FBXW7_ENST00000393956.3_Missense_Mutation_p.N503S|FBXW7_ENST00000263981.5_Missense_Mutation_p.N599S|FBXW7_ENST00000603548.1_Missense_Mutation_p.N679S|RP11-461L13.3_ENST00000603766.1_lincRNA|FBXW7_ENST00000603841.1_Missense_Mutation_p.N679S|FBXW7_ENST00000296555.5_Missense_Mutation_p.N561S	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	679					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CAGCTTTGTGTTTGAGGCTCT	0.493			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																p.N679S		Atlas-SNP	.		Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	.	FBXW7	2157	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.A2036G						.						187.0	182.0	184.0					4																	153244121		2203	4300	6503	SO:0001583	missense	55294	exon12			TTTGTGTTTGAGG	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.2036A>G	chr4.hg19:g.153244121T>C	ENSP00000281708:p.Asn679Ser	198.0	0.0		198.0	90.0	NM_033632	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	hg19	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	T	2.458	-0.324730	0.05350	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);	0.127285	0.64402	D	0.000001	T	0.11707	0.0285	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.13145	0.001;0.006;0.004;0.007	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.14282	-1.0478	10	0.25751	T	0.34	-17.8896	15.9087	0.79450	0.0:0.0:0.0:1.0	.	503;679;561;599	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	S	679;561;599;503	ENSP00000281708:N679S;ENSP00000296555:N561S;ENSP00000263981:N599S;ENSP00000377528:N503S	ENSP00000263981:N599S	N	-	2	0	FBXW7	153463571	1.000000	0.71417	0.986000	0.45419	0.991000	0.79684	8.015000	0.88690	2.165000	0.68154	0.533000	0.62120	AAC	.	.		0.493	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
NPY2R	4887	hgsc.bcm.edu	37	4	156135360	156135360	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:156135360C>T	ENST00000329476.3	+	2	758	c.269C>T	c.(268-270)gCc>gTc	p.A90V	NPY2R_ENST00000506608.1_Missense_Mutation_p.A90V	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	90					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TTTTTCATTGCCAATCTGGCT	0.468																																					p.A90V		Atlas-SNP	.											.	NPY2R	87	.	0			c.C269T						.						109.0	109.0	109.0					4																	156135360		2203	4300	6503	SO:0001583	missense	4887	exon2			TCATTGCCAATCT	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"""GPCR / Class A : Neuropeptide receptors : Y"""	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.269C>T	chr4.hg19:g.156135360C>T	ENSP00000332591:p.Ala90Val	76.0	0.0		80.0	6.0	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.222658	0.39300	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.69561	-0.41;-0.41	5.51	5.51	0.81932	GPCR, rhodopsin-like superfamily (1);	0.052025	0.85682	D	0.000000	T	0.41419	0.1158	N	0.11201	0.11	0.46542	D	0.999094	P	0.38300	0.626	B	0.36092	0.217	T	0.50189	-0.8857	10	0.02654	T	1	.	12.1441	0.54014	0.0:0.9216:0.0:0.0784	.	90	P49146	NPY2R_HUMAN	V	90	ENSP00000332591:A90V;ENSP00000426366:A90V	ENSP00000332591:A90V	A	+	2	0	NPY2R	156354810	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.002000	0.40835	2.732000	0.93576	0.643000	0.83706	GCC	.	.		0.468	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
ETFDH	2110	hgsc.bcm.edu	37	4	159620153	159620153	+	Nonsense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:159620153T>A	ENST00000511912.1	+	9	1319	c.987T>A	c.(985-987)taT>taA	p.Y329*	U3_ENST00000607547.1_RNA|ETFDH_ENST00000307738.5_Nonsense_Mutation_p.Y282*	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	329					cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		GTCTAGACTATCAGAATCCAT	0.343																																					p.Y329X		Atlas-SNP	.											.	ETFDH	57	.	0			c.T987A						.						73.0	71.0	72.0					4																	159620153		2203	4300	6503	SO:0001587	stop_gained	2110	exon9			AGACTATCAGAAT	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.987T>A	chr4.hg19:g.159620153T>A	ENSP00000426638:p.Tyr329*	403.0	0.0		373.0	145.0	NM_004453	B4E3R9|J3KND9|Q7Z347	Nonsense_Mutation	SNP	ENST00000511912.1	hg19	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.150465	0.78001	.	.	ENSG00000171503	ENST00000511912;ENST00000507475;ENST00000307738	.	.	.	5.98	-0.254	0.12992	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8195	10.2326	0.43264	0.0:0.3431:0.0:0.6569	.	.	.	.	X	329;164;282	.	ENSP00000303552:Y282X	Y	+	3	2	ETFDH	159839603	0.998000	0.40836	0.996000	0.52242	0.950000	0.60333	0.491000	0.22419	0.169000	0.19679	-0.326000	0.08463	TAT	.	.		0.343	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2		
RAPGEF2	9693	hgsc.bcm.edu	37	4	160264434	160264434	+	Splice_Site	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:160264434A>T	ENST00000264431.4	+	16	3068	c.2649A>T	c.(2647-2649)ggA>ggT	p.G883G		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	883	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CAATTTCAGGAAATGACTCAA	0.423																																					p.G883G		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.A2649T						.						103.0	98.0	99.0					4																	160264434		1855	4093	5948	SO:0001630	splice_region_variant	9693	exon16			TTCAGGAAATGAC	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.2648-1A>T	chr4.hg19:g.160264434A>T		205.0	0.0		194.0	73.0	NM_014247	D3DP27	Silent	SNP	ENST00000264431.4	hg19	CCDS43277.1																																																																																			.	.		0.423	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	Silent
NPY1R	4886	hgsc.bcm.edu	37	4	164246566	164246566	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:164246566T>A	ENST00000296533.2	-	3	1575	c.1044A>T	c.(1042-1044)gaA>gaT	p.E348D	NPY1R_ENST00000509586.1_Missense_Mutation_p.E105D	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	348					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TGGCTATTGTTTCATAATCAT	0.388																																					p.E348D		Atlas-SNP	.											.	NPY1R	72	.	0			c.A1044T						.						152.0	158.0	156.0					4																	164246566		2203	4300	6503	SO:0001583	missense	4886	exon3			TATTGTTTCATAA		CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128		"""GPCR / Class A : Neuropeptide receptors : Y"""	7956	protein-coding gene	gene with protein product		162641		NPYR		8095935	Standard	NM_000909		Approved		uc003iqm.2	P25929		ENST00000296533.2:c.1044A>T	chr4.hg19:g.164246566T>A	ENSP00000354652:p.Glu348Asp	140.0	0.0		140.0	53.0	NM_000909	B2R6H5	Missense_Mutation	SNP	ENST00000296533.2	hg19	CCDS34089.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.117630	0.37339	.	.	ENSG00000164128	ENST00000296533;ENST00000509586	T;T	0.37752	1.18;1.18	5.69	1.94	0.25998	.	0.220246	0.38663	N	0.001615	T	0.28632	0.0709	L	0.42632	1.34	0.49687	D	0.999814	B	0.22800	0.075	B	0.19391	0.025	T	0.07770	-1.0755	10	0.48119	T	0.1	.	10.0344	0.42120	0.0:0.7263:0.0:0.2737	.	348	P25929	NPY1R_HUMAN	D	348;105	ENSP00000354652:E348D;ENSP00000427284:E105D	ENSP00000354652:E348D	E	-	3	2	NPY1R	164466016	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.348000	0.33987	0.336000	0.23639	-0.177000	0.13119	GAA	.	.		0.388	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364685.1		
NPY5R	4889	hgsc.bcm.edu	37	4	164272694	164272694	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:164272694T>C	ENST00000515560.1	+	4	2791	c.1269T>C	c.(1267-1269)atT>atC	p.I423I	NPY5R_ENST00000338566.3_Silent_p.I423I|NPY5R_ENST00000506953.1_Silent_p.I423I			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	423					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				TTAATCCAATTCTATATGGGT	0.318																																					p.I423I	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.T1269C						.						99.0	101.0	100.0					4																	164272694		2202	4300	6502	SO:0001819	synonymous_variant	4889	exon4			TCCAATTCTATAT	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"""GPCR / Class A : Neuropeptide receptors : Y"""	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.1269T>C	chr4.hg19:g.164272694T>C		131.0	0.0		121.0	47.0	NM_006174	Q6GTR7|Q92916	Silent	SNP	ENST00000515560.1	hg19	CCDS3804.1																																																																																			.	.		0.318	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174	
TLL1	7092	hgsc.bcm.edu	37	4	166987010	166987010	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:166987010T>C	ENST00000061240.2	+	16	2830	c.2183T>C	c.(2182-2184)tTc>tCc	p.F728S	TLL1_ENST00000507499.1_Missense_Mutation_p.F751S	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	728	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GCACATTTTTTCTCAGGTATA	0.333																																					p.F728S		Atlas-SNP	.											.	TLL1	194	.	0			c.T2183C						.						103.0	101.0	102.0					4																	166987010		2203	4299	6502	SO:0001583	missense	7092	exon16			ATTTTTTCTCAGG	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2183T>C	chr4.hg19:g.166987010T>C	ENSP00000061240:p.Phe728Ser	135.0	0.0		134.0	49.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.259036	0.80246	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;D	0.81659	1.77;-1.52	6.02	6.02	0.97574	CUB (3);	0.000000	0.85682	U	0.000000	D	0.85071	0.5613	L	0.37561	1.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.83562	0.0107	10	0.32370	T	0.25	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	751;728	E9PD25;O43897	.;TLL1_HUMAN	S	728;751	ENSP00000061240:F728S;ENSP00000426082:F751S	ENSP00000061240:F728S	F	+	2	0	TLL1	167206460	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	7.997000	0.88414	2.311000	0.77944	0.533000	0.62120	TTC	.	.		0.333	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
CLCN3	1182	hgsc.bcm.edu	37	4	170625277	170625277	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:170625277C>T	ENST00000513761.1	+	10	2251	c.1692C>T	c.(1690-1692)gtC>gtT	p.V564V	CLCN3_ENST00000347613.4_Silent_p.V564V|CLCN3_ENST00000360642.3_Silent_p.V537V|CLCN3_ENST00000504131.2_Silent_p.V547V	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	564					chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		GGTGTGAGGTCGGGGCTGATT	0.522																																					p.V564V		Atlas-SNP	.											.	CLCN3	85	.	0			c.C1692T						.						235.0	198.0	211.0					4																	170625277		2203	4300	6503	SO:0001819	synonymous_variant	1182	exon10			TGAGGTCGGGGCT	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"""Ion channels / Chloride channels : Voltage-sensitive"""	2021	protein-coding gene	gene with protein product		600580	"""chloride channel 3"""				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.1692C>T	chr4.hg19:g.170625277C>T		109.0	0.0		133.0	50.0	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Silent	SNP	ENST00000513761.1	hg19	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	C	9.300	1.052853	0.19907	.	.	ENSG00000109572	ENST00000515420	.	.	.	5.22	-9.53	0.00575	.	.	.	.	.	T	0.51686	0.1689	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63143	-0.6703	4	.	.	.	-1.8187	12.5309	0.56115	0.0:0.5393:0.0949:0.3658	.	.	.	.	L	219	.	.	S	+	2	0	CLCN3	170861852	0.001000	0.12720	0.880000	0.34516	0.941000	0.58515	-2.071000	0.01378	-1.434000	0.01975	-1.238000	0.01547	TCG	.	.		0.522	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2		
HAND2	9464	hgsc.bcm.edu	37	4	174450400	174450400	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:174450400T>C	ENST00000359562.4	-	1	980	c.41A>G	c.(40-42)cAc>cGc	p.H14R	HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000503474.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2_ENST00000505300.1_5'UTR|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502896.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000505032.1_RNA	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	14					adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|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 regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		GCCCTCGTGGTGCACCACCGG	0.741																																					p.H14R		Atlas-SNP	.											.	HAND2	25	.	0			c.A41G						.						2.0	3.0	3.0					4																	174450400		1327	2919	4246	SO:0001583	missense	9464	exon1			TCGTGGTGCACCA	AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"""Basic helix-loop-helix proteins"""	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.41A>G	chr4.hg19:g.174450400T>C	ENSP00000352565:p.His14Arg	63.0	0.0		50.0	19.0	NM_021973	B6ECG9|O95300|O95301|P97833|Q494T1	Missense_Mutation	SNP	ENST00000359562.4	hg19	CCDS3819.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030347	0.35797	.	.	ENSG00000164107	ENST00000359562;ENST00000393686	D	0.96745	-4.11	3.32	0.703	0.18116	.	0.056789	0.64402	D	0.000001	D	0.89639	0.6773	L	0.32530	0.975	0.47153	D	0.999333	B;P;B	0.47409	0.004;0.895;0.004	B;B;B	0.38056	0.004;0.264;0.007	T	0.82827	-0.0265	10	0.25106	T	0.35	-3.4584	5.6199	0.17451	0.0:0.0951:0.172:0.7329	.	14;14;14	B6ECG9;P61296;E9PCP7	.;HAND2_HUMAN;.	R	14	ENSP00000352565:H14R	ENSP00000352565:H14R	H	-	2	0	HAND2	174686975	1.000000	0.71417	0.447000	0.26932	0.942000	0.58702	4.109000	0.57824	-0.029000	0.13827	0.329000	0.21502	CAC	.	.		0.741	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3		
NEIL3	55247	hgsc.bcm.edu	37	4	178283576	178283576	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:178283576T>C	ENST00000264596.3	+	10	1887	c.1769T>C	c.(1768-1770)tTc>tCc	p.F590S		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	590					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		TGCAATTTTTTCCAGTGGGCA	0.373								Base excision repair (BER), DNA glycosylases																													p.F590S		Atlas-SNP	.											.	NEIL3	89	.	0			c.T1769C						.						74.0	82.0	79.0					4																	178283576		2202	4300	6502	SO:0001583	missense	55247	exon10			ATTTTTTCCAGTG	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1769T>C	chr4.hg19:g.178283576T>C	ENSP00000264596:p.Phe590Ser	248.0	0.0		258.0	113.0	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	hg19	CCDS3828.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454920	0.84209	.	.	ENSG00000109674	ENST00000264596	T	0.58940	0.3	5.16	5.16	0.70880	Zinc finger, GRF-type (1);	0.000000	0.85682	D	0.000000	D	0.83820	0.5337	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89525	0.3781	10	0.87932	D	0	-18.0468	15.3044	0.73982	0.0:0.0:0.0:1.0	.	590	Q8TAT5	NEIL3_HUMAN	S	590	ENSP00000264596:F590S	ENSP00000264596:F590S	F	+	2	0	NEIL3	178520570	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.811000	0.86092	2.096000	0.63516	0.402000	0.26972	TTC	.	.		0.373	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
DCTD	1635	hgsc.bcm.edu	37	4	183815749	183815749	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:183815749G>A	ENST00000438320.2	-	4	544	c.254C>T	c.(253-255)gCg>gTg	p.A85V	DCTD_ENST00000357067.3_Missense_Mutation_p.A96V|DCTD_ENST00000510370.1_Missense_Mutation_p.A85V	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	85					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	dCMP deaminase activity (GO:0004132)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|urinary_tract(1)	18		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)	Cytarabine(DB00987)	ATTCAGCTCCGCATGGCACAC	0.423																																					p.A96V		Atlas-SNP	.											.	DCTD	30	.	0			c.C287T						.						160.0	135.0	143.0					4																	183815749		2203	4300	6503	SO:0001583	missense	1635	exon4			AGCTCCGCATGGC	L12136	CCDS3831.1, CCDS34108.1	4q35.1	2008-08-01			ENSG00000129187	ENSG00000129187	3.5.4.12		2710	protein-coding gene	gene with protein product		607638					Standard	XM_005262778		Approved		uc003ivg.3	P32321	OTTHUMG00000160685	ENST00000438320.2:c.254C>T	chr4.hg19:g.183815749G>A	ENSP00000398194:p.Ala85Val	101.0	0.0		95.0	23.0	NM_001012732	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Missense_Mutation	SNP	ENST00000438320.2	hg19	CCDS3831.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.527635	0.64860	.	.	ENSG00000129187	ENST00000357067;ENST00000438320;ENST00000510370;ENST00000503182;ENST00000510307;ENST00000512766;ENST00000514754	T;T;T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	5.53	3.79	0.43588	APOBEC/CMP deaminase, zinc-binding (1);Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.094486	0.64402	D	0.000001	D	0.91693	0.7374	H	0.99464	4.58	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.93991	0.7267	10	0.87932	D	0	-2.1914	12.4035	0.55426	0.1389:0.0:0.8611:0.0	.	85;26;96;85	D6RBJ9;B4DDC2;P32321-2;P32321	.;.;.;DCTD_HUMAN	V	96;85;85;85;85;85;85	ENSP00000349576:A96V;ENSP00000398194:A85V;ENSP00000424017:A85V;ENSP00000422662:A85V;ENSP00000424050:A85V;ENSP00000423182:A85V;ENSP00000423894:A85V	ENSP00000349576:A96V	A	-	2	0	DCTD	184052743	1.000000	0.71417	0.068000	0.19968	0.426000	0.31534	9.813000	0.99286	1.337000	0.45525	0.650000	0.86243	GCG	.	.		0.423	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2		
ADCY2	108	hgsc.bcm.edu	37	5	7706967	7706967	+	Nonsense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:7706967C>A	ENST00000338316.4	+	8	1309	c.1220C>A	c.(1219-1221)tCa>tAa	p.S407*	RP11-711G10.1_ENST00000514105.2_RNA|ADCY2_ENST00000537121.1_Nonsense_Mutation_p.S227*	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	407					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						GATGTGTGGTCACATGATGTG	0.502																																					p.S407X		Atlas-SNP	.											.	ADCY2	337	.	0			c.C1220A						.						218.0	191.0	200.0					5																	7706967		2203	4300	6503	SO:0001587	stop_gained	108	exon8			TGTGGTCACATGA	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1220C>A	chr5.hg19:g.7706967C>A	ENSP00000342952:p.Ser407*	131.0	0.0		141.0	32.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Nonsense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	39	7.303778	0.98200	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.964	0.92687	0.0:1.0:0.0:0.0	.	.	.	.	X	407;258;227	.	ENSP00000342952:S407X	S	+	2	0	ADCY2	7759967	1.000000	0.71417	0.987000	0.45799	0.983000	0.72400	7.602000	0.82796	2.480000	0.83734	0.655000	0.94253	TCA	.	.		0.502	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
FASTKD3	79072	hgsc.bcm.edu	37	5	7867406	7867406	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:7867406T>C	ENST00000264669.5	-	2	927	c.791A>G	c.(790-792)cAg>cGg	p.Q264R	MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000502509.1_Intron|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000341013.6_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	264					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						AGTACATGCCTGCAAGATTCT	0.353																																					p.Q264R		Atlas-SNP	.											.	FASTKD3	88	.	0			c.A791G						.						81.0	89.0	86.0					5																	7867406		2202	4300	6502	SO:0001583	missense	79072	exon2			CATGCCTGCAAGA	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.791A>G	chr5.hg19:g.7867406T>C	ENSP00000264669:p.Gln264Arg	57.0	0.0		64.0	27.0	NM_024091	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	hg19	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	T	19.85	3.904177	0.72754	.	.	ENSG00000124279	ENST00000264669	T	0.32753	1.44	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	M	0.76002	2.32	0.47374	D	0.999407	D	0.76494	0.999	D	0.66351	0.943	T	0.48758	-0.9007	10	0.15066	T	0.55	-21.4257	14.6078	0.68493	0.0:0.0:0.0:1.0	.	264	Q14CZ7	FAKD3_HUMAN	R	264	ENSP00000264669:Q264R	ENSP00000264669:Q264R	Q	-	2	0	FASTKD3	7920406	1.000000	0.71417	0.896000	0.35187	0.956000	0.61745	4.060000	0.57477	2.024000	0.59613	0.528000	0.53228	CAG	.	.		0.353	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
DNAH5	1767	hgsc.bcm.edu	37	5	13911493	13911493	+	Splice_Site	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:13911493A>C	ENST00000265104.4	-	12	1749		c.e12+1			NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TATACAACCTACATGAAGGTC	0.363									Kartagener syndrome																												.		Atlas-SNP	.											.	DNAH5	868	.	0			c.1644+2T>G						.						116.0	113.0	114.0					5																	13911493		2202	4300	6502	SO:0001630	splice_region_variant	1767	exon13	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAACCTACATGAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.1644+1T>G	chr5.hg19:g.13911493A>C		67.0	0.0		64.0	26.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Splice_Site	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306232	0.81247	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0858	0.81049	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNAH5	13964493	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.320000	0.89995	2.264000	0.75181	0.533000	0.62120	.	.	.		0.363	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	Intron
MYO10	4651	hgsc.bcm.edu	37	5	16818199	16818199	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:16818199A>G	ENST00000513610.1	-	3	652	c.198T>C	c.(196-198)gaT>gaC	p.D66D	MYO10_ENST00000507288.1_Silent_p.D66D	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	66	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						ACGCCATGTCATCCACGCCCT	0.468																																					p.D66D		Atlas-SNP	.											.	MYO10	198	.	0			c.T198C						.						70.0	70.0	70.0					5																	16818199		1986	4158	6144	SO:0001819	synonymous_variant	4651	exon3			CATGTCATCCACG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.198T>C	chr5.hg19:g.16818199A>G		77.0	0.0		67.0	29.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.468	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
CDH10	1008	hgsc.bcm.edu	37	5	24509863	24509863	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:24509863A>T	ENST00000264463.4	-	7	1575	c.1068T>A	c.(1066-1068)gaT>gaA	p.D356E		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	356	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		AAAAACGGGGATCTACATGGG	0.373										HNSCC(23;0.051)																											p.D356E		Atlas-SNP	.											.	CDH10	391	.	0			c.T1068A						.						73.0	75.0	74.0					5																	24509863		2203	4300	6503	SO:0001583	missense	1008	exon7			ACGGGGATCTACA	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"""Cadherins / Major cadherins"""	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1068T>A	chr5.hg19:g.24509863A>T	ENSP00000264463:p.Asp356Glu	238.0	0.0		246.0	57.0	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	hg19	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358179	0.41801	.	.	ENSG00000040731	ENST00000264463	T	0.50001	0.76	5.03	1.21	0.21127	Cadherin (4);Cadherin-like (1);	0.047005	0.85682	D	0.000000	T	0.36580	0.0972	L	0.43554	1.36	0.34979	D	0.75387	B	0.17465	0.022	B	0.24394	0.053	T	0.31364	-0.9946	10	0.42905	T	0.14	.	8.0783	0.30729	0.6816:0.0:0.3184:0.0	.	356	Q9Y6N8	CAD10_HUMAN	E	356	ENSP00000264463:D356E	ENSP00000264463:D356E	D	-	3	2	CDH10	24545620	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	0.773000	0.26661	0.036000	0.15547	0.459000	0.35465	GAT	.	.		0.373	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
PDZD2	23037	hgsc.bcm.edu	37	5	32088757	32088757	+	Nonsense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:32088757G>T	ENST00000438447.1	+	20	5591	c.5203G>T	c.(5203-5205)Gaa>Taa	p.E1735*	PDZD2_ENST00000282493.3_Nonsense_Mutation_p.E1735*			O15018	PDZD2_HUMAN	PDZ domain containing 2	1735					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						AAATGGCTTGGAACATGACCT	0.493																																					p.E1735X		Atlas-SNP	.											PDZD2,NS,malignant_melanoma,0,1	PDZD2	306	.	0			c.G5203T						.						129.0	105.0	113.0					5																	32088757		2203	4300	6503	SO:0001587	stop_gained	23037	exon19			GGCTTGGAACATG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.5203G>T	chr5.hg19:g.32088757G>T	ENSP00000402033:p.Glu1735*	157.0	0.0		122.0	48.0	NM_178140	Q9BXD4	Nonsense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	46	12.771677	0.99695	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	.	.	.	5.84	5.84	0.93424	.	0.864075	0.10208	N	0.702481	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	15.6279	0.76878	0.0:0.0:1.0:0.0	.	.	.	.	X	1735;1536;1735	.	ENSP00000282493:E1735X	E	+	1	0	PDZD2	32124514	0.790000	0.28787	0.007000	0.13788	0.002000	0.02628	2.805000	0.47939	2.768000	0.95171	0.561000	0.74099	GAA	.	.		0.493	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
DNAJC21	134218	hgsc.bcm.edu	37	5	34935891	34935891	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:34935891C>T	ENST00000342382.4	+	3	495	c.268C>T	c.(268-270)Cgc>Tgc	p.R90C	DNAJC21_ENST00000382021.2_Missense_Mutation_p.R90C|DNAJC21_ENST00000303525.7_Missense_Mutation_p.R90C			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	90					protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			AGATTTGCTACGCTATTTCAC	0.363																																					p.R90C		Atlas-SNP	.											.	DNAJC21	54	.	0			c.C268T						.						151.0	148.0	149.0					5																	34935891		2203	4300	6503	SO:0001583	missense	134218	exon3			TTGCTACGCTATT		CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"""Heat shock proteins / DNAJ (HSP40)"""	27030	protein-coding gene	gene with protein product	"""JJJ1 DnaJ domain protein homolog (S. cerevisiae)"""					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.268C>T	chr5.hg19:g.34935891C>T	ENSP00000343728:p.Arg90Cys	122.0	0.0		115.0	46.0	NM_001012339	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Missense_Mutation	SNP	ENST00000342382.4	hg19	CCDS34144.1	.	.	.	.	.	.	.	.	.	.	C	16.32	3.090522	0.55968	.	.	ENSG00000168724	ENST00000342382;ENST00000382021;ENST00000303525	T;T;T	0.73152	-0.72;-0.72;-0.72	5.62	4.75	0.60458	.	0.267930	0.44097	D	0.000488	T	0.58836	0.2150	L	0.31476	0.935	0.48975	D	0.999737	B;B	0.11235	0.002;0.004	B;B	0.06405	0.002;0.001	T	0.54827	-0.8235	10	0.37606	T	0.19	-3.5566	13.9574	0.64157	0.0:0.928:0.0:0.072	.	90;90	Q5F1R6;Q5F1R6-2	DJC21_HUMAN;.	C	90	ENSP00000343728:R90C;ENSP00000371451:R90C;ENSP00000306289:R90C	ENSP00000306289:R90C	R	+	1	0	DNAJC21	34971648	1.000000	0.71417	0.998000	0.56505	0.920000	0.55202	4.580000	0.60942	2.648000	0.89879	0.650000	0.86243	CGC	.	.		0.363	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283	
UTP15	84135	hgsc.bcm.edu	37	5	72864403	72864403	+	Silent	SNP	C	C	T	rs112684902		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:72864403C>T	ENST00000296792.4	+	4	597	c.342C>T	c.(340-342)ccC>ccT	p.P114P	UTP15_ENST00000543251.1_5'UTR|UTP15_ENST00000508491.1_Silent_p.P95P|ANKRA2_ENST00000296785.3_5'Flank	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	114					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GGAGGGCTCCCCTCAGGCAGT	0.423																																					p.P114P		Atlas-SNP	.											.	UTP15	30	.	0			c.C342T						.						83.0	85.0	85.0					5																	72864403		2203	4300	6503	SO:0001819	synonymous_variant	84135	exon4			GGCTCCCCTCAGG	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"""WD repeat domain containing"""	25758	protein-coding gene	gene with protein product			"""UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.342C>T	chr5.hg19:g.72864403C>T		89.0	0.0		104.0	43.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Silent	SNP	ENST00000296792.4	hg19	CCDS34186.1	.	.	.	.	.	.	.	.	.	.	C	9.184	1.024234	0.19433	.	.	ENSG00000164338	ENST00000509005	T	0.60299	0.2	5.55	-6.61	0.01818	.	0.114641	0.64402	D	0.000004	T	0.39489	0.1080	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27123	-1.0083	6	.	.	.	.	1.4894	0.02453	0.1935:0.3001:0.2796:0.2268	.	.	.	.	L	141	ENSP00000421669:P141L	.	P	+	2	0	UTP15	72900159	0.009000	0.17119	0.933000	0.37362	0.999000	0.98932	-1.208000	0.03005	-0.892000	0.03935	0.655000	0.94253	CCC	.	C|0.500;T|0.500		0.423	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73128204	73128204	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:73128204A>G	ENST00000426542.2	+	9	1086	c.1066A>G	c.(1066-1068)Aca>Gca	p.T356A	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.T356A|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.T356A|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.T356A|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.T356A|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.T43A|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.T356A			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	356					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)										GCCGCCCTCGACATTGCTTGC	0.443																																					p.T356A		Atlas-SNP	.											.	.	.	.	0			c.A1066G						.						82.0	74.0	77.0					5																	73128204		1904	4118	6022	SO:0001583	missense	64283	exon10			CCCTCGACATTGC		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.1066A>G	chr5.hg19:g.73128204A>G	ENSP00000412175:p.Thr356Ala	108.0	0.0		96.0	7.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	4.301	0.055104	0.08291	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.12879	2.9;2.9;2.9;2.64;2.9;2.9;2.77	5.48	-11.0	0.00169	.	.	.	.	.	T	0.04543	0.0124	N	0.10874	0.06	0.09310	N	1	B;B;B;B;B	0.09022	0.001;0.002;0.0;0.001;0.001	B;B;B;B;B	0.08055	0.002;0.003;0.002;0.003;0.003	T	0.30238	-0.9985	9	0.26408	T	0.33	.	4.6539	0.12608	0.2743:0.1912:0.4408:0.0937	.	43;356;356;356;356	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	A	356;356;356;356;356;356;43	ENSP00000296794:T356A;ENSP00000441913:T356A;ENSP00000441436:T356A;ENSP00000287898:T356A;ENSP00000411459:T356A;ENSP00000412175:T356A;ENSP00000296799:T43A	ENSP00000287898:T356A	T	+	1	0	RP11-428C6.1	73163960	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.004000	0.03678	-2.654000	0.00422	-0.263000	0.10527	ACA	.	.		0.443	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73179659	73179659	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:73179659G>A	ENST00000426542.2	+	23	3025	c.3005G>A	c.(3004-3006)cGt>cAt	p.R1002H	ARHGEF28_ENST00000512883.1_5'Flank|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.R1002H|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.R689H|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.R1002H			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1002	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)										GTCACTCAGCGTATTACAAAA	0.363																																					p.R1002H		Atlas-SNP	.											.	.	.	.	0			c.G3005A						.						56.0	54.0	55.0					5																	73179659		1847	4074	5921	SO:0001583	missense	64283	exon24			CTCAGCGTATTAC		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.3005G>A	chr5.hg19:g.73179659G>A	ENSP00000412175:p.Arg1002His	175.0	0.0		144.0	61.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	G	34	5.388581	0.95988	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	D;D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.75	5.75	0.90469	Dbl homology (DH) domain (5);	.	.	.	.	D	0.95268	0.8465	M	0.91140	3.18	0.54753	D	0.999986	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95620	0.8680	9	0.87932	D	0	.	19.9433	0.97172	0.0:0.0:1.0:0.0	.	689;1002;1002;1002	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	H	1002;1002;1002;1002;1002;1002;689	ENSP00000296794:R1002H;ENSP00000441913:R1002H;ENSP00000441436:R1002H;ENSP00000287898:R1002H;ENSP00000411459:R1002H;ENSP00000412175:R1002H;ENSP00000296799:R689H	ENSP00000287898:R1002H	R	+	2	0	RP11-428C6.1	73215415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.390000	0.97246	2.716000	0.92895	0.655000	0.94253	CGT	.	.		0.363	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
HMGCR	3156	hgsc.bcm.edu	37	5	74650434	74650434	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:74650434T>C	ENST00000287936.4	+	12	1631	c.1475T>C	c.(1474-1476)gTa>gCa	p.V492A	HMGCR_ENST00000511206.1_Missense_Mutation_p.V492A|HMGCR_ENST00000343975.5_Missense_Mutation_p.V492A	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	492	Catalytic.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	GAGCGTGGTGTATCTATTCGC	0.408																																					p.V492A		Atlas-SNP	.											.	HMGCR	53	.	0			c.T1475C						.						136.0	117.0	123.0					5																	74650434		2203	4300	6503	SO:0001583	missense	3156	exon12			GTGGTGTATCTAT		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"""hydroxymethylglutaryl-CoA reductase"", ""3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"""	142910	"""3-hydroxy-3-methylglutaryl-Coenzyme A reductase"""				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.1475T>C	chr5.hg19:g.74650434T>C	ENSP00000287936:p.Val492Ala	154.0	0.0		124.0	57.0	NM_001130996	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	hg19	CCDS4027.1	.	.	.	.	.	.	.	.	.	.	T	19.59	3.855882	0.71834	.	.	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.48201	0.82;0.82;0.87	5.14	3.94	0.45596	Hydroxymethylglutaryl-CoA reductase, N-terminal (1);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);	0.000000	0.85682	D	0.000000	T	0.59569	0.2203	L	0.48935	1.535	0.80722	D	1	P;D;P	0.89917	0.474;1.0;0.474	P;D;P	0.87578	0.785;0.998;0.785	T	0.57093	-0.7870	10	0.42905	T	0.14	-12.7489	12.1695	0.54150	0.0:0.0:0.1432:0.8568	.	492;492;492	B2R649;P04035-2;P04035	.;.;HMDH_HUMAN	A	492;423;492;492	ENSP00000426745:V492A;ENSP00000287936:V492A;ENSP00000340816:V492A	ENSP00000287936:V492A	V	+	2	0	HMGCR	74686190	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	7.667000	0.83888	0.878000	0.35920	0.383000	0.25322	GTA	.	.		0.408	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2		
AGGF1	55109	hgsc.bcm.edu	37	5	76342271	76342271	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:76342271A>G	ENST00000312916.7	+	6	1352	c.970A>G	c.(970-972)Att>Gtt	p.I324V		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	324					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		CAAAATAGGCATTCATCACAA	0.363																																					p.I324V		Atlas-SNP	.											.	AGGF1	71	.	0			c.A970G						.						112.0	120.0	117.0					5																	76342271		2203	4300	6503	SO:0001583	missense	55109	exon6			ATAGGCATTCATC	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.970A>G	chr5.hg19:g.76342271A>G	ENSP00000316109:p.Ile324Val	291.0	0.0		277.0	14.0	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	hg19	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.357510	0.00214	.	.	ENSG00000164252	ENST00000312916	T	0.35236	1.32	5.29	0.123	0.14709	.	1.373260	0.04317	N	0.349998	T	0.20941	0.0504	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16808	-1.0390	10	0.27082	T	0.32	-26.3289	4.8384	0.13476	0.5717:0.0:0.297:0.1314	.	324	Q8N302	AGGF1_HUMAN	V	324	ENSP00000316109:I324V	ENSP00000316109:I324V	I	+	1	0	AGGF1	76378027	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	0.453000	0.21811	0.010000	0.14839	0.482000	0.46254	ATT	.	.		0.363	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
AP3B1	8546	hgsc.bcm.edu	37	5	77423904	77423904	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:77423904G>A	ENST00000255194.6	-	17	2093	c.1918C>T	c.(1918-1920)Cca>Tca	p.P640S	AP3B1_ENST00000519295.1_Missense_Mutation_p.P591S	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	640					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GCCACCTCTGGCCAATTAGAT	0.393									Hermansky-Pudlak syndrome																												p.P640S		Atlas-SNP	.											.	AP3B1	94	.	0			c.C1918T						.						74.0	76.0	75.0					5																	77423904		2203	4300	6503	SO:0001583	missense	8546	exon17	Familial Cancer Database	HPS, HPS1-8	CCTCTGGCCAATT	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1918C>T	chr5.hg19:g.77423904G>A	ENSP00000255194:p.Pro640Ser	106.0	0.0		113.0	39.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.910962	0.72983	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.58358	0.34;0.34	5.91	5.91	0.95273	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.77150	0.4088	M	0.88704	2.975	0.80722	D	1	D	0.60160	0.987	P	0.62298	0.9	T	0.80529	-0.1342	10	0.87932	D	0	-13.6369	20.2983	0.98569	0.0:0.0:1.0:0.0	.	640	O00203	AP3B1_HUMAN	S	640;591;640;544	ENSP00000255194:P640S;ENSP00000430597:P591S	ENSP00000255194:P640S	P	-	1	0	AP3B1	77459660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.845000	0.99498	2.802000	0.96397	0.655000	0.94253	CCA	.	.		0.393	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
CMYA5	202333	hgsc.bcm.edu	37	5	79033682	79033682	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:79033682T>A	ENST00000446378.2	+	2	9125	c.9094T>A	c.(9094-9096)Tcc>Acc	p.S3032T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3032					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AGAAGAGATATCCACAGATTC	0.313																																					p.S3032T		Atlas-SNP	.											.	CMYA5	643	.	0			c.T9094A						.						54.0	52.0	53.0					5																	79033682		1798	4067	5865	SO:0001583	missense	202333	exon2			GAGATATCCACAG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9094T>A	chr5.hg19:g.79033682T>A	ENSP00000394770:p.Ser3032Thr	473.0	0.0		440.0	179.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	T	6.040	0.375720	0.11409	.	.	ENSG00000164309	ENST00000446378	T	0.15952	2.38	5.93	-11.7	0.00046	.	1.351940	0.04712	N	0.417809	T	0.13286	0.0322	L	0.56769	1.78	0.09310	N	1	B	0.21381	0.055	B	0.20955	0.032	T	0.24048	-1.0171	10	0.59425	D	0.04	.	5.4465	0.16537	0.0849:0.3216:0.4121:0.1815	.	3032	Q8N3K9	CMYA5_HUMAN	T	3032	ENSP00000394770:S3032T	ENSP00000394770:S3032T	S	+	1	0	CMYA5	79069438	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.914000	0.04038	-2.465000	0.00533	-0.313000	0.08912	TCC	.	.		0.313	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ZFYVE16	9765	hgsc.bcm.edu	37	5	79734315	79734315	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:79734315C>T	ENST00000338008.5	+	3	1991	c.1811C>T	c.(1810-1812)aCa>aTa	p.T604I	ZFYVE16_ENST00000510158.1_Missense_Mutation_p.T604I|ZFYVE16_ENST00000505560.1_Missense_Mutation_p.T604I	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	604					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		AAACAAAATACAATAGAAAAT	0.323																																					p.T604I	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.C1811T						.						67.0	78.0	74.0					5																	79734315		2202	4295	6497	SO:0001583	missense	9765	exon4			AAAATACAATAGA	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"""Zinc fingers, FYVE domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20756	protein-coding gene	gene with protein product	"""endofin"", ""protein phosphatase 1, regulatory subunit 69"""	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.1811C>T	chr5.hg19:g.79734315C>T	ENSP00000337159:p.Thr604Ile	418.0	0.0		456.0	202.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	hg19	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	C	2.829	-0.242975	0.05906	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.39592	1.07;1.07;1.07	5.42	-0.906	0.10524	.	1.075510	0.07096	N	0.839533	T	0.29716	0.0742	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.32241	-0.9914	10	0.56958	D	0.05	0.35	5.4894	0.16767	0.1424:0.3281:0.0:0.5295	.	604;604	Q7Z3T8-3;Q7Z3T8	.;ZFY16_HUMAN	I	604	ENSP00000337159:T604I;ENSP00000423663:T604I;ENSP00000426848:T604I	ENSP00000337159:T604I	T	+	2	0	ZFYVE16	79770071	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-0.198000	0.09505	-0.097000	0.12307	0.650000	0.86243	ACA	.	.		0.323	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733	
NR2F1	7025	hgsc.bcm.edu	37	5	92923770	92923770	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:92923770G>A	ENST00000327111.3	+	2	2298	c.611G>A	c.(610-612)gGc>gAc	p.G204D	NR2F1-AS1_ENST00000513055.1_RNA	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	204					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		TCGCGCTACGGCAGCCAGTGC	0.657																																					p.G204D		Atlas-SNP	.											.	NR2F1	56	.	0			c.G611A						.						66.0	66.0	66.0					5																	92923770		2203	4299	6502	SO:0001583	missense	7025	exon2			GCTACGGCAGCCA	BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"""Nuclear hormone receptors"""	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.611G>A	chr5.hg19:g.92923770G>A	ENSP00000325819:p.Gly204Asp	179.0	0.0		193.0	80.0	NM_005654		Missense_Mutation	SNP	ENST00000327111.3	hg19	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994603	0.93167	.	.	ENSG00000175745	ENST00000327111	T	0.51574	0.7	4.39	4.39	0.52855	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	T	0.55847	0.1946	L	0.58583	1.82	0.80722	D	1	P	0.41673	0.759	P	0.49853	0.624	T	0.53613	-0.8414	10	0.30078	T	0.28	.	17.1166	0.86690	0.0:0.0:1.0:0.0	.	204	P10589	COT1_HUMAN	D	204	ENSP00000325819:G204D	ENSP00000325819:G204D	G	+	2	0	NR2F1	92949526	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	9.554000	0.98121	2.250000	0.74265	0.462000	0.41574	GGC	.	.		0.657	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654	
TRIM36	55521	hgsc.bcm.edu	37	5	114462349	114462349	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:114462349A>G	ENST00000282369.3	-	10	2159	c.2038T>C	c.(2038-2040)Tat>Cat	p.Y680H	TRIM36_ENST00000513154.1_Missense_Mutation_p.Y668H|TRIM36_ENST00000514154.1_Missense_Mutation_p.Y525H	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	680	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		TCCATATCATAGAAATCTACT	0.398																																					p.Y680H		Atlas-SNP	.											.	TRIM36	126	.	0			c.T2038C						.						98.0	90.0	93.0					5																	114462349		2202	4300	6502	SO:0001583	missense	55521	exon10			TATCATAGAAATC	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16280	protein-coding gene	gene with protein product	"""zinc-binding protein Rbcc728"", ""tripartite motif protein 36"", ""RING finger protein 98"""	609317	"""tripartite motif-containing 36"""			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.2038T>C	chr5.hg19:g.114462349A>G	ENSP00000282369:p.Tyr680His	141.0	0.0		136.0	62.0	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	hg19	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.112104	0.77210	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.65549	-0.16;-0.16;-0.16	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.058778	0.64402	D	0.000001	D	0.83050	0.5170	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86561	0.1841	10	0.72032	D	0.01	.	16.3197	0.82945	1.0:0.0:0.0:0.0	.	668;680	E9PFI8;Q9NQ86	.;TRI36_HUMAN	H	680;668;525	ENSP00000282369:Y680H;ENSP00000423934:Y668H;ENSP00000424259:Y525H	ENSP00000282369:Y680H	Y	-	1	0	TRIM36	114490248	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.920000	0.75799	2.302000	0.77476	0.533000	0.62120	TAT	.	.		0.398	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700	
TICAM2	353376	hgsc.bcm.edu	37	5	114916490	114916490	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:114916490G>A	ENST00000427199.2	-	2	905	c.464C>T	c.(463-465)aCg>aTg	p.T155M	TICAM2_ENST00000513729.1_5'Flank|TMED7-TICAM2_ENST00000282382.4_Missense_Mutation_p.T324M|TICAM2_ENST00000408996.4_Missense_Mutation_p.T324M|TMED7-TICAM2_ENST00000333314.3_3'UTR	NM_021649.6	NP_067681.1	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2	155	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to lipopolysaccharide (GO:0071222)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18-mediated signaling pathway (GO:2000494)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|response to interleukin-12 (GO:0070671)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			cervix(1)|kidney(1)|lung(2)|soft_tissue(1)	5		all_cancers(142;0.0223)|all_epithelial(76;0.000869)|Prostate(80;0.0115)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;4.38e-07)|Epithelial(69;1.62e-06)|all cancers(49;6.93e-05)		CATTAGGGACGTATAGAACTG	0.418																																					p.T324M		Atlas-SNP	.											.	.	.	.	0			c.C971T						.						69.0	72.0	71.0					5																	114916490		2202	4300	6502	SO:0001583	missense	100302736	exon4			AGGGACGTATAGA	AY232653	CCDS4119.1	5q22.3	2012-11-21			ENSG00000243414	ENSG00000243414			21354	protein-coding gene	gene with protein product		608321					Standard	NM_021649		Approved	TRAM, TICAM-2, TIRP		Q86XR7	OTTHUMG00000162905	ENST00000427199.2:c.464C>T	chr5.hg19:g.114916490G>A	ENSP00000415139:p.Thr155Met	125.0	0.0		123.0	42.0	NM_001164468	B3Y698|Q6JUT2	Missense_Mutation	SNP	ENST00000427199.2	hg19	CCDS4119.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.744707	0.49151	.	.	ENSG00000243414;ENSG00000243414;ENSG00000251201	ENST00000408996;ENST00000427199;ENST00000282382	T;T;T	0.46063	0.88;0.88;0.88	5.74	4.87	0.63330	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.481755	0.19085	N	0.123129	T	0.49133	0.1539	L	0.29908	0.895	0.23962	N	0.996337	D;D	0.76494	0.999;0.999	P;D	0.65323	0.85;0.934	T	0.39563	-0.9608	10	0.52906	T	0.07	.	11.9164	0.52767	0.0818:0.0:0.9182:0.0	.	324;155	Q6JUT2;Q86XR7	.;TCAM2_HUMAN	M	324;155;324	ENSP00000386341:T324M;ENSP00000415139:T155M;ENSP00000282382:T324M	ENSP00000415139:T155M	T	-	2	0	TICAM2;TMED7-TICAM2	114944389	0.379000	0.25123	0.029000	0.17559	0.302000	0.27658	2.573000	0.46007	1.421000	0.47157	0.585000	0.79938	ACG	.	.		0.418	TICAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338755.1	NM_021649	
SRFBP1	153443	hgsc.bcm.edu	37	5	121356208	121356208	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:121356208T>A	ENST00000339397.4	+	6	850	c.778T>A	c.(778-780)Tat>Aat	p.Y260N		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)		GGAGAAGGAATATTTTGATGA	0.403																																					p.Y260N		Atlas-SNP	.											.	SRFBP1	47	.	0			c.T778A						.						132.0	119.0	123.0					5																	121356208		1876	4119	5995	SO:0001583	missense	153443	exon6			AAGGAATATTTTG	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.778T>A	chr5.hg19:g.121356208T>A	ENSP00000341324:p.Tyr260Asn	284.0	0.0		300.0	118.0	NM_152546		Missense_Mutation	SNP	ENST00000339397.4	hg19	CCDS43354.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.852647	0.51270	.	.	ENSG00000151304	ENST00000339397	.	.	.	5.71	4.54	0.55810	.	0.055267	0.85682	D	0.000000	T	0.68531	0.3011	M	0.67397	2.05	0.58432	D	0.999992	D	0.61080	0.989	P	0.57057	0.812	T	0.71513	-0.4570	9	0.72032	D	0.01	-12.1589	13.0005	0.58672	0.0:0.0:0.1351:0.8649	.	260	Q8NEF9	SRFB1_HUMAN	N	260	.	ENSP00000341324:Y260N	Y	+	1	0	SRFBP1	121384107	1.000000	0.71417	0.975000	0.42487	0.491000	0.33493	4.744000	0.62118	0.974000	0.38366	0.460000	0.39030	TAT	.	.		0.403	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
FNIP1	96459	hgsc.bcm.edu	37	5	131007515	131007515	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:131007515A>G	ENST00000510461.1	-	14	2717	c.2622T>C	c.(2620-2622)tgT>tgC	p.C874C	CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Silent_p.C846C|FNIP1_ENST00000307954.8_Silent_p.C829C	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	874					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TATTTTTTGTACACAATATTT	0.323																																					p.C874C		Atlas-SNP	.											.	FNIP1	104	.	0			c.T2622C						.						62.0	64.0	63.0					5																	131007515		2203	4300	6503	SO:0001819	synonymous_variant	96459	exon14			TTTTGTACACAAT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.2622T>C	chr5.hg19:g.131007515A>G		114.0	0.0		103.0	6.0	NM_133372	D6RJH5|Q86T47|Q9BUT0	Silent	SNP	ENST00000510461.1	hg19	CCDS34227.1																																																																																			.	.		0.323	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372	
KIF3A	11127	hgsc.bcm.edu	37	5	132069913	132069913	+	Silent	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:132069913T>A	ENST00000378746.4	-	2	482	c.264A>T	c.(262-264)gtA>gtT	p.V88V	KIF3A_ENST00000378735.1_Silent_p.V88V|KIF3A_ENST00000403231.1_Silent_p.V88V	NM_007054.5	NP_008985.3	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	88	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterior/posterior pattern specification (GO:0009952)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|organelle organization (GO:0006996)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of receptor-mediated endocytosis (GO:0048260)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|spectrin binding (GO:0030507)			endometrium(1)|kidney(4)|large_intestine(8)|lung(3)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	25		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCCTTCAAGTACAGAATCAA	0.328																																					p.V88V		Atlas-SNP	.											.	KIF3A	117	.	0			c.A264T						.						98.0	101.0	100.0					5																	132069913		2203	4300	6503	SO:0001819	synonymous_variant	11127	exon2			TTCAAGTACAGAA	AF041853	CCDS34235.1, CCDS75295.1, CCDS75296.1	5q31	2012-08-01			ENSG00000131437	ENSG00000131437		"""Kinesins"""	6319	protein-coding gene	gene with protein product	"""kinesin family protein 3A"""	604683				1054846	Standard	XM_005271868		Approved	FLA10, KLP-20	uc003kxo.3	Q9Y496	OTTHUMG00000059725	ENST00000378746.4:c.264A>T	chr5.hg19:g.132069913T>A		183.0	0.0		177.0	71.0	NM_007054	A8MSW9|Q59EN1|Q86XE9|Q9Y6V4	Silent	SNP	ENST00000378746.4	hg19	CCDS34235.1																																																																																			.	.		0.328	KIF3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132788.3	NM_007054	
SOWAHA	134548	hgsc.bcm.edu	37	5	132150795	132150795	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:132150795A>G	ENST00000378693.2	+	1	1763	c.1482A>G	c.(1480-1482)cgA>cgG	p.R494R	AC004775.5_ENST00000607389.1_lincRNA	NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	494																	ACCTGGCCCGAGGCTTGAAGA	0.612																																					p.R494R		Atlas-SNP	.											.	.	.	.	0			c.A1482G						.						44.0	46.0	45.0					5																	132150795		2203	4300	6503	SO:0001819	synonymous_variant	134548	exon1			GGCCCGAGGCTTG	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"""Ankyrin repeat domain containing"""	27033	protein-coding gene	gene with protein product			"""ankyrin repeat domain 43"""	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.1482A>G	chr5.hg19:g.132150795A>G		82.0	0.0		103.0	43.0	NM_175873	Q8NAE7	Silent	SNP	ENST00000378693.2	hg19	CCDS43361.1																																																																																			.	.		0.612	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873	
SHROOM1	134549	hgsc.bcm.edu	37	5	132159057	132159057	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:132159057C>T	ENST00000378679.3	-	9	2915	c.2111G>A	c.(2110-2112)cGg>cAg	p.R704Q	SHROOM1_ENST00000319854.3_Missense_Mutation_p.R704Q|SHROOM1_ENST00000488072.1_5'UTR|SHROOM1_ENST00000378676.1_Missense_Mutation_p.R635Q	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	704	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGCCATGAACCGGCTGAACCG	0.736																																					p.R704Q		Atlas-SNP	.											.	SHROOM1	35	.	0			c.G2111A						.						13.0	15.0	14.0					5																	132159057		2175	4257	6432	SO:0001583	missense	134549	exon6			ATGAACCGGCTGA	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.2111G>A	chr5.hg19:g.132159057C>T	ENSP00000367950:p.Arg704Gln	72.0	0.0		65.0	24.0	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	hg19	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668504	0.88348	.	.	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676	T;T;T	0.30714	1.52;1.52;1.52	4.91	4.04	0.47022	Apx/shroom, ASD2 (2);	0.258925	0.32314	N	0.006270	T	0.38719	0.1051	L	0.46741	1.465	0.28487	N	0.914656	D;D	0.89917	0.988;1.0	P;D	0.80764	0.737;0.994	T	0.24440	-1.0160	10	0.16420	T	0.52	-27.3311	5.52	0.16927	0.1996:0.7023:0.0:0.0982	.	704;704	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	Q	704;704;635	ENSP00000367950:R704Q;ENSP00000324245:R704Q;ENSP00000367947:R635Q	ENSP00000324245:R704Q	R	-	2	0	SHROOM1	132186956	0.060000	0.20803	1.000000	0.80357	0.981000	0.71138	1.570000	0.36439	2.673000	0.90976	0.555000	0.69702	CGG	.	.		0.736	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456	
PKD2L2	27039	hgsc.bcm.edu	37	5	137228299	137228299	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:137228299G>T	ENST00000508883.1	+	3	290	c.264G>T	c.(262-264)tgG>tgT	p.W88C	PKD2L2_ENST00000290431.5_Missense_Mutation_p.W88C|PKD2L2_ENST00000350250.4_Missense_Mutation_p.W54C|PKD2L2_ENST00000502810.1_Missense_Mutation_p.W88C|PKD2L2_ENST00000508638.1_Missense_Mutation_p.W88C			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	88					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTGATTTTTGGAAGGTAAAGT	0.378																																					p.W88C		Atlas-SNP	.											.	PKD2L2	68	.	0			c.G264T						.						142.0	136.0	138.0					5																	137228299		1884	4126	6010	SO:0001583	missense	27039	exon3			TTTTTGGAAGGTA	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.264G>T	chr5.hg19:g.137228299G>T	ENSP00000424725:p.Trp88Cys	152.0	0.0		125.0	52.0	NM_001258448	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	G	24.6	4.546161	0.86022	.	.	ENSG00000078795	ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73	5.84	5.84	0.93424	Polycystin cation channel, PKD1/PKD2 (1);	0.000000	0.64402	D	0.000007	D	0.86723	0.6001	M	0.85777	2.775	0.80722	D	1	D;D;D	0.89917	0.997;1.0;0.994	D;D;P	0.85130	0.997;0.972;0.77	D	0.87797	0.2622	10	0.87932	D	0	-4.9854	19.7449	0.96248	0.0:0.0:1.0:0.0	.	88;88;88	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	C	54;88;88;88;88	ENSP00000344177:W54C;ENSP00000423382:W88C;ENSP00000425513:W88C;ENSP00000424725:W88C;ENSP00000290431:W88C	ENSP00000290431:W88C	W	+	3	0	PKD2L2	137256198	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.692000	0.91284	2.768000	0.95171	0.609000	0.83330	TGG	.	.		0.378	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386	
APBB3	10307	hgsc.bcm.edu	37	5	139939980	139939980	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:139939980C>A	ENST00000357560.4	-	12	1585	c.1142G>T	c.(1141-1143)gGc>gTc	p.G381V	SRA1_ENST00000336283.6_5'Flank|APBB3_ENST00000508496.2_Missense_Mutation_p.G158V|APBB3_ENST00000507279.1_5'Flank|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000354402.5_Missense_Mutation_p.G388V|APBB3_ENST00000356738.2_Missense_Mutation_p.G386V|SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000412920.3_Missense_Mutation_p.G379V	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	381	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTCTGACGGCCCAGGTCAGC	0.602																																					p.G388V		Atlas-SNP	.											.	APBB3	34	.	0			c.G1163T						.						59.0	53.0	55.0					5																	139939980		2203	4300	6503	SO:0001583	missense	10307	exon11			TGACGGCCCAGGT	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1142G>T	chr5.hg19:g.139939980C>A	ENSP00000350171:p.Gly381Val	213.0	0.0		223.0	52.0	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	hg19	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434687	0.83885	.	.	ENSG00000113108	ENST00000356738;ENST00000354402;ENST00000357560;ENST00000508496;ENST00000412920	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.59252	0.2180	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.57177	-0.7856	9	.	.	.	-19.9488	18.9073	0.92467	0.0:1.0:0.0:0.0	.	379;386	O95704-2;O95704-3	.;.	V	386;388;381;158;379	ENSP00000349177:G386V;ENSP00000346378:G388V;ENSP00000350171:G381V;ENSP00000444013:G158V;ENSP00000402591:G379V	.	G	-	2	0	APBB3	139920164	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.678000	0.84035	2.468000	0.83385	0.655000	0.94253	GGC	.	.		0.602	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167660	140167660	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140167660C>T	ENST00000504120.2	+	1	1785	c.1785C>T	c.(1783-1785)cgC>cgT	p.R595R	PCDHA1_ENST00000378133.3_Silent_p.R595R|PCDHA1_ENST00000394633.3_Intron	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	595	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGAAGGTGCGCGCAGTGGACG	0.692																																					p.R595R		Atlas-SNP	.											.	PCDHA1	387	.	0			c.C1785T						.						103.0	97.0	99.0					5																	140167660		2203	4299	6502	SO:0001819	synonymous_variant	56147	exon1			GGTGCGCGCAGTG	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1785C>T	chr5.hg19:g.140167660C>T		126.0	0.0		153.0	60.0	NM_031410	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	hg19	CCDS54913.1																																																																																			.	.		0.692	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237443	140237443	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140237443G>T	ENST00000307360.5	+	1	1810	c.1810G>T	c.(1810-1812)Gcg>Tcg	p.A604S	PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	604	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGATACAACGCGTGGCTGTC	0.652																																					p.A604S		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1810T						.						90.0	91.0	91.0					5																	140237443		1323	2289	3612	SO:0001583	missense	56139	exon1			TACAACGCGTGGC	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1810G>T	chr5.hg19:g.140237443G>T	ENSP00000304234:p.Ala604Ser	165.0	0.0		141.0	65.0	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	hg19	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.733841	0.48939	.	.	ENSG00000250120	ENST00000307360	T	0.37752	1.18	3.68	3.68	0.42216	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.59985	0.2234	M	0.78801	2.425	0.39875	D	0.973556	D;D	0.89917	1.0;0.999	D;D	0.74674	0.954;0.984	T	0.66626	-0.5876	9	0.46703	T	0.11	.	15.9591	0.79914	0.0:0.0:1.0:0.0	.	604;604	Q9Y5I2-3;Q9Y5I2	.;PCDAA_HUMAN	S	604	ENSP00000304234:A604S	ENSP00000304234:A604S	A	+	1	0	PCDHA10	140217627	0.986000	0.35501	1.000000	0.80357	0.245000	0.25701	3.266000	0.51569	2.041000	0.60428	0.491000	0.48974	GCG	.	.		0.652	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347456	140347456	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140347456G>A	ENST00000289269.5	+	1	1637	c.1105G>A	c.(1105-1107)Gac>Aac	p.D369N	PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	369					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(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGCTCACGGACCTGTATAG	0.587																																					p.D369N	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.G1105A						.						93.0	78.0	83.0					5																	140347456		2203	4300	6503	SO:0001583	missense	56134	exon1			CTCACGGACCTGT	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1105G>A	chr5.hg19:g.140347456G>A	ENSP00000289269:p.Asp369Asn	68.0	0.0		61.0	17.0	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	hg19	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.220364	0.39201	.	.	ENSG00000243232	ENST00000289269	T	0.67171	-0.25	5.6	5.6	0.85130	Cadherin-like (1);	0.000000	0.43747	D	0.000532	T	0.45438	0.1342	N	0.05510	-0.035	0.40517	D	0.980794	B;P	0.35174	0.352;0.488	B;B	0.30943	0.122;0.11	T	0.55724	-0.8096	10	0.72032	D	0.01	.	12.6865	0.56949	0.0:0.0:0.7245:0.2755	.	369;369	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	N	369	ENSP00000289269:D369N	ENSP00000289269:D369N	D	+	1	0	PCDHAC2	140327640	1.000000	0.71417	0.880000	0.34516	0.746000	0.42486	4.005000	0.57075	2.636000	0.89361	0.655000	0.94253	GAC	.	.		0.587	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
PCDHB14	56122	hgsc.bcm.edu	37	5	140605037	140605037	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140605037G>A	ENST00000239449.4	+	1	1960	c.1960G>A	c.(1960-1962)Gcc>Acc	p.A654T	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A501T	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	654	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCTCGCTCGGCCACCGCCAC	0.721																																					p.A654T	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1960A						.						16.0	20.0	18.0					5																	140605037		1894	3876	5770	SO:0001583	missense	56122	exon1			CGCTCGGCCACCG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1960G>A	chr5.hg19:g.140605037G>A	ENSP00000239449:p.Ala654Thr	59.0	0.0		46.0	16.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	hg19	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	N	8.920	0.960874	0.18583	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.51071	0.72;0.72	3.83	1.49	0.22878	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.42562	0.1208	L	0.40543	1.245	0.28057	N	0.933136	P	0.39424	0.673	P	0.44696	0.458	T	0.33574	-0.9863	9	0.46703	T	0.11	.	8.054	0.30593	0.3389:0.0:0.6611:0.0	.	654	Q9Y5E9	PCDBE_HUMAN	T	501;654	ENSP00000444518:A501T;ENSP00000239449:A654T	ENSP00000239449:A654T	A	+	1	0	PCDHB14	140585221	0.001000	0.12720	0.797000	0.32132	0.017000	0.09413	0.432000	0.21461	0.722000	0.32252	-0.199000	0.12753	GCC	.	.		0.721	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
PCDHGA7	56108	hgsc.bcm.edu	37	5	140764204	140764204	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140764204C>T	ENST00000518325.1	+	1	1738	c.1738C>T	c.(1738-1740)Cgc>Tgc	p.R580C	PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	580	Cadherin 6. {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)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGCACCCCGCTCCGCAGA	0.622																																					p.R580C		Atlas-SNP	.											PCDHGA7,NS,carcinoma,0,1	PCDHGA7	130	.	0			c.C1738T						.						83.0	98.0	93.0					5																	140764204		2202	4300	6502	SO:0001583	missense	56108	exon1			GCACCCCGCTCCG	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"""Cadherins / Protocadherins : Clustered"""	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.1738C>T	chr5.hg19:g.140764204C>T	ENSP00000430024:p.Arg580Cys	103.0	0.0		129.0	50.0	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	hg19	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	17.73	3.462042	0.63513	.	.	ENSG00000253537	ENST00000518325	T	0.59772	0.24	5.01	5.01	0.66863	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.81004	0.4733	H	0.95004	3.61	0.38846	D	0.95616	D;D	0.89917	1.0;1.0	D;D	0.79108	0.988;0.992	D	0.86378	0.1727	9	0.87932	D	0	.	11.8056	0.52152	0.0:0.9186:0.0:0.0814	.	580;580	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	C	580	ENSP00000430024:R580C	ENSP00000430024:R580C	R	+	1	0	PCDHGA7	140744388	0.937000	0.31787	0.959000	0.39883	0.972000	0.66771	2.006000	0.40874	2.484000	0.83849	0.655000	0.94253	CGC	.	.		0.622	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
DIAPH1	1729	hgsc.bcm.edu	37	5	140955840	140955840	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140955840T>G	ENST00000398557.4	-	14	1558	c.1418A>C	c.(1417-1419)aAg>aCg	p.K473T	DIAPH1_ENST00000389054.3_Missense_Mutation_p.K473T|DIAPH1_ENST00000520569.1_Missense_Mutation_p.K419T|DIAPH1_ENST00000398562.2_Missense_Mutation_p.K464T|DIAPH1_ENST00000398566.3_Missense_Mutation_p.K464T|DIAPH1_ENST00000389057.5_Missense_Mutation_p.K464T|DIAPH1_ENST00000518047.1_Missense_Mutation_p.K464T|DIAPH1_ENST00000253811.6_Missense_Mutation_p.K473T	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	473					actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCTCCACCTTTGTCTTATC	0.363																																					p.K473T		Atlas-SNP	.											.	DIAPH1	64	.	0			c.A1418C						.						158.0	143.0	148.0					5																	140955840		1854	4101	5955	SO:0001583	missense	1729	exon14			TCCACCTTTGTCT	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"""diaphanous (Drosophila, homolog) 1"", ""diaphanous homolog 1 (Drosophila)"""	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1418A>C	chr5.hg19:g.140955840T>G	ENSP00000381565:p.Lys473Thr	228.0	0.0		190.0	76.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.657790	0.88154	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;T;T;T;T;T;T	0.22336	1.96;1.96;2.0;1.96;1.96;1.96;1.96;1.96	5.78	5.78	0.91487	Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.51143	0.1657	M	0.84948	2.725	0.58432	D	0.999995	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	T	0.58434	-0.7637	10	0.87932	D	0	.	15.0913	0.72195	0.0:0.0:0.0:1.0	.	464;473	E9PEZ2;O60610	.;DIAP1_HUMAN	T	473;419;464;464;464;473;473;464	ENSP00000373706:K473T;ENSP00000429282:K419T;ENSP00000381570:K464T;ENSP00000373709:K464T;ENSP00000381572:K464T;ENSP00000381565:K473T;ENSP00000253811:K473T;ENSP00000428268:K464T	ENSP00000253811:K473T	K	-	2	0	DIAPH1	140936024	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.356000	0.79445	2.204000	0.70986	0.528000	0.53228	AAG	.	.		0.363	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219	
PCDH12	51294	hgsc.bcm.edu	37	5	141336556	141336556	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:141336556C>A	ENST00000231484.3	-	1	2071	c.861G>T	c.(859-861)atG>atT	p.M287I	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	287	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCTGGAGGCATGTGCTTAC	0.537																																					p.M287I		Atlas-SNP	.											.	PCDH12	133	.	0			c.G861T						.						99.0	92.0	94.0					5																	141336556		2203	4300	6503	SO:0001583	missense	51294	exon1			TGGAGGCATGTGC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.861G>T	chr5.hg19:g.141336556C>A	ENSP00000231484:p.Met287Ile	124.0	0.0		92.0	8.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	C	10.14	1.267319	0.23136	.	.	ENSG00000113555	ENST00000231484	T	0.50548	0.74	5.32	4.45	0.53987	Cadherin (4);Cadherin-like (1);	0.505224	0.22091	N	0.064750	T	0.21881	0.0527	N	0.02842	-0.48	0.22378	N	0.999151	B	0.02656	0.0	B	0.04013	0.001	T	0.13176	-1.0519	10	0.13108	T	0.6	.	11.6919	0.51521	0.0:0.9149:0.0:0.0851	.	287	Q9NPG4	PCD12_HUMAN	I	287	ENSP00000231484:M287I	ENSP00000231484:M287I	M	-	3	0	PCDH12	141316740	0.013000	0.17824	0.994000	0.49952	0.968000	0.65278	-0.866000	0.04245	1.471000	0.48121	0.655000	0.94253	ATG	.	.		0.537	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
RBM27	54439	hgsc.bcm.edu	37	5	145634549	145634549	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:145634549T>C	ENST00000265271.5	+	10	1654	c.1488T>C	c.(1486-1488)atT>atC	p.I496I	RBM27_ENST00000506502.1_Silent_p.I441I	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	496					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTCCTAGTATTACTAGTTCTG	0.403																																					p.I496I		Atlas-SNP	.											.	RBM27	119	.	0			c.T1488C						.						106.0	93.0	97.0					5																	145634549		1568	3582	5150	SO:0001819	synonymous_variant	54439	exon10			TAGTATTACTAGT	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1488T>C	chr5.hg19:g.145634549T>C		97.0	0.0		105.0	30.0	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.403	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
C5orf46	389336	hgsc.bcm.edu	37	5	147281302	147281302	+	Silent	SNP	G	G	A	rs368375161		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:147281302G>A	ENST00000318315.4	-	2	105	c.105C>T	c.(103-105)gaC>gaT	p.D35D	C5orf46_ENST00000515291.1_Silent_p.D35D|C5orf46_ENST00000510432.1_5'UTR	NM_206966.2	NP_996849.2	Q6UWT4	CE046_HUMAN	chromosome 5 open reading frame 46	35						extracellular vesicular exosome (GO:0070062)				NS(1)|lung(1)|prostate(1)	3						TGCCCGAgtcgtctggcttgt	0.488																																					p.D35D		Atlas-SNP	.											.	C5orf46	8	.	0			c.C105T						.	A		2,4404	826.0+/-416.6	0,2,2201	226.0	200.0	208.0		105	-7.7	0.1	5		208	0,8600		0,0,4300	no	coding-synonymous	C5orf46	NM_206966.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		35/88	147281302	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	389336	exon2			CGAGTCGTCTGGC		CCDS34267.1	5q33.1	2013-12-13			ENSG00000178776	ENSG00000178776			33768	protein-coding gene	gene with protein product	"""skin and saliva secreted protein 1"""						Standard	NM_206966		Approved	MGC23985, SSSP1	uc003lou.3	Q6UWT4	OTTHUMG00000163420	ENST00000318315.4:c.105C>T	chr5.hg19:g.147281302G>A		178.0	0.0		195.0	73.0	NM_206966	A8K038|Q8WU04	Silent	SNP	ENST00000318315.4	hg19	CCDS34267.1																																																																																			.	.		0.488	C5orf46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373314.1	NM_206966	
PDE6A	5145	hgsc.bcm.edu	37	5	149324081	149324081	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:149324081C>T	ENST00000255266.5	-	1	275	c.156G>A	c.(154-156)ccG>ccA	p.P52P		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	52					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CCATGCTGCTCGGGGAGTGGT	0.517																																					p.P52P		Atlas-SNP	.											.	PDE6A	98	.	0			c.G156A						.						63.0	61.0	62.0					5																	149324081		2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GCTGCTCGGGGAG		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.156G>A	chr5.hg19:g.149324081C>T		128.0	0.0		116.0	43.0	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	hg19	CCDS4299.1																																																																																			.	.		0.517	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
HMGXB3	22993	hgsc.bcm.edu	37	5	149421470	149421470	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:149421470G>A	ENST00000502717.1	+	15	3132	c.2668G>A	c.(2668-2670)Gcc>Acc	p.A890T	HMGXB3_ENST00000503427.1_Missense_Mutation_p.A858T	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	1136					phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						CTGTGGTGTGGCCCCCAAAGT	0.552																																					p.A890T		Atlas-SNP	.											.	HMGXB3	31	.	0			c.G2668A						.						113.0	91.0	98.0					5																	149421470		692	1591	2283	SO:0001583	missense	22993	exon15			GGTGTGGCCCCCA	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.2668G>A	chr5.hg19:g.149421470G>A	ENSP00000421917:p.Ala890Thr	106.0	0.0		88.0	24.0	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Missense_Mutation	SNP	ENST00000502717.1	hg19	CCDS54935.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.985823	0.74589	.	.	ENSG00000113716	ENST00000503427;ENST00000502717	T;T	0.46063	0.88;0.88	5.84	5.84	0.93424	.	0.048342	0.85682	D	0.000000	T	0.34221	0.0890	L	0.41236	1.265	0.53005	D	0.999963	P	0.39809	0.689	B	0.34489	0.184	T	0.25641	-1.0126	10	0.87932	D	0	-18.8263	13.7705	0.63021	0.0791:0.0:0.9209:0.0	.	1136	Q12766	HMGX3_HUMAN	T	858;890	ENSP00000422231:A858T;ENSP00000421917:A890T	ENSP00000421917:A890T	A	+	1	0	HMGXB3	149401663	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.589000	0.82641	2.751000	0.94390	0.650000	0.86243	GCC	.	.		0.552	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
NDST1	3340	hgsc.bcm.edu	37	5	149901211	149901211	+	Missense_Mutation	SNP	G	G	A	rs141135213		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:149901211G>A	ENST00000261797.6	+	2	897	c.395G>A	c.(394-396)cGc>cAc	p.R132H	NDST1_ENST00000523767.1_Missense_Mutation_p.R132H	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	132	Heparan sulfate N-deacetylase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCCGTGGCCGCTTCGCCCTC	0.607																																					p.R132H		Atlas-SNP	.											.	NDST1	79	.	0			c.G395A						.	G	HIS/ARG	0,4406		0,0,2203	107.0	112.0	110.0		395	5.4	1.0	5	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	missense	NDST1	NM_001543.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	132/883	149901211	1,13005	2203	4300	6503	SO:0001583	missense	3340	exon2			GTGGCCGCTTCGC	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"""Sulfotransferases, membrane-bound"""	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.395G>A	chr5.hg19:g.149901211G>A	ENSP00000261797:p.Arg132His	160.0	0.0		126.0	46.0	NM_001543	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	hg19	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.880758	0.91740	0.0	1.16E-4	ENSG00000070614	ENST00000519157;ENST00000523767;ENST00000261797	T;T;T	0.59083	0.29;0.58;0.91	5.39	5.39	0.77823	.	0.061246	0.64402	D	0.000001	T	0.78214	0.4248	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.977;0.984;0.977	T	0.79381	-0.1827	10	0.54805	T	0.06	.	19.5078	0.95127	0.0:0.0:1.0:0.0	.	132;132;132	E7EVJ3;P52848-2;P52848	.;.;NDST1_HUMAN	H	132	ENSP00000427813:R132H;ENSP00000428604:R132H;ENSP00000261797:R132H	ENSP00000261797:R132H	R	+	2	0	NDST1	149881404	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.950000	0.87804	2.676000	0.91093	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.607	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
SLC36A3	285641	hgsc.bcm.edu	37	5	150660598	150660598	+	Missense_Mutation	SNP	C	C	T	rs201585244		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:150660598C>T	ENST00000335230.3	-	9	1532	c.1121G>A	c.(1120-1122)cGc>cAc	p.R374H	SLC36A3_ENST00000377713.3_Missense_Mutation_p.R415H	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	374						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAGGCTGAGCGGACAGACAG	0.552																																					p.R415H		Atlas-SNP	.											.	SLC36A3	54	.	0			c.G1244A						.						141.0	120.0	127.0					5																	150660598		2203	4300	6503	SO:0001583	missense	285641	exon10			GCTGAGCGGACAG	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"""Solute carriers"""	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.1121G>A	chr5.hg19:g.150660598C>T	ENSP00000334750:p.Arg374His	130.0	0.0		122.0	39.0	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.345514	0.82022	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.03920	3.76;3.76	3.82	2.95	0.34219	.	0.110120	0.64402	N	0.000010	T	0.28267	0.0698	H	0.94503	3.545	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.998	T	0.29852	-0.9998	10	0.87932	D	0	.	11.5293	0.50599	0.0:0.9119:0.0:0.0881	.	415;374;359	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	H	374;415	ENSP00000334750:R374H;ENSP00000366942:R415H	ENSP00000334750:R374H	R	-	2	0	SLC36A3	150640791	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	3.880000	0.56145	0.955000	0.37878	0.561000	0.74099	CGC	.	C|1.000;A|0.000		0.552	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
GRIA1	2890	hgsc.bcm.edu	37	5	153030021	153030021	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:153030021C>T	ENST00000285900.5	+	4	935	c.592C>T	c.(592-594)Cgg>Tgg	p.R198W	GRIA1_ENST00000340592.5_Missense_Mutation_p.R198W|GRIA1_ENST00000448073.4_Missense_Mutation_p.R208W|GRIA1_ENST00000518783.1_Missense_Mutation_p.R208W|GRIA1_ENST00000518142.1_Missense_Mutation_p.R118W|GRIA1_ENST00000518862.1_3'UTR|GRIA1_ENST00000521843.2_Missense_Mutation_p.R129W	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	198					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GAAAAAGGAGCGGCTGGTGGT	0.542																																					p.R208W		Atlas-SNP	.											.	GRIA1	321	.	0			c.C622T						.						108.0	103.0	105.0					5																	153030021		2203	4300	6503	SO:0001583	missense	2890	exon4			AAGGAGCGGCTGG		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.592C>T	chr5.hg19:g.153030021C>T	ENSP00000285900:p.Arg198Trp	151.0	0.0		132.0	48.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.003695	0.54254	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38;1.38;1.38	5.33	-1.32	0.09201	Extracellular ligand-binding receptor (1);	0.055015	0.64402	D	0.000001	T	0.42877	0.1222	L	0.39898	1.24	0.45662	D	0.998588	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;0.999;1.0	P;P;D;P;P;D	0.67103	0.901;0.901;0.949;0.901;0.841;0.949	T	0.07654	-1.0761	10	0.37606	T	0.19	.	11.2657	0.49110	0.6337:0.3015:0.0:0.0648	.	208;208;118;208;198;198	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	W	198;198;118;152;198;129;129;208;208	ENSP00000285900:R198W;ENSP00000427920:R118W;ENSP00000339343:R198W;ENSP00000427864:R129W;ENSP00000442108:R129W;ENSP00000428994:R208W;ENSP00000415569:R208W	ENSP00000285900:R198W	R	+	1	2	GRIA1	153010214	0.634000	0.27190	0.814000	0.32528	0.577000	0.36160	-0.178000	0.09782	-0.654000	0.05394	-0.142000	0.14014	CGG	.	.		0.542	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3		
TIMD4	91937	hgsc.bcm.edu	37	5	156353300	156353300	+	Nonsense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:156353300G>A	ENST00000274532.2	-	6	924	c.868C>T	c.(868-870)Cag>Tag	p.Q290*	TIMD4_ENST00000406964.1_5'UTR|TIMD4_ENST00000407087.3_Nonsense_Mutation_p.Q262*	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	290						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTTTTGTTCTGCTCAGGAACT	0.373																																					p.Q290X		Atlas-SNP	.											.	TIMD4	94	.	0			c.C868T						.						178.0	159.0	165.0					5																	156353300		2203	4300	6503	SO:0001587	stop_gained	91937	exon6			TGTTCTGCTCAGG	BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850		"""Immunoglobulin superfamily / V-set domain containing"""	25132	protein-coding gene	gene with protein product		610096				12477932	Standard	NM_001146726		Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.868C>T	chr5.hg19:g.156353300G>A	ENSP00000274532:p.Gln290*	70.0	0.0		63.0	19.0	NM_138379	B5MCL9	Nonsense_Mutation	SNP	ENST00000274532.2	hg19	CCDS4332.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638706	0.47153	.	.	ENSG00000145850	ENST00000274532;ENST00000407087	.	.	.	4.06	-0.165	0.13355	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	3.919	7.3801	0.26851	0.1019:0.5089:0.3892:0.0	.	.	.	.	X	290;262	.	ENSP00000274532:Q290X	Q	-	1	0	TIMD4	156285878	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.959000	0.03853	-0.153000	0.11137	0.650000	0.86243	CAG	.	.		0.373	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379	
CYFIP2	26999	hgsc.bcm.edu	37	5	156816337	156816337	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:156816337C>T	ENST00000521420.1	+	28	3361	c.3270C>T	c.(3268-3270)ggC>ggT	p.G1090G	CYFIP2_ENST00000377576.3_Silent_p.G1116G|CYFIP2_ENST00000347377.6_Silent_p.G1116G|CYFIP2_ENST00000435847.2_Silent_p.G815G|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000522463.1_Silent_p.G920G|CYFIP2_ENST00000318218.6_Silent_p.G1141G|CYFIP2_ENST00000541131.1_Silent_p.G1041G					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCACCAATGGCGTCATGCACG	0.617																																					p.G1116G		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C3348T						.						59.0	68.0	65.0					5																	156816337		2169	4284	6453	SO:0001819	synonymous_variant	26999	exon29			CAATGGCGTCATG	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3270C>T	chr5.hg19:g.156816337C>T		71.0	0.0		79.0	18.0	NM_001037332		Silent	SNP	ENST00000521420.1	hg19																																																																																				.	.		0.617	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
NUDCD2	134492	hgsc.bcm.edu	37	5	162887001	162887001	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:162887001C>T	ENST00000302764.4	-	1	145	c.56G>A	c.(55-57)gGc>gAc	p.G19D	HMMR_ENST00000353866.3_5'Flank|NUDCD2_ENST00000519395.1_5'Flank|HMMR_ENST00000393915.4_5'Flank|HMMR_ENST00000358715.3_5'Flank|NUDCD2_ENST00000517501.1_Missense_Mutation_p.G19D|HMMR_ENST00000432118.2_5'Flank	NM_145266.4	NP_660309.1	Q8WVJ2	NUDC2_HUMAN	NudC domain containing 2	19	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)				large_intestine(1)|prostate(1)	2	Renal(175;0.000281)	Medulloblastoma(196;0.0207)|all_neural(177;0.0966)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0981)|OV - Ovarian serous cystadenocarcinoma(192;0.183)|Epithelial(171;0.247)		GTACCACTGGCCCCACGGGGT	0.687																																					p.G19D		Atlas-SNP	.											.	NUDCD2	12	.	0			c.G56A						.						78.0	92.0	87.0					5																	162887001		2203	4300	6503	SO:0001583	missense	134492	exon1			CACTGGCCCCACG	BX538290	CCDS4361.1	5q34	2008-02-05			ENSG00000170584	ENSG00000170584			30535	protein-coding gene	gene with protein product							Standard	NM_145266		Approved	DKFZp686E10109	uc003lze.3	Q8WVJ2	OTTHUMG00000130378	ENST00000302764.4:c.56G>A	chr5.hg19:g.162887001C>T	ENSP00000304854:p.Gly19Asp	413.0	0.0		408.0	163.0	NM_145266	B2R4V0	Missense_Mutation	SNP	ENST00000302764.4	hg19	CCDS4361.1	.	.	.	.	.	.	.	.	.	.	C	36	5.728119	0.96856	.	.	ENSG00000170584	ENST00000302764;ENST00000517501	T;T	0.42900	0.96;0.96	5.94	5.94	0.96194	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.000000	0.85682	D	0.000000	T	0.66982	0.2845	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63400	-0.6646	10	0.06891	T	0.86	0.0013	20.3736	0.98901	0.0:1.0:0.0:0.0	.	19	Q8WVJ2	NUDC2_HUMAN	D	19	ENSP00000304854:G19D;ENSP00000430347:G19D	ENSP00000304854:G19D	G	-	2	0	NUDCD2	162819579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.207000	0.77899	2.820000	0.97059	0.650000	0.86243	GGC	.	.		0.687	NUDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252747.3	NM_145266	
DOCK2	1794	hgsc.bcm.edu	37	5	169116263	169116263	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:169116263T>C	ENST00000256935.8	+	9	849	c.769T>C	c.(769-771)Tac>Cac	p.Y257H		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	257					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGTGAGAACTACCTAGTGCG	0.517																																					p.Y257H		Atlas-SNP	.											.	DOCK2	389	.	0			c.T769C						.						112.0	98.0	102.0					5																	169116263		2203	4300	6503	SO:0001583	missense	1794	exon9			GAGAACTACCTAG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.769T>C	chr5.hg19:g.169116263T>C	ENSP00000256935:p.Tyr257His	74.0	0.0		90.0	35.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849042	0.91277	.	.	ENSG00000134516	ENST00000256935	T	0.17528	2.27	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	M	0.85710	2.77	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.54139	-0.8338	10	0.87932	D	0	.	16.4484	0.83959	0.0:0.0:0.0:1.0	.	257	Q92608	DOCK2_HUMAN	H	257	ENSP00000256935:Y257H	ENSP00000256935:Y257H	Y	+	1	0	DOCK2	169048841	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.965000	0.87945	2.285000	0.76669	0.533000	0.62120	TAC	.	.		0.517	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
GPRIN1	114787	hgsc.bcm.edu	37	5	176025680	176025680	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:176025680G>A	ENST00000303991.4	-	2	1333	c.1156C>T	c.(1156-1158)Cgt>Tgt	p.R386C		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	386					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACACAGGACGCCCCTCTCCT	0.537																																					p.R386C		Atlas-SNP	.											GPRIN1,colon,carcinoma,0,1	GPRIN1	77	.	0			c.C1156T						.						61.0	57.0	58.0					5																	176025680		2203	4300	6503	SO:0001583	missense	114787	exon2			CAGGACGCCCCTC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.1156C>T	chr5.hg19:g.176025680G>A	ENSP00000305839:p.Arg386Cys	132.0	1.0		112.0	50.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	hg19	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.706135	0.30232	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.08720	3.06	4.72	0.659	0.17861	.	1.951490	0.03101	N	0.161082	T	0.08403	0.0209	L	0.36672	1.1	0.09310	N	1	P	0.39782	0.688	B	0.37780	0.258	T	0.29088	-1.0023	10	0.56958	D	0.05	14.3433	4.9434	0.13976	0.1413:0.3297:0.4452:0.0838	.	386	Q7Z2K8	GRIN1_HUMAN	C	386	ENSP00000305839:R386C	ENSP00000305839:R386C	R	-	1	0	GPRIN1	175958286	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.592000	0.05747	0.215000	0.20761	-1.576000	0.00868	CGT	.	.		0.537	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
FGFR4	2264	hgsc.bcm.edu	37	5	176520464	176520464	+	Missense_Mutation	SNP	C	C	T	rs558220864	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:176520464C>T	ENST00000292408.4	+	10	1554	c.1309C>T	c.(1309-1311)Cgt>Tgt	p.R437C	FGFR4_ENST00000393637.1_Missense_Mutation_p.R397C|FGFR4_ENST00000292410.3_Missense_Mutation_p.R397C|FGFR4_ENST00000393648.2_Silent_p.C385C|FGFR4_ENST00000502906.1_Missense_Mutation_p.R437C	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	437					alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	ACGAGGCGTGCGTCTCTCCTC	0.627										TSP Lung(9;0.080)			C|||	2	0.000399361	0.0	0.0	5008	,	,		16618	0.0		0.0	False		,,,				2504	0.002				p.R437C		Atlas-SNP	.											.	FGFR4	174	.	0			c.C1309T						.						77.0	79.0	78.0					5																	176520464		2203	4299	6502	SO:0001583	missense	2264	exon10			GGCGTGCGTCTCT	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1309C>T	chr5.hg19:g.176520464C>T	ENSP00000292408:p.Arg437Cys	94.0	0.0		78.0	28.0	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.25|18.25	3.582520|3.582520	0.65992|0.65992	.|.	.|.	ENSG00000160867|ENSG00000160867	ENST00000511076|ENST00000292408;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	.|D;D;D;D	.|0.88664	.|-2.41;-2.41;-2.41;-2.41	4.44|4.44	3.57|3.57	0.40892|0.40892	.|.	.|0.103824	.|0.64402	.|D	.|0.000002	D|D	0.94598|0.94598	0.8259|0.8259	M|M	0.88450|0.88450	2.955|2.955	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.997;1.0	.|P;D	.|0.83275	.|0.681;0.996	D|D	0.94860|0.94860	0.8021|0.8021	5|10	.|0.87932	.|D	.|0	.|.	11.9644|11.9644	0.53027|0.53027	0.0:0.9148:0.0:0.0852|0.0:0.9148:0.0:0.0852	.|.	.|397;437	.|P22455-2;P22455	.|.;FGFR4_HUMAN	V|C	68|437;437;397;397;665	.|ENSP00000292408:R437C;ENSP00000424960:R437C;ENSP00000292410:R397C;ENSP00000377254:R397C	.|ENSP00000292408:R437C	A|R	+|+	2|1	0|0	FGFR4|FGFR4	176453070|176453070	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.204000|0.204000	0.24138|0.24138	5.863000|5.863000	0.69568|0.69568	1.097000|1.097000	0.41459|0.41459	0.555000|0.555000	0.69702|0.69702	GCG|CGT	.	.		0.627	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
PFN3	345456	hgsc.bcm.edu	37	5	176827232	176827232	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:176827232C>T	ENST00000358571.2	-	1	405	c.346G>A	c.(346-348)Gta>Ata	p.V116I	F12_ENST00000514943.1_5'Flank	NM_001029886.2	NP_001025057.1	P60673	PROF3_HUMAN	profilin 3	116					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	lipid binding (GO:0008289)			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCCCATGTACGCCGCGTCGG	0.726																																					p.V116I		Atlas-SNP	.											.	PFN3	4	.	0			c.G346A						.						17.0	19.0	18.0					5																	176827232		2076	4198	6274	SO:0001583	missense	345456	exon1			CATGTACGCCGCG	AC090063	CCDS34301.1	5q35.2	2008-08-26			ENSG00000196570	ENSG00000196570			18627	protein-coding gene	gene with protein product		612812				11867228	Standard	NM_001029886		Approved		uc003mgl.2	P60673	OTTHUMG00000163408	ENST00000358571.2:c.346G>A	chr5.hg19:g.176827232C>T	ENSP00000351379:p.Val116Ile	249.0	0.0		195.0	75.0	NM_001029886	A2RUL3	Missense_Mutation	SNP	ENST00000358571.2	hg19	CCDS34301.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.345624	0.61073	.	.	ENSG00000196570	ENST00000358571	D	0.86865	-2.18	4.76	4.76	0.60689	.	0.175856	0.37761	N	0.001954	T	0.80819	0.4696	L	0.44542	1.39	0.26464	N	0.975398	P	0.43431	0.807	B	0.35655	0.207	T	0.76055	-0.3099	10	0.42905	T	0.14	.	13.3416	0.60549	0.0:1.0:0.0:0.0	.	116	P60673	PROF3_HUMAN	I	116	ENSP00000351379:V116I	ENSP00000351379:V116I	V	-	1	0	PFN3	176759838	0.994000	0.37717	1.000000	0.80357	0.857000	0.48899	1.993000	0.40747	2.209000	0.71365	0.485000	0.47835	GTA	.	.		0.726	PFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373234.1	NM_001029886	
ZNF354B	117608	hgsc.bcm.edu	37	5	178310742	178310742	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:178310742T>A	ENST00000322434.3	+	5	1515	c.1289T>A	c.(1288-1290)aTa>aAa	p.I430K	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	430					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(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGACACCGAATAATTCATACT	0.358																																					p.I430K		Atlas-SNP	.											.	ZNF354B	67	.	0			c.T1289A						.						70.0	74.0	73.0					5																	178310742		2203	4300	6503	SO:0001583	missense	117608	exon5			ACCGAATAATTCA	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.1289T>A	chr5.hg19:g.178310742T>A	ENSP00000327143:p.Ile430Lys	235.0	0.0		214.0	79.0	NM_058230	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	hg19	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.023794	0.35701	.	.	ENSG00000178338	ENST00000322434	T	0.12774	2.65	3.69	2.51	0.30379	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03011	0.0089	N	0.00315	-1.66	0.45490	D	0.998451	B	0.21905	0.062	B	0.23716	0.048	T	0.30090	-0.9990	9	0.41790	T	0.15	-1.6144	3.8088	0.08788	0.1987:0.0:0.2387:0.5626	.	430	Q96LW1	Z354B_HUMAN	K	430	ENSP00000327143:I430K	ENSP00000327143:I430K	I	+	2	0	ZNF354B	178243348	0.000000	0.05858	0.999000	0.59377	0.985000	0.73830	0.440000	0.21592	1.545000	0.49373	0.454000	0.30748	ATA	.	.		0.358	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
MAML1	9794	hgsc.bcm.edu	37	5	179201140	179201140	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:179201140G>A	ENST00000292599.3	+	5	2576	c.2313G>A	c.(2311-2313)ccG>ccA	p.P771P	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAGCCCCCGCCACAGGCCA	0.602																																					p.P771P		Atlas-SNP	.											.	MAML1	118	.	0			c.G2313A						.						38.0	39.0	39.0					5																	179201140		2203	4300	6503	SO:0001819	synonymous_variant	9794	exon5			GCCCCCGCCACAG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2313G>A	chr5.hg19:g.179201140G>A		70.0	0.0		52.0	18.0	NM_014757		Silent	SNP	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.		0.602	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
BTNL9	153579	hgsc.bcm.edu	37	5	180472566	180472566	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:180472566T>C	ENST00000327705.9	+	2	308	c.77T>C	c.(76-78)cTc>cCc	p.L26P	BTNL9_ENST00000515271.1_Intron|BTNL9_ENST00000376841.2_Missense_Mutation_p.L26P|BTNL9_ENST00000376842.3_Missense_Mutation_p.L26P	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	26						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCATGCACCTCCTCCTCCTT	0.622																																					p.L26P		Atlas-SNP	.											.	BTNL9	58	.	0			c.T77C						.						114.0	97.0	103.0					5																	180472566		2203	4297	6500	SO:0001583	missense	153579	exon2			TGCACCTCCTCCT	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.77T>C	chr5.hg19:g.180472566T>C	ENSP00000330200:p.Leu26Pro	49.0	0.0		45.0	15.0	NM_152547	A6NL42|Q6P660|Q96DM5	Missense_Mutation	SNP	ENST00000327705.9	hg19	CCDS4460.2	.	.	.	.	.	.	.	.	.	.	T	16.36	3.101136	0.56183	.	.	ENSG00000165810	ENST00000376841;ENST00000327705;ENST00000376842;ENST00000376850	T;T;T	0.54279	3.81;0.6;0.58	4.73	4.73	0.59995	.	0.952130	0.08578	N	0.925046	T	0.66046	0.2750	M	0.64170	1.965	0.18873	N	0.999981	D	0.58970	0.984	P	0.57371	0.819	T	0.54682	-0.8257	10	0.87932	D	0	.	10.9292	0.47207	0.0:0.0:0.0:1.0	.	26	Q6UXG8	BTNL9_HUMAN	P	26	ENSP00000366037:L26P;ENSP00000330200:L26P;ENSP00000366038:L26P	ENSP00000330200:L26P	L	+	2	0	BTNL9	180405172	0.111000	0.22076	0.007000	0.13788	0.033000	0.12548	2.431000	0.44775	1.911000	0.55334	0.454000	0.30748	CTC	.	.		0.622	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
RREB1	6239	hgsc.bcm.edu	37	6	7231535	7231535	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:7231535T>C	ENST00000349384.6	+	10	3517	c.3203T>C	c.(3202-3204)aTt>aCt	p.I1068T	RREB1_ENST00000334984.6_Missense_Mutation_p.I1068T|RREB1_ENST00000379938.2_Missense_Mutation_p.I1068T|RREB1_ENST00000379933.3_Missense_Mutation_p.I1068T	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1068					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CTGGCCTCCATTGCCCAGATC	0.642																																					p.I1068T		Atlas-SNP	.											.	RREB1	242	.	0			c.T3203C						.						37.0	44.0	42.0					6																	7231535		2203	4300	6503	SO:0001583	missense	6239	exon10			CCTCCATTGCCCA	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3203T>C	chr6.hg19:g.7231535T>C	ENSP00000305560:p.Ile1068Thr	96.0	0.0		73.0	54.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	hg19	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.729279	0.89390	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.25579	1.95;1.94;1.95;1.79	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000009	T	0.42245	0.1194	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.36529	-0.9744	10	0.59425	D	0.04	-27.7182	16.2302	0.82332	0.0:0.0:0.0:1.0	.	1068;1068;1068	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	T	1068	ENSP00000369265:I1068T;ENSP00000369270:I1068T;ENSP00000305560:I1068T;ENSP00000335574:I1068T	ENSP00000335574:I1068T	I	+	2	0	RREB1	7176534	1.000000	0.71417	0.950000	0.38849	0.993000	0.82548	5.855000	0.69510	2.228000	0.72767	0.533000	0.62120	ATT	.	.		0.642	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
MBOAT1	154141	hgsc.bcm.edu	37	6	20152967	20152967	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:20152967A>G	ENST00000324607.7	-	2	297	c.133T>C	c.(133-135)Ttt>Ctt	p.F45L	MBOAT1_ENST00000536798.1_Missense_Mutation_p.F45L|MBOAT1_ENST00000541730.1_5'UTR	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	45					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			AAAGCAGCAAACAGAGCAACA	0.428																																					p.F45L		Atlas-SNP	.											.	MBOAT1	48	.	0			c.T133C						.						92.0	91.0	91.0					6																	20152967		2203	4300	6503	SO:0001583	missense	154141	exon2			CAGCAAACAGAGC	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"""lysophosphatidylethanolamine acyltransferase 1"""	611732	"""O-acyltransferase (membrane bound) domain containing 1"""	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.133T>C	chr6.hg19:g.20152967A>G	ENSP00000324944:p.Phe45Leu	191.0	0.0		198.0	25.0	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	hg19	CCDS34346.1	.	.	.	.	.	.	.	.	.	.	A	3.231	-0.157379	0.06544	.	.	ENSG00000172197	ENST00000324607;ENST00000536798	T;T	0.21031	2.86;2.03	5.37	-4.69	0.03299	.	0.942499	0.09062	N	0.854219	T	0.01387	0.0045	N	0.02202	-0.64	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.46541	-0.9184	10	0.07482	T	0.82	-13.2751	6.7811	0.23646	0.4674:0.2126:0.3201:0.0	.	45	Q6ZNC8	MBOA1_HUMAN	L	45	ENSP00000324944:F45L;ENSP00000439814:F45L	ENSP00000324944:F45L	F	-	1	0	MBOAT1	20260946	0.000000	0.05858	0.013000	0.15412	0.831000	0.47069	-0.589000	0.05767	-0.745000	0.04772	0.533000	0.62120	TTT	.	.		0.428	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1		
HDGFL1	154150	hgsc.bcm.edu	37	6	22570437	22570437	+	Silent	SNP	C	C	T	rs371376684		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:22570437C>T	ENST00000230012.3	+	1	760	c.633C>T	c.(631-633)ggC>ggT	p.G211G	HDGFL1_ENST00000510882.2_Silent_p.G211G	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	211	Glu-rich.									kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					GCGAGCCGGGCCTGGTCTGCG	0.741																																					p.G211G		Atlas-SNP	.											.	HDGFL1	33	.	0			c.C633T						.						4.0	6.0	5.0					6																	22570437		1937	3989	5926	SO:0001819	synonymous_variant	154150	exon1			GCCGGGCCTGGTC	AK056824	CCDS34347.1	6p22.2	2008-02-05	2005-04-07	2005-04-07	ENSG00000112273	ENSG00000112273			21095	protein-coding gene	gene with protein product			"""PWWP domain containing 1"""	PWWP1			Standard	NM_138574		Approved	dJ309H15.1	uc003nds.3	Q5TGJ6	OTTHUMG00000016206	ENST00000230012.3:c.633C>T	chr6.hg19:g.22570437C>T		54.0	0.0		73.0	13.0	NM_138574	Q96MJ6	Silent	SNP	ENST00000230012.3	hg19	CCDS34347.1																																																																																			.	.		0.741	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574	
LRRC16A	55604	hgsc.bcm.edu	37	6	25538179	25538179	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:25538179C>T	ENST00000329474.6	+	25	2532	c.2164C>T	c.(2164-2166)Cgg>Tgg	p.R722W		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	722					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)			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						ATCAGCAGAGCGGCTCATGCG	0.393																																					p.R722W		Atlas-SNP	.											.	LRRC16A	168	.	0			c.C2164T						.						50.0	48.0	48.0					6																	25538179		1889	4117	6006	SO:0001583	missense	55604	exon25			GCAGAGCGGCTCA	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.2164C>T	chr6.hg19:g.25538179C>T	ENSP00000331983:p.Arg722Trp	48.0	0.0		57.0	11.0	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	hg19	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167125	0.78339	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.16597	2.33	5.79	3.67	0.42095	.	0.090383	0.85682	D	0.000000	T	0.17662	0.0424	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.70935	0.937;0.937;0.971;0.937	T	0.01492	-1.1341	10	0.66056	D	0.02	-18.7033	12.3661	0.55230	0.5598:0.4402:0.0:0.0	.	722;722;722;722	Q5VZK9;B2RTQ5;Q5VZK9-2;B8X1J0	LR16A_HUMAN;.;.;.	W	722	ENSP00000331983:R722W	ENSP00000331983:R722W	R	+	1	2	LRRC16A	25646158	1.000000	0.71417	0.961000	0.40146	0.991000	0.79684	3.670000	0.54569	0.614000	0.30107	0.591000	0.81541	CGG	.	.		0.393	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056197	26056197	+	Missense_Mutation	SNP	T	T	C	rs548795634		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:26056197T>C	ENST00000343677.2	-	1	502	c.460A>G	c.(460-462)Aca>Gca	p.T154A		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	154					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TTCTTCGGTGTTTTCTTAGCG	0.562													T|||	1	0.000199681	0.0	0.0	5008	,	,		14270	0.001		0.0	False		,,,				2504	0.0				p.T154A		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.A460G						.						75.0	89.0	85.0					6																	26056197		2201	4297	6498	SO:0001583	missense	3006	exon1			TCGGTGTTTTCTT	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.460A>G	chr6.hg19:g.26056197T>C	ENSP00000339566:p.Thr154Ala	118.0	0.0		146.0	40.0	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	T	2.271	-0.367071	0.05069	.	.	ENSG00000187837	ENST00000343677	T	0.15834	2.39	5.47	5.47	0.80525	.	0.381500	0.23472	N	0.047801	T	0.03520	0.0101	N	0.14661	0.345	0.34798	D	0.736415	B	0.30406	0.278	B	0.24974	0.057	T	0.38542	-0.9656	10	0.25751	T	0.34	-34.9918	9.5155	0.39102	0.0:0.0793:0.0:0.9207	.	154	P16403	H12_HUMAN	A	154	ENSP00000339566:T154A	ENSP00000339566:T154A	T	-	1	0	HIST1H1C	26164176	0.998000	0.40836	1.000000	0.80357	0.012000	0.07955	1.305000	0.33493	2.198000	0.70561	0.528000	0.53228	ACA	.	.		0.562	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
ABT1	29777	hgsc.bcm.edu	37	6	26598247	26598247	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:26598247G>A	ENST00000274849.1	+	2	378	c.347G>A	c.(346-348)cGc>cAc	p.R116H		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	116	RRM.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron differentiation (GO:0021522)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11						CGTGACAAGCGCATAGCCAAG	0.582																																					p.R116H		Atlas-SNP	.											.	ABT1	39	.	0			c.G347A						.						62.0	56.0	58.0					6																	26598247		2203	4300	6503	SO:0001583	missense	29777	exon2			ACAAGCGCATAGC	AB027258	CCDS4616.1	6p21.31	2008-07-07			ENSG00000146109	ENSG00000146109			17369	protein-coding gene	gene with protein product						10648625	Standard	NM_013375		Approved		uc003nii.3	Q9ULW3	OTTHUMG00000016319	ENST00000274849.1:c.347G>A	chr6.hg19:g.26598247G>A	ENSP00000274849:p.Arg116His	345.0	0.0		394.0	114.0	NM_013375		Missense_Mutation	SNP	ENST00000274849.1	hg19	CCDS4616.1	.	.	.	.	.	.	.	.	.	.	G	35	5.527269	0.96431	.	.	ENSG00000146109	ENST00000274849	T	0.43294	0.95	5.23	5.23	0.72850	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.60971	0.2310	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.64433	-0.6409	10	0.59425	D	0.04	-33.4763	16.6701	0.85263	0.0:0.0:1.0:0.0	.	116	Q9ULW3	ABT1_HUMAN	H	116	ENSP00000274849:R116H	ENSP00000274849:R116H	R	+	2	0	ABT1	26706226	1.000000	0.71417	0.959000	0.39883	0.903000	0.53119	8.296000	0.89940	2.629000	0.89072	0.563000	0.77884	CGC	.	.		0.582	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1		
HIST1H4I	8294	hgsc.bcm.edu	37	6	27107217	27107217	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:27107217G>A	ENST00000354348.2	+	1	142	c.130G>A	c.(130-132)Gtg>Atg	p.V44M	HIST1H2BK_ENST00000396891.4_Intron	NM_003495.2	NP_003486.1	P62805	H4_HUMAN	histone cluster 1, H4i	44					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(1)	1						CCGCGGCGGCGTGAAGCGCAT	0.642			T	BCL6	NHL																																p.V44M		Atlas-SNP	.		Dom	yes		6	6p21.3	8294	"""histone 1, H4i (H4FM)"""		L	.	HIST1H4I	26	.	0			c.G130A						.						57.0	59.0	58.0					6																	27107217		2203	4300	6503	SO:0001583	missense	8294	exon1			GGCGGCGTGAAGC	AB000905	CCDS4620.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198339	ENSG00000276180		"""Histones / Replication-dependent"""	4793	protein-coding gene	gene with protein product		602833	"""H4 histone family, member M"", ""histone 1, H4i"""	H4FM		8988030, 9439656, 12408966	Standard	NM_003495		Approved	H4/m	uc003niy.1	P62805	OTTHUMG00000014471	ENST00000354348.2:c.130G>A	chr6.hg19:g.27107217G>A	ENSP00000346316:p.Val44Met	202.0	0.0		254.0	41.0	NM_003495	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000354348.2	hg19	CCDS4620.1	.	.	.	.	.	.	.	.	.	.	.	17.13	3.309732	0.60414	.	.	ENSG00000198339	ENST00000354348	T	0.68624	-0.34	3.95	3.95	0.45737	.	0.000000	0.36444	U	0.002585	D	0.86171	0.5869	H	0.98089	4.145	0.48236	D	0.999618	.	.	.	.	.	.	D	0.90533	0.4497	8	0.62326	D	0.03	.	14.3124	0.66424	0.0:0.0:1.0:0.0	.	.	.	.	M	44	ENSP00000346316:V44M	ENSP00000346316:V44M	V	+	1	0	HIST1H4I	27215196	1.000000	0.71417	0.626000	0.29213	0.049000	0.14656	8.868000	0.92320	2.158000	0.67659	0.655000	0.94253	GTG	.	.		0.642	HIST1H4I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040139.1	NM_003495	
OR12D2	26529	hgsc.bcm.edu	37	6	29365183	29365183	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:29365183C>T	ENST00000383555.2	+	1	768	c.707C>T	c.(706-708)gCa>gTa	p.A236V	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CTCTGTAAAGCACTGTCCACT	0.438																																					p.A236V		Atlas-SNP	.											.	OR12D2	42	.	0			c.C707T						.						223.0	216.0	218.0					6																	29365183		1511	2708	4219	SO:0001583	missense	26529	exon1			GTAAAGCACTGTC		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.707C>T	chr6.hg19:g.29365183C>T	ENSP00000373047:p.Ala236Val	116.0	0.0		140.0	48.0	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	hg19	CCDS4659.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.394839	0.42512	.	.	ENSG00000168787	ENST00000383555	T	0.00342	8.03	3.94	3.94	0.45596	GPCR, rhodopsin-like superfamily (1);	0.213717	0.32736	N	0.005710	T	0.00440	0.0014	M	0.79614	2.46	0.37040	D	0.897106	D	0.64830	0.994	D	0.68765	0.96	T	0.76454	-0.2953	10	0.54805	T	0.06	.	15.7562	0.78030	0.0:1.0:0.0:0.0	.	236	P58182	O12D2_HUMAN	V	236	ENSP00000373047:A236V	ENSP00000373047:A236V	A	+	2	0	OR12D2	29473162	1.000000	0.71417	0.042000	0.18584	0.184000	0.23303	5.014000	0.64029	2.019000	0.59389	0.205000	0.17691	GCA	.	.		0.438	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
HLA-G	3135	hgsc.bcm.edu	37	6	29797328	29797328	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:29797328C>T	ENST00000360323.6	+	4	777	c.753C>T	c.(751-753)gaC>gaT	p.D251D	HLA-G_ENST00000428701.1_Silent_p.D251D|HLA-G_ENST00000376828.2_Silent_p.D256D|HLA-G_ENST00000376818.3_Silent_p.D159D|HLA-G_ENST00000376815.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	251	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						AGACCCAGGACGTGGAGCTCG	0.617																																					p.D251D		Atlas-SNP	.											.	HLA-G	90	.	0			c.C753T						.						79.0	72.0	75.0					6																	29797328		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			CCAGGACGTGGAG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.753C>T	chr6.hg19:g.29797328C>T		129.0	0.0		197.0	55.0	NM_002127		Silent	SNP	ENST00000360323.6	hg19	CCDS4668.1																																																																																			.	.		0.617	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
ZNRD1	30834	hgsc.bcm.edu	37	6	30029708	30029708	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30029708G>A	ENST00000332435.5	+	2	431	c.160G>A	c.(160-162)Gtt>Att	p.V54I	ZNRD1_ENST00000376785.2_Missense_Mutation_p.V54I|ZNRD1_ENST00000376782.2_Missense_Mutation_p.V54I|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1_ENST00000463141.1_Intron|ZNRD1-AS1_ENST00000376797.3_RNA|ZNRD1_ENST00000359374.4_Missense_Mutation_p.V54I|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000421692.1_RNA|ZNRD1-AS1_ENST00000431012.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000452229.1_RNA|ZNRD1-AS1_ENST00000437417.1_RNA	NM_170783.2	NP_740753.1	Q9P1U0	RPA12_HUMAN	zinc ribbon domain containing 1	54					nucleobase-containing compound metabolic process (GO:0006139)|termination of RNA polymerase I transcription (GO:0006363)	DNA-directed RNA polymerase I complex (GO:0005736)	DNA-directed RNA polymerase activity (GO:0003899)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)										TGAGGGGAAGGTTGTGAAGAC	0.552																																					p.V54I		Atlas-SNP	.											.	.	.	.	0			c.G160A						.						191.0	196.0	194.0					6																	30029708		1511	2709	4220	SO:0001583	missense	30834	exon2			GGGAAGGTTGTGA	AF024617	CCDS4670.1	6p21	2011-02-18	2006-04-04		ENSG00000066379	ENSG00000066379			13182	protein-coding gene	gene with protein product		607525	"""zinc ribbon domain containing, 1"""			8938444, 10662553	Standard	NM_170783		Approved	hZR14, HTEX-6, tctex-6, RPA12	uc003npa.3	Q9P1U0	OTTHUMG00000031149	ENST00000332435.5:c.160G>A	chr6.hg19:g.30029708G>A	ENSP00000331111:p.Val54Ile	149.0	0.0		186.0	65.0	NM_170783		Missense_Mutation	SNP	ENST00000332435.5	hg19	CCDS4670.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730110	0.48939	.	.	ENSG00000066379	ENST00000332435;ENST00000376782;ENST00000359374;ENST00000376785	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.9	1.94	0.25998	.	0.295653	0.31246	N	0.008000	T	0.15739	0.0379	L	0.50333	1.59	0.39330	D	0.965392	B	0.11235	0.004	B	0.08055	0.003	T	0.04467	-1.0949	10	0.34782	T	0.22	-35.9902	5.7269	0.18018	0.1652:0.3046:0.5301:0.0	.	54	Q9P1U0	RPA12_HUMAN	I	54	ENSP00000331111:V54I;ENSP00000365978:V54I;ENSP00000352333:V54I;ENSP00000365981:V54I	ENSP00000331111:V54I	V	+	1	0	ZNRD1	30137687	0.998000	0.40836	0.958000	0.39756	0.993000	0.82548	1.193000	0.32162	0.404000	0.25506	0.637000	0.83480	GTT	.	.		0.552	ZNRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076272.2		
RNF39	80352	hgsc.bcm.edu	37	6	30039027	30039027	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30039027C>T	ENST00000244360.6	-	4	1221	c.1124G>A	c.(1123-1125)cGc>cAc	p.R375H	RNF39_ENST00000376751.3_Intron	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	375	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										GAAGGCCACGCGGCCCCGCTC	0.726																																					p.R375H	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.G1124A						.						13.0	10.0	11.0					6																	30039027		1489	2677	4166	SO:0001583	missense	80352	exon4			GCCACGCGGCCCC	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"""RING-type (C3HC4) zinc fingers"""	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.1124G>A	chr6.hg19:g.30039027C>T	ENSP00000244360:p.Arg375His	148.0	0.0		224.0	9.0	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	hg19	CCDS4673.1	.	.	.	.	.	.	.	.	.	.	c	14.95	2.688513	0.48097	.	.	ENSG00000204618	ENST00000244360	T	0.69175	-0.38	4.43	4.43	0.53597	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.43579	D	0.000552	T	0.45357	0.1338	L	0.47716	1.5	0.29863	N	0.82749	B	0.31413	0.322	B	0.37780	0.258	T	0.38243	-0.9670	9	.	.	.	-17.3663	10.2818	0.43543	0.1975:0.8025:0.0:0.0	.	375	Q9H2S5	RNF39_HUMAN	H	375	ENSP00000244360:R375H	.	R	-	2	0	RNF39	30147006	0.000000	0.05858	0.974000	0.42286	0.251000	0.25915	0.140000	0.16056	2.195000	0.70347	0.282000	0.19409	CGC	.	.		0.726	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769	
DDR1	780	hgsc.bcm.edu	37	6	30864468	30864468	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30864468C>T	ENST00000324771.8	+	15	2243	c.1695C>T	c.(1693-1695)agC>agT	p.S565S	DDR1_ENST00000418800.2_Silent_p.S528S|DDR1_ENST00000376568.3_Silent_p.S565S|DDR1_ENST00000376575.3_Silent_p.S565S|DDR1_ENST00000508312.1_Silent_p.S546S|DDR1_ENST00000452441.1_Silent_p.S565S|DDR1_ENST00000376569.3_Silent_p.S528S|DDR1_ENST00000361741.4_Intron|DDR1_ENST00000376570.4_Silent_p.S528S|DDR1_ENST00000513240.1_Silent_p.S565S|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000376567.2_Silent_p.S528S|DDR1_ENST00000454612.2_Silent_p.S528S			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	565	Gly/Pro-rich.				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)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CCCAGAACAGCGTCCCCCATT	0.642																																					p.S565S		Atlas-SNP	.											.	DDR1	213	.	0			c.C1695T						.						49.0	55.0	53.0					6																	30864468		2203	4300	6503	SO:0001819	synonymous_variant	780	exon12			GAACAGCGTCCCC	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.1695C>T	chr6.hg19:g.30864468C>T		250.0	0.0		309.0	60.0	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	hg19	CCDS34385.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.377265	0.24944	.	.	ENSG00000204580	ENST00000514434	.	.	.	5.21	0.774	0.18521	.	.	.	.	.	T	0.38532	0.1044	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	.	6.739	0.23424	0.0:0.6021:0.1374:0.2606	.	.	.	.	C	57	.	.	R	+	1	0	DDR1	30972447	0.902000	0.30710	0.994000	0.49952	0.987000	0.75469	-0.032000	0.12266	0.205000	0.20568	0.561000	0.74099	CGT	.	.		0.642	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
GTF2H4	2968	hgsc.bcm.edu	37	6	30881751	30881751	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30881751T>G	ENST00000259895.4	+	14	1603	c.1380T>G	c.(1378-1380)caT>caG	p.H460Q	VARS2_ENST00000321897.5_5'Flank|VARS2_ENST00000541562.1_5'Flank|VARS2_ENST00000416670.2_5'Flank|VARS2_ENST00000542001.1_5'Flank|GTF2H4_ENST00000376316.2_Missense_Mutation_p.H460Q	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	460					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|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)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						GGCAGAAACATAGCTCCTGAG	0.637								Nucleotide excision repair (NER)																													p.H460Q		Atlas-SNP	.											.	GTF2H4	38	.	0			c.T1380G						.						15.0	17.0	16.0					6																	30881751		1508	2707	4215	SO:0001583	missense	2968	exon14			GAAACATAGCTCC	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	4658	protein-coding gene	gene with protein product		601760	"""general transcription factor IIH, polypeptide 4 (52kD subunit)"""			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.1380T>G	chr6.hg19:g.30881751T>G	ENSP00000259895:p.His460Gln	191.0	0.0		283.0	86.0	NM_001517	B4DTJ5|Q76KU4	Missense_Mutation	SNP	ENST00000259895.4	hg19	CCDS34386.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.035880	0.54896	.	.	ENSG00000213780	ENST00000259895;ENST00000376316	T;T	0.40476	1.03;1.03	5.86	5.0	0.66597	.	0.802978	0.11020	U	0.608480	T	0.08447	0.0210	N	0.02213	-0.635	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17018	-1.0383	10	0.29301	T	0.29	-4.7331	10.8614	0.46829	0.0:0.8469:0.0:0.1531	.	460	Q92759	TF2H4_HUMAN	Q	460	ENSP00000259895:H460Q;ENSP00000365493:H460Q	ENSP00000259895:H460Q	H	+	3	2	GTF2H4	30989730	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	1.143000	0.31553	0.845000	0.35118	-0.186000	0.12905	CAT	.	.		0.637	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084588	31084588	+	Intron	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:31084588A>C	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Silent_p.V268V	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGGGACCTTGAACCACTCCAG	0.622																																					p.V268V		Atlas-SNP	.											.	CDSN	48	.	0			c.T804G						.						29.0	29.0	29.0					6																	31084588		2158	4232	6390	SO:0001627	intron_variant	1041	exon2			ACCTTGAACCACT	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1920A>C	chr6.hg19:g.31084588A>C		61.0	0.0		107.0	24.0	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	hg19	CCDS34390.1																																																																																			.	.		0.622	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
DDX39B	7919	hgsc.bcm.edu	37	6	31507027	31507027	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:31507027G>A	ENST00000396172.1	-	3	866	c.236C>T	c.(235-237)gCc>gTc	p.A79V	DDX39B_ENST00000415382.2_Intron|DDX39B_ENST00000453105.2_Intron|DDX39B_ENST00000449074.2_Missense_Mutation_p.A79V|ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank|DDX39B_ENST00000458640.1_Missense_Mutation_p.A79V|SNORD117_ENST00000364915.1_RNA|SNORD84_ENST00000584275.1_RNA|DDX39B_ENST00000376177.2_Missense_Mutation_p.A79V|DDX39B_ENST00000417556.2_Missense_Mutation_p.A79V|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	79	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)	p.A79V(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TCCCAGAATGGCCTGAGGGAT	0.522																																					p.A79V		Atlas-SNP	.											DDX39B,face,carcinoma,0,1	DDX39B	38	.	1	Substitution - Missense(1)	skin(1)	c.C236T						.						117.0	122.0	120.0					6																	31507027		1511	2709	4220	SO:0001583	missense	7919	exon3			AGAATGGCCTGAG	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"""DEAD-boxes"""	13917	protein-coding gene	gene with protein product	"""U2AF65-associated protein 56"""	142560	"""HLA-B associated transcript 1"""	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.236C>T	chr6.hg19:g.31507027G>A	ENSP00000379475:p.Ala79Val	92.0	0.0		143.0	48.0	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	hg19	CCDS4697.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504374	0.85176	.	.	ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000427214;ENST00000428098;ENST00000419338;ENST00000456662;ENST00000449074;ENST00000428450;ENST00000449757;ENST00000456976;ENST00000418897;ENST00000419020;ENST00000458215	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55;2.55	5.53	5.53	0.82687	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.065486	0.64402	D	0.000017	T	0.11452	0.0279	L	0.41824	1.3	0.80722	D	1	P;B;P	0.47962	0.903;0.35;0.831	P;B;P	0.47470	0.521;0.177;0.548	T	0.01405	-1.1363	10	0.49607	T	0.09	-9.5406	16.9509	0.86245	0.0:0.0:1.0:0.0	.	99;79;79	Q59G92;Q13838;Q5STU3	.;DX39B_HUMAN;.	V	79;79;79;79;79;79;79;79;79;79;102;79;94;79;79	ENSP00000365347:A79V;ENSP00000416269:A79V;ENSP00000379475:A79V;ENSP00000412582:A79V;ENSP00000399371:A79V;ENSP00000392672:A79V;ENSP00000410313:A79V;ENSP00000416350:A79V;ENSP00000391946:A79V;ENSP00000405707:A79V;ENSP00000409426:A102V;ENSP00000393984:A79V;ENSP00000399841:A94V;ENSP00000405245:A79V	ENSP00000365347:A79V	A	-	2	0	DDX39B	31615006	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.262000	0.95591	2.592000	0.87571	0.563000	0.77884	GCC	.	.		0.522	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640	
AGPAT1	10554	hgsc.bcm.edu	37	6	32138331	32138331	+	Silent	SNP	G	G	A	rs528693769	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:32138331G>A	ENST00000395499.1	-	4	960	c.381C>T	c.(379-381)cgC>cgT	p.R127R	AGPAT1_ENST00000375107.3_Silent_p.R127R|AGPAT1_ENST00000412465.2_Silent_p.R15R|AGPAT1_ENST00000490711.1_Intron|AGPAT1_ENST00000395497.1_Silent_p.R127R|AGPAT1_ENST00000395496.1_Silent_p.R127R|AGPAT1_ENST00000375104.2_Silent_p.R127R|AGPAT1_ENST00000336984.6_Silent_p.R127R|PPT2-EGFL8_ENST00000422437.1_3'UTR			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	127					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						ACAGTAGCTCGCGCTTGGCAA	0.637													G|||	2	0.000399361	0.0	0.0029	5008	,	,		18391	0.0		0.0	False		,,,				2504	0.0				p.R127R		Atlas-SNP	.											.	AGPAT1	22	.	0			c.C381T						.						64.0	70.0	67.0					6																	32138331		1510	2708	4218	SO:0001819	synonymous_variant	10554	exon4			TAGCTCGCGCTTG	U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	324	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, alpha"""	603099	"""1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"""			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.381C>T	chr6.hg19:g.32138331G>A		84.0	0.0		106.0	28.0	NM_006411	A2BFI5|Q5BL03	Silent	SNP	ENST00000395499.1	hg19	CCDS4744.1																																																																																			.	.		0.637	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411	
AGER	177	hgsc.bcm.edu	37	6	32149317	32149317	+	Intron	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:32149317A>G	ENST00000375076.4	-	10	1093				AGER_ENST00000375055.2_3'UTR|AGER_ENST00000375067.3_Intron|AGER_ENST00000375070.3_Intron|AGER_ENST00000438221.2_3'UTR|AGER_ENST00000375065.5_Intron|AGER_ENST00000375069.3_Intron|RNF5_ENST00000427134.2_Intron	NM_001136.4|NM_001206929.1|NM_001206932.1	NP_001127.1|NP_001193858.1|NP_001193861.1	Q15109	RAGE_HUMAN	advanced glycosylation end product-specific receptor						cell surface receptor signaling pathway (GO:0007166)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|neuron projection development (GO:0031175)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|response to wounding (GO:0009611)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor activity (GO:0004872)|S100 protein binding (GO:0044548)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|lung(5)|pancreas(2)	9						TTTCTTGTTGACCATCCCCCC	0.557																																					p.G335G		Atlas-SNP	.											.	AGER	15	.	0			c.T1005C						.																																			SO:0001627	intron_variant	177	exon9			TTGTTGACCATCC	M91211	CCDS4746.1, CCDS4747.1, CCDS56417.1, CCDS56418.1, CCDS75429.1	6p21.3	2013-01-29			ENSG00000204305	ENSG00000204305		"""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	320	protein-coding gene	gene with protein product		600214				7713518	Standard	NM_001136		Approved	RAGE	uc003oap.2	Q15109	OTTHUMG00000031120	ENST00000375076.4:c.992-63T>C	chr6.hg19:g.32149317A>G		115.0	0.0		154.0	43.0	NM_001206936	A2BFI7|A6NKF0|A7Y2U9|B0V176|Q15279|Q3L1R4|Q3L1R5|Q3L1R6|Q3L1R7|Q3L1R8|Q3L1S0|Q86SN1|Q9H2X7|Q9Y3R3|V5R6A3	Silent	SNP	ENST00000375076.4	hg19	CCDS4746.1																																																																																			.	.		0.557	AGER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076200.1	NM_001136	
ITPR3	3710	hgsc.bcm.edu	37	6	33608281	33608281	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:33608281T>C	ENST00000374316.5	+	3	1170	c.110T>C	c.(109-111)gTg>gCg	p.V37A	ITPR3_ENST00000605930.1_Missense_Mutation_p.V37A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	37					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GACCGCTGTGTGGTGGAGCCC	0.632																																					p.V37A		Atlas-SNP	.											.	ITPR3	409	.	0			c.T110C						.						148.0	161.0	157.0					6																	33608281		2203	4300	6503	SO:0001583	missense	3710	exon2			GCTGTGTGGTGGA	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.110T>C	chr6.hg19:g.33608281T>C	ENSP00000363435:p.Val37Ala	114.0	0.0		137.0	43.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.623529	0.87460	.	.	ENSG00000096433	ENST00000374316	D	0.98649	-5.05	5.15	5.15	0.70609	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.000000	0.85682	D	0.000000	D	0.99180	0.9716	M	0.92459	3.31	0.44745	D	0.997747	D	0.89917	1.0	D	0.91635	0.999	D	0.99568	1.0970	10	0.87932	D	0	-30.931	11.3587	0.49630	0.0:0.0:0.0:1.0	.	37	Q14573	ITPR3_HUMAN	A	37	ENSP00000363435:V37A	ENSP00000363435:V37A	V	+	2	0	ITPR3	33716259	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.007000	0.70731	1.936000	0.56123	0.402000	0.26972	GTG	.	.		0.632	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
IP6K3	117283	hgsc.bcm.edu	37	6	33693356	33693356	+	Silent	SNP	C	C	T	rs200747722		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:33693356C>T	ENST00000293756.4	-	5	953	c.627G>A	c.(625-627)acG>acA	p.T209T	IP6K3_ENST00000451316.1_Silent_p.T209T	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	209					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						CACAGGGATGCGTGTACTGTG	0.552																																					p.T209T		Atlas-SNP	.											.	IP6K3	52	.	0			c.G627A						.						99.0	86.0	90.0					6																	33693356		2203	4300	6503	SO:0001819	synonymous_variant	117283	exon6			GGGATGCGTGTAC	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.627G>A	chr6.hg19:g.33693356C>T		118.0	0.0		119.0	36.0	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	hg19	CCDS34435.1																																																																																			.	C|0.999;T|0.001		0.552	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
C6orf89	221477	hgsc.bcm.edu	37	6	36867219	36867219	+	5'UTR	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:36867219A>T	ENST00000480824.2	+	0	293				C6orf89_ENST00000510325.2_5'UTR|C6orf89_ENST00000359359.2_5'UTR|C6orf89_ENST00000373685.1_5'UTR|C6orf89_ENST00000355190.3_Missense_Mutation_p.D7V			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89						epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						ATATTGGAAGACATGGATCTT	0.418																																					p.D7V		Atlas-SNP	.											.	C6orf89	39	.	0			c.A20T						.						75.0	76.0	76.0					6																	36867219		2203	4300	6503	SO:0001623	5_prime_UTR_variant	221477	exon2			TGGAAGACATGGA	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"""bombesin receptor activated protein"""					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.-2A>T	chr6.hg19:g.36867219A>T		113.0	0.0		54.0	23.0	NM_152734	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000480824.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.27	3.587111	0.66105	.	.	ENSG00000198663	ENST00000355190;ENST00000416621;ENST00000540072	.	.	.	5.91	3.32	0.38043	.	0.000000	0.56097	D	0.000033	T	0.26304	0.0642	L	0.36672	1.1	0.80722	D	1	P	0.39480	0.675	B	0.39258	0.295	T	0.15378	-1.0439	9	0.87932	D	0	-0.8288	7.8253	0.29311	0.7142:0.2102:0.0756:0.0	.	7	Q6UWU4-2	.	V	7;7;6	.	ENSP00000347322:D7V	D	+	2	0	C6orf89	36975197	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.146000	0.42216	1.023000	0.39654	0.533000	0.62120	GAC	.	.		0.418	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734	
TRERF1	55809	hgsc.bcm.edu	37	6	42200601	42200601	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42200601G>A	ENST00000372922.4	-	17	3658	c.3096C>T	c.(3094-3096)ggC>ggT	p.G1032G	TRERF1_ENST00000340840.2_Silent_p.G961G|TRERF1_ENST00000354325.2_Silent_p.G949G|TRERF1_ENST00000372917.4_Silent_p.G961G|TRERF1_ENST00000541110.1_Silent_p.G1052G	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1032	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGCGGGCATGGCCATTCAGTG	0.562																																					p.G1032G		Atlas-SNP	.											.	TRERF1	124	.	0			c.C3096T						.						37.0	35.0	36.0					6																	42200601		2203	4300	6503	SO:0001819	synonymous_variant	55809	exon17			GGCATGGCCATTC	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3096C>T	chr6.hg19:g.42200601G>A		55.0	0.0		127.0	19.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	hg19	CCDS4867.1																																																																																			.	.		0.562	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42796557	42796557	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42796557G>A	ENST00000314073.5	+	6	662	c.486G>A	c.(484-486)acG>acA	p.T162T	GLTSCR1L_ENST00000394168.1_Silent_p.T162T			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	162																	CAGGTCAGACGCTGCAGCCTA	0.468																																					p.T162T		Atlas-SNP	.											.	.	.	.	0			c.G486A						.						134.0	124.0	128.0					6																	42796557		2203	4300	6503	SO:0001819	synonymous_variant	23506	exon5			TCAGACGCTGCAG	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"""KIAA0240"""	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.486G>A	chr6.hg19:g.42796557G>A		109.0	0.0		313.0	76.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	hg19	CCDS34451.1																																																																																			.	.		0.468	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	
PPP2R5D	5528	hgsc.bcm.edu	37	6	42975948	42975948	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42975948C>T	ENST00000485511.1	+	8	1046	c.867C>T	c.(865-867)taC>taT	p.Y289Y	PPP2R5D_ENST00000394110.3_Silent_p.Y257Y|PPP2R5D_ENST00000461010.1_Silent_p.Y183Y|PPP2R5D_ENST00000472118.1_Silent_p.Y281Y	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	289					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGTTCATCTACGAGACGGAGC	0.582																																					p.Y289Y	Melanoma(63;587 1613 29742 31770)	Atlas-SNP	.											.	PPP2R5D	47	.	0			c.C867T						.						136.0	139.0	138.0					6																	42975948		2203	4300	6503	SO:0001819	synonymous_variant	5528	exon8			CATCTACGAGACG	L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9312	protein-coding gene	gene with protein product		601646	"""protein phosphatase 2, regulatory subunit B (B56), delta isoform"", ""protein phosphatase 2, regulatory subunit B', delta isoform"""			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.867C>T	chr6.hg19:g.42975948C>T		133.0	0.0		281.0	36.0	NM_006245	A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Silent	SNP	ENST00000485511.1	hg19	CCDS4878.1	.	.	.	.	.	.	.	.	.	.	C	6.120	0.390354	0.11581	.	.	ENSG00000112640	ENST00000470467	.	.	.	5.84	-4.83	0.03161	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.3824	14.3121	0.66422	0.0:0.4819:0.0:0.5181	.	.	.	.	X	209	.	.	R	+	1	2	PPP2R5D	43083926	0.980000	0.34600	0.973000	0.42090	0.946000	0.59487	0.095000	0.15127	-0.641000	0.05487	-1.152000	0.01820	CGA	.	.		0.582	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245	
MRPL2	51069	hgsc.bcm.edu	37	6	43023917	43023917	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43023917A>G	ENST00000388752.3	-	4	846	c.422T>C	c.(421-423)cTg>cCg	p.L141P	MRPL2_ENST00000230413.5_Missense_Mutation_p.L141P|MRPL2_ENST00000489623.1_Intron|CUL7_ENST00000265348.3_5'Flank|CUL7_ENST00000535468.1_5'Flank	NM_015950.3	NP_057034.2	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2	141					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(2)	9		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		CCCAGCAACCAGAGCTATGTC	0.522																																					p.L141P		Atlas-SNP	.											.	MRPL2	30	.	0			c.T422C						.						113.0	104.0	107.0					6																	43023917		2203	4300	6503	SO:0001583	missense	51069	exon4			GCAACCAGAGCTA	AB051617	CCDS34454.1, CCDS75458.1	6p21.3	2012-09-13			ENSG00000112651	ENSG00000112651		"""Mitochondrial ribosomal proteins / large subunits"""	14056	protein-coding gene	gene with protein product		611822					Standard	XM_005249161		Approved	MRP-L14, RPML14, CGI-22	uc003ots.1	Q5T653	OTTHUMG00000014719	ENST00000388752.3:c.422T>C	chr6.hg19:g.43023917A>G	ENSP00000373404:p.Leu141Pro	72.0	0.0		172.0	67.0	NM_015950	B2RC56|Q8WUL1|Q96Q56|Q9Y311	Missense_Mutation	SNP	ENST00000388752.3	hg19	CCDS34454.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.535022	0.85812	.	.	ENSG00000112651	ENST00000388752;ENST00000230413	T	0.60040	0.22	5.7	5.7	0.88788	Nucleic acid-binding, OB-fold-like (1);Ribosomal Proteins L2, RNA binding domain (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.64402	D	0.000001	T	0.81283	0.4790	H	0.96604	3.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.87741	0.2585	10	0.87932	D	0	-12.5297	14.5373	0.67969	1.0:0.0:0.0:0.0	.	141;141	B4DVE2;Q5T653	.;RM02_HUMAN	P	141	ENSP00000373404:L141P	ENSP00000230413:L141P	L	-	2	0	MRPL2	43131895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.831000	0.92068	2.170000	0.68504	0.533000	0.62120	CTG	.	.		0.522	MRPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040577.2		
CUL9	23113	hgsc.bcm.edu	37	6	43190596	43190596	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43190596A>G	ENST00000252050.4	+	38	7196	c.7112A>G	c.(7111-7113)aAc>aGc	p.N2371S	CUL9_ENST00000354495.3_Missense_Mutation_p.N2261S|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000372647.2_Missense_Mutation_p.N2343S	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2371					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CAGACAGAGAACCTGGAGCTG	0.642																																					p.N2371S		Atlas-SNP	.											.	CUL9	248	.	0			c.A7112G						.						88.0	89.0	89.0					6																	43190596		2203	4300	6503	SO:0001583	missense	23113	exon38			CAGAGAACCTGGA	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.7112A>G	chr6.hg19:g.43190596A>G	ENSP00000252050:p.Asn2371Ser	94.0	0.0		207.0	49.0	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.650741	0.29336	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.72282	-0.64;-0.64;-0.53	5.04	-3.13	0.05266	.	0.627181	0.16955	N	0.192706	T	0.22742	0.0549	N	0.08118	0	0.34091	D	0.660774	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.01781	-1.1275	10	0.25106	T	0.35	-3.2484	8.481	0.33043	0.4044:0.125:0.4706:0.0	.	2261;2343;2371	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	S	2371;2261;2343	ENSP00000252050:N2371S;ENSP00000346490:N2261S;ENSP00000361730:N2343S	ENSP00000252050:N2371S	N	+	2	0	CUL9	43298574	0.645000	0.27286	0.893000	0.35052	0.787000	0.44495	-0.025000	0.12413	-0.610000	0.05716	-0.366000	0.07423	AAC	.	.		0.642	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
SLC22A7	10864	hgsc.bcm.edu	37	6	43267678	43267678	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43267678T>C	ENST00000372585.5	+	5	796	c.701T>C	c.(700-702)gTc>gCc	p.V234A	SLC22A7_ENST00000487175.1_3'UTR|SLC22A7_ENST00000372574.3_Missense_Mutation_p.V232A|SLC22A7_ENST00000372589.3_Missense_Mutation_p.V232A	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	234					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	GTGGCTGGAGTCCTGAGCAGC	0.617																																					p.V234A		Atlas-SNP	.											.	SLC22A7	69	.	0			c.T701C						.						152.0	121.0	131.0					6																	43267678		2203	4300	6503	SO:0001583	missense	10864	exon4			CTGGAGTCCTGAG	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"""Solute carriers"""	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.701T>C	chr6.hg19:g.43267678T>C	ENSP00000361666:p.Val234Ala	145.0	0.0		325.0	31.0	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	hg19	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	T	13.83	2.353384	0.41700	.	.	ENSG00000137204	ENST00000451757;ENST00000372589;ENST00000372585;ENST00000372574	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.68	5.68	0.88126	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.290888	0.32901	N	0.005504	T	0.51941	0.1704	M	0.66378	2.025	0.33870	D	0.634833	P;P;P	0.49862	0.929;0.913;0.913	P;P;P	0.59115	0.852;0.769;0.769	T	0.58239	-0.7671	10	0.42905	T	0.14	.	13.4565	0.61201	0.0:0.0:0.0:1.0	.	234;232;232	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	A	106;232;234;232	ENSP00000416052:V106A;ENSP00000361670:V232A;ENSP00000361666:V234A;ENSP00000361655:V232A	ENSP00000361655:V232A	V	+	2	0	SLC22A7	43375656	0.710000	0.27896	0.308000	0.25141	0.002000	0.02628	1.607000	0.36836	2.160000	0.67779	0.455000	0.32223	GTC	.	.		0.617	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1		
ABCC10	89845	hgsc.bcm.edu	37	6	43402386	43402386	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43402386C>T	ENST00000372530.4	+	4	1623	c.1408C>T	c.(1408-1410)Cgg>Tgg	p.R470W	ABCC10_ENST00000443426.2_3'UTR|ABCC10_ENST00000244533.3_Missense_Mutation_p.R427W	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	470	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GAGTGGCATTCGGGTCATCAA	0.612																																					p.R470W		Atlas-SNP	.											.	ABCC10	118	.	0			c.C1408T						.						100.0	105.0	103.0					6																	43402386		2203	4300	6503	SO:0001583	missense	89845	exon4			GGCATTCGGGTCA	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.1408C>T	chr6.hg19:g.43402386C>T	ENSP00000361608:p.Arg470Trp	53.0	0.0		193.0	21.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	32	5.160422	0.94727	.	.	ENSG00000124574	ENST00000372515;ENST00000372530;ENST00000244533	D;D;D	0.91843	-2.92;-2.92;-2.92	5.93	5.93	0.95920	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.96374	0.8817	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	0.991;1.0	P;D	0.97110	0.786;1.0	D	0.96555	0.9411	10	0.87932	D	0	-25.7653	15.9036	0.79403	0.1357:0.8643:0.0:0.0	.	427;470	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	W	26;470;427	ENSP00000361593:R26W;ENSP00000361608:R470W;ENSP00000244533:R427W	ENSP00000244533:R427W	R	+	1	2	ABCC10	43510364	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	3.885000	0.56182	2.826000	0.97356	0.655000	0.94253	CGG	.	.		0.612	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
ABCC10	89845	hgsc.bcm.edu	37	6	43412531	43412531	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43412531C>T	ENST00000372530.4	+	13	2910	c.2695C>T	c.(2695-2697)Cgg>Tgg	p.R899W	ABCC10_ENST00000244533.3_Missense_Mutation_p.R871W	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	899	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.R871W(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	CCCAGCCACGCGGAACGCTGC	0.587																																					p.R899W		Atlas-SNP	.											ABCC10,bladder,carcinoma,0,1	ABCC10	118	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C2695T						.						70.0	67.0	68.0					6																	43412531		2203	4300	6503	SO:0001583	missense	89845	exon13			GCCACGCGGAACG	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2695C>T	chr6.hg19:g.43412531C>T	ENSP00000361608:p.Arg899Trp	55.0	1.0		139.0	24.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.445368	0.63178	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	T;T	0.42900	0.96;0.96	5.22	2.07	0.26955	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.351077	0.30043	N	0.010549	T	0.52419	0.1733	M	0.78285	2.405	0.42656	D	0.993467	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	T	0.56547	-0.7961	10	0.40728	T	0.16	-37.1748	13.796	0.63171	0.6701:0.3299:0.0:0.0	.	871;899	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	W	899;871	ENSP00000361608:R899W;ENSP00000244533:R871W	ENSP00000244533:R871W	R	+	1	2	ABCC10	43520509	0.735000	0.28153	0.244000	0.24202	0.947000	0.59692	1.451000	0.35145	0.448000	0.26722	0.563000	0.77884	CGG	.	.		0.587	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
XPO5	57510	hgsc.bcm.edu	37	6	43526266	43526266	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43526266G>A	ENST00000265351.7	-	12	1494	c.1284C>T	c.(1282-1284)agC>agT	p.S428S	XPO5_ENST00000424378.2_5'UTR	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	428					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)			AGTCCTCATCGCTATCAAAAT	0.408																																					p.S428S		Atlas-SNP	.											.	XPO5	79	.	0			c.C1284T						.						79.0	74.0	76.0					6																	43526266		1870	4097	5967	SO:0001819	synonymous_variant	57510	exon12			CTCATCGCTATCA	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.1284C>T	chr6.hg19:g.43526266G>A		168.0	0.0		459.0	49.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.408	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
RUNX2	860	hgsc.bcm.edu	37	6	45390466	45390466	+	Silent	SNP	A	A	G	rs575896136	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:45390466A>G	ENST00000371438.1	+	2	553	c.195A>G	c.(193-195)caA>caG	p.Q65Q	RUNX2_ENST00000465038.2_Silent_p.Q65Q|RUNX2_ENST00000576263.1_Silent_p.Q65Q|RUNX2_ENST00000352853.5_Silent_p.Q133Q|RUNX2_ENST00000541979.1_Silent_p.Q133Q|RUNX2_ENST00000371432.3_Silent_p.Q51Q|RUNX2_ENST00000359524.5_Silent_p.Q51Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Silent_p.Q65Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	65	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	8	0.00159744	0.0023	0.0	5008	,	,		7675	0.002		0.0	False		,,,				2504	0.0031				p.Q65Q		Atlas-SNP	.											.	RUNX2	128	.	0			c.A195G						.						10.0	15.0	14.0					6																	45390466		1452	3071	4523	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.195A>G	chr6.hg19:g.45390466A>G		57.0	0.0		109.0	5.0	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348	
TDRD6	221400	hgsc.bcm.edu	37	6	46656045	46656045	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:46656045G>T	ENST00000316081.6	+	1	180	c.180G>T	c.(178-180)tgG>tgT	p.W60C	RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000434329.2_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.W60C|RP11-446F17.3_ENST00000422284.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	60					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GCGGCCAGTGGGCGCTGGGCA	0.741																																					p.W60C		Atlas-SNP	.											.	TDRD6	205	.	0			c.G180T						.						2.0	3.0	3.0					6																	46656045		1504	3094	4598	SO:0001583	missense	221400	exon1			CCAGTGGGCGCTG	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.180G>T	chr6.hg19:g.46656045G>T	ENSP00000346065:p.Trp60Cys	63.0	0.0		103.0	11.0	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.358668	0.24598	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09255	3.0;3.0	5.2	4.32	0.51571	Maternal tudor protein (1);	0.879250	0.10003	N	0.728190	T	0.04227	0.0117	N	0.14661	0.345	0.18873	N	0.999987	P;D	0.53151	0.948;0.958	P;P	0.50754	0.517;0.649	T	0.33954	-0.9848	10	0.42905	T	0.14	-7.235	6.8771	0.24153	0.1443:0.1607:0.695:0.0	.	60;60	F5H5M3;O60522	.;TDRD6_HUMAN	C	60	ENSP00000443299:W60C;ENSP00000346065:W60C	ENSP00000346065:W60C	W	+	3	0	TDRD6	46764004	1.000000	0.71417	0.999000	0.59377	0.771000	0.43674	2.134000	0.42102	2.425000	0.82216	0.563000	0.77884	TGG	.	.		0.741	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
GPR116	221395	hgsc.bcm.edu	37	6	46874483	46874483	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:46874483C>G	ENST00000283296.7	-	2	305	c.17G>C	c.(16-18)aGa>aCa	p.R6T	GPR116_ENST00000265417.7_Missense_Mutation_p.R6T|GPR116_ENST00000362015.4_Missense_Mutation_p.R6T|RP3-365O12.2_ENST00000451135.1_RNA|GPR116_ENST00000456426.2_Missense_Mutation_p.R6T	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	6					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R6I(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CAAAGTGGTTCTCCTTGGGGA	0.358																																					p.R6T	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											GPR116,colon,carcinoma,0,1	GPR116	133	.	1	Substitution - Missense(1)	large_intestine(1)	c.G17C						.						138.0	140.0	139.0					6																	46874483		2203	4300	6503	SO:0001583	missense	221395	exon2			GTGGTTCTCCTTG	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.17G>C	chr6.hg19:g.46874483C>G	ENSP00000283296:p.Arg6Thr	154.0	0.0		222.0	74.0	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	hg19	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	3.779	-0.046105	0.07407	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.30182	1.54;1.92;1.6;1.54	5.73	2.6	0.31112	.	0.453074	0.19217	N	0.119775	T	0.04452	0.0122	N	0.12182	0.205	0.09310	N	0.999996	B;B;B	0.21381	0.055;0.017;0.004	B;B;B	0.12837	0.008;0.007;0.003	T	0.40327	-0.9569	10	0.25751	T	0.34	-0.5277	4.8602	0.13579	0.0:0.5998:0.1752:0.2251	.	6;6;6	A8K0D8;Q8IZF2-3;Q8IZF2	.;.;GP116_HUMAN	T	6	ENSP00000283296:R6T;ENSP00000354563:R6T;ENSP00000412866:R6T;ENSP00000265417:R6T	ENSP00000265417:R6T	R	-	2	0	GPR116	46982442	0.011000	0.17503	0.030000	0.17652	0.079000	0.17450	-0.122000	0.10627	0.280000	0.22209	0.557000	0.71058	AGA	.	.		0.358	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
GPR115	221393	hgsc.bcm.edu	37	6	47682484	47682484	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:47682484A>G	ENST00000283303.2	+	6	1761	c.1503A>G	c.(1501-1503)ggA>ggG	p.G501G	GPR115_ENST00000327753.3_Silent_p.G501G|GPR115_ENST00000371220.1_Silent_p.G558G|RN7SKP116_ENST00000516902.1_RNA	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	501					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						TCATTTATGGAATATTGGTCA	0.423																																					p.G501G	GBM(22;431 510 9010 26644 32828)	Atlas-SNP	.											.	GPR115	140	.	0			c.A1503G						.						205.0	193.0	197.0					6																	47682484		2203	4300	6503	SO:0001819	synonymous_variant	221393	exon6			TTATGGAATATTG	AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"""-"", ""GPCR / Class B : Orphans"""	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.1503A>G	chr6.hg19:g.47682484A>G		75.0	0.0		155.0	54.0	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	hg19	CCDS4922.2																																																																																			.	.		0.423	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838	
COL19A1	1310	hgsc.bcm.edu	37	6	70866035	70866035	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:70866035G>A	ENST00000322773.4	+	32	2198	c.2096G>A	c.(2095-2097)tGc>tAc	p.C699Y	COL19A1_ENST00000393344.1_Missense_Mutation_p.C321Y	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	699					cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						TGTGGCAACTGCCAAGCCAGT	0.453																																					p.C699Y		Atlas-SNP	.											.	COL19A1	232	.	0			c.G2096A						.						70.0	64.0	66.0					6																	70866035		2203	4300	6503	SO:0001583	missense	1310	exon32			GCAACTGCCAAGC		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2096G>A	chr6.hg19:g.70866035G>A	ENSP00000316030:p.Cys699Tyr	152.0	0.0		72.0	6.0	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.408196	0.42715	.	.	ENSG00000082293	ENST00000322773;ENST00000393344	D;D	0.92099	-2.97;-2.88	5.41	5.41	0.78517	.	0.062427	0.64402	D	0.000007	D	0.96846	0.8970	H	0.95712	3.71	0.50039	D	0.999846	D	0.71674	0.998	D	0.80764	0.994	D	0.96789	0.9581	10	0.46703	T	0.11	.	14.7103	0.69225	0.0:0.0:1.0:0.0	.	699	Q14993	COJA1_HUMAN	Y	699;321	ENSP00000316030:C699Y;ENSP00000377013:C321Y	ENSP00000316030:C699Y	C	+	2	0	COL19A1	70922756	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	4.422000	0.59854	2.546000	0.85860	0.563000	0.77884	TGC	.	.		0.453	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
B3GAT2	135152	hgsc.bcm.edu	37	6	71603972	71603972	+	Nonsense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:71603972G>A	ENST00000230053.6	-	2	1203	c.595C>T	c.(595-597)Cga>Tga	p.R199*		NM_080742.2	NP_542780.1	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2	199					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)	p.R199G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						CGGGTGGTTCGCATCTATAAA	0.502																																					p.R199X		Atlas-SNP	.											B3GAT2,NS,carcinoma,0,1	B3GAT2	33	.	1	Substitution - Missense(1)	lung(1)	c.C595T						.						55.0	59.0	58.0					6																	71603972		2203	4300	6503	SO:0001587	stop_gained	135152	exon2			TGGTTCGCATCTA	AB075843	CCDS4974.1	6q12	2014-07-08	2014-07-08		ENSG00000112309	ENSG00000112309	2.4.1.135	"""Beta-1,3-glucuronyltransferases"""	922	protein-coding gene	gene with protein product	"""glucuronosyltransferase S"", ""galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2"""	607497				12383500	Standard	NM_080742		Approved	GlcAT-S	uc003pfv.3	Q9NPZ5	OTTHUMG00000014997	ENST00000230053.6:c.595C>T	chr6.hg19:g.71603972G>A	ENSP00000230053:p.Arg199*	186.0	0.0		117.0	99.0	NM_080742	Q5JS09|Q8TF38|Q96NK4	Nonsense_Mutation	SNP	ENST00000230053.6	hg19	CCDS4974.1	.	.	.	.	.	.	.	.	.	.	G	40	8.154060	0.98680	.	.	ENSG00000112309	ENST00000230053	.	.	.	6.07	3.24	0.37175	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.3395	15.333	0.74229	0.0:0.0:0.634:0.366	.	.	.	.	X	199	.	ENSP00000230053:R199X	R	-	1	2	B3GAT2	71660693	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	3.976000	0.56867	0.392000	0.25172	0.650000	0.86243	CGA	.	.		0.502	B3GAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041150.2	NM_080742	
SYNCRIP	10492	hgsc.bcm.edu	37	6	86333797	86333797	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:86333797T>C	ENST00000369622.3	-	7	1200	c.700A>G	c.(700-702)Att>Gtt	p.I234V	SYNCRIP_ENST00000355238.6_Missense_Mutation_p.I234V	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	234	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		CAGACACCAATATGTTTTCCA	0.323																																					p.I234V		Atlas-SNP	.											.	SYNCRIP	80	.	0			c.A700G						.						87.0	84.0	85.0					6																	86333797		2203	4300	6503	SO:0001583	missense	10492	exon7			CACCAATATGTTT	AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"""RNA binding motif (RRM) containing"""	16918	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein Q"""					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.700A>G	chr6.hg19:g.86333797T>C	ENSP00000358635:p.Ile234Val	79.0	0.0		55.0	5.0	NM_006372	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Missense_Mutation	SNP	ENST00000369622.3	hg19	CCDS5005.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.348593	0.82132	.	.	ENSG00000135316	ENST00000355238;ENST00000369622	T;T	0.49139	1.12;0.79	5.75	5.75	0.90469	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.49201	0.1543	L	0.49571	1.57	0.54753	D	0.999982	P;P;P;P;B;P;P	0.50943	0.475;0.544;0.787;0.94;0.12;0.61;0.475	B;B;B;P;B;B;B	0.55011	0.196;0.439;0.387;0.766;0.219;0.358;0.196	T	0.54423	-0.8296	10	0.87932	D	0	.	16.066	0.80870	0.0:0.0:0.0:1.0	.	234;234;136;82;234;234;234	O60506;O60506-2;B7Z645;O60506-5;O60506-4;O60506-3;B2R8Z8	HNRPQ_HUMAN;.;.;.;.;.;.	V	234	ENSP00000347380:I234V;ENSP00000358635:I234V	ENSP00000347380:I234V	I	-	1	0	SYNCRIP	86390516	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.121000	0.64691	2.196000	0.70406	0.455000	0.32223	ATT	.	.		0.323	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372	
KIAA1244	57221	hgsc.bcm.edu	37	6	138576784	138576784	+	Missense_Mutation	SNP	G	G	A	rs370057378		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:138576784G>A	ENST00000251691.4	+	10	1148	c.982G>A	c.(982-984)Gag>Aag	p.E328K		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CATCGCAGCCGAGCTGGTCCG	0.662																																					p.E328K		Atlas-SNP	.											KIAA1244_ENST00000251691,NS,carcinoma,0,2	KIAA1244	236	.	0			c.G982A						.	G	LYS/GLU	0,4406		0,0,2203	27.0	28.0	27.0		982	5.7	1.0	6		27	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1244	NM_020340.4	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	328/2178	138576784	1,13005	2203	4300	6503	SO:0001583	missense	57221	exon10			GCAGCCGAGCTGG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.982G>A	chr6.hg19:g.138576784G>A	ENSP00000251691:p.Glu328Lys	103.0	0.0		52.0	26.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	36	5.810796	0.96975	0.0	1.16E-4	ENSG00000112379	ENST00000251691	T	0.04654	3.58	5.68	5.68	0.88126	.	0.046372	0.85682	D	0.000000	T	0.15392	0.0371	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.00475	-1.1717	10	0.72032	D	0.01	-23.604	19.7964	0.96487	0.0:0.0:1.0:0.0	.	328	Q5TH69	BIG3_HUMAN	K	328	ENSP00000251691:E328K	ENSP00000251691:E328K	E	+	1	0	KIAA1244	138618477	1.000000	0.71417	0.976000	0.42696	0.935000	0.57460	9.869000	0.99810	2.702000	0.92279	0.655000	0.94253	GAG	.	.		0.662	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
KIAA1244	57221	hgsc.bcm.edu	37	6	138584499	138584499	+	Missense_Mutation	SNP	G	G	A	rs376236619		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:138584499G>A	ENST00000251691.4	+	12	2045	c.1879G>A	c.(1879-1881)Gtg>Atg	p.V627M		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CAGGTCCGACGTGTCAGACAT	0.547																																					p.V627M		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G1879A						.	G	MET/VAL	0,4406		0,0,2203	133.0	146.0	142.0		1879	5.3	1.0	6		142	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1244	NM_020340.4	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	627/2178	138584499	1,13005	2203	4300	6503	SO:0001583	missense	57221	exon12			TCCGACGTGTCAG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1879G>A	chr6.hg19:g.138584499G>A	ENSP00000251691:p.Val627Met	124.0	0.0		86.0	33.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	18.99	3.740392	0.69304	0.0	1.16E-4	ENSG00000112379	ENST00000251691	T	0.21734	1.99	5.32	5.32	0.75619	SEC7-like (1);	0.231513	0.34411	N	0.003983	T	0.18676	0.0448	L	0.57536	1.79	0.48185	D	0.999605	D	0.64830	0.994	P	0.48488	0.579	T	0.01114	-1.1447	10	0.54805	T	0.06	-22.0588	12.3695	0.55246	0.0773:0.0:0.9227:0.0	.	627	Q5TH69	BIG3_HUMAN	M	627	ENSP00000251691:V627M	ENSP00000251691:V627M	V	+	1	0	KIAA1244	138626192	1.000000	0.71417	0.962000	0.40283	0.649000	0.38597	7.524000	0.81866	2.482000	0.83794	0.655000	0.94253	GTG	.	.		0.547	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
ESR1	2099	hgsc.bcm.edu	37	6	152332874	152332874	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:152332874C>T	ENST00000206249.3	+	5	1542	c.1180C>T	c.(1180-1182)Cgc>Tgc	p.R394C	ESR1_ENST00000443427.1_Missense_Mutation_p.R394C|ESR1_ENST00000427531.2_Missense_Mutation_p.R221C|ESR1_ENST00000456483.2_Missense_Mutation_p.R282C|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000440973.1_Missense_Mutation_p.R394C|ESR1_ENST00000338799.5_Missense_Mutation_p.R394C	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	394	Interaction with AKAP13.|Self-association.|Steroid-binding.|Transactivation AF-2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	TCTCGTCTGGCGCTCCATGGA	0.493																																					p.R394C		Atlas-SNP	.											.	ESR1	94	.	0			c.C1180T						.						142.0	127.0	132.0					6																	152332874		2203	4300	6503	SO:0001583	missense	2099	exon5			GTCTGGCGCTCCA	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.1180C>T	chr6.hg19:g.152332874C>T	ENSP00000206249:p.Arg394Cys	117.0	0.0		69.0	17.0	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483500	0.84854	.	.	ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000456483;ENST00000431219;ENST00000443427;ENST00000206249;ENST00000431590;ENST00000544394;ENST00000415488	D;D;D;D;D;D;T	0.97256	-4.31;-4.31;-4.31;-4.31;-4.31;-4.31;0.35	5.42	5.42	0.78866	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.98535	0.9511	M	0.90814	3.15	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.997;0.998	D;D;D;D;P;D	0.97110	1.0;0.999;0.999;1.0;0.856;0.911	D	0.99513	1.0956	10	0.87932	D	0	.	14.0967	0.65027	0.1504:0.8495:0.0:0.0	.	298;175;89;393;394;394	B0QYW6;E7EVR3;C8CJL6;A8KAF4;G4XH65;P03372	.;.;.;.;.;ESR1_HUMAN	C	394;394;282;175;394;394;322;221;67	ENSP00000405330:R394C;ENSP00000342630:R394C;ENSP00000415934:R282C;ENSP00000387500:R394C;ENSP00000206249:R394C;ENSP00000445454:R221C;ENSP00000401995:R67C	ENSP00000206249:R394C	R	+	1	0	ESR1	152374567	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.719000	0.54926	2.541000	0.85698	0.591000	0.81541	CGC	.	.		0.493	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
TFB1M	51106	hgsc.bcm.edu	37	6	155578991	155578991	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:155578991G>A	ENST00000367166.4	-	7	1075	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D	RP11-477D19.2_ENST00000435295.1_RNA	NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		AATTCTCTGCGTCATCCTCTT	0.418																																					p.D340D		Atlas-SNP	.											.	TFB1M	30	.	0			c.C1020T						.						104.0	94.0	97.0					6																	155578991		2203	4300	6503	SO:0001819	synonymous_variant	51106	exon7			CTCTGCGTCATCC	AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"""dimethyladenosine transferase 1, mitochondrial"""	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.1020C>T	chr6.hg19:g.155578991G>A		73.0	0.0		54.0	27.0	NM_016020	Q05DR0|Q9Y384	Silent	SNP	ENST00000367166.4	hg19	CCDS5248.1																																																																																			.	.		0.418	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1		
TTLL2	83887	hgsc.bcm.edu	37	6	167754936	167754936	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:167754936G>A	ENST00000239587.5	+	3	1636	c.1548G>A	c.(1546-1548)acG>acA	p.T516T		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	516					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GCAGGCACACGCCTCACAAGA	0.577																																					p.T516T		Atlas-SNP	.											.	TTLL2	82	.	0			c.G1548A						.						147.0	120.0	129.0					6																	167754936		2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			GCACACGCCTCAC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1548G>A	chr6.hg19:g.167754936G>A		135.0	0.0		61.0	40.0	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	hg19	CCDS5301.1																																																																																			.	.		0.577	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
PRKAR1B	5575	hgsc.bcm.edu	37	7	618965	618965	+	Silent	SNP	G	G	T	rs199622718		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:618965G>T	ENST00000406797.1	-	9	993	c.819C>A	c.(817-819)ccC>ccA	p.P273P	PRKAR1B_ENST00000544935.1_Silent_p.P273P|PRKAR1B_ENST00000360274.4_Silent_p.P273P|PRKAR1B_ENST00000403562.1_Silent_p.P273P|PRKAR1B_ENST00000537384.1_Silent_p.P273P	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	273					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CAAACTGGACGGGCTCCAGCG	0.627																																					p.P273P		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.C819A						.						130.0	102.0	111.0					7																	618965		2203	4296	6499	SO:0001819	synonymous_variant	5575	exon9			CTGGACGGGCTCC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.819C>A	chr7.hg19:g.618965G>T		103.0	0.0		140.0	42.0	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	hg19	CCDS34579.1	.	.	.	.	.	.	.	.	.	.	G	8.252	0.809138	0.16537	.	.	ENSG00000188191	ENST00000400758	T	0.71579	-0.58	5.14	-10.3	0.00346	.	0.057139	0.64402	U	0.000001	T	0.63283	0.2498	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70861	-0.4757	7	0.51188	T	0.08	-8.0692	6.2906	0.21057	0.2876:0.0998:0.5146:0.098	.	.	.	.	Q	134	ENSP00000383569:P134Q	ENSP00000383569:P134Q	P	-	2	0	PRKAR1B	585491	0.004000	0.15560	0.682000	0.30024	0.800000	0.45204	-1.351000	0.02622	-2.277000	0.00677	-1.104000	0.02111	CCG	.	G|1.000;A|0.000		0.627	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
INTS1	26173	hgsc.bcm.edu	37	7	1518116	1518116	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:1518116C>T	ENST00000404767.3	-	33	4601	c.4516G>A	c.(4516-4518)Gag>Aag	p.E1506K	INTS1_ENST00000389470.4_Missense_Mutation_p.E1705K	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1506					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GCCAGGGCCTCGGCCAGGCGC	0.697																																					p.E1506K		Atlas-SNP	.											.	INTS1	145	.	0			c.G4516A						.						23.0	30.0	27.0					7																	1518116		2114	4214	6328	SO:0001583	missense	26173	exon33			GGGCCTCGGCCAG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.4516G>A	chr7.hg19:g.1518116C>T	ENSP00000385722:p.Glu1506Lys	253.0	0.0		273.0	145.0	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.139569	0.37728	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.57907	0.54;0.37	4.51	3.62	0.41486	.	0.105841	0.64402	D	0.000005	T	0.37100	0.0991	L	0.34521	1.04	0.41207	D	0.986411	P	0.45428	0.858	B	0.34346	0.18	T	0.19778	-1.0295	10	0.36615	T	0.2	.	13.8353	0.63406	0.1542:0.8458:0.0:0.0	.	1506	Q8N201	INT1_HUMAN	K	1506;1705	ENSP00000385722:E1506K;ENSP00000374121:E1705K	ENSP00000374121:E1705K	E	-	1	0	INTS1	1484642	1.000000	0.71417	0.142000	0.22268	0.000000	0.00434	7.407000	0.80029	0.875000	0.35847	-0.310000	0.09108	GAG	.	.		0.697	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
AP5Z1	9907	hgsc.bcm.edu	37	7	4825084	4825084	+	Splice_Site	SNP	G	G	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:4825084G>C	ENST00000348624.4	+	8	1063		c.e8+1		AP5Z1_ENST00000401897.1_Splice_Site	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit						cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											GCAGAAAGCTGTAAGTGGCTG	0.632																																					.		Atlas-SNP	.											.	.	.	.	0			c.969+1G>C						.						37.0	44.0	42.0					7																	4825084		2132	4234	6366	SO:0001630	splice_region_variant	9907	exon8			AAAGCTGTAAGTG	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.969+1G>C	chr7.hg19:g.4825084G>C		101.0	0.0		119.0	31.0	NM_014855	Q8N3X2|Q96H80	Splice_Site	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001907	0.54254	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3295	0.90263	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA0415	4791610	1.000000	0.71417	0.160000	0.22671	0.483000	0.33249	8.164000	0.89661	2.573000	0.86826	0.561000	0.74099	.	.	.		0.632	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		Intron
AIMP2	7965	hgsc.bcm.edu	37	7	6054890	6054890	+	Silent	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:6054890A>C	ENST00000223029.3	+	2	368	c.249A>C	c.(247-249)ccA>ccC	p.P83P	AIMP2_ENST00000400479.2_Silent_p.P5P|SNORA42_ENST00000384488.1_RNA|AIMP2_ENST00000395236.2_Intron	NM_006303.3	NP_006294.2	Q13155	AIMP2_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 2	83	Interaction with PARK2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|tRNA aminoacylation for protein translation (GO:0006418)|Type II pneumocyte differentiation (GO:0060510)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						TTCAAACACCAGATGCAGACT	0.458																																					p.P83P		Atlas-SNP	.											.	AIMP2	32	.	0			c.A249C						.						146.0	137.0	140.0					7																	6054890		2203	4300	6503	SO:0001819	synonymous_variant	7965	exon2			AACACCAGATGCA	U24169	CCDS5344.1	7p22.1	2009-05-29			ENSG00000106305	ENSG00000106305			20609	protein-coding gene	gene with protein product		600859				8666379, 18695251	Standard	NM_006303		Approved	p38, PRO0992, JTV-1, JTV1	uc003spo.3	Q13155	OTTHUMG00000122077	ENST00000223029.3:c.249A>C	chr7.hg19:g.6054890A>C		183.0	0.0		219.0	68.0	NM_006303	Q75MR1|Q96CZ5|Q9P1L2	Silent	SNP	ENST00000223029.3	hg19	CCDS5344.1																																																																																			.	.		0.458	AIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242834.2	NM_006303	
VWDE	221806	hgsc.bcm.edu	37	7	12381716	12381716	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:12381716T>C	ENST00000275358.3	-	23	4427	c.4239A>G	c.(4237-4239)aaA>aaG	p.K1413K		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1413						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						ACCAGCCAGGTTTGCACTGGC	0.383																																					p.K1413K		Atlas-SNP	.											.	VWDE	123	.	0			c.A4239G						.						107.0	98.0	101.0					7																	12381716		692	1591	2283	SO:0001819	synonymous_variant	221806	exon23			GCCAGGTTTGCAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.4239A>G	chr7.hg19:g.12381716T>C		79.0	0.0		93.0	47.0	NM_001135924	B7ZM77|Q96SQ3	Silent	SNP	ENST00000275358.3	hg19	CCDS47544.1																																																																																			.	.		0.383	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
AVL9	23080	hgsc.bcm.edu	37	7	32612909	32612909	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:32612909C>T	ENST00000318709.4	+	12	1670	c.1449C>T	c.(1447-1449)caC>caT	p.H483H	AVL9_ENST00000404479.1_Intron|AVL9_ENST00000409301.1_Silent_p.H483H	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	483					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TAGTGAGGCACGTGACTGAGA	0.547																																					p.H483H		Atlas-SNP	.											.	AVL9	66	.	0			c.C1449T						.						141.0	107.0	118.0					7																	32612909		2203	4300	6503	SO:0001819	synonymous_variant	23080	exon12			GAGGCACGTGACT	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1449C>T	chr7.hg19:g.32612909C>T		177.0	0.0		209.0	119.0	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	hg19	CCDS34613.1																																																																																			.	.		0.547	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
SEPT7	989	hgsc.bcm.edu	37	7	35913370	35913370	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:35913370C>A	ENST00000435235.1	+	5	770	c.338C>A	c.(337-339)gCt>gAt	p.A113D	SEPT7_ENST00000469679.2_Missense_Mutation_p.A165D|SEPT7_ENST00000350320.6_Missense_Mutation_p.A165D|SEPT7_ENST00000399034.2_Missense_Mutation_p.A167D|SEPT7_ENST00000475109.1_3'UTR|SEPT7_ENST00000399035.3_Missense_Mutation_p.A165D|SEPT7_ENST00000494488.2_Missense_Mutation_p.A152D			Q16181	SEPT7_HUMAN	septin 7	166	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						TACTTCATTGCTCCTTCAGGA	0.373																																					p.A165D		Atlas-SNP	.											.	SEPT7	24	.	0			c.C494A						.						101.0	92.0	95.0					7																	35913370		1913	4129	6042	SO:0001583	missense	989	exon5			TCATTGCTCCTTC	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"""Septins"""	1717	protein-coding gene	gene with protein product		603151	"""CDC10 cell division cycle 10 homolog (S. cerevisiae)"""	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.338C>A	chr7.hg19:g.35913370C>A	ENSP00000413507:p.Ala113Asp	136.0	0.0		212.0	76.0	NM_001011553	Q52M76|Q6NX50	Missense_Mutation	SNP	ENST00000435235.1	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.235523	0.95240	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000469679;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	T;T;T;T;T;T	0.69175	-0.38;2.2;2.2;2.2;2.2;2.2	5.09	5.09	0.68999	.	0.000000	0.85682	U	0.000000	T	0.78285	0.4259	L	0.60455	1.87	0.80722	D	1	D;D;D	0.53151	0.958;0.958;0.958	P;P;P	0.60541	0.876;0.876;0.876	T	0.80151	-0.1502	10	0.72032	D	0.01	.	18.918	0.92513	0.0:1.0:0.0:0.0	.	111;165;166	B4DNE4;E7EPK1;Q16181	.;.;SEPT7_HUMAN	D	113;167;165;165;165;111;113;152	ENSP00000413507:A113D;ENSP00000381992:A167D;ENSP00000344868:A165D;ENSP00000444501:A165D;ENSP00000381993:A165D;ENSP00000438395:A152D	ENSP00000344868:A165D	A	+	2	0	SEPT7	35879895	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.815000	0.86186	2.557000	0.86248	0.644000	0.83932	GCT	.	.		0.373	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788	
STK17A	9263	hgsc.bcm.edu	37	7	43664380	43664380	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:43664380C>T	ENST00000319357.5	+	7	1363	c.1184C>T	c.(1183-1185)tCc>tTc	p.S395F		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	395					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						AAGGCCATTTCCAAACGATTT	0.343																																					p.S395F		Atlas-SNP	.											.	STK17A	31	.	0			c.C1184T						.						64.0	66.0	65.0					7																	43664380		2203	4300	6503	SO:0001583	missense	9263	exon7			CCATTTCCAAACG	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 1"""	604726	"""serine/threonine kinase 17a (apoptosis-inducing)"""			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.1184C>T	chr7.hg19:g.43664380C>T	ENSP00000319192:p.Ser395Phe	163.0	0.0		118.0	40.0	NM_004760	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	hg19	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.451697	0.84209	.	.	ENSG00000164543	ENST00000319357	T	0.68479	-0.33	4.95	4.95	0.65309	.	0.000000	0.47455	D	0.000235	T	0.66684	0.2814	L	0.34521	1.04	0.80722	D	1	D	0.54207	0.965	P	0.50537	0.643	T	0.69745	-0.5062	10	0.51188	T	0.08	.	18.1719	0.89747	0.0:1.0:0.0:0.0	.	395	Q9UEE5	ST17A_HUMAN	F	395	ENSP00000319192:S395F	ENSP00000319192:S395F	S	+	2	0	STK17A	43630905	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.175000	0.71949	2.264000	0.75181	0.563000	0.77884	TCC	.	.		0.343	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
ADCY1	107	hgsc.bcm.edu	37	7	45743231	45743231	+	Silent	SNP	C	C	T	rs138836914		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:45743231C>T	ENST00000297323.7	+	16	2626	c.2604C>T	c.(2602-2604)ggC>ggT	p.G868G		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	868					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCCAGGTGGGCGTCATGTTTG	0.567																																					p.G868G		Atlas-SNP	.											.	ADCY1	187	.	0			c.C2604T						.	C		0,4406		0,0,2203	138.0	117.0	124.0		2604	-2.2	1.0	7	dbSNP_134	124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADCY1	NM_021116.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		868/1120	45743231	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	107	exon16			GGTGGGCGTCATG	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"""Adenylate cyclases"""	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2604C>T	chr7.hg19:g.45743231C>T		165.0	0.0		148.0	47.0	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	hg19	CCDS34631.1																																																																																			.	C|1.000;T|0.000		0.567	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116	
IKZF1	10320	hgsc.bcm.edu	37	7	50467747	50467747	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:50467747C>T	ENST00000331340.3	+	8	1137	c.982C>T	c.(982-984)Cgc>Tgc	p.R328C	IKZF1_ENST00000346667.4_Missense_Mutation_p.R98C|IKZF1_ENST00000357364.4_Missense_Mutation_p.R241C|IKZF1_ENST00000343574.5_Missense_Mutation_p.R241C|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000439701.1_Missense_Mutation_p.R286C|IKZF1_ENST00000438033.1_Missense_Mutation_p.R241C|IKZF1_ENST00000359197.5_Missense_Mutation_p.R286C|IKZF1_ENST00000349824.4_Missense_Mutation_p.R185C	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	328					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				CGAGTCCCTGCGCCCGCTGGT	0.657			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.R328C		Atlas-SNP	.		"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.C982T						.						19.0	21.0	20.0					7																	50467747		2076	4234	6310	SO:0001583	missense	10320	exon8			TCCCTGCGCCCGC	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.982C>T	chr7.hg19:g.50467747C>T	ENSP00000331614:p.Arg328Cys	124.0	0.0		140.0	55.0	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.256041	0.95336	.	.	ENSG00000185811	ENST00000346667;ENST00000343574;ENST00000359197;ENST00000349824;ENST00000357364;ENST00000331340;ENST00000438033;ENST00000439701	T;T;T;T;T;T;T;T	0.08634	4.38;3.07;3.12;3.9;3.29;3.14;3.07;3.12	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.31765	0.0807	.	.	.	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.997;0.998	T	0.01090	-1.1455	9	0.52906	T	0.07	-22.584	19.3925	0.94590	0.0:1.0:0.0:0.0	.	241;98;241;286;328	Q13422-2;Q13422-6;Q13422-3;Q13422-7;Q13422	.;.;.;.;IKZF1_HUMAN	C	98;241;286;185;241;328;241;286	ENSP00000340080:R98C;ENSP00000342750:R241C;ENSP00000352123:R286C;ENSP00000342485:R185C;ENSP00000349928:R241C;ENSP00000331614:R328C;ENSP00000396554:R241C;ENSP00000413025:R286C	ENSP00000331614:R328C	R	+	1	0	IKZF1	50435241	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.757000	0.85209	2.591000	0.87537	0.650000	0.86243	CGC	.	.		0.657	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
POM121L12	285877	hgsc.bcm.edu	37	7	53103947	53103947	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:53103947C>T	ENST00000408890.4	+	1	599	c.583C>T	c.(583-585)Ccg>Tcg	p.P195S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	195										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GTTCGACGGGCCGTTGTGGTT	0.682																																					p.P195S		Atlas-SNP	.											POM121L12,NS,carcinoma,-2,1	POM121L12	146	.	0			c.C583T						.						48.0	56.0	53.0					7																	53103947		1973	4142	6115	SO:0001583	missense	285877	exon1			GACGGGCCGTTGT		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.583C>T	chr7.hg19:g.53103947C>T	ENSP00000386133:p.Pro195Ser	72.0	0.0		63.0	23.0	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	hg19	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.251504	0.39797	.	.	ENSG00000221900	ENST00000408890	T	0.12984	2.63	2.21	2.21	0.28008	.	.	.	.	.	T	0.26122	0.0637	L	0.46157	1.445	0.09310	N	1	D	0.71674	0.998	D	0.74023	0.982	T	0.03166	-1.1065	9	0.62326	D	0.03	.	8.0049	0.30319	0.0:1.0:0.0:0.0	.	195	Q8N7R1	P1L12_HUMAN	S	195	ENSP00000386133:P195S	ENSP00000386133:P195S	P	+	1	0	POM121L12	53071441	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.522000	0.22909	1.561000	0.49584	0.561000	0.74099	CCG	.	.		0.682	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
GUSB	2990	hgsc.bcm.edu	37	7	65440028	65440028	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:65440028G>T	ENST00000304895.4	-	6	1073	c.943C>A	c.(943-945)Cct>Act	p.P315T	GUSB_ENST00000345660.6_Intron|GUSB_ENST00000476486.1_5'UTR|GUSB_ENST00000421103.1_Missense_Mutation_p.P169T	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	315					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)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TCAGACACAGGCCCCAGTGAC	0.587																																					p.P315T		Atlas-SNP	.											.	GUSB	52	.	0			c.C943A						.						84.0	78.0	80.0					7																	65440028		2203	4300	6503	SO:0001583	missense	2990	exon6			ACACAGGCCCCAG	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.943C>A	chr7.hg19:g.65440028G>T	ENSP00000302728:p.Pro315Thr	117.0	0.0		82.0	8.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Missense_Mutation	SNP	ENST00000304895.4	hg19	CCDS5530.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271784	0.23221	.	.	ENSG00000169919	ENST00000304895;ENST00000421103	D;D	0.94897	-1.91;-3.55	4.99	-4.7	0.03288	Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich (2);Glycoside hydrolase, family 2/20, immunoglobulin-like beta-sandwich domain (1);	0.584044	0.18926	N	0.127351	D	0.84781	0.5548	N	0.21448	0.665	0.09310	N	0.999998	B;B	0.10296	0.003;0.0	B;B	0.08055	0.001;0.003	T	0.72587	-0.4248	10	0.14656	T	0.56	.	8.6134	0.33817	0.5727:0.0:0.3183:0.109	.	169;315	E9PCV0;P08236	.;BGLR_HUMAN	T	315;169	ENSP00000302728:P315T;ENSP00000391390:P169T	ENSP00000302728:P315T	P	-	1	0	GUSB	65077463	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.667000	0.05274	-0.772000	0.04602	0.511000	0.50034	CCT	.	.		0.587	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
AUTS2	26053	hgsc.bcm.edu	37	7	70254962	70254962	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:70254962C>T	ENST00000342771.4	+	19	3081	c.2760C>T	c.(2758-2760)gaC>gaT	p.D920D	AUTS2_ENST00000406775.2_Silent_p.D896D	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	920										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CCGAGAAGGACGGGCACGGCC	0.697																																					p.D920D		Atlas-SNP	.											.	AUTS2	173	.	0			c.C2760T						.						21.0	22.0	22.0					7																	70254962		2197	4294	6491	SO:0001819	synonymous_variant	26053	exon19			GAAGGACGGGCAC	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.2760C>T	chr7.hg19:g.70254962C>T		108.0	0.0		89.0	36.0	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	hg19	CCDS5539.1																																																																																			.	.		0.697	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
DTX2	113878	hgsc.bcm.edu	37	7	76131756	76131756	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:76131756T>C	ENST00000324432.5	+	9	1882	c.1372T>C	c.(1372-1374)Tac>Cac	p.Y458H	DTX2_ENST00000430490.2_Missense_Mutation_p.Y458H|DTX2_ENST00000307569.8_Missense_Mutation_p.Y411H|DTX2_ENST00000446820.2_Missense_Mutation_p.Y411H|DTX2_ENST00000413936.2_Missense_Mutation_p.Y458H|DTX2_ENST00000446600.1_Missense_Mutation_p.Y367H	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	458					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						CCTGGCCATGTACTGCAACGG	0.662																																					p.Y458H		Atlas-SNP	.											.	DTX2	64	.	0			c.T1372C						.						59.0	43.0	48.0					7																	76131756		2201	4297	6498	SO:0001583	missense	113878	exon8			GCCATGTACTGCA		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1372T>C	chr7.hg19:g.76131756T>C	ENSP00000322885:p.Tyr458His	128.0	0.0		110.0	42.0	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	hg19	CCDS5587.1	.	.	.	.	.	.	.	.	.	.	.	24.4	4.526779	0.85706	.	.	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490;ENST00000446820	T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.48	5.48	0.80851	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.122676	0.56097	D	0.000024	D	0.82628	0.5078	M	0.83012	2.62	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991	D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.998	D	0.84817	0.0794	10	0.56958	D	0.05	-34.3157	14.7255	0.69341	0.0:0.0:0.0:1.0	.	367;89;367;411;458	F5GX89;Q6P2H0;E7ET89;Q86UW9-2;Q86UW9	.;.;.;.;DTX2_HUMAN	H	458;411;367;367;458;458;411	ENSP00000322885:Y458H;ENSP00000305242:Y411H;ENSP00000397648:Y367H;ENSP00000390218:Y458H;ENSP00000411986:Y458H;ENSP00000392545:Y411H	ENSP00000305242:Y411H	Y	+	1	0	AC005522.1	75969692	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	7.958000	0.87877	2.081000	0.62600	0.533000	0.62120	TAC	.	.		0.662	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
CACNA2D1	781	hgsc.bcm.edu	37	7	81579773	81579773	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:81579773A>G	ENST00000356253.5	-	39	3502	c.3247T>C	c.(3247-3249)Tat>Cat	p.Y1083H	CACNA2D1_ENST00000535308.1_Missense_Mutation_p.Y283H|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.Y1071H			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	1083					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CCAATGATATACCACAGGGAG	0.368																																					p.Y1071H		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.T3211C						.						82.0	81.0	82.0					7																	81579773		2203	4300	6503	SO:0001583	missense	781	exon39			TGATATACCACAG	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.3247T>C	chr7.hg19:g.81579773A>G	ENSP00000348589:p.Tyr1083His	114.0	0.0		111.0	38.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	4.185	0.033043	0.08101	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	T;T;T	0.30714	3.27;3.27;1.52	4.89	2.4	0.29515	.	0.124078	0.56097	D	0.000027	T	0.13841	0.0335	N	0.08118	0	0.23823	N	0.996745	B;B	0.17038	0.02;0.02	B;B	0.13407	0.005;0.009	T	0.28490	-1.0042	10	0.15952	T	0.53	-7.9207	10.2042	0.43103	0.7348:0.0:0.0:0.2652	.	283;1071	B7Z658;P54289-2	.;.	H	1071;1090;1083;283	ENSP00000349320:Y1071H;ENSP00000348589:Y1083H;ENSP00000443124:Y283H	ENSP00000284088:Y1090H	Y	-	1	0	CACNA2D1	81417709	1.000000	0.71417	0.524000	0.27887	0.405000	0.30901	5.100000	0.64560	0.259000	0.21709	0.528000	0.53228	TAT	.	.		0.368	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
CCDC132	55610	hgsc.bcm.edu	37	7	92970851	92970851	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:92970851A>G	ENST00000305866.5	+	23	2299	c.2171A>G	c.(2170-2172)tAt>tGt	p.Y724C	CCDC132_ENST00000474412.1_3'UTR|CCDC132_ENST00000535481.1_Missense_Mutation_p.Y444C|CCDC132_ENST00000541136.1_Missense_Mutation_p.Y535C|CCDC132_ENST00000544910.1_Missense_Mutation_p.Y694C	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	724						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GATACGCTGTATGGGTTGGCA	0.438																																					p.Y724C		Atlas-SNP	.											.	CCDC132	136	.	0			c.A2171G						.						131.0	139.0	137.0					7																	92970851		1953	4158	6111	SO:0001583	missense	55610	exon23			CGCTGTATGGGTT	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.2171A>G	chr7.hg19:g.92970851A>G	ENSP00000307666:p.Tyr724Cys	132.0	0.0		143.0	7.0	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829345	0.71258	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481	.	.	.	5.69	5.69	0.88448	Protein of unknown function DUF2451, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79936	0.4532	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.997;0.997	T	0.82335	-0.0508	9	0.72032	D	0.01	-13.3761	16.2703	0.82612	1.0:0.0:0.0:0.0	.	444;694;724	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	C	724;694;535;444	.	ENSP00000307666:Y724C	Y	+	2	0	CCDC132	92808787	1.000000	0.71417	0.999000	0.59377	0.397000	0.30659	9.270000	0.95690	2.311000	0.77944	0.533000	0.62120	TAT	.	.		0.438	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97946608	97946608	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:97946608G>T	ENST00000005260.8	-	6	624	c.409C>A	c.(409-411)Caa>Aaa	p.Q137K	BAIAP2L1_ENST00000462558.1_5'UTR	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	137	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			AACTCAGCTTGGGATTTCTCC	0.378																																					p.Q137K		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.C409A						.						259.0	247.0	251.0					7																	97946608		2203	4300	6503	SO:0001583	missense	55971	exon6			CAGCTTGGGATTT	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.409C>A	chr7.hg19:g.97946608G>T	ENSP00000005260:p.Gln137Lys	137.0	0.0		84.0	26.0	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Missense_Mutation	SNP	ENST00000005260.8	hg19	CCDS34687.1	.	.	.	.	.	.	.	.	.	.	G	16.04	3.011341	0.54361	.	.	ENSG00000006453	ENST00000005260	T	0.23552	1.9	5.53	5.53	0.82687	IRSp53/MIM homology domain (IMD) (3);	0.108634	0.64402	D	0.000005	T	0.22859	0.0552	L	0.39467	1.215	0.49798	D	0.999825	B	0.14012	0.009	B	0.17098	0.017	T	0.05321	-1.0892	10	0.14656	T	0.56	-5.5035	16.6084	0.84837	0.0:0.0:1.0:0.0	.	137	Q9UHR4	BI2L1_HUMAN	K	137	ENSP00000005260:Q137K	ENSP00000005260:Q137K	Q	-	1	0	AC093799.1	97784544	1.000000	0.71417	0.942000	0.38095	0.933000	0.57130	7.479000	0.81095	2.597000	0.87782	0.603000	0.83216	CAA	.	.		0.378	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
TAF6	6878	hgsc.bcm.edu	37	7	99706132	99706132	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:99706132C>T	ENST00000344095.4	-	13	1841	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H	TAF6_ENST00000437822.2_Missense_Mutation_p.R476H|TAF6_ENST00000452041.1_Missense_Mutation_p.R439H|TAF6_ENST00000453269.2_Missense_Mutation_p.R439H|TAF6_ENST00000418432.2_Missense_Mutation_p.R363H|TAF6_ENST00000472509.1_Missense_Mutation_p.R496H|AP4M1_ENST00000421755.1_Intron	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	439					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGGCGGTGGGCGCAGCTTTGC	0.607																																					p.R476H		Atlas-SNP	.											.	TAF6	55	.	0			c.G1427A						.						61.0	68.0	66.0					7																	99706132		2203	4300	6503	SO:0001583	missense	6878	exon13			GGTGGGCGCAGCT		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"""TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD"", ""transcription initiation factor TFIID 70 kD subunit"""	602955	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"""	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.1316G>A	chr7.hg19:g.99706132C>T	ENSP00000344537:p.Arg439His	84.0	0.0		100.0	43.0	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	hg19	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.683357	0.68157	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822	T;T;T;T;T	0.59906	0.3;0.23;0.3;0.3;0.24	5.69	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	L	0.43757	1.38	0.53005	D	0.999967	P;D;P;P;P	0.53462	0.933;0.96;0.933;0.933;0.933	B;B;B;B;B	0.40982	0.187;0.345;0.187;0.187;0.187	T	0.47886	-0.9082	10	0.38643	T	0.18	-11.6419	12.2687	0.54693	0.0:0.9179:0.0:0.0821	.	476;439;429;439;363	B4DT11;P49848-2;A4D299;P49848;B3KUR4	.;.;.;TAF6_HUMAN;.	H	439;496;439;439;363;476	ENSP00000389575:R439H;ENSP00000419760:R496H;ENSP00000416396:R439H;ENSP00000344537:R439H;ENSP00000399982:R476H	ENSP00000344537:R439H	R	-	2	0	TAF6	99544068	0.999000	0.42202	0.984000	0.44739	0.901000	0.52897	4.026000	0.57232	1.413000	0.46997	0.491000	0.48974	CGC	.	.		0.607	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641	
NYAP1	222950	hgsc.bcm.edu	37	7	100084550	100084550	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100084550G>T	ENST00000300179.2	+	3	334	c.175G>T	c.(175-177)Ggt>Tgt	p.G59C	NYAP1_ENST00000423930.1_Missense_Mutation_p.G59C|NYAP1_ENST00000454988.1_Missense_Mutation_p.G2C	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	59					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CCTCAGGATGGGTTTCATGAC	0.741																																					p.G59C		Atlas-SNP	.											.	.	.	.	0			c.G175T						.						9.0	10.0	10.0					7																	100084550		2162	4247	6409	SO:0001583	missense	222950	exon3			AGGATGGGTTTCA	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"""chromosome 7 open reading frame 51"", ""KIAA1486-like"""	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.175G>T	chr7.hg19:g.100084550G>T	ENSP00000300179:p.Gly59Cys	160.0	0.0		162.0	11.0	NM_173564	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	hg19	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843378	0.91197	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.52295	0.67;0.67;0.67	5.03	5.03	0.67393	.	0.000000	0.52532	D	0.000078	T	0.65481	0.2695	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67891	-0.5553	10	0.87932	D	0	-16.4094	15.8881	0.79269	0.0:0.0:1.0:0.0	.	59	Q6ZVC0	CG051_HUMAN	C	59;59;2	ENSP00000300179:G59C;ENSP00000411861:G59C;ENSP00000394424:G2C	ENSP00000300179:G59C	G	+	1	0	C7orf51	99922486	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.591000	0.74090	2.606000	0.88127	0.462000	0.41574	GGT	.	.		0.741	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564	
AGFG2	3268	hgsc.bcm.edu	37	7	100159952	100159952	+	Silent	SNP	C	C	T	rs550739522		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100159952C>T	ENST00000300176.4	+	7	1070	c.948C>T	c.(946-948)gaC>gaT	p.D316D	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	316					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.D316D(2)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCCTCGCAGACGTGGGCAGCT	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		17703	0.0		0.001	False		,,,				2504	0.0				p.D316D		Atlas-SNP	.											AGFG2,NS,carcinoma,0,2	AGFG2	44	.	2	Substitution - coding silent(2)	lung(2)	c.C948T						.						43.0	47.0	46.0					7																	100159952		2203	4300	6503	SO:0001819	synonymous_variant	3268	exon7			CGCAGACGTGGGC	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.948C>T	chr7.hg19:g.100159952C>T		156.0	0.0		132.0	56.0	NM_006076	O75429|Q96AB9|Q96GL4	Silent	SNP	ENST00000300176.4	hg19	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	C	3.110	-0.182952	0.06340	.	.	ENSG00000106351	ENST00000429987	.	.	.	4.61	-3.03	0.05429	.	.	.	.	.	T	0.47783	0.1464	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39418	-0.9615	4	.	.	.	-23.1344	5.1848	0.15178	0.0:0.3746:0.1604:0.465	.	.	.	.	M	58	.	.	T	+	2	0	AGFG2	99997888	0.140000	0.22579	0.373000	0.26003	0.380000	0.30137	-0.905000	0.04075	-0.629000	0.05575	-0.477000	0.04895	ACG	.	.		0.637	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
MUC17	140453	hgsc.bcm.edu	37	7	100678585	100678585	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100678585C>T	ENST00000306151.4	+	3	3952	c.3888C>T	c.(3886-3888)agC>agT	p.S1296S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1296	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CTGAGGCTAGCACCCTTTTAA	0.478																																					p.S1296S		Atlas-SNP	.											.	MUC17	804	.	0			c.C3888T						.						263.0	250.0	254.0					7																	100678585		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			GGCTAGCACCCTT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3888C>T	chr7.hg19:g.100678585C>T		83.0	0.0		49.0	24.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SLC26A5	375611	hgsc.bcm.edu	37	7	103014890	103014890	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:103014890C>T	ENST00000306312.3	-	20	2452	c.2191G>A	c.(2191-2193)Gag>Aag	p.E731K	SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000339444.6_Intron|SLC26A5_ENST00000393723.1_Missense_Mutation_p.E701K|SLC26A5_ENST00000393730.1_Missense_Mutation_p.E699K|SLC26A5_ENST00000354356.4_Missense_Mutation_p.E164K|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000432958.2_Missense_Mutation_p.E699K|SLC26A5_ENST00000393727.1_Missense_Mutation_p.E733K|SLC26A5_ENST00000393729.1_Missense_Mutation_p.E694K	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	731					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TCCAAGTCCTCCTGGGAAGGG	0.527																																					p.E731K		Atlas-SNP	.											SLC26A5,NS,malignant_melanoma,0,1	SLC26A5	231	.	0			c.G2191A						.						59.0	52.0	55.0					7																	103014890		2203	4300	6503	SO:0001583	missense	375611	exon20			AGTCCTCCTGGGA	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"""Solute carriers"""	9359	protein-coding gene	gene with protein product	"""deafness, neurosensory, autosomal recessive, 61"""	604943	"""prestin (motor protein)"""	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.2191G>A	chr7.hg19:g.103014890C>T	ENSP00000304783:p.Glu731Lys	116.0	0.0		89.0	39.0	NM_198999	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	hg19	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.331971	0.60853	.	.	ENSG00000170615	ENST00000306312;ENST00000393730;ENST00000432958;ENST00000354356;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D	0.96232	-3.2;-3.22;-3.22;-3.95;-3.13;-3.2;-3.22	5.69	5.69	0.88448	.	0.330752	0.29587	N	0.011738	D	0.89280	0.6670	N	0.08118	0	0.28654	N	0.906519	B;B	0.27559	0.181;0.155	B;B	0.21360	0.024;0.034	T	0.83186	-0.0086	10	0.72032	D	0.01	.	8.3886	0.32516	0.0:0.8347:0.0:0.1653	.	731;699	P58743;Q496J2	S26A5_HUMAN;.	K	731;699;699;164;694;733;701	ENSP00000304783:E731K;ENSP00000377331:E699K;ENSP00000389733:E699K;ENSP00000346325:E164K;ENSP00000377330:E694K;ENSP00000377328:E733K;ENSP00000377324:E701K	ENSP00000304783:E731K	E	-	1	0	SLC26A5	102802126	0.996000	0.38824	1.000000	0.80357	0.665000	0.39181	2.163000	0.42377	2.699000	0.92147	0.454000	0.30748	GAG	.	.		0.527	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999	
DOCK4	9732	hgsc.bcm.edu	37	7	111584884	111584884	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:111584884C>T	ENST00000437633.1	-	10	1082	c.826G>A	c.(826-828)Gtg>Atg	p.V276M	DOCK4_ENST00000428084.1_Missense_Mutation_p.V276M|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	276					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				ATAATGTGCACGGTGATATAA	0.418																																					p.V276M		Atlas-SNP	.											.	DOCK4	365	.	0			c.G826A						.						136.0	130.0	132.0					7																	111584884		1913	4119	6032	SO:0001583	missense	9732	exon10			TGTGCACGGTGAT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.826G>A	chr7.hg19:g.111584884C>T	ENSP00000404179:p.Val276Met	89.0	0.0		118.0	49.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.715839	0.89112	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	T;T	0.03272	3.99;3.99	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.12305	0.0299	L	0.50333	1.59	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.997	P;P;P	0.56088	0.791;0.791;0.791	T	0.00064	-1.2152	10	0.72032	D	0.01	.	20.2406	0.98372	0.0:1.0:0.0:0.0	.	276;276;276	A4D0S8;Q149N5;Q8N1I0	.;.;DOCK4_HUMAN	M	264;276;276;264;275	ENSP00000410746:V276M;ENSP00000404179:V276M	ENSP00000345432:V264M	V	-	1	0	DOCK4	111372120	1.000000	0.71417	0.978000	0.43139	0.993000	0.82548	6.730000	0.74780	2.857000	0.98124	0.650000	0.86243	GTG	.	.		0.418	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
AASS	10157	hgsc.bcm.edu	37	7	121733126	121733126	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:121733126G>A	ENST00000393376.1	-	15	1837	c.1742C>T	c.(1741-1743)cCa>cTa	p.P581L	AASS_ENST00000417368.2_Missense_Mutation_p.P581L|AASS_ENST00000473553.1_5'UTR			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	581	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTTTAGTGCTGGTGTGATGTA	0.368																																					p.P581L		Atlas-SNP	.											.	AASS	123	.	0			c.C1742T						.						173.0	177.0	176.0					7																	121733126		2203	4300	6503	SO:0001583	missense	10157	exon16			AGTGCTGGTGTGA	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.1742C>T	chr7.hg19:g.121733126G>A	ENSP00000377040:p.Pro581Leu	191.0	0.0		162.0	58.0	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824335	0.90955	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	T;T	0.44482	0.92;0.92	6.07	6.07	0.98685	NAD(P)-binding domain (1);	0.046355	0.85682	D	0.000000	T	0.71953	0.3401	M	0.92459	3.31	0.80722	D	1	D	0.55605	0.972	P	0.59825	0.864	T	0.77230	-0.2664	10	0.66056	D	0.02	-14.8046	20.2544	0.98414	0.0:0.0:1.0:0.0	.	581	Q9UDR5	AASS_HUMAN	L	581	ENSP00000377040:P581L;ENSP00000403768:P581L	ENSP00000351834:P581L	P	-	2	0	AASS	121520362	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	9.159000	0.94728	2.885000	0.99019	0.655000	0.94253	CCA	.	.		0.368	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763	
STRA8	346673	hgsc.bcm.edu	37	7	134931258	134931258	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:134931258C>T	ENST00000275764.3	+	6	536	c.536C>T	c.(535-537)gCg>gTg	p.A179V		NM_182489.1	NP_872295.1			stimulated by retinoic acid 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(1)	16						ATCGTCTCCGCGGCCATCTCC	0.642																																					p.A179V		Atlas-SNP	.											.	STRA8	39	.	0			c.C536T						.						13.0	13.0	13.0					7																	134931258		2194	4279	6473	SO:0001583	missense	346673	exon6			TCTCCGCGGCCAT	AF513502	CCDS5839.1	7q33	2012-12-07	2012-12-07		ENSG00000146857	ENSG00000146857			30653	protein-coding gene	gene with protein product		609987	"""stimulated by retinoic acid gene 8 homolog (mouse)"", ""stimulated by retinoic acid 8 homolog (mouse)"""			12489526	Standard	NM_182489		Approved		uc011kpx.2	Q7Z7C7	OTTHUMG00000155415	ENST00000275764.3:c.536C>T	chr7.hg19:g.134931258C>T	ENSP00000275764:p.Ala179Val	114.0	0.0		114.0	39.0	NM_182489		Missense_Mutation	SNP	ENST00000275764.3	hg19	CCDS5839.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.079253	0.76528	.	.	ENSG00000146857	ENST00000275764	.	.	.	5.92	5.92	0.95590	.	0.250984	0.33772	N	0.004569	T	0.49795	0.1578	M	0.63428	1.95	0.20074	N	0.999936	D	0.65815	0.995	P	0.48795	0.59	T	0.52697	-0.8541	9	0.56958	D	0.05	-20.8075	15.0829	0.72127	0.1417:0.8583:0.0:0.0	.	179	Q7Z7C7	STRA8_HUMAN	V	179	.	ENSP00000275764:A179V	A	+	2	0	STRA8	134581798	0.616000	0.27035	0.613000	0.29037	0.711000	0.40976	2.012000	0.40932	2.809000	0.96659	0.655000	0.94253	GCG	.	.		0.642	STRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340028.1	NM_182489	
FAM131B	9715	hgsc.bcm.edu	37	7	143055964	143055964	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:143055964T>C	ENST00000409408.1	-	4	2046	c.338A>G	c.(337-339)tAc>tGc	p.Y113C	FAM131B_ENST00000409578.1_Missense_Mutation_p.Y129C|FAM131B_ENST00000409222.3_Missense_Mutation_p.Y113C|FAM131B_ENST00000443739.2_Missense_Mutation_p.Y141C|FAM131B_ENST00000409346.1_Missense_Mutation_p.Y113C			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	113										breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					GAGGTCGGAGTAGGCATCCGT	0.597																																					p.Y141C		Atlas-SNP	.											.	FAM131B	104	.	0			c.A422G						.						98.0	85.0	89.0					7																	143055964		2203	4300	6503	SO:0001583	missense	9715	exon5			TCGGAGTAGGCAT	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.338A>G	chr7.hg19:g.143055964T>C	ENSP00000387017:p.Tyr113Cys	90.0	0.0		68.0	12.0	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	hg19	CCDS5882.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.495513	0.64186	.	.	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.26	5.26	0.73747	.	0.115379	0.64402	D	0.000009	T	0.63331	0.2502	M	0.71206	2.165	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	T	0.67558	-0.5640	10	0.87932	D	0	-15.5113	13.7328	0.62799	0.0:0.0:0.0:1.0	.	129;113	Q86XD5-2;Q86XD5	.;F131B_HUMAN	C	141;129;113;117;113;113	ENSP00000410603:Y141C;ENSP00000386568:Y129C;ENSP00000386984:Y113C;ENSP00000387017:Y113C;ENSP00000387147:Y113C	ENSP00000387147:Y113C	Y	-	2	0	FAM131B	142766086	1.000000	0.71417	1.000000	0.80357	0.349000	0.29174	7.686000	0.84128	1.977000	0.57605	0.459000	0.35465	TAC	.	.		0.597	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690	
TAS2R41	259287	hgsc.bcm.edu	37	7	143175777	143175777	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:143175777C>T	ENST00000408916.1	+	1	812	c.812C>T	c.(811-813)gCa>gTa	p.A271V	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	271					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					TGGCAAATTGCAGTCTACCTG	0.478																																					p.A271V		Atlas-SNP	.											.	TAS2R41	43	.	0			c.C812T						.						148.0	142.0	144.0					7																	143175777		2061	4205	6266	SO:0001583	missense	259287	exon1			AAATTGCAGTCTA	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.812C>T	chr7.hg19:g.143175777C>T	ENSP00000386201:p.Ala271Val	127.0	0.0		111.0	42.0	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	hg19	CCDS43663.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.049140	0.00394	.	.	ENSG00000221855	ENST00000408916	T	0.35973	1.28	6.0	2.42	0.29668	.	2.338580	0.03182	U	0.172136	T	0.18923	0.0454	N	0.05467	-0.045	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.22977	-1.0201	10	0.02654	T	1	.	8.2919	0.31963	0.0:0.2292:0.0:0.7708	.	271	P59536	T2R41_HUMAN	V	271	ENSP00000386201:A271V	ENSP00000386201:A271V	A	+	2	0	TAS2R41	142885899	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.187000	0.16998	0.180000	0.19960	-0.302000	0.09304	GCA	.	.		0.478	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1		
KCNH2	3757	hgsc.bcm.edu	37	7	150648807	150648807	+	Silent	SNP	C	C	T	rs554855472	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150648807C>T	ENST00000262186.5	-	7	2075	c.1674G>A	c.(1672-1674)gcG>gcA	p.A558A	KCNH2_ENST00000392968.2_Silent_p.A462A|KCNH2_ENST00000330883.4_Silent_p.A218A|KCNH2_ENST00000430723.3_Silent_p.A558A	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	558			A -> P (in LQT2). {ECO:0000269|PubMed:10220144}.		cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GCGCGATGAGCGCAAAGGTGC	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		16943	0.0		0.0	False		,,,				2504	0.002				p.A558A	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.G1674A						.						77.0	63.0	68.0					7																	150648807		2203	4300	6503	SO:0001819	synonymous_variant	3757	exon7			GATGAGCGCAAAG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1674G>A	chr7.hg19:g.150648807C>T		97.0	0.0		87.0	33.0	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	hg19	CCDS5910.1																																																																																			.	.		0.647	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
SLC4A2	6522	hgsc.bcm.edu	37	7	150772569	150772569	+	Missense_Mutation	SNP	C	C	T	rs370805035		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150772569C>T	ENST00000485713.1	+	20	4315	c.3275C>T	c.(3274-3276)aCg>aTg	p.T1092M	SLC4A2_ENST00000310317.5_Missense_Mutation_p.T1010M|SLC4A2_ENST00000413384.2_Missense_Mutation_p.T1092M|RP11-148K1.12_ENST00000485974.1_RNA|SLC4A2_ENST00000461735.1_Missense_Mutation_p.T1078M|SLC4A2_ENST00000392826.2_Missense_Mutation_p.T1083M|FASTK_ENST00000489884.1_5'Flank	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	1092	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGCGGGTGACGGGGCTGCTG	0.637																																					p.T1092M		Atlas-SNP	.											SLC4A2,NS,carcinoma,0,1	SLC4A2	98	.	0			c.C3275T						.	C	MET/THR,MET/THR,MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	136.0	145.0	142.0		3275,3248,3233,3275	5.1	1.0	7		142	0,8600		0,0,4300	no	missense,missense,missense,missense	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	81,81,81,81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1092/1242,1083/1233,1078/1228,1092/1242	150772569	1,13005	2203	4300	6503	SO:0001583	missense	6522	exon20			GGGTGACGGGGCT		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.3275C>T	chr7.hg19:g.150772569C>T	ENSP00000419412:p.Thr1092Met	20.0	0.0		10.0	6.0	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.297317	0.81025	2.27E-4	0.0	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	5.07	5.07	0.68467	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93684	0.7982	H	0.94306	3.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.993;0.993;0.996	D	0.95169	0.8288	10	0.87932	D	0	.	17.6106	0.88051	0.0:1.0:0.0:0.0	.	1083;1078;1092	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	M	1092;1092;1010;1083;1078	ENSP00000419412:T1092M;ENSP00000405600:T1092M;ENSP00000311402:T1010M;ENSP00000376571:T1083M;ENSP00000419164:T1078M	ENSP00000311402:T1010M	T	+	2	0	SLC4A2	150403502	1.000000	0.71417	0.958000	0.39756	0.958000	0.62258	5.934000	0.70138	2.639000	0.89480	0.561000	0.74099	ACG	.	.		0.637	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
FASTK	10922	hgsc.bcm.edu	37	7	150776623	150776623	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150776623T>C	ENST00000297532.6	-	2	546	c.469A>G	c.(469-471)Acc>Gcc	p.T157A	FASTK_ENST00000353841.2_Intron|FASTK_ENST00000540185.1_Missense_Mutation_p.T123A|FASTK_ENST00000482571.1_Missense_Mutation_p.T157A|FASTK_ENST00000489884.1_Intron	NM_006712.4	NP_006703.1	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase	157					apoptotic signaling pathway (GO:0097190)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|Fas-activated serine/threonine kinase activity (GO:0033867)|protein serine/threonine kinase activity (GO:0004674)			lung(4)|stomach(2)	6			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		ACGTGGATGGTGTGAATGTCA	0.577																																					p.T157A		Atlas-SNP	.											.	FASTK	29	.	0			c.A469G						.						63.0	59.0	60.0					7																	150776623		2202	4300	6502	SO:0001583	missense	10922	exon2			GGATGGTGTGAAT		CCDS5918.1, CCDS5919.1, CCDS59088.1	7q35	2006-07-06			ENSG00000164896	ENSG00000164896			24676	protein-coding gene	gene with protein product		606965				7544399, 15572676	Standard	NM_006712		Approved	FAST	uc003wix.2	Q14296	OTTHUMG00000158694	ENST00000297532.6:c.469A>G	chr7.hg19:g.150776623T>C	ENSP00000297532:p.Thr157Ala	259.0	1.0		246.0	98.0	NM_006712	A8K867|F8VTW9|Q59EM8|Q8IVA0	Missense_Mutation	SNP	ENST00000297532.6	hg19	CCDS5918.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.198786	0.58126	.	.	ENSG00000164896	ENST00000483105;ENST00000297530;ENST00000297532;ENST00000482571;ENST00000540185	T;T;T	0.45276	0.9;0.9;0.9	4.61	4.61	0.57282	.	0.268618	0.24779	N	0.035674	T	0.47451	0.1446	N	0.24115	0.695	0.41923	D	0.990523	D;P;P	0.67145	0.996;0.954;0.787	D;B;B	0.76071	0.987;0.446;0.219	T	0.40136	-0.9579	10	0.33141	T	0.24	-24.2934	12.1032	0.53796	0.0:0.0:0.0:1.0	.	123;157;157	G3V1R6;F8VTW9;Q14296	.;.;FASTK_HUMAN	A	157;157;157;157;123	ENSP00000297532:T157A;ENSP00000418516:T157A;ENSP00000444498:T123A	ENSP00000297530:T157A	T	-	1	0	FASTK	150407556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.294000	0.65687	2.012000	0.59069	0.533000	0.62120	ACC	.	.		0.577	FASTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351832.2	NM_006712	
SMARCD3	6604	hgsc.bcm.edu	37	7	150938679	150938679	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:150938679G>A	ENST00000262188.8	-	8	1248	c.838C>T	c.(838-840)Cgc>Tgc	p.R280C	RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000392811.2_Missense_Mutation_p.R267C|SMARCD3_ENST00000356800.2_Missense_Mutation_p.R267C|SMARCD3_ENST00000477169.1_5'Flank	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	280	SWIB.				cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGGCTGAGCGGCTCTGTGTG	0.562																																					p.R280C		Atlas-SNP	.											.	SMARCD3	92	.	0			c.C838T						.						35.0	32.0	33.0					7																	150938679		2203	4300	6503	SO:0001583	missense	6604	exon8			CTGAGCGGCTCTG	U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60C"", ""Swp73-like protein"", ""SWI/SNF complex 60 kDa subunit C"", ""60kDa BRG-1/Brm associated factor subunit c"""	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.838C>T	chr7.hg19:g.150938679G>A	ENSP00000262188:p.Arg280Cys	68.0	0.0		69.0	33.0	NM_001003801	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Missense_Mutation	SNP	ENST00000262188.8	hg19	CCDS34780.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.374349	0.82573	.	.	ENSG00000082014	ENST00000262188;ENST00000392811;ENST00000356800;ENST00000347683	T;T;T	0.56103	0.48;0.49;0.49	5.48	4.57	0.56435	SWIB domain (1);SWIB/MDM2 domain (2);	0.000000	0.85682	D	0.000000	T	0.76248	0.3961	M	0.90145	3.09	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.941	D;D;P	0.87578	0.998;0.992;0.584	T	0.81256	-0.1015	10	0.87932	D	0	-12.7736	13.5304	0.61619	0.0:0.0:0.8444:0.1556	.	280;267;280	B7Z4U8;Q6STE5-2;Q6STE5	.;.;SMRD3_HUMAN	C	280;267;267;232	ENSP00000262188:R280C;ENSP00000376558:R267C;ENSP00000349254:R267C	ENSP00000262188:R280C	R	-	1	0	SMARCD3	150569612	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.001000	0.88508	2.572000	0.86782	0.655000	0.94253	CGC	.	.		0.562	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801	
RHEB	6009	hgsc.bcm.edu	37	7	151188049	151188049	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:151188049T>C	ENST00000262187.5	-	2	516	c.104A>G	c.(103-105)tAc>tGc	p.Y35C	RHEB_ENST00000472642.1_5'UTR|RHEB_ENST00000496004.1_5'UTR	NM_005614.3	NP_005605.1	Q15382	RHEB_HUMAN	Ras homolog enriched in brain	35					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|positive regulation of TOR signaling (GO:0032008)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)	14			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)		GGTTGGATCGTAGGAGTCCAC	0.358																																					p.Y35C	Pancreas(98;671 892 8111 15140 36556 39178 39939 44184)	Atlas-SNP	.											.	RHEB	30	.	0			c.A104G						.						103.0	100.0	101.0					7																	151188049		2203	4300	6503	SO:0001583	missense	6009	exon2			GGATCGTAGGAGT	D78132	CCDS5927.1	7q36	2014-05-09	2003-07-14	2003-07-14	ENSG00000106615	ENSG00000106615			10011	protein-coding gene	gene with protein product		601293	"""Ras homolog enriched in brain 2"""	RHEB2		8661031	Standard	NM_005614		Approved		uc003wkh.1	Q15382	OTTHUMG00000157330	ENST00000262187.5:c.104A>G	chr7.hg19:g.151188049T>C	ENSP00000262187:p.Tyr35Cys	106.0	0.0		99.0	5.0	NM_005614	B3KWN6|D3DX13|Q53Y56|Q99444	Missense_Mutation	SNP	ENST00000262187.5	hg19	CCDS5927.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.379908	0.82682	.	.	ENSG00000106615	ENST00000262187	D	0.81659	-1.52	5.42	5.42	0.78866	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90700	0.7082	M	0.88512	2.96	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92314	0.5860	10	0.87932	D	0	.	13.3975	0.60863	0.0:0.0:0.0:1.0	.	35	Q15382	RHEB_HUMAN	C	35	ENSP00000262187:Y35C	ENSP00000262187:Y35C	Y	-	2	0	RHEB	150818982	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.016000	0.76393	2.051000	0.60960	0.533000	0.62120	TAC	.	.		0.358	RHEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348468.2	NM_005614	
LMBR1	64327	hgsc.bcm.edu	37	7	156521354	156521354	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:156521354A>C	ENST00000353442.5	-	11	1135	c.899T>G	c.(898-900)cTc>cGc	p.L300R	LMBR1_ENST00000354505.4_Missense_Mutation_p.L341R|LMBR1_ENST00000359422.4_Missense_Mutation_p.L148R|LMBR1_ENST00000540390.1_Missense_Mutation_p.L279R	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	300					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		AATAAGAAGGAGAACCATAAC	0.333																																					p.L300R		Atlas-SNP	.											.	LMBR1	35	.	0			c.T899G						.						98.0	102.0	101.0					7																	156521354		2203	4299	6502	SO:0001583	missense	64327	exon11			AGAAGGAGAACCA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.899T>G	chr7.hg19:g.156521354A>C	ENSP00000326604:p.Leu300Arg	314.0	0.0		280.0	93.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Missense_Mutation	SNP	ENST00000353442.5	hg19	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.885158	0.51908	.	.	ENSG00000105983	ENST00000353442;ENST00000359422;ENST00000415428;ENST00000354505;ENST00000540390	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	4.83	4.83	0.62350	LMBR1-like membrane protein (1);	0.061993	0.64402	D	0.000004	T	0.50514	0.1620	L	0.60455	1.87	0.58432	D	0.999995	D;D;D	0.71674	0.986;0.998;0.979	P;D;P	0.70935	0.899;0.971;0.837	T	0.53641	-0.8410	10	0.72032	D	0.01	-10.086	14.0874	0.64968	1.0:0.0:0.0:0.0	.	279;341;300	B7Z633;Q8WVP7-3;Q8WVP7	.;.;LMBR1_HUMAN	R	300;148;339;341;279	ENSP00000326604:L300R;ENSP00000352392:L148R;ENSP00000408256:L339R;ENSP00000346500:L341R;ENSP00000445509:L279R	ENSP00000326604:L300R	L	-	2	0	LMBR1	156214115	1.000000	0.71417	0.969000	0.41365	0.335000	0.28730	7.780000	0.85658	1.806000	0.52798	0.533000	0.62120	CTC	.	.		0.333	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
FBXO25	26260	hgsc.bcm.edu	37	8	363195	363195	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:363195G>A	ENST00000276326.5	+	2	235	c.116G>A	c.(115-117)tGt>tAt	p.C39Y	FBXO25_ENST00000350302.3_Missense_Mutation_p.C39Y|FBXO25_ENST00000352684.2_5'UTR|FBXO25_ENST00000382824.1_5'UTR	NM_183421.1	NP_904357.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25	39	Interaction with beta-actin.				protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		AATAACCGTTGTAACATCAGT	0.433																																					p.C39Y		Atlas-SNP	.											.	FBXO25	25	.	0			c.G116A						.						95.0	139.0	124.0					8																	363195		2203	4300	6503	SO:0001583	missense	26260	exon2			ACCGTTGTAACAT	AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364		"""F-boxes /  ""other"""""	13596	protein-coding gene	gene with protein product		609098	"""F-box only protein 25"""			10531035, 10531037	Standard	NM_012173		Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000276326.5:c.116G>A	chr8.hg19:g.363195G>A	ENSP00000276326:p.Cys39Tyr	179.0	0.0		175.0	52.0	NM_183420	Q6PJ83|Q7Z4V4|Q9UKB8	Missense_Mutation	SNP	ENST00000276326.5	hg19	CCDS5953.1	.	.	.	.	.	.	.	.	.	.	.	0.426	-0.905601	0.02453	.	.	ENSG00000147364	ENST00000518240;ENST00000350302;ENST00000276326;ENST00000447233	T;T;T	0.17854	2.25;2.25;2.25	3.45	1.57	0.23409	.	1.416530	0.04389	N	0.362038	T	0.19886	0.0478	M	0.80183	2.485	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48636	-0.9018	10	0.02654	T	1	-13.5167	5.8083	0.18452	0.274:0.0:0.726:0.0	.	39;39	Q8TCJ0-2;Q8TCJ0	.;FBX25_HUMAN	Y	39	ENSP00000428872:C39Y;ENSP00000342077:C39Y;ENSP00000276326:C39Y	ENSP00000276326:C39Y	C	+	2	0	FBXO25	353195	0.000000	0.05858	0.000000	0.03702	0.943000	0.58893	0.506000	0.22658	0.113000	0.18004	0.298000	0.19748	TGT	.	.		0.433	FBXO25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206710.2	NM_012173	
CLN8	2055	hgsc.bcm.edu	37	8	1719730	1719730	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:1719730G>A	ENST00000331222.4	+	2	757	c.510G>A	c.(508-510)acG>acA	p.T170T		NM_018941.3	NP_061764.2	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)	170	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.		T -> M (in CLN8; associated with M-16 on the same allele; dbSNP:rs188259026). {ECO:0000269|PubMed:15024724}.		adult walking behavior (GO:0007628)|age-dependent response to oxidative stress (GO:0001306)|associative learning (GO:0008306)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|ceramide biosynthetic process (GO:0046513)|ceramide metabolic process (GO:0006672)|cholesterol metabolic process (GO:0008203)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|lipid biosynthetic process (GO:0008610)|lipid transport (GO:0006869)|lysosome organization (GO:0007040)|mitochondrial membrane organization (GO:0007006)|musculoskeletal movement (GO:0050881)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteolysis (GO:0045861)|negative regulation of transferase activity (GO:0051348)|nervous system development (GO:0007399)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|phospholipid metabolic process (GO:0006644)|photoreceptor cell maintenance (GO:0045494)|protein catabolic process (GO:0030163)|regulation of cell size (GO:0008361)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic motor neuron differentiation (GO:0021523)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		AGATGAGCACGCCCTTTACCT	0.493																																					p.T170T	Pancreas(155;338 1942 6138 10888 50612)	Atlas-SNP	.											.	CLN8	64	.	0			c.G510A						.						74.0	71.0	72.0					8																	1719730		2203	4300	6503	SO:0001819	synonymous_variant	2055	exon2			GAGCACGCCCTTT	AF123761	CCDS5956.1	8p23.3	2014-09-17			ENSG00000182372	ENSG00000182372			2079	protein-coding gene	gene with protein product		607837	"""chromosome 8 open reading frame 61"""	EPMR, C8orf61		10508524	Standard	NM_018941		Approved	FLJ39417	uc003wpo.4	Q9UBY8	OTTHUMG00000090343	ENST00000331222.4:c.510G>A	chr8.hg19:g.1719730G>A		61.0	0.0		47.0	6.0	NM_018941	Q86U71|Q96I95	Silent	SNP	ENST00000331222.4	hg19	CCDS5956.1																																																																																			.	.		0.493	CLN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206715.2	NM_018941	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1842674	1842674	+	Missense_Mutation	SNP	C	C	T	rs144726787		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:1842674C>T	ENST00000398564.1	+	13	1451	c.1451C>T	c.(1450-1452)gCg>gTg	p.A484V	ARHGEF10_ENST00000518288.1_Missense_Mutation_p.A484V|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.A459V|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.A421V|ARHGEF10_ENST00000398560.1_Missense_Mutation_p.A445V|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.A484V			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	484	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		TTTCAGATCGCGCTGGCCAGC	0.547																																					p.A459V		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C1376T						.	C	VAL/ALA	0,4406		0,0,2203	83.0	74.0	77.0		1376	5.2	0.9	8	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARHGEF10	NM_014629.2	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	459/1345	1842674	1,13005	2203	4300	6503	SO:0001583	missense	9639	exon13			AGATCGCGCTGGC	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.1451C>T	chr8.hg19:g.1842674C>T	ENSP00000381571:p.Ala484Val	116.0	0.0		119.0	29.0	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	hg19		.	.	.	.	.	.	.	.	.	.	C	32	5.122600	0.94429	0.0	1.16E-4	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398560;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.23	5.23	0.72850	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.82157	0.4976	M	0.84683	2.71	0.80722	D	1	D;D;D;D	0.89917	1.0;0.994;1.0;1.0	D;D;D;D	0.91635	0.999;0.911;0.999;0.998	D	0.85289	0.1066	10	0.87932	D	0	-44.9466	18.7871	0.91960	0.0:1.0:0.0:0.0	.	484;445;421;459	O15013;E9PB39;O15013-7;O15013-5	ARHGA_HUMAN;.;.;.	V	459;421;484;445;484;484;132	ENSP00000340297:A459V;ENSP00000427909:A421V;ENSP00000431012:A484V;ENSP00000381568:A445V;ENSP00000381571:A484V;ENSP00000262112:A484V;ENSP00000427768:A132V	ENSP00000262112:A484V	A	+	2	0	ARHGEF10	1830081	1.000000	0.71417	0.873000	0.34254	0.661000	0.39034	7.073000	0.76784	2.418000	0.82041	0.655000	0.94253	GCG	.	C|1.000;T|0.000		0.547	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
AGPAT5	55326	hgsc.bcm.edu	37	8	6590108	6590108	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:6590108T>C	ENST00000285518.6	+	4	744	c.432T>C	c.(430-432)agT>agC	p.S144S		NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	144					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		TAAAGCGCAGTGCCAAATTTA	0.423																																					p.S144S		Atlas-SNP	.											.	AGPAT5	31	.	0			c.T432C						.						69.0	66.0	67.0					8																	6590108		2203	4300	6503	SO:0001819	synonymous_variant	55326	exon4			GCGCAGTGCCAAA	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20886	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, epsilon"""	614796	"""1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"""				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.432T>C	chr8.hg19:g.6590108T>C		539.0	0.0		569.0	37.0	NM_018361	Q8IZ47|Q9BQG4	Silent	SNP	ENST00000285518.6	hg19	CCDS34796.1																																																																																			.	.		0.423	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361	
KIAA1456	57604	hgsc.bcm.edu	37	8	12879351	12879351	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:12879351A>G	ENST00000524591.2	+	5	1652	c.1163A>G	c.(1162-1164)aAc>aGc	p.N388S	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	388							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						ACAGATTTCAACCCAGATGAT	0.433																																					p.N388S		Atlas-SNP	.											.	KIAA1456	20	.	0			c.A1163G						.						72.0	68.0	70.0					8																	12879351		1909	4140	6049	SO:0001583	missense	57604	exon5			ATTTCAACCCAGA	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"""chromosome 8 open reading frame 79"""	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.1163A>G	chr8.hg19:g.12879351A>G	ENSP00000432695:p.Asn388Ser	154.0	0.0		156.0	48.0	NM_020844	Q96AW6	Missense_Mutation	SNP	ENST00000524591.2	hg19	CCDS47808.1	.	.	.	.	.	.	.	.	.	.	A	4.129	0.022214	0.08006	.	.	ENSG00000250305	ENST00000524591;ENST00000529978	T	0.08634	3.07	4.75	-4.95	0.03048	.	1.141070	0.06094	N	0.664072	T	0.05273	0.0140	L	0.48362	1.52	0.09310	N	1	B	0.16396	0.017	B	0.06405	0.002	T	0.45145	-0.9281	10	0.08599	T	0.76	-0.5598	1.3292	0.02131	0.1528:0.2811:0.1501:0.416	.	388	Q9P272	K1456_HUMAN	S	388;301	ENSP00000432695:N388S	ENSP00000432695:N388S	N	+	2	0	AC135352.2	12923722	0.000000	0.05858	0.003000	0.11579	0.084000	0.17831	0.125000	0.15749	-0.553000	0.06158	0.533000	0.62120	AAC	.	.		0.433	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
PPP2R2A	5520	hgsc.bcm.edu	37	8	26223877	26223877	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:26223877A>G	ENST00000380737.3	+	9	1348	c.1019A>G	c.(1018-1020)gAc>gGc	p.D340G	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.D350G	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	340					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		TATGAAAATGACTGCATATTT	0.308																																					p.D350G		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.A1049G						.						136.0	136.0	136.0					8																	26223877		2203	4299	6502	SO:0001583	missense	5520	exon9			AAAATGACTGCAT	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9304	protein-coding gene	gene with protein product	"""PP2A subunit B isoform alpha"""	604941	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"""			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1019A>G	chr8.hg19:g.26223877A>G	ENSP00000370113:p.Asp340Gly	112.0	0.0		106.0	34.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	hg19	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.852848	0.91355	.	.	ENSG00000221914	ENST00000380737;ENST00000524169;ENST00000315985	T;T;T	0.71461	0.88;-0.57;0.86	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	U	0.000000	D	0.87341	0.6153	M	0.91300	3.195	0.80722	D	1	D;D;D	0.69078	0.996;0.997;0.985	D;D;D	0.72338	0.946;0.946;0.977	D	0.89813	0.3983	10	0.66056	D	0.02	-13.965	16.4484	0.83959	1.0:0.0:0.0:0.0	.	350;340;341	B4E1T7;P63151;Q6ZP32	.;2ABA_HUMAN;.	G	340;119;350	ENSP00000370113:D340G;ENSP00000430320:D119G;ENSP00000325074:D350G	ENSP00000325074:D350G	D	+	2	0	PPP2R2A	26279794	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.308	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717	
SCARA3	51435	hgsc.bcm.edu	37	8	27516318	27516318	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:27516318C>A	ENST00000301904.3	+	5	651	c.631C>A	c.(631-633)Cag>Aag	p.Q211K	SCARA3_ENST00000337221.4_Missense_Mutation_p.Q211K	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	211					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		GGACCTCACCCAGGAGTGCTA	0.607																																					p.Q211K		Atlas-SNP	.											.	SCARA3	93	.	0			c.C631A						.						36.0	37.0	37.0					8																	27516318		2203	4300	6503	SO:0001583	missense	51435	exon5			CTCACCCAGGAGT	AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"""macrophage scavenger receptor-like 1"""	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.631C>A	chr8.hg19:g.27516318C>A	ENSP00000301904:p.Gln211Lys	123.0	0.0		152.0	7.0	NM_182826	Q9UM15|Q9UM16	Missense_Mutation	SNP	ENST00000301904.3	hg19	CCDS34871.1	.	.	.	.	.	.	.	.	.	.	C	15.21	2.764823	0.49574	.	.	ENSG00000168077	ENST00000337221;ENST00000301904	T;T	0.75367	-0.93;2.01	6.17	6.17	0.99709	.	0.102956	0.64402	D	0.000002	T	0.66799	0.2826	L	0.27053	0.805	0.43766	D	0.996289	P;P	0.46859	0.885;0.817	P;B	0.44946	0.465;0.275	T	0.61676	-0.7014	10	0.12430	T	0.62	-18.7305	18.3732	0.90420	0.0:1.0:0.0:0.0	.	211;211	Q6AZY7-2;Q6AZY7	.;SCAR3_HUMAN	K	211	ENSP00000337985:Q211K;ENSP00000301904:Q211K	ENSP00000301904:Q211K	Q	+	1	0	SCARA3	27572237	0.992000	0.36948	1.000000	0.80357	0.994000	0.84299	2.839000	0.48207	2.941000	0.99782	0.655000	0.94253	CAG	.	.		0.607	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240	
ESCO2	157570	hgsc.bcm.edu	37	8	27646450	27646450	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:27646450G>A	ENST00000305188.8	+	7	1456	c.1218G>A	c.(1216-1218)caG>caA	p.Q406Q	ESCO2_ENST00000397418.2_Silent_p.Q54Q	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	406					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		ATGAAATGCAGCATGTACAGC	0.413									SC Phocomelia syndrome																												p.Q406Q		Atlas-SNP	.											.	ESCO2	50	.	0			c.G1218A						.						128.0	117.0	121.0					8																	27646450		2203	4300	6503	SO:0001819	synonymous_variant	157570	exon7	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AATGCAGCATGTA	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"""Roberts syndrome"", ""establishment of cohesion 1 homolog 2 (S. cerevisiae)"""	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.1218G>A	chr8.hg19:g.27646450G>A		82.0	0.0		108.0	40.0	NM_001017420	B3KW59|Q49AP4	Silent	SNP	ENST00000305188.8	hg19	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	G	9.386	1.074229	0.20227	.	.	ENSG00000171320	ENST00000518262	.	.	.	6.03	-1.5	0.08691	.	.	.	.	.	T	0.57403	0.2051	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54794	-0.8240	4	.	.	.	-10.9913	10.9164	0.47139	0.7521:0.0:0.2479:0.0	.	.	.	.	N	111	.	.	S	+	2	0	ESCO2	27702369	0.986000	0.35501	0.975000	0.42487	0.992000	0.81027	0.115000	0.15540	-0.140000	0.11394	-0.137000	0.14449	AGC	.	.		0.413	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420	
PBK	55872	hgsc.bcm.edu	37	8	27667883	27667883	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:27667883T>A	ENST00000301905.4	-	8	1371	c.908A>T	c.(907-909)gAa>gTa	p.E303V	PBK_ENST00000522944.1_Missense_Mutation_p.E314V|ESCO2_ENST00000397418.2_Intron	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	303	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		TTTAGGGTCTTCATTAGTGCA	0.423																																					p.E303V		Atlas-SNP	.											.	PBK	29	.	0			c.A908T						.						168.0	138.0	149.0					8																	27667883		2203	4300	6503	SO:0001583	missense	55872	exon8			GGGTCTTCATTAG	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.908A>T	chr8.hg19:g.27667883T>A	ENSP00000301905:p.Glu303Val	114.0	0.0		103.0	51.0	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Missense_Mutation	SNP	ENST00000301905.4	hg19	CCDS6063.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.180811	0.78677	.	.	ENSG00000168078	ENST00000301905;ENST00000522944	T;T	0.33216	1.42;1.42	6.11	6.11	0.99139	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.37433	0.1003	L	0.39245	1.2	0.80722	D	1	P;P	0.51057	0.883;0.941	P;P	0.51657	0.676;0.676	T	0.04333	-1.0959	10	0.37606	T	0.19	-28.0105	14.6542	0.68820	0.0:0.0:0.0:1.0	.	314;303	B4DX68;Q96KB5	.;TOPK_HUMAN	V	303;314	ENSP00000301905:E303V;ENSP00000428489:E314V	ENSP00000301905:E303V	E	-	2	0	PBK	27723802	1.000000	0.71417	0.996000	0.52242	0.624000	0.37722	7.765000	0.85310	2.343000	0.79666	0.533000	0.62120	GAA	.	.		0.423	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
EXTL3	2137	hgsc.bcm.edu	37	8	28608212	28608212	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:28608212T>C	ENST00000220562.4	+	7	3491	c.2589T>C	c.(2587-2589)ccT>ccC	p.P863P	EXTL3_ENST00000519886.1_Intron|EXTL3_ENST00000523149.1_Silent_p.P479P	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	863					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)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		CAGGATGCCCTCAGGCCCTGT	0.562																																					p.P863P		Atlas-SNP	.											.	EXTL3	83	.	0			c.T2589C						.						146.0	115.0	125.0					8																	28608212		2203	4300	6503	SO:0001819	synonymous_variant	2137	exon7			ATGCCCTCAGGCC	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"""Exostosin glycosyltransferase family"""	3518	protein-coding gene	gene with protein product	"""REG receptor"", ""glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"""	605744	"""exostoses (multiple)-like 3"""			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.2589T>C	chr8.hg19:g.28608212T>C		66.0	0.0		48.0	21.0	NM_001440	D3DST8|O00225|Q53XT3	Silent	SNP	ENST00000220562.4	hg19	CCDS6070.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.325950	0.24080	.	.	ENSG00000012232	ENST00000521473	.	.	.	5.61	-7.8	0.01214	.	.	.	.	.	T	0.36690	0.0976	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	-20.6994	3.7169	0.08441	0.0924:0.2857:0.375:0.2469	.	.	.	.	P	154	.	.	S	+	1	0	EXTL3	28664131	0.780000	0.28664	0.965000	0.40720	0.902000	0.53008	-0.181000	0.09740	-0.895000	0.03920	-0.478000	0.04885	TCA	.	.		0.562	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440	
SARAF	51669	hgsc.bcm.edu	37	8	29924389	29924389	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:29924389G>A	ENST00000256255.6	-	4	1003	c.746C>T	c.(745-747)gCt>gTt	p.A249V	TMEM66_ENST00000545648.1_Missense_Mutation_p.A77V|TMEM66_ENST00000536273.1_Missense_Mutation_p.A77V	NM_016127.4	NP_057211.4	Q96BY9	SARAF_HUMAN		249					calcium ion transport (GO:0006816)|regulation of store-operated calcium entry (GO:2001256)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|large_intestine(1)|lung(11)	14				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)		TCCTGTAAAAGCACTGCCAAA	0.393																																					p.A249V		Atlas-SNP	.											.	TMEM66	23	.	0			c.C746T						.						147.0	143.0	144.0					8																	29924389		2203	4300	6503	SO:0001583	missense	51669	exon4			GTAAAAGCACTGC																												ENST00000256255.6:c.746C>T	chr8.hg19:g.29924389G>A	ENSP00000256255:p.Ala249Val	165.0	0.0		183.0	19.0	NM_016127	B3KQQ4|B7Z9J1|D3DSU7|H9MHJ8|H9MHJ9|Q53HE8|Q9UNZ3|Q9Y683	Missense_Mutation	SNP	ENST00000256255.6	hg19	CCDS6074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.47|19.47	3.832781|3.832781	0.71258|0.71258	.|.	.|.	ENSG00000133872|ENSG00000133872	ENST00000256255;ENST00000545648;ENST00000541035;ENST00000536273;ENST00000523127|ENST00000521265	T;T;T;T|.	0.44482|.	0.92;0.92;0.92;0.92|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.470266|.	0.24217|.	N|.	0.040472|.	T|T	0.50650|0.50650	0.1628|0.1628	L|L	0.55103|0.55103	1.725|1.725	0.29310|0.29310	N|N	0.868108|0.868108	P;P|.	0.52170|.	0.951;0.951|.	P;P|.	0.52646|.	0.705;0.705|.	T|T	0.50338|0.50338	-0.8840|-0.8840	10|5	0.48119|.	T|.	0.1|.	-20.6171|-20.6171	9.8225|9.8225	0.40891|0.40891	0.0936:0.0:0.9064:0.0|0.0936:0.0:0.9064:0.0	.|.	249;249|.	B3KQQ4;Q96BY9|.	.;TMM66_HUMAN|.	V|F	249;77;213;77;147|249	ENSP00000256255:A249V;ENSP00000441351:A77V;ENSP00000441723:A77V;ENSP00000428323:A147V|.	ENSP00000256255:A249V|.	A|L	-|-	2|1	0|0	TMEM66|TMEM66	30043931|30043931	0.980000|0.980000	0.34600|0.34600	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	1.720000|1.720000	0.38022|0.38022	2.442000|2.442000	0.82660|0.82660	0.580000|0.580000	0.79431|0.79431	GCT|CTT	.	.		0.393	TMEM66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257254.4		
UNC5D	137970	hgsc.bcm.edu	37	8	35541099	35541099	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:35541099C>A	ENST00000404895.2	+	5	933	c.605C>A	c.(604-606)tCt>tAt	p.S202Y	UNC5D_ENST00000416672.1_Missense_Mutation_p.S202Y|UNC5D_ENST00000453357.2_Missense_Mutation_p.S197Y|UNC5D_ENST00000287272.2_Missense_Mutation_p.S202Y|UNC5D_ENST00000420357.1_Missense_Mutation_p.S202Y	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	202	Ig-like C2-type.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		CCCATTGACTCTGAACAAGAC	0.448																																					p.S202Y		Atlas-SNP	.											.	UNC5D	393	.	0			c.C605A						.						94.0	83.0	87.0					8																	35541099		2203	4300	6503	SO:0001583	missense	137970	exon5			TTGACTCTGAACA	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.605C>A	chr8.hg19:g.35541099C>A	ENSP00000385143:p.Ser202Tyr	124.0	0.0		121.0	53.0	NM_080872	Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	hg19	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	C	20.3	3.963810	0.74131	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357	T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46	5.39	5.39	0.77823	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.051625	0.85682	D	0.000000	T	0.68705	0.3030	L	0.37561	1.115	0.80722	D	1	P;P	0.44241	0.823;0.829	P;P	0.48795	0.59;0.544	T	0.71856	-0.4466	10	0.87932	D	0	-16.6379	19.5354	0.95251	0.0:1.0:0.0:0.0	.	197;202	Q6UXZ4-2;Q6UXZ4	.;UNC5D_HUMAN	Y	202;202;202;202;197	ENSP00000385143:S202Y;ENSP00000392739:S202Y;ENSP00000287272:S202Y;ENSP00000412652:S202Y;ENSP00000394303:S197Y	ENSP00000287272:S202Y	S	+	2	0	UNC5D	35660641	1.000000	0.71417	0.994000	0.49952	0.863000	0.49368	5.905000	0.69893	2.709000	0.92574	0.655000	0.94253	TCT	.	.		0.448	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		
WHSC1L1	54904	hgsc.bcm.edu	37	8	38184373	38184373	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:38184373C>T	ENST00000317025.8	-	7	2100	c.1583G>A	c.(1582-1584)gGa>gAa	p.G528E	WHSC1L1_ENST00000527502.1_Splice_Site_p.G528E|WHSC1L1_ENST00000433384.2_Splice_Site_p.G528E|WHSC1L1_ENST00000316985.3_Splice_Site_p.G528E	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	528					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)			GTTACCAATTCCCTTTAAAAT	0.368			T	NUP98	AML																																p.G528E		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.G1583A						.						112.0	99.0	103.0					8																	38184373		2203	4300	6503	SO:0001630	splice_region_variant	54904	exon7			CCAATTCCCTTTA	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.1582-1G>A	chr8.hg19:g.38184373C>T		73.0	0.0		87.0	34.0	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.842584	0.51057	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985	D;D;D;T	0.94537	-3.42;-3.45;-3.45;0.01	5.79	5.79	0.91817	.	0.000000	0.47093	U	0.000245	D	0.89382	0.6699	N	0.19112	0.55	0.46437	D	0.999041	B;B;B;B	0.29301	0.012;0.082;0.241;0.049	B;B;B;B	0.30855	0.009;0.039;0.121;0.018	D	0.86763	0.1968	10	0.40728	T	0.16	.	13.2527	0.60060	0.0:0.9276:0.0:0.0724	.	528;528;528;528	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	E	528;528;465;528;528	ENSP00000393284:G528E;ENSP00000313983:G528E;ENSP00000434730:G528E;ENSP00000313410:G528E	ENSP00000313410:G528E	G	-	2	0	WHSC1L1	38303530	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.655000	0.54460	2.718000	0.92993	0.655000	0.94253	GGA	.	.		0.368	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	Missense_Mutation
RB1CC1	9821	hgsc.bcm.edu	37	8	53555118	53555118	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:53555118C>T	ENST00000025008.5	-	18	4653	c.4130G>A	c.(4129-4131)cGt>cAt	p.R1377H	RB1CC1_ENST00000539297.1_Missense_Mutation_p.R1377H|RB1CC1_ENST00000435644.2_Missense_Mutation_p.R1377H|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1377					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CTCAAGCAAACGAGCTCGATC	0.358																																					p.R1377H	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.G4130A						.						80.0	76.0	77.0					8																	53555118		2203	4300	6503	SO:0001583	missense	9821	exon18			AGCAAACGAGCTC	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4130G>A	chr8.hg19:g.53555118C>T	ENSP00000025008:p.Arg1377His	110.0	0.0		103.0	30.0	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	hg19	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831119	0.91036	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.15487	2.42;2.42;2.42	5.61	5.61	0.85477	.	0.053357	0.85682	D	0.000000	T	0.30823	0.0777	L	0.32530	0.975	0.44104	D	0.996878	D;D	0.76494	0.999;0.998	P;P	0.61592	0.891;0.781	T	0.01460	-1.1349	10	0.72032	D	0.01	-13.615	18.6201	0.91318	0.0:1.0:0.0:0.0	.	1377;1377	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	H	1377	ENSP00000025008:R1377H;ENSP00000396067:R1377H;ENSP00000445960:R1377H	ENSP00000025008:R1377H	R	-	2	0	RB1CC1	53717671	0.998000	0.40836	0.994000	0.49952	0.998000	0.95712	3.761000	0.55242	2.632000	0.89209	0.655000	0.94253	CGT	.	.		0.358	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
NSMAF	8439	hgsc.bcm.edu	37	8	59511898	59511898	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:59511898C>T	ENST00000038176.3	-	19	1690	c.1478G>A	c.(1477-1479)aGc>aAc	p.S493N	NSMAF_ENST00000427130.2_Missense_Mutation_p.S524N|NSMAF_ENST00000519858.1_5'Flank	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	493	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TGCATCTTTGCTCTTCTGGAG	0.398																																					p.S524N		Atlas-SNP	.											.	NSMAF	156	.	0			c.G1571A						.						139.0	139.0	139.0					8																	59511898		2203	4300	6503	SO:0001583	missense	8439	exon19			TCTTTGCTCTTCT	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"""WD repeat domain containing"""	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1478G>A	chr8.hg19:g.59511898C>T	ENSP00000038176:p.Ser493Asn	93.0	0.0		89.0	37.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	hg19	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.558695	0.27827	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	T;T	0.78595	-1.19;-1.19	6.17	4.37	0.52481	BEACH domain (4);	0.181464	0.64402	N	0.000006	T	0.38321	0.1036	N	0.00178	-1.915	0.32582	N	0.528327	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.001	T	0.42430	-0.9452	9	.	.	.	.	9.386	0.38342	0.0:0.7848:0.0:0.2152	.	524;493	Q92636-2;Q92636	.;FAN_HUMAN	N	493;524	ENSP00000038176:S493N;ENSP00000411012:S524N	.	S	-	2	0	NSMAF	59674452	1.000000	0.71417	0.999000	0.59377	0.864000	0.49448	2.248000	0.43160	0.923000	0.37045	0.655000	0.94253	AGC	.	.		0.398	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580	
PDE7A	5150	hgsc.bcm.edu	37	8	66651737	66651737	+	Splice_Site	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:66651737C>A	ENST00000401827.3	-	6	1038	c.595G>T	c.(595-597)Gtt>Ttt	p.V199F	PDE7A_ENST00000396642.3_Splice_Site_p.V199F|PDE7A_ENST00000518667.1_5'UTR|PDE7A_ENST00000379419.4_Splice_Site_p.V173F	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	199	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	AATCACTTACCTAAAAATCTA	0.289																																					p.V199F		Atlas-SNP	.											.	PDE7A	78	.	0			c.G595T						.						55.0	56.0	56.0					8																	66651737		2195	4292	6487	SO:0001630	splice_region_variant	5150	exon6			ACTTACCTAAAAA	L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	3.1.4.17	"""Phosphodiesterases"""	8791	protein-coding gene	gene with protein product		171885				8389765, 9521885	Standard	NM_001242318		Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.595+1G>T	chr8.hg19:g.66651737C>A		268.0	0.0		239.0	92.0	NM_001242318	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	Missense_Mutation	SNP	ENST00000401827.3	hg19	CCDS56538.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756829	0.89843	.	.	ENSG00000205268	ENST00000401827;ENST00000379419;ENST00000396642	T;T;T	0.76316	-1.01;-1.01;-0.44	5.37	5.37	0.77165	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.85405	0.5689	L	0.52573	1.65	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.995;0.952;0.995	D	0.84150	0.0422	9	.	.	.	.	19.107	0.93300	0.0:1.0:0.0:0.0	.	199;199;173	Q13946-3;Q13946;Q13946-2	.;PDE7A_HUMAN;.	F	199;173;199	ENSP00000385632:V199F;ENSP00000368730:V173F;ENSP00000379881:V199F	.	V	-	1	0	PDE7A	66814291	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.565000	0.82337	2.502000	0.84385	0.655000	0.94253	GTT	.	.		0.289	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378905.1		Missense_Mutation
PREX2	80243	hgsc.bcm.edu	37	8	69020402	69020402	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:69020402T>A	ENST00000288368.4	+	24	3051	c.2774T>A	c.(2773-2775)aTc>aAc	p.I925N		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	925					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AAATCTAAAATCTCCCCACTG	0.408																																					p.I925N		Atlas-SNP	.											.	PREX2	614	.	0			c.T2774A						.						93.0	83.0	86.0					8																	69020402		2203	4300	6503	SO:0001583	missense	80243	exon24			CTAAAATCTCCCC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2774T>A	chr8.hg19:g.69020402T>A	ENSP00000288368:p.Ile925Asn	87.0	0.0		114.0	40.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964171	0.53507	.	.	ENSG00000046889	ENST00000288368;ENST00000396539	T	0.34667	1.35	5.85	5.85	0.93711	.	0.184790	0.48767	D	0.000170	T	0.24890	0.0604	N	0.22421	0.69	0.41335	D	0.987262	P;B	0.35944	0.529;0.047	B;B	0.36922	0.236;0.042	T	0.09952	-1.0651	10	0.22706	T	0.39	.	10.5554	0.45114	0.0:0.0716:0.0:0.9284	.	990;925	Q70Z35-2;Q70Z35	.;PREX2_HUMAN	N	925;991	ENSP00000288368:I925N	ENSP00000288368:I925N	I	+	2	0	PREX2	69182956	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.162000	0.64942	2.238000	0.73509	0.533000	0.62120	ATC	.	.		0.408	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
ZFHX4	79776	hgsc.bcm.edu	37	8	77776151	77776151	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:77776151T>C	ENST00000521891.2	+	11	10649	c.10201T>C	c.(10201-10203)Tat>Cat	p.Y3401H	ZFHX4_ENST00000518282.1_Missense_Mutation_p.Y3375H|ZFHX4_ENST00000050961.6_Missense_Mutation_p.Y3352H|ZFHX4_ENST00000455469.2_Missense_Mutation_p.Y3356H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3352					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)			ATTCGTCAAGTATGAGTTTAT	0.398										HNSCC(33;0.089)																											p.Y3401H		Atlas-SNP	.											.	ZFHX4	878	.	0			c.T10201C						.						48.0	45.0	46.0					8																	77776151		1876	4116	5992	SO:0001583	missense	79776	exon11			GTCAAGTATGAGT		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.10201T>C	chr8.hg19:g.77776151T>C	ENSP00000430497:p.Tyr3401His	70.0	0.0		71.0	31.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	T	6.636	0.485890	0.12641	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.51817	0.69;0.75;0.72;0.71	4.85	4.85	0.62838	.	0.000000	0.40469	U	0.001088	T	0.26412	0.0645	N	0.05510	-0.035	0.36159	D	0.847962	B	0.09022	0.002	B	0.11329	0.006	T	0.20706	-1.0267	10	0.37606	T	0.19	.	9.1643	0.37041	0.0:0.0811:0.0:0.9189	.	3356	Q86UP3-4	.	H	3401;3385;3356;3352;3375	ENSP00000430497:Y3401H;ENSP00000399605:Y3356H;ENSP00000050961:Y3352H;ENSP00000430848:Y3375H	ENSP00000050961:Y3352H	Y	+	1	0	ZFHX4	77938706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.142000	0.50601	2.056000	0.61249	0.496000	0.49642	TAT	.	.		0.398	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
PSKH2	85481	hgsc.bcm.edu	37	8	87076416	87076416	+	Silent	SNP	G	G	A	rs376242267		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:87076416G>A	ENST00000276616.2	-	2	704	c.630C>T	c.(628-630)tcC>tcT	p.S210S	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	210	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			TTTTTTTCCCGGAGTATGCCA	0.423																																					p.S210S		Atlas-SNP	.											PSKH2,rectum,carcinoma,0,1	PSKH2	79	.	0			c.C630T						.	G		1,4405	2.1+/-5.4	0,1,2202	72.0	76.0	75.0		630	-1.9	1.0	8		75	0,8600		0,0,4300	no	coding-synonymous	PSKH2	NM_033126.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		210/386	87076416	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	85481	exon2			TTTCCCGGAGTAT	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.630C>T	chr8.hg19:g.87076416G>A		127.0	0.0		130.0	52.0	NM_033126	A0AV22	Silent	SNP	ENST00000276616.2	hg19	CCDS6240.1																																																																																			.	.		0.423	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
ESRP1	54845	hgsc.bcm.edu	37	8	95680213	95680213	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:95680213A>G	ENST00000433389.2	+	10	1158	c.968A>G	c.(967-969)gAa>gGa	p.E323G	ESRP1_ENST00000454170.2_Missense_Mutation_p.E323G|ESRP1_ENST00000358397.5_Missense_Mutation_p.E323G|ESRP1_ENST00000423620.2_Missense_Mutation_p.E323G	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	323					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)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						CTCTCCAAGGAAAATCAAGTC	0.468																																					p.E323G		Atlas-SNP	.											.	ESRP1	148	.	0			c.A968G						.						60.0	58.0	58.0					8																	95680213		1849	4088	5937	SO:0001583	missense	54845	exon10			CCAAGGAAAATCA	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.968A>G	chr8.hg19:g.95680213A>G	ENSP00000405738:p.Glu323Gly	131.0	0.0		121.0	45.0	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Missense_Mutation	SNP	ENST00000433389.2	hg19	CCDS47897.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.588378	0.46110	.	.	ENSG00000104413	ENST00000423620;ENST00000433389;ENST00000358397;ENST00000454170;ENST00000517610	T;T;T;T;T	0.29397	1.57;3.39;3.39;2.8;3.39	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.36608	0.0973	N	0.16567	0.415	0.80722	D	1	P;D;B;B;B;B	0.56746	0.589;0.977;0.005;0.003;0.014;0.431	B;D;B;B;B;B	0.64506	0.346;0.926;0.029;0.013;0.029;0.254	T	0.13575	-1.0504	10	0.19147	T	0.46	-14.893	16.1146	0.81295	1.0:0.0:0.0:0.0	.	323;323;323;323;323;323	D7PBN3;Q6NXG1-4;Q6NXG1-2;E9PB47;Q6NXG1-3;Q6NXG1	.;.;.;.;.;ESRP1_HUMAN	G	323;323;323;323;182	ENSP00000407349:E323G;ENSP00000405738:E323G;ENSP00000351168:E323G;ENSP00000402766:E323G;ENSP00000429125:E182G	ENSP00000351168:E323G	E	+	2	0	ESRP1	95749389	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.200000	0.70718	0.460000	0.39030	GAA	.	.		0.468	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
CTHRC1	115908	hgsc.bcm.edu	37	8	104394725	104394725	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:104394725A>T	ENST00000330295.5	+	4	771	c.629A>T	c.(628-630)gAt>gTt	p.D210V	RNU6-1011P_ENST00000384668.1_RNA|CTHRC1_ENST00000520880.1_Missense_Mutation_p.D80V|CTHRC1_ENST00000520337.1_Missense_Mutation_p.D196V|RP11-1C8.6_ENST00000577199.1_lincRNA	NM_138455.3	NP_612464.1	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	210					cell migration (GO:0016477)|cochlea morphogenesis (GO:0090103)|establishment of planar polarity involved in neural tube closure (GO:0090177)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|ossification involved in bone remodeling (GO:0043932)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein binding (GO:0032092)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				endometrium(1)|large_intestine(5)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)			GGATTAGTGGATGTTGCTATC	0.378																																					p.D210V		Atlas-SNP	.											.	CTHRC1	29	.	0			c.A629T						.						306.0	289.0	295.0					8																	104394725		2203	4300	6503	SO:0001583	missense	115908	exon4			TAGTGGATGTTGC	BC014245	CCDS6299.1, CCDS59110.1	8q22.3	2008-08-07			ENSG00000164932	ENSG00000164932			18831	protein-coding gene	gene with protein product		610635				15618538	Standard	NM_138455		Approved		uc003ylk.4	Q96CG8	OTTHUMG00000164887	ENST00000330295.5:c.629A>T	chr8.hg19:g.104394725A>T	ENSP00000330523:p.Asp210Val	152.0	0.0		121.0	48.0	NM_138455	G3V141|Q6UW91|Q8IX63	Missense_Mutation	SNP	ENST00000330295.5	hg19	CCDS6299.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.418834	0.83559	.	.	ENSG00000164932	ENST00000330295;ENST00000520337;ENST00000297577;ENST00000520880	T;T	0.66815	-0.23;0.8	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.80934	0.4719	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.83202	-0.0078	10	0.72032	D	0.01	-10.7745	15.4021	0.74849	1.0:0.0:0.0:0.0	.	210	Q96CG8	CTHR1_HUMAN	V	210;196;196;80	ENSP00000330523:D210V;ENSP00000430550:D196V	ENSP00000297577:D196V	D	+	2	0	CTHRC1	104463901	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	8.962000	0.93254	2.048000	0.60808	0.533000	0.62120	GAT	.	.		0.378	CTHRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380792.1	NM_138455	
DCAF13	25879	hgsc.bcm.edu	37	8	104447934	104447934	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:104447934A>G	ENST00000297579.5	+	8	1599	c.1322A>G	c.(1321-1323)gAt>gGt	p.D441G	DCAF13_ENST00000521999.1_3'UTR	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	289					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						CTTGATGTGGATTACTCTCCC	0.398																																					p.D441G		Atlas-SNP	.											.	DCAF13	66	.	0			c.A1322G						.						150.0	129.0	136.0					8																	104447934		2203	4300	6503	SO:0001583	missense	25879	exon8			ATGTGGATTACTC	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	24535	protein-coding gene	gene with protein product			"""WD repeats and SOF1 domain containing"""	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.1322A>G	chr8.hg19:g.104447934A>G	ENSP00000297579:p.Asp441Gly	46.0	0.0		63.0	24.0	NM_015420	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	hg19	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.530671	0.85706	.	.	ENSG00000164934	ENST00000297579	T	0.61510	0.1	4.99	4.99	0.66335	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.74268	0.3694	M	0.73217	2.22	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.78097	-0.2337	10	0.87932	D	0	-23.3527	14.9911	0.71390	1.0:0.0:0.0:0.0	.	289	Q9NV06	DCA13_HUMAN	G	441	ENSP00000297579:D441G	ENSP00000297579:D441G	D	+	2	0	DCAF13	104517110	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.906000	0.92626	1.998000	0.58463	0.528000	0.53228	GAT	.	.		0.398	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420	
ATAD2	29028	hgsc.bcm.edu	37	8	124340665	124340665	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:124340665A>T	ENST00000287394.5	-	25	3740	c.3633T>A	c.(3631-3633)gaT>gaA	p.D1211E	ATAD2_ENST00000521903.1_Missense_Mutation_p.D529E	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	1211					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TCTCATTATGATCTACACTTG	0.383																																					p.D1211E		Atlas-SNP	.											.	ATAD2	160	.	0			c.T3633A						.						175.0	165.0	169.0					8																	124340665		2203	4300	6503	SO:0001583	missense	29028	exon25			ATTATGATCTACA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.3633T>A	chr8.hg19:g.124340665A>T	ENSP00000287394:p.Asp1211Glu	124.0	0.0		141.0	58.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	A	10.13	1.266032	0.23136	.	.	ENSG00000156802	ENST00000287394;ENST00000521903	D;T	0.91792	-2.91;1.53	5.03	-1.74	0.08056	.	1.645960	0.02670	N	0.108427	T	0.79924	0.4530	N	0.08118	0	0.31420	N	0.674386	B	0.06786	0.001	B	0.06405	0.002	T	0.74140	-0.3761	10	0.07990	T	0.79	-4.3289	4.8821	0.13685	0.5084:0.253:0.2385:0.0	.	1211	Q6PL18	ATAD2_HUMAN	E	1211;529	ENSP00000287394:D1211E;ENSP00000429213:D529E	ENSP00000287394:D1211E	D	-	3	2	ATAD2	124409846	0.422000	0.25473	0.876000	0.34364	0.946000	0.59487	-0.469000	0.06648	-0.095000	0.12351	-0.345000	0.07892	GAT	.	.		0.383	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
ATAD2	29028	hgsc.bcm.edu	37	8	124383532	124383532	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:124383532G>A	ENST00000287394.5	-	5	690	c.583C>T	c.(583-585)Cgt>Tgt	p.R195C	ATAD2_ENST00000521903.1_5'UTR|ATAD2_ENST00000534257.1_5'Flank	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	195					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			CGCTGTCTACGCATCTTCTTC	0.313																																					p.R195C		Atlas-SNP	.											.	ATAD2	160	.	0			c.C583T						.						94.0	92.0	93.0					8																	124383532		2203	4298	6501	SO:0001583	missense	29028	exon5			GTCTACGCATCTT	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.583C>T	chr8.hg19:g.124383532G>A	ENSP00000287394:p.Arg195Cys	212.0	0.0		198.0	71.0	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	hg19	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.984142	0.74474	.	.	ENSG00000156802	ENST00000287394	T	0.08102	3.13	5.06	4.16	0.48862	.	3.441010	0.01712	U	0.027766	T	0.33904	0.0879	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00003	-1.2586	10	0.87932	D	0	-11.072	13.9126	0.63876	0.0:0.0:0.8343:0.1657	.	25;195	Q6PL18-2;Q6PL18	.;ATAD2_HUMAN	C	195	ENSP00000287394:R195C	ENSP00000287394:R195C	R	-	1	0	ATAD2	124452713	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.008000	0.70739	1.057000	0.40506	0.555000	0.69702	CGT	.	.		0.313	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
TMEM71	137835	hgsc.bcm.edu	37	8	133764034	133764034	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:133764034A>C	ENST00000356838.3	-	4	453	c.311T>G	c.(310-312)gTt>gGt	p.V104G	TMEM71_ENST00000517538.1_5'UTR|TMEM71_ENST00000523829.1_Missense_Mutation_p.V104G|TMEM71_ENST00000377901.4_Missense_Mutation_p.V104G	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	104						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGCTTACCTAACTAAGTTCTC	0.378																																					p.V104G		Atlas-SNP	.											.	TMEM71	55	.	0			c.T311G						.						131.0	120.0	124.0					8																	133764034		2203	4300	6503	SO:0001583	missense	137835	exon4			TACCTAACTAAGT	AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.311T>G	chr8.hg19:g.133764034A>C	ENSP00000349296:p.Val104Gly	126.0	0.0		119.0	40.0	NM_144649	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	hg19	CCDS6366.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.352347	0.61293	.	.	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901;ENST00000522334;ENST00000519016	.	.	.	5.95	5.95	0.96441	.	0.073213	0.53938	D	0.000046	T	0.79311	0.4424	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.993;0.962;0.999	T	0.81906	-0.0718	9	0.87932	D	0	.	14.1698	0.65503	1.0:0.0:0.0:0.0	.	104;104;104	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	G	104;104;104;7;7	.	ENSP00000349296:V104G	V	-	2	0	TMEM71	133833216	0.996000	0.38824	0.989000	0.46669	0.252000	0.25951	5.934000	0.70138	2.282000	0.76494	0.533000	0.62120	GTT	.	.		0.378	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649	
PHF20L1	51105	hgsc.bcm.edu	37	8	133848922	133848922	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:133848922C>T	ENST00000395386.2	+	16	2346	c.2047C>T	c.(2047-2049)Cga>Tga	p.R683*	AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000395390.2_Nonsense_Mutation_p.R658*|PHF20L1_ENST00000220847.7_Nonsense_Mutation_p.R70*|AF230666.2_ENST00000429151.1_RNA	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	683							zinc ion binding (GO:0008270)	p.R657*(2)		breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGAAATTGTGCGATGTATTTG	0.408																																					p.R683X		Atlas-SNP	.											Q86U89_HUMAN,NS,carcinoma,0,4	PHF20L1	129	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2047T						.						190.0	183.0	185.0					8																	133848922		1969	4147	6116	SO:0001587	stop_gained	51105	exon16			ATTGTGCGATGTA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2047C>T	chr8.hg19:g.133848922C>T	ENSP00000378784:p.Arg683*	159.0	0.0		158.0	55.0	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Nonsense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	C	38	7.083629	0.98051	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	.	.	.	5.14	3.02	0.34903	.	0.103999	0.38111	U	0.001810	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6783	12.4875	0.55881	0.3889:0.6111:0.0:0.0	.	.	.	.	X	683;70;658	.	ENSP00000220847:R70X	R	+	1	2	PHF20L1	133918104	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.219000	0.42899	1.289000	0.44618	0.544000	0.68410	CGA	.	.		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
LYNX1	66004	hgsc.bcm.edu	37	8	143857040	143857040	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:143857040A>G	ENST00000335822.5	-	3	752	c.125T>C	c.(124-126)aTg>aCg	p.M42T	LYNX1_ENST00000522906.1_Intron|LYNX1_ENST00000523332.1_Missense_Mutation_p.M42T|LYNX1_ENST00000345173.6_Missense_Mutation_p.M42T|LYNX1_ENST00000395192.2_Missense_Mutation_p.M42T|LYNX1_ENST00000398906.1_Missense_Mutation_p.M42T	NM_023946.2	NP_076435.1	Q9BZG9	LYNX1_HUMAN	Ly6/neurotoxin 1	42						anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|lung(2)|skin(1)	4	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GTAGGCAACCATAGCCGGGCA	0.657																																					p.M42T		Atlas-SNP	.											.	LYNX1	40	.	0			c.T125C						.						73.0	59.0	64.0					8																	143857040		2201	4299	6500	SO:0001583	missense	66004	exon3			GCAACCATAGCCG	AF321824	CCDS6389.1, CCDS34951.1, CCDS34952.1	8q24.3	2008-03-12			ENSG00000180155	ENSG00000180155			29604	protein-coding gene	gene with protein product		606110				12573258, 10402197	Standard	NM_023946		Approved	SLURP2	uc003yxd.1	Q9BZG9	OTTHUMG00000164694	ENST00000335822.5:c.125T>C	chr8.hg19:g.143857040A>G	ENSP00000337950:p.Met42Thr	116.0	0.0		99.0	40.0	NM_177477	D3DWI7|G3XAC2|Q86SR0	Missense_Mutation	SNP	ENST00000335822.5	hg19	CCDS34951.1	.	.	.	.	.	.	.	.	.	.	a	11.89	1.774863	0.31411	.	.	ENSG00000180155	ENST00000523332;ENST00000335822;ENST00000395192;ENST00000398906;ENST00000345173;ENST00000522929;ENST00000520131	T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06	4.82	3.51	0.40186	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.465370	0.03948	N	0.288053	T	0.26738	0.0654	N	0.22421	0.69	0.09310	N	1	P;D	0.56968	0.802;0.978	B;P	0.53649	0.43;0.731	T	0.26883	-1.0090	10	0.72032	D	0.01	-19.2184	8.1989	0.31413	0.808:0.0:0.0:0.192	.	42;42	Q9BZG9;G3XAC2	LYNX1_HUMAN;.	T	42	ENSP00000428713:M42T;ENSP00000337950:M42T;ENSP00000378618:M42T;ENSP00000381878:M42T;ENSP00000332495:M42T;ENSP00000429261:M42T;ENSP00000428157:M42T	ENSP00000337950:M42T	M	-	2	0	LYNX1	143854042	0.996000	0.38824	0.992000	0.48379	0.602000	0.36980	2.589000	0.46145	1.827000	0.53221	0.529000	0.55759	ATG	.	.		0.657	LYNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379786.3	NM_177476	
FAM83H	286077	hgsc.bcm.edu	37	8	144809309	144809309	+	Silent	SNP	C	C	T	rs566224492		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:144809309C>T	ENST00000388913.3	-	5	2447	c.2322G>A	c.(2320-2322)gcG>gcA	p.A774A		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	774					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CACCTGGGGCCGCCACCTCTT	0.741													c|||	1	0.000199681	0.0	0.0	5008	,	,		10370	0.0		0.0	False		,,,				2504	0.001				p.A774A		Atlas-SNP	.											.	FAM83H	68	.	0			c.G2322A						.						2.0	3.0	2.0					8																	144809309		1498	3149	4647	SO:0001819	synonymous_variant	286077	exon5			TGGGGCCGCCACC	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.2322G>A	chr8.hg19:g.144809309C>T		914.0	1.0		952.0	247.0	NM_198488	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	hg19	CCDS6410.2																																																																																			.	.		0.741	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
FAM83H	286077	hgsc.bcm.edu	37	8	144812634	144812634	+	Missense_Mutation	SNP	G	G	A	rs371078447		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:144812634G>A	ENST00000388913.3	-	2	244	c.119C>T	c.(118-120)tCg>tTg	p.S40L	MIR4664_ENST00000583819.1_RNA	NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	40					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GTAGGCCTCCGAGCCACCCTC	0.647																																					p.S40L		Atlas-SNP	.											.	FAM83H	68	.	0			c.C119T						.	G	LEU/SER	1,3997		0,1,1998	29.0	33.0	32.0		119	3.0	0.0	8		32	0,8314		0,0,4157	no	missense	FAM83H	NM_198488.3	145	0,1,6155	AA,AG,GG		0.0,0.025,0.0081	benign	40/1180	144812634	1,12311	1999	4157	6156	SO:0001583	missense	286077	exon2			GCCTCCGAGCCAC	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.119C>T	chr8.hg19:g.144812634G>A	ENSP00000373565:p.Ser40Leu	1440.0	2.0		1310.0	554.0	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	g	3.815	-0.038928	0.07497	2.5E-4	0.0	ENSG00000180921	ENST00000388913	T	0.11277	2.79	4.87	2.97	0.34412	.	0.602886	0.15663	N	0.250787	T	0.02970	0.0088	N	0.00521	-1.4	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.44097	-0.9350	10	0.23302	T	0.38	.	9.5268	0.39169	0.0:0.1291:0.575:0.2959	.	40	Q6ZRV2	FA83H_HUMAN	L	40	ENSP00000373565:S40L	ENSP00000373565:S40L	S	-	2	0	FAM83H	144884622	0.000000	0.05858	0.015000	0.15790	0.181000	0.23173	0.271000	0.18626	0.517000	0.28361	0.561000	0.74099	TCG	.	.		0.647	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
EPPK1	83481	hgsc.bcm.edu	37	8	144942558	144942558	+	Nonsense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:144942558T>A	ENST00000525985.1	-	2	4935	c.4864A>T	c.(4864-4866)Aag>Tag	p.K1622*				P58107	EPIPL_HUMAN	epiplakin 1	1622						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACGGTCAGCTTCCGGTTCTCC	0.642																																					p.K1622X		Atlas-SNP	.											.	EPPK1	199	.	0			c.A4864T						.						50.0	57.0	55.0					8																	144942558		2037	4186	6223	SO:0001587	stop_gained	83481	exon1			TCAGCTTCCGGTT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4864A>T	chr8.hg19:g.144942558T>A	ENSP00000436337:p.Lys1622*	73.0	0.0		90.0	15.0	NM_031308	Q76E58|Q9NSU9	Nonsense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	T	44	11.034399	0.99506	.	.	ENSG00000227184	ENST00000525985	.	.	.	4.41	1.91	0.25777	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5429	0.39262	0.0:0.0:0.3414:0.6586	.	.	.	.	X	1622	.	ENSP00000436337:K1622X	K	-	1	0	EPPK1	145014546	0.817000	0.29147	0.537000	0.28052	0.847000	0.48162	1.977000	0.40589	0.204000	0.20548	0.482000	0.46254	AAG	.	.		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
SPATC1	375686	hgsc.bcm.edu	37	8	145095689	145095689	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145095689C>T	ENST00000377470.3	+	3	1089	c.987C>T	c.(985-987)tcC>tcT	p.S329S	SPATC1_ENST00000447830.2_Silent_p.S329S	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	329						centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ccaccacctcccccacggtca	0.677																																					p.S329S		Atlas-SNP	.											.	SPATC1	77	.	0			c.C987T						.						67.0	29.0	42.0					8																	145095689		2198	4289	6487	SO:0001819	synonymous_variant	375686	exon3			CACCTCCCCCACG	BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.987C>T	chr8.hg19:g.145095689C>T		134.0	0.0		125.0	40.0	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Silent	SNP	ENST00000377470.3	hg19	CCDS6413.2																																																																																			.	.		0.677	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572	
VPS28	51160	hgsc.bcm.edu	37	8	145649444	145649444	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145649444G>A	ENST00000526054.1	-	8	565	c.528C>T	c.(526-528)ggC>ggT	p.G176G	VPS28_ENST00000377348.2_Silent_p.G176G|VPS28_ENST00000529182.1_Silent_p.G176G|VPS28_ENST00000526734.1_5'Flank|VPS28_ENST00000292510.4_Silent_p.G176G			Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 homolog (S. cerevisiae)	176	VPS28 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00642}.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|negative regulation of protein ubiquitination (GO:0031397)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CCGTCTGGCGGCCCTCAAAGT	0.697																																					p.G176G		Atlas-SNP	.											.	VPS28	23	.	0			c.C528T						.						49.0	57.0	54.0					8																	145649444		2203	4298	6501	SO:0001819	synonymous_variant	51160	exon9			CTGGCGGCCCTCA	AF316887	CCDS6425.1, CCDS34967.1	8q24.3	2014-08-12	2006-04-04		ENSG00000160948	ENSG00000160948			18178	protein-coding gene	gene with protein product		611952	"""vacuolar protein sorting 28 (yeast)"""				Standard	NM_183057		Approved		uc003zct.1	Q9UK41	OTTHUMG00000165209	ENST00000526054.1:c.528C>T	chr8.hg19:g.145649444G>A		145.0	0.0		139.0	62.0	NM_016208	Q86VK0	Silent	SNP	ENST00000526054.1	hg19	CCDS6425.1																																																																																			.	.		0.697	VPS28-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382694.1		
FOXH1	8928	hgsc.bcm.edu	37	8	145700399	145700399	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145700399A>G	ENST00000377317.4	-	3	898	c.320T>C	c.(319-321)tTc>tCc	p.F107S	FOXH1_ENST00000525197.1_5'UTR	NM_003923.2	NP_003914.1	O75593	FOXH1_HUMAN	forkhead box H1	107					aorta morphogenesis (GO:0035909)|axial mesoderm development (GO:0048318)|cardiac right ventricle morphogenesis (GO:0003215)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|heart looping (GO:0001947)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|secondary heart field specification (GO:0003139)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular trabecula myocardium morphogenesis (GO:0003222)	activin responsive factor complex (GO:0032444)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|bHLH transcription factor binding (GO:0043425)|co-SMAD binding (GO:0070410)|enhancer binding (GO:0035326)|protein domain specific binding (GO:0019904)|R-SMAD binding (GO:0070412)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.76e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GACCGCCCAGAAGTTGCCCTT	0.677																																					p.F107S		Atlas-SNP	.											.	FOXH1	17	.	0			c.T320C						.						15.0	12.0	13.0					8																	145700399		2189	4271	6460	SO:0001583	missense	8928	exon3			GCCCAGAAGTTGC	AF076292	CCDS6428.1	8q24.3	2014-08-12			ENSG00000160973			"""Forkhead boxes"""	3814	protein-coding gene	gene with protein product		603621				9702198	Standard	NM_003923		Approved	FAST1	uc003zdc.3	O75593	OTTHUMG00000165172	ENST00000377317.4:c.320T>C	chr8.hg19:g.145700399A>G	ENSP00000366534:p.Phe107Ser	72.0	0.0		96.0	42.0	NM_003923	D3DWM4	Missense_Mutation	SNP	ENST00000377317.4	hg19	CCDS6428.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.267893	0.80469	.	.	ENSG00000160973	ENST00000377317;ENST00000292541	D	0.95588	-3.75	4.63	3.38	0.38709	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.96463	0.8846	M	0.69248	2.105	0.49915	D	0.999839	D	0.89917	1.0	D	0.77557	0.99	D	0.95942	0.8947	10	0.87932	D	0	-47.1348	8.3518	0.32307	0.6509:0.349:0.0:0.0	.	107	O75593	FOXH1_HUMAN	S	107;134	ENSP00000366534:F107S	ENSP00000292541:F134S	F	-	2	0	FOXH1	145671207	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.947000	0.63583	1.723000	0.51488	0.379000	0.24179	TTC	.	.		0.677	FOXH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382451.1		
LRRC14	9684	hgsc.bcm.edu	37	8	145746113	145746113	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145746113G>A	ENST00000292524.1	+	3	967	c.821G>A	c.(820-822)cGc>cAc	p.R274H	LRRC14_ENST00000529022.1_Missense_Mutation_p.R274H|RECQL4_ENST00000532237.1_5'Flank|RECQL4_ENST00000428558.2_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	274										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GACAACTTCCGCTACTTCCTT	0.632																																					p.R274H		Atlas-SNP	.											.	LRRC14	25	.	0			c.G821A						.						56.0	52.0	53.0					8																	145746113		2202	4300	6502	SO:0001583	missense	9684	exon4			ACTTCCGCTACTT	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.821G>A	chr8.hg19:g.145746113G>A	ENSP00000292524:p.Arg274His	18.0	0.0		19.0	9.0	NM_001272036	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.599259	0.46318	.	.	ENSG00000160959	ENST00000527730;ENST00000529022;ENST00000292524	T;T;T	0.53640	0.61;0.61;0.61	4.44	1.2	0.21068	.	0.165156	0.45606	D	0.000344	T	0.42854	0.1221	L	0.55990	1.75	0.20638	N	0.99987	D	0.69078	0.997	P	0.50708	0.648	T	0.24870	-1.0148	10	0.35671	T	0.21	.	2.9598	0.05889	0.1838:0.0:0.3831:0.4331	.	274	Q15048	LRC14_HUMAN	H	274	ENSP00000436452:R274H;ENSP00000434768:R274H;ENSP00000292524:R274H	ENSP00000292524:R274H	R	+	2	0	LRRC14	145716921	0.309000	0.24518	0.938000	0.37757	0.947000	0.59692	1.385000	0.34408	0.446000	0.26666	0.313000	0.20887	CGC	.	.		0.632	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
LRRC14	9684	hgsc.bcm.edu	37	8	145746554	145746554	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145746554T>C	ENST00000292524.1	+	4	1320	c.1174T>C	c.(1174-1176)Tgc>Cgc	p.C392R	LRRC14_ENST00000529022.1_Missense_Mutation_p.C392R	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	392										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCTGACTCAGTGCGCCAGTCT	0.607																																					p.C392R		Atlas-SNP	.											.	LRRC14	25	.	0			c.T1174C						.						79.0	68.0	71.0					8																	145746554		2203	4300	6503	SO:0001583	missense	9684	exon5			ACTCAGTGCGCCA	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.1174T>C	chr8.hg19:g.145746554T>C	ENSP00000292524:p.Cys392Arg	71.0	0.0		49.0	15.0	NM_001272036	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.821321	0.32237	.	.	ENSG00000160959	ENST00000529022;ENST00000292524	T;T	0.12984	2.63;2.63	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.42966	0.1226	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.52162	-0.8612	10	0.87932	D	0	.	11.9975	0.53212	0.0:0.0:0.0:1.0	.	392	Q15048	LRC14_HUMAN	R	392	ENSP00000434768:C392R;ENSP00000292524:C392R	ENSP00000292524:C392R	C	+	1	0	LRRC14	145717362	0.989000	0.36119	0.036000	0.18154	0.001000	0.01503	2.808000	0.47963	1.932000	0.55993	0.533000	0.62120	TGC	.	.		0.607	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
LRRC24	441381	hgsc.bcm.edu	37	8	145750253	145750253	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145750253A>G	ENST00000529415.2	-	2	223	c.106T>C	c.(106-108)Tgt>Cgt	p.C36R	LRRC14_ENST00000292524.1_3'UTR|LRRC24_ENST00000533758.1_Missense_Mutation_p.C36R			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	36	LRRNT.					integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			AGGGCGCCACACTCCACCGTG	0.746																																					p.C36R		Atlas-SNP	.											.	LRRC24	11	.	0			c.T106C						.						3.0	4.0	4.0					8																	145750253		1503	2917	4420	SO:0001583	missense	441381	exon2			CGCCACACTCCAC	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"""Immunoglobulin superfamily / I-set domain containing"""	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.106T>C	chr8.hg19:g.145750253A>G	ENSP00000434849:p.Cys36Arg	62.0	0.0		67.0	21.0	NM_001024678		Missense_Mutation	SNP	ENST00000529415.2	hg19	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677044	0.88445	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.53857	0.6;3.97	4.84	4.84	0.62591	Leucine-rich repeat-containing N-terminal (1);	0.059704	0.64402	D	0.000002	T	0.77445	0.4131	M	0.93854	3.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.82548	-0.0402	10	0.87932	D	0	.	10.7106	0.45982	1.0:0.0:0.0:0.0	.	36;36	G3V1D8;Q50LG9	.;LRC24_HUMAN	R	36	ENSP00000434849:C36R;ENSP00000435653:C36R	ENSP00000434849:C36R	C	-	1	0	LRRC24	145721061	1.000000	0.71417	0.989000	0.46669	0.682000	0.39822	3.478000	0.53158	2.022000	0.59522	0.533000	0.62120	TGT	.	.		0.746	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678	
C8orf82	414919	hgsc.bcm.edu	37	8	145752948	145752948	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:145752948C>T	ENST00000524821.1	-	3	644	c.429G>A	c.(427-429)gcG>gcA	p.A143A	C8orf82_ENST00000313465.5_3'UTR|LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	143										endometrium(1)|urinary_tract(1)	2						GCAGCAGGCGCGCCGGCTCGA	0.776																																					p.A143A		Atlas-SNP	.											.	C8orf82	7	.	0			c.G429A						.						1.0	2.0	2.0					8																	145752948		924	2176	3100	SO:0001819	synonymous_variant	414919	exon3			CAGGCGCGCCGGC		CCDS34970.1	8q24	2012-04-18			ENSG00000213563	ENSG00000213563			33826	protein-coding gene	gene with protein product						12477932	Standard	NM_001001795		Approved	MGC70857	uc003zdp.1	Q6P1X6	OTTHUMG00000165181	ENST00000524821.1:c.429G>A	chr8.hg19:g.145752948C>T		15.0	0.0		8.0	7.0	NM_001001795	Q6GMR2|Q6P2Q7	Silent	SNP	ENST00000524821.1	hg19	CCDS34970.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686159	0.29962	.	.	ENSG00000213563	ENST00000532827	.	.	.	3.96	-0.875	0.10628	.	0.118857	0.34932	U	0.003561	T	0.49609	0.1567	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.30327	-0.9982	6	0.31617	T	0.26	-11.1577	5.177	0.15141	0.5791:0.3077:0.0:0.1131	.	.	.	.	T	188	.	ENSP00000437092:A188T	A	-	1	0	C8orf82	145723756	0.009000	0.17119	0.857000	0.33713	0.944000	0.59088	0.076000	0.14712	-0.008000	0.14320	-0.262000	0.10625	GCG	.	.		0.776	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795	
ZNF517	340385	hgsc.bcm.edu	37	8	146033090	146033090	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:146033090C>T	ENST00000531720.1	+	4	834	c.789C>T	c.(787-789)tgC>tgT	p.C263C	ZNF517_ENST00000359971.3_Silent_p.C263C|ZNF517_ENST00000525105.1_Intron|ZNF517_ENST00000526178.1_Intron			Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CCTACGCATGCGGCGAGTGCG	0.697																																					p.C263C		Atlas-SNP	.											.	ZNF517	30	.	0			c.C789T						.						22.0	23.0	22.0					8																	146033090		2201	4298	6499	SO:0001819	synonymous_variant	340385	exon5			CGCATGCGGCGAG	AK096527	CCDS6434.1	8q24.3	2013-01-08				ENSG00000197363		"""Zinc fingers, C2H2-type"", ""-"""	27984	protein-coding gene	gene with protein product							Standard	NM_213605		Approved		uc003zed.1	Q6ZMY9		ENST00000531720.1:c.789C>T	chr8.hg19:g.146033090C>T		83.0	0.0		69.0	29.0	NM_213605		Silent	SNP	ENST00000531720.1	hg19	CCDS6434.1	.	.	.	.	.	.	.	.	.	.	C	0.046	-1.264883	0.01433	.	.	ENSG00000197363	ENST00000529429	.	.	.	2.37	-2.12	0.07165	.	.	.	.	.	T	0.52141	0.1716	.	.	.	0.53005	D	0.999962	.	.	.	.	.	.	T	0.45644	-0.9247	4	.	.	.	.	8.1165	0.30946	0.0:0.2622:0.0:0.7378	.	.	.	.	V	230	.	.	A	+	2	0	ZNF517	146003894	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.344000	0.02639	-0.443000	0.07180	0.462000	0.41574	GCG	.	.		0.697	ZNF517-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382642.1	XM_291261	
SMARCA2	6595	hgsc.bcm.edu	37	9	2047346	2047346	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:2047346C>A	ENST00000382203.1	+	5	1117	c.908C>A	c.(907-909)cCc>cAc	p.P303H	SMARCA2_ENST00000382194.1_Missense_Mutation_p.P303H|SMARCA2_ENST00000349721.2_Missense_Mutation_p.P303H|SMARCA2_ENST00000357248.2_Missense_Mutation_p.P303H|RP11-264I13.2_ENST00000426860.1_RNA			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	303					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		gccgcAGTGCCCGGGCCCTCA	0.801																																					p.P303H		Atlas-SNP	.											.	SMARCA2	313	.	0			c.C908A						.						4.0	5.0	4.0					9																	2047346		1937	3815	5752	SO:0001583	missense	6595	exon5			CAGTGCCCGGGCC	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.908C>A	chr9.hg19:g.2047346C>A	ENSP00000371638:p.Pro303His	367.0	0.0		358.0	17.0	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.505499	0.64410	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	D;D;T;D;D	0.87256	-2.23;-2.23;0.7;-2.23;-2.23	5.72	4.82	0.62117	.	0.844539	0.10410	N	0.677990	D	0.83514	0.5271	L	0.38175	1.15	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.75731	-0.3215	10	0.66056	D	0.02	-9.6039	14.4802	0.67576	0.0:0.9288:0.0:0.0712	.	303;303	P51531-2;P51531	.;SMCA2_HUMAN	H	303	ENSP00000265773:P303H;ENSP00000349788:P303H;ENSP00000392081:P303H;ENSP00000371638:P303H;ENSP00000371629:P303H	ENSP00000265773:P303H	P	+	2	0	SMARCA2	2037346	1.000000	0.71417	0.532000	0.27989	0.390000	0.30446	3.327000	0.52045	1.435000	0.47434	0.551000	0.68910	CCC	.	.		0.801	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
GLIS3	169792	hgsc.bcm.edu	37	9	4118184	4118184	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:4118184G>A	ENST00000324333.10	-	3	1022	c.829C>T	c.(829-831)Cgc>Tgc	p.R277C	GLIS3_ENST00000381971.3_Missense_Mutation_p.R432C	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	277					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TCCTCCAGGCGTTCGGTCTTG	0.726																																					p.R432C		Atlas-SNP	.											.	GLIS3	152	.	0			c.C1294T						.						6.0	8.0	7.0					9																	4118184		1687	3372	5059	SO:0001583	missense	169792	exon4			CCAGGCGTTCGGT	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.829C>T	chr9.hg19:g.4118184G>A	ENSP00000325494:p.Arg277Cys	114.0	0.0		111.0	42.0	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	hg19	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.688228	0.48097	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.11604	2.78;2.76	5.51	5.51	0.81932	.	0.000000	0.45606	D	0.000358	T	0.12518	0.0304	M	0.63428	1.95	0.37725	D	0.925057	B;B	0.21381	0.055;0.033	B;B	0.12156	0.007;0.003	T	0.04522	-1.0945	10	0.51188	T	0.08	.	8.7194	0.34432	0.0757:0.0:0.7731:0.1512	.	432;277	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	C	277;432	ENSP00000325494:R277C;ENSP00000371398:R432C	ENSP00000325494:R277C	R	-	1	0	GLIS3	4108184	0.998000	0.40836	1.000000	0.80357	0.688000	0.40055	3.821000	0.55700	2.583000	0.87209	0.655000	0.94253	CGC	.	.		0.726	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
RIC1	57589	hgsc.bcm.edu	37	9	5772941	5772941	+	Missense_Mutation	SNP	G	G	A	rs565348578		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:5772941G>A	ENST00000414202.2	+	25	4035	c.3844G>A	c.(3844-3846)Gtt>Att	p.V1282I	KIAA1432_ENST00000449720.2_Missense_Mutation_p.V1166I|KIAA1432_ENST00000418622.3_Missense_Mutation_p.V1203I	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		CTGGTGCATCGTTATAGGCCT	0.358													G|||	1	0.000199681	0.0	0.0	5008	,	,		17787	0.0		0.0	False		,,,				2504	0.001				p.V1282I		Atlas-SNP	.											.	KIAA1432	97	.	0			c.G3844A						.						114.0	107.0	110.0					9																	5772941		2203	4300	6503	SO:0001583	missense	57589	exon25			TGCATCGTTATAG																												ENST00000414202.2:c.3844G>A	chr9.hg19:g.5772941G>A	ENSP00000416696:p.Val1282Ile	93.0	0.0		88.0	35.0	NM_020829		Missense_Mutation	SNP	ENST00000414202.2	hg19	CCDS34982.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.92|11.92	1.781261|1.781261	0.31502|0.31502	.|.	.|.	ENSG00000107036|ENSG00000107036	ENST00000545641|ENST00000414202;ENST00000418622;ENST00000449720;ENST00000490816	.|.	.|.	.|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.125811	.|0.53938	.|D	.|0.000053	T|T	0.40322|0.40322	0.1112|0.1112	N|N	0.21583|0.21583	0.68|0.68	0.80722|0.80722	D|D	1|1	.|B;B	.|0.16166	.|0.016;0.016	.|B;B	.|0.09377	.|0.004;0.004	T|T	0.25606|0.25606	-1.0127|-1.0127	5|9	.|0.27785	.|T	.|0.31	-17.6829|-17.6829	9.3842|9.3842	0.38333|0.38333	0.1974:0.0:0.8026:0.0|0.1974:0.0:0.8026:0.0	.|.	.|1166;1282	.|B7ZM67;Q4ADV7	.|.;RIC1_HUMAN	H|I	1173|1282;1203;1166;101	.|.	.|ENSP00000416696:V1282I	R|V	+|+	2|1	0|0	KIAA1432|KIAA1432	5762941|5762941	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.991000|0.991000	0.79684|0.79684	3.349000|3.349000	0.52217|0.52217	2.590000|2.590000	0.87494|0.87494	0.555000|0.555000	0.69702|0.69702	CGT|GTT	.	.		0.358	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3		
MPDZ	8777	hgsc.bcm.edu	37	9	13192209	13192209	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:13192209C>T	ENST00000319217.7	-	15	2136	c.1889G>A	c.(1888-1890)tGc>tAc	p.C630Y	MPDZ_ENST00000381022.2_Missense_Mutation_p.C630Y|MPDZ_ENST00000381015.4_Missense_Mutation_p.C630Y|MPDZ_ENST00000447879.1_Missense_Mutation_p.C630Y|MPDZ_ENST00000536827.1_Missense_Mutation_p.C630Y|MPDZ_ENST00000546205.1_Missense_Mutation_p.C630Y|MPDZ_ENST00000541718.1_Missense_Mutation_p.C630Y	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	630	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TCGACGACAGCACACCATTGT	0.398																																					p.C630Y		Atlas-SNP	.											.	MPDZ	324	.	0			c.G1889A						.						132.0	123.0	126.0					9																	13192209		1926	4138	6064	SO:0001583	missense	8777	exon15			CGACAGCACACCA	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.1889G>A	chr9.hg19:g.13192209C>T	ENSP00000320006:p.Cys630Tyr	110.0	0.0		110.0	39.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	C	24.9	4.580177	0.86645	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13;1.13	5.77	5.77	0.91146	.	0.000000	0.49305	D	0.000160	T	0.71710	0.3372	M	0.86953	2.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.75838	-0.3176	10	0.87932	D	0	.	19.9915	0.97366	0.0:1.0:0.0:0.0	.	630;630;630	B7ZMI4;O75970-3;O75970-2	.;.;.	Y	630	ENSP00000320006:C630Y;ENSP00000439807:C630Y;ENSP00000370410:C630Y;ENSP00000444151:C630Y;ENSP00000415208:C630Y;ENSP00000370403:C630Y;ENSP00000446358:C630Y	ENSP00000320006:C630Y	C	-	2	0	MPDZ	13182209	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.487000	0.81328	2.723000	0.93209	0.655000	0.94253	TGC	.	.		0.398	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
ACO1	48	hgsc.bcm.edu	37	9	32450103	32450103	+	Silent	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:32450103C>G	ENST00000309951.6	+	21	2802	c.2664C>G	c.(2662-2664)gcC>gcG	p.A888A	ACO1_ENST00000379923.1_Silent_p.A888A|ACO1_ENST00000541043.1_Silent_p.A789A	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	888					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GCAAGATGGCCAAGTAGGAGA	0.607																																					p.A888A		Atlas-SNP	.											.	ACO1	149	.	0			c.C2664G						.						106.0	95.0	98.0					9																	32450103		2203	4300	6503	SO:0001819	synonymous_variant	48	exon21			GATGGCCAAGTAG	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.2664C>G	chr9.hg19:g.32450103C>G		163.0	0.0		130.0	60.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	hg19	CCDS6525.1																																																																																			.	.		0.607	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
UNC13B	10497	hgsc.bcm.edu	37	9	35399263	35399263	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35399263C>A	ENST00000378495.3	+	33	4155	c.3933C>A	c.(3931-3933)ccC>ccA	p.P1311P	UNC13B_ENST00000396787.1_Silent_p.P1323P|UNC13B_ENST00000378496.4_Silent_p.P1311P	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1311	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TTGTTCTGCCCCCACTCACTG	0.562																																					p.P1311P		Atlas-SNP	.											.	UNC13B	153	.	0			c.C3933A						.						190.0	167.0	175.0					9																	35399263		2203	4300	6503	SO:0001819	synonymous_variant	10497	exon33			TCTGCCCCCACTC	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3933C>A	chr9.hg19:g.35399263C>A		138.0	0.0		147.0	53.0	NM_006377	Q5VYM8	Silent	SNP	ENST00000378495.3	hg19	CCDS6579.1																																																																																			.	.		0.562	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
RUSC2	9853	hgsc.bcm.edu	37	9	35558293	35558293	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35558293G>A	ENST00000455600.1	+	7	3729	c.3160G>A	c.(3160-3162)Gcc>Acc	p.A1054T		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1054	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			TGGGCTCAAGGCCTTTGTACT	0.592																																					p.A1054T		Atlas-SNP	.											.	RUSC2	88	.	0			c.G3160A						.						102.0	89.0	94.0					9																	35558293		2203	4300	6503	SO:0001583	missense	9853	exon7			CTCAAGGCCTTTG	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.3160G>A	chr9.hg19:g.35558293G>A	ENSP00000393922:p.Ala1054Thr	64.0	0.0		53.0	11.0	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Missense_Mutation	SNP	ENST00000455600.1	hg19	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.019289	0.75275	.	.	ENSG00000198853	ENST00000361226;ENST00000455600	T;T	0.30182	1.54;1.54	5.72	2.75	0.32379	RUN (2);	0.235880	0.42053	D	0.000764	T	0.28366	0.0701	L	0.44542	1.39	0.47183	D	0.999348	B	0.31752	0.338	B	0.37015	0.239	T	0.05699	-1.0869	10	0.59425	D	0.04	-6.8154	9.9291	0.41512	0.0:0.1246:0.4483:0.4271	.	1054	Q8N2Y8	RUSC2_HUMAN	T	1054	ENSP00000355177:A1054T;ENSP00000393922:A1054T	ENSP00000355177:A1054T	A	+	1	0	RUSC2	35548293	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	2.263000	0.43293	0.283000	0.22279	0.655000	0.94253	GCC	.	.		0.592	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462	
CA9	768	hgsc.bcm.edu	37	9	35674060	35674060	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35674060T>G	ENST00000378357.4	+	1	208	c.104T>G	c.(103-105)gTc>gGc	p.V35G	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	35					bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CTGGTGCCTGTCCATCCCCAG	0.647																																					p.V35G		Atlas-SNP	.											.	CA9	48	.	0			c.T104G						.						61.0	56.0	57.0					9																	35674060		2203	4300	6503	SO:0001583	missense	768	exon1			TGCCTGTCCATCC	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.104T>G	chr9.hg19:g.35674060T>G	ENSP00000367608:p.Val35Gly	84.0	0.0		91.0	32.0	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	hg19	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	T	6.793	0.515345	0.12944	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.63417	-0.04	5.01	0.922	0.19408	.	1.897240	0.02339	N	0.074648	T	0.45558	0.1348	N	0.14661	0.345	0.29156	N	0.878054	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40365	-0.9567	10	0.72032	D	0.01	.	4.4005	0.11385	0.0:0.5452:0.1616:0.2932	.	35;35	F5H404;Q16790	.;CAH9_HUMAN	G	35	ENSP00000367608:V35G	ENSP00000367608:V35G	V	+	2	0	CA9	35664060	0.116000	0.22171	0.979000	0.43373	0.020000	0.10135	0.458000	0.21892	0.001000	0.14605	-2.130000	0.00343	GTC	.	.		0.647	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
TLN1	7094	hgsc.bcm.edu	37	9	35705588	35705588	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:35705588G>A	ENST00000314888.9	-	43	6046	c.5693C>T	c.(5692-5694)tCg>tTg	p.S1898L	TLN1_ENST00000540444.1_Intron|TLN1_ENST00000464379.1_Intron	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1898	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTTGGCCTCCGAGGCCAGACG	0.577																																					p.S1898L		Atlas-SNP	.											.	TLN1	185	.	0			c.C5693T						.						61.0	63.0	62.0					9																	35705588		2203	4299	6502	SO:0001583	missense	7094	exon43			GCCTCCGAGGCCA	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.5693C>T	chr9.hg19:g.35705588G>A	ENSP00000316029:p.Ser1898Leu	80.0	0.0		80.0	37.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	G	5.199	0.222180	0.09863	.	.	ENSG00000137076	ENST00000314888	T	0.14640	2.49	5.66	1.26	0.21427	Vinculin-binding site-containing domain (1);	0.834466	0.11111	N	0.598613	T	0.07369	0.0186	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39781	-0.9597	10	0.27082	T	0.32	-0.6165	5.1951	0.15232	0.3907:0.0:0.446:0.1633	.	1898	Q9Y490	TLN1_HUMAN	L	1898	ENSP00000316029:S1898L	ENSP00000316029:S1898L	S	-	2	0	TLN1	35695588	0.400000	0.25295	0.336000	0.25522	0.931000	0.56810	0.836000	0.27545	0.342000	0.23796	0.555000	0.69702	TCG	.	.		0.577	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
FRMPD1	22844	hgsc.bcm.edu	37	9	37707440	37707440	+	Silent	SNP	C	C	T	rs139243880	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:37707440C>T	ENST00000539465.1	+	3	722	c.129C>T	c.(127-129)ccC>ccT	p.P43P	FRMPD1_ENST00000377765.3_Silent_p.P43P|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	43						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CTGATGGGCCCGCCAGGAACC	0.498													C|||	2	0.000399361	0.0	0.0	5008	,	,		18943	0.0		0.001	False		,,,				2504	0.001				p.P43P		Atlas-SNP	.											.	FRMPD1	237	.	0			c.C129T						.	C		0,4406		0,0,2203	91.0	93.0	92.0		129	0.8	0.1	9	dbSNP_134	92	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FRMPD1	NM_014907.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		43/1579	37707440	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	22844	exon3			TGGGCCCGCCAGG	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.129C>T	chr9.hg19:g.37707440C>T		115.0	0.0		155.0	68.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	hg19	CCDS6612.1																																																																																			.	C|1.000;T|0.000		0.498	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
SLC25A51	92014	hgsc.bcm.edu	37	9	37888305	37888305	+	Nonsense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:37888305A>T	ENST00000377716.2	-	3	986	c.243T>A	c.(241-243)taT>taA	p.Y81*	SLC25A51_ENST00000242275.6_Nonsense_Mutation_p.Y81*|SLC25A51_ENST00000496760.1_Intron|SLC25A51_ENST00000380590.3_Nonsense_Mutation_p.Y81*|RP11-613M10.9_ENST00000540557.1_Intron			Q9H1U9	S2551_HUMAN	solute carrier family 25, member 51	81					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											GGATTCCACGATACAAATTTC	0.448																																					p.Y81X		Atlas-SNP	.											.	.	.	.	0			c.T243A						.						119.0	106.0	110.0					9																	37888305		2203	4300	6503	SO:0001587	stop_gained	92014	exon3			TCCACGATACAAA	BC008500	CCDS6614.1	9p13.3-p12	2013-05-22	2012-03-29	2012-03-29	ENSG00000122696	ENSG00000122696		"""Solute carriers"""	23323	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 1"""	MCART1		12477932	Standard	NM_033412		Approved	MGC14836, CG7943	uc004aav.2	Q9H1U9	OTTHUMG00000019935	ENST00000377716.2:c.243T>A	chr9.hg19:g.37888305A>T	ENSP00000366945:p.Tyr81*	144.0	0.0		159.0	52.0	NM_033412		Nonsense_Mutation	SNP	ENST00000377716.2	hg19	CCDS6614.1	.	.	.	.	.	.	.	.	.	.	.	41	8.893163	0.98992	.	.	ENSG00000122696	ENST00000380590;ENST00000377716;ENST00000242275	.	.	.	4.94	-3.85	0.04243	.	0.078063	0.53938	D	0.000059	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7727	0.69691	0.2702:0.0:0.7298:0.0	.	.	.	.	X	81	.	ENSP00000242275:Y81X	Y	-	3	2	MCART1	37878305	0.979000	0.34478	0.988000	0.46212	0.918000	0.54935	0.140000	0.16056	-0.554000	0.06150	-0.361000	0.07541	TAT	.	.		0.448	SLC25A51-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313746.1	NM_033412	
C9orf135	138255	hgsc.bcm.edu	37	9	72435841	72435841	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:72435841C>T	ENST00000377197.3	+	1	133	c.46C>T	c.(46-48)Caa>Taa	p.Q16*	C9orf135_ENST00000527647.1_Nonsense_Mutation_p.Q16*|C9orf135_ENST00000466872.2_3'UTR|C9orf135-AS1_ENST00000439418.1_lincRNA	NM_001010940.1	NP_001010940.1	Q5VTT2	CI135_HUMAN	chromosome 9 open reading frame 135	16						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						CGACAGGAAGCAACACTGGTT	0.592																																					p.Q16X		Atlas-SNP	.											.	C9orf135	25	.	0			c.C46T						.						76.0	66.0	69.0					9																	72435841		2203	4300	6503	SO:0001587	stop_gained	138255	exon1			AGGAAGCAACACT		CCDS35041.1	9q21.11	2013-06-07	2013-06-07	2013-06-07	ENSG00000204711	ENSG00000204711			31422	protein-coding gene	gene with protein product							Standard	XM_005251705		Approved		uc004ahl.3	Q5VTT2	OTTHUMG00000019985	ENST00000377197.3:c.46C>T	chr9.hg19:g.72435841C>T	ENSP00000366402:p.Gln16*	84.0	0.0		82.0	24.0	NM_001010940	A7E2U4|B2RN61	Nonsense_Mutation	SNP	ENST00000377197.3	hg19	CCDS35041.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.123022	0.56613	.	.	ENSG00000204711	ENST00000377197;ENST00000527647	.	.	.	4.5	-1.42	0.08913	.	1.087950	0.07217	N	0.860239	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-8.5176	10.4441	0.44483	0.1434:0.2605:0.5961:0.0	.	.	.	.	X	16	.	ENSP00000366402:Q16X	Q	+	1	0	C9orf135	71625661	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.284000	0.08422	-0.054000	0.13266	-0.176000	0.13171	CAA	.	.		0.592	C9orf135-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052591.1	NM_001010940	
ALDH1A1	216	hgsc.bcm.edu	37	9	75567885	75567885	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:75567885A>T	ENST00000297785.3	-	1	86	c.32T>A	c.(31-33)gTc>gAc	p.V11D	ALDH1A1_ENST00000482210.1_5'Flank|ALDH1A1_ENST00000376939.1_Missense_Mutation_p.V11D	NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	11					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	GGTGAGTAGGACAGGTAAGTC	0.418																																					p.V11D		Atlas-SNP	.											.	ALDH1A1	98	.	0			c.T32A						.						116.0	105.0	109.0					9																	75567885		2203	4299	6502	SO:0001583	missense	216	exon1			AGTAGGACAGGTA	K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"""Aldehyde dehydrogenases"""	402	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 1"""	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.32T>A	chr9.hg19:g.75567885A>T	ENSP00000297785:p.Val11Asp	136.0	0.0		142.0	51.0	NM_000689	O00768|Q5SYR1	Missense_Mutation	SNP	ENST00000297785.3	hg19	CCDS6644.1	.	.	.	.	.	.	.	.	.	.	A	5.234	0.228572	0.09916	.	.	ENSG00000165092	ENST00000297785;ENST00000376939;ENST00000428593;ENST00000419959;ENST00000446946	T;T;T;T	0.76060	-0.99;-0.34;-0.27;0.01	5.96	-11.3	0.00108	Aldehyde/histidinol dehydrogenase (1);	1.017990	0.07854	N	0.965112	T	0.51601	0.1684	N	0.03608	-0.345	0.23806	N	0.996792	B	0.18968	0.032	B	0.15484	0.013	T	0.50065	-0.8871	10	0.33141	T	0.24	.	24.0269	0.99987	0.0905:0.0:0.8261:0.0834	.	11	P00352	AL1A1_HUMAN	D	11;11;25;11;11	ENSP00000297785:V11D;ENSP00000366138:V11D;ENSP00000388026:V11D;ENSP00000401361:V11D	ENSP00000297785:V11D	V	-	2	0	ALDH1A1	74757705	0.125000	0.22332	0.001000	0.08648	0.118000	0.20060	-0.686000	0.05161	-2.366000	0.00606	-1.054000	0.02325	GTC	.	.		0.418	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1		
TLE4	7091	hgsc.bcm.edu	37	9	82333837	82333837	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:82333837A>T	ENST00000376552.2	+	15	2559	c.1541A>T	c.(1540-1542)gAc>gTc	p.D514V	TLE4_ENST00000376544.3_Missense_Mutation_p.D445V|TLE4_ENST00000265284.6_Missense_Mutation_p.D489V|TLE4_ENST00000376537.4_Missense_Mutation_p.D546V|TLE4_ENST00000376520.4_Missense_Mutation_p.D546V|TLE4_ENST00000376534.4_Missense_Mutation_p.D151V	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	514					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AAGGTCTGGGACATCAGCCAC	0.552																																					p.D514V		Atlas-SNP	.											.	TLE4	187	.	0			c.A1541T						.						109.0	108.0	109.0					9																	82333837		2203	4300	6503	SO:0001583	missense	7091	exon15			TCTGGGACATCAG	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"""WD repeat domain containing"""	11840	protein-coding gene	gene with protein product		605132	"""transducin-like enhancer of split 4, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.1541A>T	chr9.hg19:g.82333837A>T	ENSP00000365735:p.Asp514Val	122.0	0.0		151.0	66.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	A	33	5.290764	0.95546	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284	T;T;T;T;T;T	0.17370	2.28;2.28;2.28;2.28;2.28;2.28	6.07	6.07	0.98685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.49474	0.1559	M	0.87547	2.89	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.995;0.998;1.0;0.997	T	0.56613	-0.7950	10	0.87932	D	0	-27.0888	16.6288	0.85011	1.0:0.0:0.0:0.0	.	489;445;546;514	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	V	514;445;546;546;151;489	ENSP00000365735:D514V;ENSP00000365727:D445V;ENSP00000365703:D546V;ENSP00000365720:D546V;ENSP00000365717:D151V;ENSP00000265284:D489V	ENSP00000265284:D489V	D	+	2	0	TLE4	81523657	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.552	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607569	84607569	+	Silent	SNP	T	T	A	rs145735905	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:84607569T>A	ENST00000344803.2	+	4	2231	c.2184T>A	c.(2182-2184)atT>atA	p.I728I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	728					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAGAGAGAATTCATGGACCGT	0.488																																					p.I728I		Atlas-SNP	.											.	.	.	.	0			c.T2184A						.						70.0	62.0	65.0					9																	84607569		1852	4099	5951	SO:0001819	synonymous_variant	389763	exon4			GAGAATTCATGGA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2184T>A	chr9.hg19:g.84607569T>A		330.0	0.0		342.0	139.0	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	T|0.998;C|0.002		0.488	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
KIF27	55582	hgsc.bcm.edu	37	9	86495341	86495341	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:86495341A>G	ENST00000297814.2	-	11	2657	c.2514T>C	c.(2512-2514)gcT>gcC	p.A838A	KIF27_ENST00000376347.1_Silent_p.A229A|KIF27_ENST00000334204.2_Silent_p.A838A|KIF27_ENST00000413982.1_Intron	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	838					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						CTAGCTCATTAGCACGTTTCT	0.358																																					p.A838A		Atlas-SNP	.											.	KIF27	103	.	0			c.T2514C						.						211.0	189.0	197.0					9																	86495341		2203	4300	6503	SO:0001819	synonymous_variant	55582	exon11			CTCATTAGCACGT	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.2514T>C	chr9.hg19:g.86495341A>G		50.0	0.0		60.0	27.0	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Silent	SNP	ENST00000297814.2	hg19	CCDS6665.1																																																																																			.	.		0.358	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
SPATA31C2	645961	hgsc.bcm.edu	37	9	90747272	90747272	+	IGR	SNP	G	G	A	rs373582239		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:90747272G>A								U6 (134022 upstream) : U3 (241911 downstream)																							GAAGCCTTTCGGAGGAGGCGG	0.587																																					p.P227L		Atlas-SNP	.											.	.	.	.	0			c.C680T						.	G	LEU/PRO	2,1382		0,2,690	92.0	82.0	85.0		680	0.1	0.0	9		85	0,3182		0,0,1591	no	missense	FAM75C2	NM_001166137.1	98	0,2,2281	AA,AG,GG		0.0,0.1445,0.0438	probably-damaging	227/1135	90747272	2,4564	692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			CCTTTCGGAGGAG																													chr9.hg19:g.90747272G>A		103.0	0.0		106.0	42.0	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.587								
NXNL2	158046	hgsc.bcm.edu	37	9	91150438	91150438	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:91150438C>T	ENST00000375854.3	+	1	423	c.89C>T	c.(88-90)gCa>gTa	p.A30V	NXNL2_ENST00000487646.2_3'UTR|NXNL2_ENST00000375855.3_Missense_Mutation_p.A30V	NM_001161625.1	NP_001155097.1	Q5VZ03	NXNL2_HUMAN	nucleoredoxin-like 2	30	Thioredoxin.				photoreceptor cell maintenance (GO:0045494)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)					lung(3)	3						AAGGTGGTGGCACTGTACTTC	0.711																																					p.A30V		Atlas-SNP	.											.	NXNL2	13	.	0			c.C89T						.						32.0	36.0	34.0					9																	91150438		2200	4297	6497	SO:0001583	missense	158046	exon1			TGGTGGCACTGTA	BC022521	CCDS6679.1, CCDS55325.1	9q22.2	2008-02-05	2007-08-16	2007-08-16	ENSG00000130045	ENSG00000130045			30482	protein-coding gene	gene with protein product		615299	"""chromosome 9 open reading frame 121"""	C9orf121		12477932	Standard	NM_001161625		Approved		uc011ltj.2	Q5VZ03	OTTHUMG00000020170	ENST00000375854.3:c.89C>T	chr9.hg19:g.91150438C>T	ENSP00000365014:p.Ala30Val	171.0	0.0		122.0	50.0	NM_145283	B1AMD0|Q8TBG6	Missense_Mutation	SNP	ENST00000375854.3	hg19	CCDS55325.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.411271	0.83340	.	.	ENSG00000130045	ENST00000375854;ENST00000375855	T;T	0.80738	1.36;-1.41	3.95	3.0	0.34707	Thioredoxin-like fold (2);	0.194164	0.42420	D	0.000702	T	0.77136	0.4086	L	0.33293	1	0.44024	D	0.996742	P;D	0.62365	0.669;0.991	B;P	0.53593	0.355;0.73	T	0.75402	-0.3330	10	0.36615	T	0.2	-9.6255	10.7547	0.46230	0.0:0.5395:0.4605:0.0	.	30;30	Q5VZ03;Q5VZ03-3	NXNL2_HUMAN;.	V	30	ENSP00000365014:A30V;ENSP00000365015:A30V	ENSP00000365014:A30V	A	+	2	0	NXNL2	90340258	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	4.960000	0.63673	2.040000	0.60383	0.491000	0.48974	GCA	.	.		0.711	NXNL2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145283	
S1PR3	1903	hgsc.bcm.edu	37	9	91617238	91617238	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:91617238A>T	ENST00000375846.3	+	1	5818	c.1123A>T	c.(1123-1125)Atc>Ttc	p.I375F	S1PR3_ENST00000358157.2_Missense_Mutation_p.I375F			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	375					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						TCAGAATGGGATCTTCTGCAA	0.557																																					p.I375F		Atlas-SNP	.											.	S1PR3	49	.	0			c.A1123T						.						68.0	65.0	66.0					9																	91617238		2203	4300	6503	SO:0001583	missense	1903	exon2			AATGGGATCTTCT	AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3167	protein-coding gene	gene with protein product	"""sphingosine-1-phosphate receptor 3"""	601965	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"""	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.1123A>T	chr9.hg19:g.91617238A>T	ENSP00000365006:p.Ile375Phe	92.0	0.0		103.0	40.0	NM_005226	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	hg19	CCDS6680.1	.	.	.	.	.	.	.	.	.	.	A	7.650	0.682612	0.14907	.	.	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.68903	-0.36;-0.36	5.07	-1.31	0.09230	.	0.891383	0.09228	N	0.831015	T	0.44644	0.1303	N	0.14661	0.345	0.23192	N	0.998142	B	0.26400	0.148	B	0.24541	0.054	T	0.30387	-0.9980	10	0.54805	T	0.06	.	5.8187	0.18516	0.587:0.1298:0.2832:0.0	.	375	Q99500	S1PR3_HUMAN	F	375	ENSP00000350878:I375F;ENSP00000365006:I375F	ENSP00000350878:I375F	I	+	1	0	S1PR3	90807058	0.072000	0.21174	0.280000	0.24747	0.027000	0.11550	0.123000	0.15708	-0.386000	0.07821	0.402000	0.26972	ATC	.	.		0.557	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226	
IARS	3376	hgsc.bcm.edu	37	9	95021242	95021242	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:95021242T>C	ENST00000375643.3	-	19	2176	c.1910A>G	c.(1909-1911)aAc>aGc	p.N637S	IARS_ENST00000443024.2_Missense_Mutation_p.N637S|IARS_ENST00000447699.2_Missense_Mutation_p.N527S|IARS_ENST00000375629.3_5'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	637					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	AAAGCGGAGGTTTTCTGCTCT	0.433																																					p.N637S		Atlas-SNP	.											.	IARS	74	.	0			c.A1910G						.						77.0	70.0	72.0					9																	95021242		2203	4300	6503	SO:0001583	missense	3376	exon19			CGGAGGTTTTCTG	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.1910A>G	chr9.hg19:g.95021242T>C	ENSP00000364794:p.Asn637Ser	86.0	0.0		78.0	33.0	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	hg19	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.045461	0.36085	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660	T;T;T	0.21031	2.03;2.03;2.03	5.45	5.45	0.79879	Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	T	0.25717	0.0626	M	0.69463	2.115	0.80722	D	1	B;B	0.32653	0.226;0.379	B;B	0.37091	0.241;0.241	T	0.04481	-1.0948	10	0.09338	T	0.73	-26.181	15.1695	0.72858	0.0:0.0:0.0:1.0	.	637;482	P41252;Q6P0M4	SYIC_HUMAN;.	S	637;637;527;637	ENSP00000364794:N637S;ENSP00000406448:N637S;ENSP00000415020:N527S	ENSP00000364794:N637S	N	-	2	0	IARS	94061063	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.004000	0.70709	2.072000	0.62099	0.459000	0.35465	AAC	.	.		0.433	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161	
ECM2	1842	hgsc.bcm.edu	37	9	95263292	95263292	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:95263292C>T	ENST00000344604.5	-	9	1797	c.1648G>A	c.(1648-1650)Gtc>Atc	p.V550I	ECM2_ENST00000444490.2_Missense_Mutation_p.V528I|CENPP_ENST00000375587.3_Intron	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	550					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						TAGGACGGGACGTGATAGAGC	0.483																																					p.V550I		Atlas-SNP	.											.	ECM2	147	.	0			c.G1648A						.						141.0	129.0	133.0					9																	95263292		2203	4300	6503	SO:0001583	missense	1842	exon9			ACGGGACGTGATA	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.1648G>A	chr9.hg19:g.95263292C>T	ENSP00000344758:p.Val550Ile	159.0	0.0		147.0	50.0	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	hg19	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.439466	0.83885	.	.	ENSG00000106823	ENST00000444490;ENST00000344604	T;T	0.20332	2.08;5.7	5.35	5.35	0.76521	.	0.115628	0.64402	D	0.000016	T	0.37571	0.1008	L	0.39566	1.225	0.80722	D	1	D;D;D	0.69078	0.996;0.997;0.997	D;D;D	0.67103	0.949;0.945;0.946	T	0.01500	-1.1339	10	0.27785	T	0.31	.	19.4519	0.94871	0.0:1.0:0.0:0.0	.	550;528;528	O94769;B4DK93;O94769-2	ECM2_HUMAN;.;.	I	528;550	ENSP00000393971:V528I;ENSP00000344758:V550I	ENSP00000344758:V550I	V	-	1	0	ECM2	94303113	1.000000	0.71417	0.926000	0.36857	0.751000	0.42716	5.740000	0.68629	2.676000	0.91093	0.591000	0.81541	GTC	.	.		0.483	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
ZNF510	22869	hgsc.bcm.edu	37	9	99521523	99521523	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:99521523T>G	ENST00000375231.1	-	6	2239	c.1589A>C	c.(1588-1590)aAc>aCc	p.N530T	ZNF510_ENST00000223428.4_Missense_Mutation_p.N530T			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	530					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)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TATTCTGAGGTTTGACTTCTG	0.403																																					p.N530T		Atlas-SNP	.											.	ZNF510	59	.	0			c.A1589C						.						161.0	161.0	161.0					9																	99521523		2203	4300	6503	SO:0001583	missense	22869	exon6			CTGAGGTTTGACT	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"""Zinc fingers, C2H2-type"", ""-"""	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.1589A>C	chr9.hg19:g.99521523T>G	ENSP00000364379:p.Asn530Thr	101.0	0.0		91.0	6.0	NM_014930	Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	hg19	CCDS35074.1	.	.	.	.	.	.	.	.	.	.	T	8.090	0.774401	0.16051	.	.	ENSG00000081386	ENST00000375231;ENST00000223428	T;T	0.22134	1.97;1.97	3.02	0.676	0.17958	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09555	0.0235	N	0.12961	0.28	0.09310	N	1	B	0.33103	0.397	B	0.29353	0.101	T	0.33727	-0.9857	9	0.21014	T	0.42	.	6.0406	0.19732	0.0:0.2425:0.0:0.7575	.	530	Q9Y2H8	ZN510_HUMAN	T	530	ENSP00000364379:N530T;ENSP00000223428:N530T	ENSP00000223428:N530T	N	-	2	0	ZNF510	98561344	0.000000	0.05858	0.923000	0.36655	0.978000	0.69477	0.141000	0.16076	0.120000	0.18254	0.533000	0.62120	AAC	.	.		0.403	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930	
ZNF782	158431	hgsc.bcm.edu	37	9	99580289	99580289	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:99580289T>C	ENST00000481138.1	-	6	2677	c.2016A>G	c.(2014-2016)aaA>aaG	p.K672K	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Silent_p.K540K	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	672					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				ATTTATAGGGTTTCTCCCCTG	0.413																																					p.K672K		Atlas-SNP	.											.	ZNF782	64	.	0			c.A2016G						.						101.0	102.0	102.0					9																	99580289		2203	4300	6503	SO:0001819	synonymous_variant	158431	exon6			ATAGGGTTTCTCC	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.2016A>G	chr9.hg19:g.99580289T>C		166.0	0.0		160.0	10.0	NM_001001662	B2RNR0	Silent	SNP	ENST00000481138.1	hg19	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	t	7.291	0.611092	0.14066	.	.	ENSG00000196597	ENST00000289032	.	.	.	2.64	0.247	0.15521	.	.	.	.	.	T	0.51466	0.1676	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38067	-0.9678	4	.	.	.	.	5.8842	0.18872	0.0:0.2581:0.0:0.7419	.	.	.	.	A	661	.	.	T	-	1	0	ZNF782	98620110	0.001000	0.12720	0.991000	0.47740	0.996000	0.88848	-0.239000	0.08965	0.028000	0.15324	0.533000	0.62120	ACC	.	.		0.413	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
INVS	27130	hgsc.bcm.edu	37	9	103054739	103054739	+	Missense_Mutation	SNP	C	C	T	rs370949695		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:103054739C>T	ENST00000262457.2	+	14	2385	c.2200C>T	c.(2200-2202)Cgg>Tgg	p.R734W	INVS_ENST00000541287.1_Missense_Mutation_p.R638W|INVS_ENST00000262456.2_Intron	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	734					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				TGGCGATGAGCGGTGTGCAAA	0.577																																					p.R734W		Atlas-SNP	.											INVS,NS,carcinoma,0,1	INVS	81	.	0			c.C2200T						.	C	TRP/ARG,	1,4405	2.1+/-5.4	0,1,2202	67.0	56.0	60.0		2200,	3.7	0.0	9		60	0,8600		0,0,4300	no	missense,intron	INVS	NM_014425.2,NM_183245.1	101,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,	734/1066,	103054739	1,13005	2203	4300	6503	SO:0001583	missense	27130	exon14			GATGAGCGGTGTG	AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"""Ankyrin repeat domain containing"""	17870	protein-coding gene	gene with protein product	"""nephrocystin 2"""	243305	"""nephronophthisis 2 (infantile)"""	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.2200C>T	chr9.hg19:g.103054739C>T	ENSP00000262457:p.Arg734Trp	250.0	0.0		223.0	91.0	NM_014425	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Missense_Mutation	SNP	ENST00000262457.2	hg19	CCDS6746.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.686349	0.47991	2.27E-4	0.0	ENSG00000119509	ENST00000262457;ENST00000541287	T;T	0.41065	1.01;1.03	5.55	3.69	0.42338	.	1.744500	0.02657	N	0.107102	T	0.38799	0.1054	N	0.24115	0.695	0.09310	N	1	D;D	0.65815	0.995;0.964	P;B	0.46975	0.533;0.232	T	0.27640	-1.0068	10	0.72032	D	0.01	.	7.2451	0.26117	0.1671:0.7459:0.0:0.087	.	638;734	F5GZH2;Q9Y283	.;INVS_HUMAN	W	734;638	ENSP00000262457:R734W;ENSP00000444454:R638W	ENSP00000262457:R734W	R	+	1	2	INVS	102094560	0.055000	0.20627	0.011000	0.14972	0.199000	0.23934	4.128000	0.57951	0.680000	0.31366	0.650000	0.86243	CGG	.	.		0.577	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425	
PLPPR1	54886	hgsc.bcm.edu	37	9	104079724	104079724	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:104079724A>G	ENST00000374874.3	+	7	1330	c.891A>G	c.(889-891)gtA>gtG	p.V297V	LPPR1_ENST00000395056.2_Silent_p.V297V	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		297					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										CCCGTGGAGTACCCCTAATGG	0.483																																					p.V297V		Atlas-SNP	.											.	.	.	.	0			c.A891G						.						122.0	129.0	127.0					9																	104079724		2203	4300	6503	SO:0001819	synonymous_variant	0	exon7			TGGAGTACCCCTA																												ENST00000374874.3:c.891A>G	chr9.hg19:g.104079724A>G		196.0	0.0		155.0	62.0	NM_207299	Q5VX23|Q9NXE2	Silent	SNP	ENST00000374874.3	hg19	CCDS6751.1																																																																																			.	.		0.483	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
GRIN3A	116443	hgsc.bcm.edu	37	9	104340102	104340102	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:104340102A>T	ENST00000361820.3	-	8	3556	c.2956T>A	c.(2956-2958)Tca>Aca	p.S986T		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	986	PPP2CB binding site. {ECO:0000250}.				calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	TCTATAAATGATGTATTTATT	0.368																																					p.S986T		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2956A						.						147.0	140.0	142.0					9																	104340102		2203	4300	6503	SO:0001583	missense	116443	exon8			TAAATGATGTATT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2956T>A	chr9.hg19:g.104340102A>T	ENSP00000355155:p.Ser986Thr	63.0	0.0		45.0	12.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	A	8.832	0.940030	0.18281	.	.	ENSG00000198785	ENST00000361820	T	0.10477	2.87	5.64	5.64	0.86602	.	0.386476	0.24056	N	0.041955	T	0.10252	0.0251	L	0.39898	1.24	0.38326	D	0.943667	B	0.11235	0.004	B	0.08055	0.003	T	0.13098	-1.0522	10	0.09084	T	0.74	.	15.8494	0.78916	1.0:0.0:0.0:0.0	.	986	Q8TCU5	NMD3A_HUMAN	T	986	ENSP00000355155:S986T	ENSP00000355155:S986T	S	-	1	0	GRIN3A	103379923	0.999000	0.42202	0.999000	0.59377	0.996000	0.88848	3.981000	0.56902	2.148000	0.66965	0.533000	0.62120	TCA	.	.		0.368	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
KIAA0368	23392	hgsc.bcm.edu	37	9	114176260	114176260	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:114176260G>A	ENST00000338205.5	-	19	2213	c.1994C>T	c.(1993-1995)cCg>cTg	p.P665L	RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Missense_Mutation_p.P843L			Q5VYK3	ECM29_HUMAN	KIAA0368	671					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GTACATAACCGGCAAACCTAA	0.353																																					p.P843L		Atlas-SNP	.											.	KIAA0368	144	.	0			c.C2528T						.						60.0	51.0	54.0					9																	114176260		1834	4087	5921	SO:0001583	missense	23392	exon21			ATAACCGGCAAAC	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1994C>T	chr9.hg19:g.114176260G>A	ENSP00000339889:p.Pro665Leu	80.0	0.0		91.0	23.0	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	hg19		.	.	.	.	.	.	.	.	.	.	G	12.49	1.953603	0.34471	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.63417	-0.04	5.53	5.53	0.82687	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.51160	0.1658	L	0.44542	1.39	0.80722	D	1	B;B	0.32731	0.382;0.27	B;B	0.20384	0.029;0.015	T	0.51076	-0.8751	10	0.36615	T	0.2	.	14.3268	0.66526	0.0:0.0:0.8516:0.1484	.	671;140	Q5VYK3;B3KXF2	ECM29_HUMAN;.	L	665;843;140	ENSP00000259335:P843L	ENSP00000259335:P843L	P	-	2	0	KIAA0368	113216081	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.126000	0.77201	2.607000	0.88179	0.563000	0.77884	CCG	.	.		0.353	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
SLC46A2	57864	hgsc.bcm.edu	37	9	115648748	115648748	+	Silent	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:115648748A>T	ENST00000374228.4	-	3	1593	c.1362T>A	c.(1360-1362)atT>atA	p.I454I	RP11-408O19.5_ENST00000605480.1_RNA	NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	454					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						ACCTAATTGGAATGATGGCCA	0.517																																					p.I454I		Atlas-SNP	.											.	SLC46A2	30	.	0			c.T1362A						.						111.0	106.0	108.0					9																	115648748		2203	4300	6503	SO:0001819	synonymous_variant	57864	exon3			AATTGGAATGATG	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"""Solute carriers"""	16055	protein-coding gene	gene with protein product		608956	"""thymic stromal co-transporter"""	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.1362T>A	chr9.hg19:g.115648748A>T		148.0	0.0		164.0	60.0	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	hg19	CCDS6786.1																																																																																			.	.		0.517	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051	
ALAD	210	hgsc.bcm.edu	37	9	116153902	116153902	+	Splice_Site	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:116153902A>G	ENST00000409155.3	-	4	362	c.166T>C	c.(166-168)Tat>Cat	p.Y56H	ALAD_ENST00000482001.1_5'UTR|ALAD_ENST00000277315.5_Splice_Site_p.Y39H	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	56					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	TTCACACCATACCTGTGTGGG	0.587																																					p.Y56H		Atlas-SNP	.											.	ALAD	36	.	0			c.T166C						.						65.0	61.0	62.0					9																	116153902		2203	4300	6503	SO:0001630	splice_region_variant	210	exon4			CACCATACCTGTG	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"""porphobilinogen synthase"""	125270	"""aminolevulinate, delta-, dehydratase"""			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.165-1T>C	chr9.hg19:g.116153902A>G		79.0	0.0		64.0	28.0	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	hg19	CCDS6794.2	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184733	0.78677	.	.	ENSG00000148218	ENST00000409155;ENST00000277315;ENST00000448137	D;D;D	0.87179	-2.22;-2.16;-2.22	5.65	5.65	0.86999	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.86343	0.5910	L	0.49778	1.585	0.80722	D	1	B;B;B	0.26935	0.015;0.054;0.164	B;B;B	0.37304	0.115;0.086;0.246	T	0.82798	-0.0279	10	0.28530	T	0.3	-7.3993	15.072	0.72046	1.0:0.0:0.0:0.0	.	56;39;85	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	H	56;39;65	ENSP00000386284:Y56H;ENSP00000277315:Y39H;ENSP00000392748:Y65H	ENSP00000277315:Y39H	Y	-	1	0	ALAD	115193723	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	6.741000	0.74837	2.146000	0.66826	0.533000	0.62120	TAT	.	.		0.587	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945	Missense_Mutation
FBXW2	26190	hgsc.bcm.edu	37	9	123533666	123533666	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:123533666C>T	ENST00000608872.1	-	7	1223	c.1036G>A	c.(1036-1038)Ggt>Agt	p.G346S	FBXW2_ENST00000493559.1_5'UTR|FBXW2_ENST00000340778.5_Missense_Mutation_p.G281S	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	346					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						TGGTAGAGACCAAGTGCTGAA	0.423																																					p.G346S		Atlas-SNP	.											.	FBXW2	34	.	0			c.G1036A						.						98.0	89.0	92.0					9																	123533666		1903	4127	6030	SO:0001583	missense	26190	exon7			AGAGACCAAGTGC	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13608	protein-coding gene	gene with protein product		609071	"""F-box and WD-40 domain protein 2"""			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1036G>A	chr9.hg19:g.123533666C>T	ENSP00000476369:p.Gly346Ser	108.0	0.0		98.0	33.0	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	hg19	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983146	0.74474	.	.	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833	T;T	0.24350	1.86;1.86	5.77	5.77	0.91146	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.093477	0.85682	D	0.000000	T	0.45577	0.1349	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.994;0.997;0.997	T	0.05903	-1.0857	10	0.15499	T	0.54	-10.6657	17.8518	0.88748	0.0:1.0:0.0:0.0	.	281;346;346	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	S	346;281;346	ENSP00000363036:G346S;ENSP00000341161:G281S	ENSP00000341161:G281S	G	-	1	0	FBXW2	122573487	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	GGT	.	.		0.423	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2		
DAB2IP	153090	hgsc.bcm.edu	37	9	124534910	124534910	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:124534910G>A	ENST00000408936.3	+	12	2285	c.2103G>A	c.(2101-2103)ccG>ccA	p.P701P	DAB2IP_ENST00000259371.2_Silent_p.P673P|DAB2IP_ENST00000309989.1_Silent_p.P577P			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	701	Necessary for interaction with AKT1.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CCCGGTTACCGTCTCCAACCC	0.557																																					p.P673P		Atlas-SNP	.											DAB2IP_ENST00000259371,NS,carcinoma,0,2	DAB2IP	150	.	0			c.G2019A						.						101.0	96.0	98.0					9																	124534910		2203	4300	6503	SO:0001819	synonymous_variant	153090	exon12			GTTACCGTCTCCA	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"""nGAP-like protein"", ""DOC-2/DAB2 interactive protein"", ""ASK-interacting protein"", ""ASK1-interacting protein 1"""	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.2103G>A	chr9.hg19:g.124534910G>A		95.0	0.0		80.0	27.0	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Silent	SNP	ENST00000408936.3	hg19																																																																																				.	.		0.557	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552	
ANGPTL2	23452	hgsc.bcm.edu	37	9	129854031	129854031	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:129854031G>A	ENST00000373425.3	-	4	1817	c.1200C>T	c.(1198-1200)taC>taT	p.Y400Y	RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000424082.2_Intron|ANGPTL2_ENST00000373417.1_Silent_p.Y98Y|RALGPS1_ENST00000394022.3_Intron|RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000373434.1_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	400	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CATTGCCATGGTAGCGCCCCA	0.542																																					p.Y400Y		Atlas-SNP	.											.	ANGPTL2	46	.	0			c.C1200T						.						175.0	173.0	173.0					9																	129854031		2203	4300	6503	SO:0001819	synonymous_variant	23452	exon4			GCCATGGTAGCGC	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"""Fibrinogen C domain containing"""	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.1200C>T	chr9.hg19:g.129854031G>A		110.0	0.0		99.0	32.0	NM_012098	Q5JT58|Q8NCH7	Silent	SNP	ENST00000373425.3	hg19	CCDS6868.1																																																																																			.	.		0.542	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098	
GARNL3	84253	hgsc.bcm.edu	37	9	130027161	130027161	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:130027161T>C	ENST00000373387.4	+	1	357	c.5T>C	c.(4-6)gTa>gCa	p.V2A	GARNL3_ENST00000435213.2_Intron|GARNL3_ENST00000314904.5_Missense_Mutation_p.V2A	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	2					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						TTGCAAATGGTAGTTGATTTT	0.502																																					p.V2A		Atlas-SNP	.											.	GARNL3	83	.	0			c.T5C						.						136.0	134.0	135.0					9																	130027161		2203	4300	6503	SO:0001583	missense	84253	exon1			AAATGGTAGTTGA	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 3"""			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.5T>C	chr9.hg19:g.130027161T>C	ENSP00000362485:p.Val2Ala	129.0	0.0		113.0	47.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	hg19	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	T	12.62	1.992302	0.35131	.	.	ENSG00000136895	ENST00000314904;ENST00000373387	D;D	0.87650	-2.28;-2.26	5.35	4.19	0.49359	.	.	.	.	.	T	0.71160	0.3307	N	0.08118	0	0.21527	N	0.99965	B	0.02656	0.0	B	0.04013	0.001	T	0.56486	-0.7971	8	.	.	.	.	6.0035	0.19533	0.0:0.0825:0.3214:0.5961	.	2	Q5VVW2	GARL3_HUMAN	A	2	ENSP00000313970:V2A;ENSP00000362485:V2A	.	V	+	2	0	GARNL3	129066982	1.000000	0.71417	0.972000	0.41901	0.991000	0.79684	1.451000	0.35145	0.840000	0.34995	0.529000	0.55759	GTA	.	.		0.502	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293	
CDK9	1025	hgsc.bcm.edu	37	9	130551527	130551527	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:130551527T>C	ENST00000373264.4	+	7	924	c.824T>C	c.(823-825)gTg>gCg	p.V275A	CDK9_ENST00000373265.2_Missense_Mutation_p.V392A	NM_001261.3	NP_001252.1	P50750	CDK9_HUMAN	cyclin-dependent kinase 9	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|DNA repair (GO:0006281)|gene expression (GO:0010467)|negative regulation of cell cycle arrest (GO:0071157)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of DNA repair (GO:0006282)|regulation of histone modification (GO:0031056)|replication fork arrest (GO:0043111)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|positive transcription elongation factor complex b (GO:0008024)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA binding (GO:0003677)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			lung(1)	1						AAGCGGAAGGTGAAGGACAGG	0.587																																					p.V275A		Atlas-SNP	.											.	CDK9	22	.	0			c.T824C						.						160.0	100.0	120.0					9																	130551527		2203	4300	6503	SO:0001583	missense	1025	exon7			GGAAGGTGAAGGA	L25676	CCDS6879.1	9q34.1	2011-11-08	2007-11-21		ENSG00000136807	ENSG00000136807		"""Cyclin-dependent kinases"""	1780	protein-coding gene	gene with protein product		603251	"""cyclin-dependent kinase 9 (CDC2-related kinase)"""	CDC2L4		8170997, 9356449	Standard	NM_001261		Approved	PITALRE, C-2k, TAK	uc004bse.2	P50750	OTTHUMG00000020715	ENST00000373264.4:c.824T>C	chr9.hg19:g.130551527T>C	ENSP00000362361:p.Val275Ala	93.0	0.0		109.0	45.0	NM_001261	Q5JU24|Q5JU25|Q5U006|Q96TF1	Missense_Mutation	SNP	ENST00000373264.4	hg19	CCDS6879.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.788860	0.90367	.	.	ENSG00000136807	ENST00000373265;ENST00000373264	T;T	0.43294	0.95;0.95	5.43	5.43	0.79202	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	0.85682	D	0.000000	T	0.51924	0.1703	N	0.25426	0.745	0.80722	D	1	D	0.63880	0.993	D	0.75484	0.986	T	0.56709	-0.7934	10	0.87932	D	0	-13.9615	14.633	0.68671	0.0:0.0:0.0:1.0	.	275	P50750	CDK9_HUMAN	A	392;275	ENSP00000362362:V392A;ENSP00000362361:V275A	ENSP00000362361:V275A	V	+	2	0	CDK9	129591348	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.798000	0.85924	2.058000	0.61347	0.482000	0.46254	GTG	.	.		0.587	CDK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054235.1		
NAIF1	203245	hgsc.bcm.edu	37	9	130829075	130829075	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:130829075G>A	ENST00000373078.4	-	1	525	c.306C>T	c.(304-306)gaC>gaT	p.D102D	SLC25A25_ENST00000373068.2_5'Flank|NAIF1_ENST00000488519.1_5'Flank|SLC25A25_ENST00000373069.5_5'Flank	NM_197956.3	NP_931045.1	Q69YI7	NAIF1_HUMAN	nuclear apoptosis inducing factor 1	102	Gly-rich.				negative regulation of cell growth (GO:0030308)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CCCCAGCTCCGTCCTCCTCAG	0.682																																					p.D102D		Atlas-SNP	.											.	NAIF1	36	.	0			c.C306T						.						33.0	35.0	34.0					9																	130829075		2200	4298	6498	SO:0001819	synonymous_variant	203245	exon1			AGCTCCGTCCTCC	AK122729	CCDS6889.1	9q34.11	2008-04-10	2008-04-10	2008-04-10	ENSG00000171169	ENSG00000171169			25446	protein-coding gene	gene with protein product	"""nuclear apoptosis-inducing factor 1"""	610673	"""chromosome 9 open reading frame 90"""	C9orf90		14702039, 16378748	Standard	NM_197956		Approved	DKFZp762G199, bA379C10.2	uc004bta.3	Q69YI7	OTTHUMG00000020727	ENST00000373078.4:c.306C>T	chr9.hg19:g.130829075G>A		90.0	0.0		72.0	29.0	NM_197956	B3KV81|Q8WU12	Silent	SNP	ENST00000373078.4	hg19	CCDS6889.1																																																																																			.	.		0.682	NAIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054330.1	NM_197956	
USP20	10868	hgsc.bcm.edu	37	9	132637022	132637022	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:132637022C>T	ENST00000315480.4	+	18	2066	c.1908C>T	c.(1906-1908)caC>caT	p.H636H	USP20_ENST00000358355.1_Silent_p.H636H|USP20_ENST00000372429.3_Silent_p.H636H			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	636	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				TCTGCCACCACGGCACGGCAG	0.657																																					p.H636H		Atlas-SNP	.											.	USP20	186	.	0			c.C1908T						.						77.0	84.0	81.0					9																	132637022		2146	4245	6391	SO:0001819	synonymous_variant	10868	exon18			CCACCACGGCACG	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1908C>T	chr9.hg19:g.132637022C>T		90.0	0.0		78.0	33.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	hg19	CCDS43892.1																																																																																			.	.		0.657	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
PRRC2B	84726	hgsc.bcm.edu	37	9	134353960	134353960	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:134353960G>A	ENST00000357304.4	+	17	4767	c.4712G>A	c.(4711-4713)cGc>cAc	p.R1571H	PRRC2B_ENST00000405995.1_Missense_Mutation_p.R877H|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.R877H	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1571							poly(A) RNA binding (GO:0044822)	p.R1571H(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AAGAAGCAGCGCCGCCTGCTG	0.637											OREG0019562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1571H		Atlas-SNP	.											PRRC2B_ENST00000357304,rectum,carcinoma,0,2	PRRC2B	266	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4712A						.						67.0	74.0	72.0					9																	134353960		1880	4109	5989	SO:0001583	missense	84726	exon17			AGCAGCGCCGCCT	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4712G>A	chr9.hg19:g.134353960G>A	ENSP00000349856:p.Arg1571His	114.0	0.0	1610	93.0	46.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.908653	0.92107	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.03124	4.04;4.3;4.04	5.42	5.42	0.78866	.	0.000000	0.42682	U	0.000676	T	0.15219	0.0367	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	T	0.00134	-1.2009	10	0.72032	D	0.01	-44.0546	18.2062	0.89855	0.0:0.0:1.0:0.0	.	304;1571	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	H	877;1571;877	ENSP00000384606:R877H;ENSP00000349856:R1571H;ENSP00000398853:R877H	ENSP00000349856:R1571H	R	+	2	0	PRRC2B	133343781	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.655000	0.67981	2.549000	0.85964	0.561000	0.74099	CGC	.	.		0.637	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SETX	23064	hgsc.bcm.edu	37	9	135140223	135140223	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:135140223T>C	ENST00000224140.5	-	26	7619	c.7437A>G	c.(7435-7437)atA>atG	p.I2479M	SETX_ENST00000477049.1_5'UTR|SETX_ENST00000372169.2_Missense_Mutation_p.I2508M|SETX_ENST00000393220.1_Missense_Mutation_p.I2446M	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2479					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CCTCTGGGGCTATGGTAGGAG	0.498																																					p.I2479M		Atlas-SNP	.											.,1	SETX	234	.	0			c.A7437G						.						100.0	104.0	103.0					9																	135140223		2203	4300	6503	SO:0001583	missense	23064	exon26			TGGGGCTATGGTA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.7437A>G	chr9.hg19:g.135140223T>C	ENSP00000224140:p.Ile2479Met	100.0	0.0		103.0	50.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131366	0.56828	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.90900	-2.09;-2.75;-2.23;-1.84	4.83	-9.65	0.00537	.	1.549250	0.04012	N	0.298360	D	0.85305	0.5666	L	0.44542	1.39	0.09310	N	1	P;P;P	0.44946	0.763;0.761;0.846	B;B;P	0.45610	0.28;0.293;0.487	T	0.82139	-0.0605	10	0.44086	T	0.13	.	4.9238	0.13883	0.0965:0.1923:0.4924:0.2189	.	2446;2479;2508	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	M	2479;750;2508;2446	ENSP00000224140:I2479M;ENSP00000409143:I750M;ENSP00000361242:I2508M;ENSP00000376913:I2446M	ENSP00000224140:I2479M	I	-	3	3	SETX	134130044	0.000000	0.05858	0.000000	0.03702	0.380000	0.30137	-4.012000	0.00314	-3.100000	0.00245	0.459000	0.35465	ATA	.	.		0.498	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
CACFD1	11094	hgsc.bcm.edu	37	9	136330530	136330530	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:136330530A>T	ENST00000316948.4	+	3	361	c.281A>T	c.(280-282)gAc>gTc	p.D94V	CACFD1_ENST00000489519.1_3'UTR|CACFD1_ENST00000542192.1_Intron|CACFD1_ENST00000540581.1_Missense_Mutation_p.D94V|CACFD1_ENST00000291722.7_Intron	NM_017586.3	NP_060056.1	Q9UGQ2	FLOWR_HUMAN	calcium channel flower domain containing 1	94					synaptic vesicle endocytosis (GO:0048488)	integral component of synaptic vesicle membrane (GO:0030285)	calcium channel activity (GO:0005262)										GAGAAGGTGGACCGGCTGCGC	0.582																																					p.D94V		Atlas-SNP	.											.	CACFD1	1	.	0			c.A281T						.						111.0	105.0	107.0					9																	136330530		2203	4300	6503	SO:0001583	missense	11094	exon3			AGGTGGACCGGCT		CCDS6974.1, CCDS48051.1, CCDS56591.1, CCDS56592.1	9q34	2012-03-06	2012-03-06	2012-03-06	ENSG00000160325	ENSG00000160325			1365	protein-coding gene	gene with protein product		613104	"""chromosome 9 open reading frame 7"""	C9orf7		19737521	Standard	NM_001242370		Approved	D9S2135, flower	uc011mdh.1	Q9UGQ2	OTTHUMG00000020875	ENST00000316948.4:c.281A>T	chr9.hg19:g.136330530A>T	ENSP00000317121:p.Asp94Val	90.0	0.0		69.0	31.0	NM_017586	B7Z3T8|B7Z5E1|F5GXX4|Q5SXD4|Q8NBM6	Missense_Mutation	SNP	ENST00000316948.4	hg19	CCDS6974.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.520414	0.85495	.	.	ENSG00000160325	ENST00000535514;ENST00000316948;ENST00000540581;ENST00000444798	T;T;T	0.46819	0.86;0.86;0.86	5.35	5.35	0.76521	Membrane protein, Golgi apparatus TVP18/Calcium channel flower (1);	0.096847	0.64402	D	0.000002	T	0.69815	0.3153	M	0.80183	2.485	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.982;0.99	T	0.74722	-0.3569	10	0.72032	D	0.01	-41.932	14.5099	0.67776	1.0:0.0:0.0:0.0	.	94;94	F5GXX4;Q9UGQ2	.;FLOWR_HUMAN	V	84;94;94;66	ENSP00000317121:D94V;ENSP00000440832:D94V;ENSP00000414495:D66V	ENSP00000317121:D94V	D	+	2	0	C9orf7	135320351	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.896000	0.92521	2.025000	0.59659	0.402000	0.26972	GAC	.	.		0.582	CACFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054915.1	NM_017586	
GPSM1	26086	hgsc.bcm.edu	37	9	139231495	139231495	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:139231495C>T	ENST00000440944.1	+	4	764	c.544C>T	c.(544-546)Cga>Tga	p.R182*	GPSM1_ENST00000392945.3_Nonsense_Mutation_p.R182*	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	182	Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GCCCGATGTCCGAGAGACCCT	0.647																																					p.R182X		Atlas-SNP	.											.	GPSM1	50	.	0			c.C544T						.						36.0	34.0	34.0					9																	139231495		2111	4156	6267	SO:0001587	stop_gained	26086	exon4			GATGTCCGAGAGA	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.544C>T	chr9.hg19:g.139231495C>T	ENSP00000392828:p.Arg182*	122.0	0.0		89.0	29.0	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Nonsense_Mutation	SNP	ENST00000440944.1	hg19	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	C	37	6.421558	0.97555	.	.	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	.	.	.	3.79	1.57	0.23409	.	0.127086	0.51477	U	0.000091	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7884	9.5393	0.39242	0.6145:0.3855:0.0:0.0	.	.	.	.	X	182;182;159	.	ENSP00000346797:R159X	R	+	1	2	GPSM1	138351316	0.996000	0.38824	0.025000	0.17156	0.792000	0.44763	2.604000	0.46274	0.821000	0.34540	0.563000	0.77884	CGA	.	.		0.647	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
SNAPC4	6621	hgsc.bcm.edu	37	9	139288750	139288750	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:139288750A>G	ENST00000298532.2	-	6	951	c.583T>C	c.(583-585)Tca>Cca	p.S195P		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CTCACCACTGACTTTCGGAGC	0.547																																					p.S195P		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T583C						.						163.0	156.0	159.0					9																	139288750		2203	4300	6503	SO:0001583	missense	6621	exon6			CCACTGACTTTCG	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.583T>C	chr9.hg19:g.139288750A>G	ENSP00000298532:p.Ser195Pro	86.0	0.0		86.0	35.0	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	hg19	CCDS6998.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.122312	0.56613	.	.	ENSG00000165684	ENST00000298532	T	0.32272	1.46	4.9	2.41	0.29592	SANT domain, DNA binding (1);	0.450738	0.22316	N	0.061677	T	0.37972	0.1023	M	0.62723	1.935	0.30814	N	0.738492	P	0.52170	0.951	P	0.49226	0.603	T	0.45862	-0.9232	10	0.72032	D	0.01	-3.9617	11.1655	0.48541	0.5364:0.4636:0.0:0.0	.	195	Q5SXM2	SNPC4_HUMAN	P	195	ENSP00000298532:S195P	ENSP00000298532:S195P	S	-	1	0	SNAPC4	138408571	0.896000	0.30565	0.216000	0.23742	0.773000	0.43773	0.866000	0.27954	0.194000	0.20326	0.529000	0.55759	TCA	.	.		0.547	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
EGFL7	51162	hgsc.bcm.edu	37	9	139564144	139564144	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:139564144C>T	ENST00000371699.1	+	5	1195	c.284C>T	c.(283-285)aCc>aTc	p.T95I	EGFL7_ENST00000406555.3_Missense_Mutation_p.T95I|MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000371698.3_Missense_Mutation_p.T95I|EGFL7_ENST00000308874.7_Missense_Mutation_p.T95I			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	95	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		TGGAAGAGGACCAGCGGGCTT	0.682																																					p.T95I		Atlas-SNP	.											.	EGFL7	11	.	0			c.C284T						.						14.0	16.0	16.0					9																	139564144		2182	4287	6469	SO:0001583	missense	51162	exon6			AGAGGACCAGCGG	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.284C>T	chr9.hg19:g.139564144C>T	ENSP00000360764:p.Thr95Ile	113.0	0.0		107.0	6.0	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	hg19	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.495338	0.26774	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	4.06	3.1	0.35709	EMI domain (2);	0.486110	0.21645	N	0.071267	T	0.26882	0.0658	L	0.35414	1.06	0.27529	N	0.951145	P	0.39809	0.689	B	0.37091	0.241	T	0.07809	-1.0753	10	0.30078	T	0.28	-17.256	6.9329	0.24451	0.0:0.7258:0.1777:0.0965	.	95	Q9UHF1	EGFL7_HUMAN	I	95	ENSP00000360764:T95I;ENSP00000307843:T95I;ENSP00000385639:T95I;ENSP00000360763:T95I	ENSP00000307843:T95I	T	+	2	0	EGFL7	138683965	0.012000	0.17670	0.696000	0.30242	0.300000	0.27592	1.251000	0.32862	2.089000	0.63090	0.313000	0.20887	ACC	.	.		0.682	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215	
ZMYND19	116225	hgsc.bcm.edu	37	9	140477533	140477533	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:140477533G>A	ENST00000298585.2	-	5	668	c.442C>T	c.(442-444)Cgg>Tgg	p.R148W		NM_138462.2	NP_612471.1	Q96E35	ZMY19_HUMAN	zinc finger, MYND-type containing 19	148						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|synapse (GO:0045202)	metal ion binding (GO:0046872)	p.R148R(1)		endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000275)|Epithelial(140;0.00047)		TTATAATACCGGGTCACATTT	0.473																																					p.R148W		Atlas-SNP	.											.	ZMYND19	16	.	1	Substitution - coding silent(1)	lung(1)	c.C442T						.						274.0	253.0	260.0					9																	140477533		2203	4300	6503	SO:0001583	missense	116225	exon5			AATACCGGGTCAC	BC012948	CCDS7048.1	9q34.3	2008-02-05			ENSG00000165724	ENSG00000165724		"""Zinc fingers, MYND-type"""	21146	protein-coding gene	gene with protein product		611424					Standard	NM_138462		Approved	MIZIP	uc004cno.1	Q96E35	OTTHUMG00000020992	ENST00000298585.2:c.442C>T	chr9.hg19:g.140477533G>A	ENSP00000298585:p.Arg148Trp	107.0	0.0		98.0	19.0	NM_138462	Q5T366	Missense_Mutation	SNP	ENST00000298585.2	hg19	CCDS7048.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552503	0.86127	.	.	ENSG00000165724	ENST00000298585	.	.	.	5.29	4.39	0.52855	.	0.060469	0.64402	D	0.000002	T	0.68109	0.2965	M	0.62723	1.935	0.54753	D	0.999984	D	0.76494	0.999	P	0.62014	0.897	T	0.70502	-0.4854	9	0.87932	D	0	-36.7711	9.8258	0.40910	0.0947:0.0:0.9053:0.0	.	148	Q96E35	ZMY19_HUMAN	W	148	.	ENSP00000298585:R148W	R	-	1	2	ZMYND19	139597354	1.000000	0.71417	0.957000	0.39632	0.973000	0.67179	7.808000	0.86044	1.228000	0.43614	0.561000	0.74099	CGG	.	.		0.473	ZMYND19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055356.1	NM_138462	
CACNA1B	774	hgsc.bcm.edu	37	9	140881287	140881287	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:140881287C>A	ENST00000371372.1	+	15	2100	c.1955C>A	c.(1954-1956)gCc>gAc	p.A652D	CACNA1B_ENST00000371357.1_Missense_Mutation_p.A653D|CACNA1B_ENST00000277551.2_Missense_Mutation_p.A652D|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371363.1_Missense_Mutation_p.A652D|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A653D	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	652					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TTCCCTGCCGCCATCCTCACT	0.602																																					p.A652D		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C1955A						.						187.0	202.0	197.0					9																	140881287		2082	4212	6294	SO:0001583	missense	774	exon15			CTGCCGCCATCCT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1955C>A	chr9.hg19:g.140881287C>A	ENSP00000360423:p.Ala652Asp	82.0	0.0		66.0	21.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.844506	0.51164	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98914	-5.23;-5.23;-5.23;-5.23;-5.23	4.12	4.12	0.48240	.	0.112726	0.64402	D	0.000012	D	0.99489	0.9818	H	0.98068	4.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97855	1.0277	10	0.87932	D	0	.	16.8462	0.85981	0.0:1.0:0.0:0.0	.	652;652	B1AQK4;B1AQK6	.;.	D	652;652;652;653;653	ENSP00000360423:A652D;ENSP00000277551:A652D;ENSP00000360414:A652D;ENSP00000360408:A653D;ENSP00000360406:A653D	ENSP00000277551:A652D	A	+	2	0	CACNA1B	140001108	1.000000	0.71417	0.995000	0.50966	0.291000	0.27294	7.538000	0.82048	2.210000	0.71456	0.448000	0.29417	GCC	.	.		0.602	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
GDI2	2665	hgsc.bcm.edu	37	10	5827986	5827986	+	Missense_Mutation	SNP	C	C	T	rs376781352		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:5827986C>T	ENST00000380191.4	-	5	706	c.416G>A	c.(415-417)cGc>cAc	p.R139H	GDI2_ENST00000380181.3_Missense_Mutation_p.R94H|GDI2_ENST00000380132.4_Missense_Mutation_p.R143H	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	139					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						TTTCCTGAAGCGACGTTTTTC	0.373																																					p.R139H		Atlas-SNP	.											.	GDI2	26	.	0			c.G416A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	100.0	99.0	99.0		281,416	4.3	1.0	10		99	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GDI2	NM_001115156.1,NM_001494.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	94/401,139/446	5827986	1,13005	2203	4300	6503	SO:0001583	missense	2665	exon5			CTGAAGCGACGTT	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"""rab GDP-dissociation"""	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.416G>A	chr10.hg19:g.5827986C>T	ENSP00000369538:p.Arg139His	60.0	0.0		36.0	13.0	NM_001494	O43928|Q5SX88|Q9UQM6	Missense_Mutation	SNP	ENST00000380191.4	hg19	CCDS7071.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.836798	0.71373	0.0	1.16E-4	ENSG00000057608	ENST00000380191;ENST00000380132;ENST00000380181;ENST00000456041;ENST00000418688;ENST00000380127	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.17	4.26	0.50523	.	0.000000	0.85682	D	0.000000	D	0.91878	0.7429	M	0.85777	2.775	0.80722	D	1	B;P;P	0.40660	0.151;0.726;0.48	B;P;B	0.46825	0.049;0.528;0.067	D	0.92440	0.5961	10	0.62326	D	0.03	0.609	13.7496	0.62899	0.0:0.9244:0.0:0.0756	.	143;94;139	E7EU23;Q5SX88;P50395	.;.;GDIB_HUMAN	H	139;143;94;129;103;143	ENSP00000369538:R139H;ENSP00000369475:R143H;ENSP00000369528:R94H;ENSP00000401733:R129H;ENSP00000394177:R103H;ENSP00000369470:R143H	ENSP00000369470:R143H	R	-	2	0	GDI2	5867992	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.664000	0.83830	1.315000	0.45114	0.655000	0.94253	CGC	.	.		0.373	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494	
ITIH5	80760	hgsc.bcm.edu	37	10	7608361	7608361	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:7608361A>G	ENST00000256861.6	-	13	2237	c.2159T>C	c.(2158-2160)gTg>gCg	p.V720A	ITIH5_ENST00000298441.6_Missense_Mutation_p.V506A|ITIH5_ENST00000446830.2_Missense_Mutation_p.V502A|ITIH5_ENST00000397146.2_Intron	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	720					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CTCTCCGTTCACTGTGACACC	0.522																																					p.V720A		Atlas-SNP	.											.	ITIH5	343	.	0			c.T2159C						.						58.0	59.0	58.0					10																	7608361		2203	4300	6503	SO:0001583	missense	80760	exon13			CCGTTCACTGTGA			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2159T>C	chr10.hg19:g.7608361A>G	ENSP00000256861:p.Val720Ala	84.0	0.0		35.0	21.0	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	A	16.29	3.082855	0.55861	.	.	ENSG00000123243	ENST00000256861;ENST00000298441;ENST00000446830	T;T;T	0.26810	1.71;1.71;1.71	5.84	5.84	0.93424	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.051547	0.85682	D	0.000000	T	0.53916	0.1826	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.58584	-0.7611	9	0.87932	D	0	-34.9487	16.1928	0.82004	1.0:0.0:0.0:0.0	.	720;506	Q86UX2;Q86UX2-3	ITIH5_HUMAN;.	A	720;506;502	ENSP00000256861:V720A;ENSP00000298441:V506A;ENSP00000387969:V502A	ENSP00000256861:V720A	V	-	2	0	ITIH5	7648367	1.000000	0.71417	0.997000	0.53966	0.086000	0.17979	7.011000	0.76359	2.216000	0.71823	0.533000	0.62120	GTG	.	.		0.522	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
RPP38	10557	hgsc.bcm.edu	37	10	15145341	15145341	+	Missense_Mutation	SNP	C	C	T	rs138934702		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:15145341C>T	ENST00000378197.4	+	3	542	c.28C>T	c.(28-30)Cgg>Tgg	p.R10W	NMT2_ENST00000466201.1_5'UTR|RPP38_ENST00000378202.5_Missense_Mutation_p.R10W|RPP38_ENST00000451677.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	10					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						AGCACCGGGGCGGGGATCTCT	0.483																																					p.R10W	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.C28T						.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	65.0	70.0	68.0		28,28,28	-1.6	0.0	10	dbSNP_134	68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	10/284,10/284,10/284	15145341	1,13005	2203	4300	6503	SO:0001583	missense	10557	exon2			CCGGGGCGGGGAT	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.28C>T	chr10.hg19:g.15145341C>T	ENSP00000367439:p.Arg10Trp	130.0	0.0		79.0	37.0	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	hg19	CCDS7108.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.959700	0.34565	0.0	1.16E-4	ENSG00000152464	ENST00000378203;ENST00000378201;ENST00000378202;ENST00000378197;ENST00000441850	T;T;T;T	0.26373	2.73;2.73;2.73;1.74	5.75	-1.56	0.08532	.	0.113772	0.56097	D	0.000030	T	0.45236	0.1332	M	0.68317	2.08	0.21064	N	0.999796	D	0.89917	1.0	D	0.69479	0.964	T	0.51044	-0.8755	10	0.87932	D	0	-27.85	16.3068	0.82852	0.2668:0.7332:0.0:0.0	.	10	P78345	RPP38_HUMAN	W	10	ENSP00000367445:R10W;ENSP00000367444:R10W;ENSP00000367439:R10W;ENSP00000402635:R10W	ENSP00000367439:R10W	R	+	1	2	RPP38	15185347	0.137000	0.22531	0.022000	0.16811	0.059000	0.15707	0.938000	0.28965	-0.545000	0.06224	-0.271000	0.10264	CGG	.	C|1.000;T|0.000		0.483	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
ITGA8	8516	hgsc.bcm.edu	37	10	15590538	15590538	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:15590538G>A	ENST00000378076.3	-	27	3149	c.2796C>T	c.(2794-2796)atC>atT	p.I932I		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	932					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						CTGCACAGGAGATTTGTAAAC	0.453																																					p.I932I		Atlas-SNP	.											.	ITGA8	230	.	0			c.C2796T						.						138.0	116.0	124.0					10																	15590538		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon27			ACAGGAGATTTGT	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"""Integrins"""	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.2796C>T	chr10.hg19:g.15590538G>A		90.0	0.0		76.0	35.0	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	.		0.453	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638	
CUBN	8029	hgsc.bcm.edu	37	10	16877086	16877086	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:16877086T>C	ENST00000377833.4	-	64	10354	c.10289A>G	c.(10288-10290)aAc>aGc	p.N3430S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3430	CUB 26. {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)	AATGGTGTGGTTCTGGGGGGC	0.448																																					p.N3430S		Atlas-SNP	.											.	CUBN	515	.	0			c.A10289G						.						162.0	137.0	146.0					10																	16877086		2203	4300	6503	SO:0001583	missense	8029	exon64			GTGTGGTTCTGGG	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.10289A>G	chr10.hg19:g.16877086T>C	ENSP00000367064:p.Asn3430Ser	153.0	0.0		111.0	8.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.373093	0.61624	.	.	ENSG00000107611	ENST00000377833;ENST00000545090	T	0.34667	1.35	4.84	4.84	0.62591	CUB (5);	0.000000	0.47093	D	0.000243	T	0.48333	0.1494	L	0.43554	1.36	0.80722	D	1	D	0.61080	0.989	D	0.63488	0.915	T	0.34875	-0.9811	10	0.30854	T	0.27	.	14.5848	0.68317	0.0:0.0:0.0:1.0	.	3430	O60494	CUBN_HUMAN	S	3430;271	ENSP00000367064:N3430S	ENSP00000367064:N3430S	N	-	2	0	CUBN	16917092	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	1.964000	0.40462	2.028000	0.59812	0.459000	0.35465	AAC	.	.		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
SKIDA1	387640	hgsc.bcm.edu	37	10	21804625	21804625	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:21804625G>A	ENST00000449193.2	-	4	4379	c.2127C>T	c.(2125-2127)tgC>tgT	p.C709C	SKIDA1_ENST00000444772.3_Silent_p.C630C	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	628						nucleus (GO:0005634)											CATTGCACTCGCACTTTAGCT	0.393																																					p.C709C		Atlas-SNP	.											C10orf140_ENST00000449193,colon,carcinoma,0,2	.	.	.	0			c.C2127T						.						213.0	215.0	215.0					10																	21804625		1933	4132	6065	SO:0001819	synonymous_variant	387640	exon4			GCACTCGCACTTT	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.2127C>T	chr10.hg19:g.21804625G>A		109.0	1.0		107.0	29.0	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	hg19	CCDS44363.1																																																																																			.	.		0.393	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371	
ARMC3	219681	hgsc.bcm.edu	37	10	23326257	23326257	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:23326257C>T	ENST00000298032.5	+	19	2552	c.2468C>T	c.(2467-2469)gCg>gTg	p.A823V	ARMC3_ENST00000409983.3_Missense_Mutation_p.A816V|ARMC3_ENST00000376528.4_Missense_Mutation_p.A560V	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	823						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TACGGTAGAGCGTGGAATGAA	0.542																																					p.A823V		Atlas-SNP	.											.	ARMC3	102	.	0			c.C2468T						.						123.0	116.0	118.0					10																	23326257		2203	4300	6503	SO:0001583	missense	219681	exon19			GTAGAGCGTGGAA	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.2468C>T	chr10.hg19:g.23326257C>T	ENSP00000298032:p.Ala823Val	124.0	0.0		133.0	52.0	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	hg19	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395601	0.62177	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376528	T;T;T	0.50548	0.74;0.74;1.99	5.68	4.76	0.60689	.	0.061426	0.64402	D	0.000005	T	0.71542	0.3352	M	0.87682	2.9	0.58432	D	0.999993	D;D	0.89917	1.0;0.999	D;D	0.65010	0.928;0.931	T	0.78698	-0.2103	10	0.87932	D	0	-25.4588	16.305	0.82844	0.0:0.8631:0.1369:0.0	.	816;823	Q5W041-4;Q5W041	.;ARMC3_HUMAN	V	823;816;560	ENSP00000298032:A823V;ENSP00000386943:A816V;ENSP00000365711:A560V	ENSP00000298032:A823V	A	+	2	0	ARMC3	23366263	0.998000	0.40836	0.727000	0.30756	0.005000	0.04900	3.693000	0.54735	1.360000	0.45960	0.655000	0.94253	GCG	.	.		0.542	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081	
SVIL	6840	hgsc.bcm.edu	37	10	29769474	29769474	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:29769474C>T	ENST00000355867.4	-	29	6121	c.5369G>A	c.(5368-5370)aGc>aAc	p.S1790N	SVIL_ENST00000375398.2_Missense_Mutation_p.S1790N|SVIL_ENST00000460007.1_Intron|SVIL_ENST00000535393.1_Missense_Mutation_p.S704N|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.S1364N|SVIL_ENST00000538146.1_Missense_Mutation_p.S582N|PTCHD3P1_ENST00000413405.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1790					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ACCTGCCGTGCTCACCATGAA	0.562																																					p.S1790N		Atlas-SNP	.											.	SVIL	226	.	0			c.G5369A						.						95.0	87.0	90.0					10																	29769474		2203	4300	6503	SO:0001583	missense	6840	exon29			GCCGTGCTCACCA	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5369G>A	chr10.hg19:g.29769474C>T	ENSP00000348128:p.Ser1790Asn	117.0	0.0		116.0	42.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404653	0.83230	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;1.7	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.47414	0.1444	L	0.58101	1.795	0.80722	D	1	B;B;B;B	0.32040	0.02;0.004;0.164;0.353	B;B;B;B	0.32211	0.029;0.018;0.142;0.118	T	0.51568	-0.8689	10	0.46703	T	0.11	-11.6278	17.4706	0.87645	0.0:1.0:0.0:0.0	.	704;582;1364;1790	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	N	1364;1790;1790;704;744;582	ENSP00000364549:S1364N;ENSP00000364547:S1790N;ENSP00000348128:S1790N;ENSP00000445472:S704N;ENSP00000440343:S582N	ENSP00000348128:S1790N	S	-	2	0	SVIL	29809480	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	5.779000	0.68948	2.337000	0.79520	0.561000	0.74099	AGC	.	.		0.562	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
EPC1	80314	hgsc.bcm.edu	37	10	32581987	32581987	+	Nonsense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:32581987G>A	ENST00000263062.8	-	4	864	c.595C>T	c.(595-597)Cga>Tga	p.R199*	EPC1_ENST00000375110.2_Nonsense_Mutation_p.R149*|EPC1_ENST00000319778.6_Nonsense_Mutation_p.R199*	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	199					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GAACCATCTCGCTTCTCTTGT	0.338																																					p.R199X		Atlas-SNP	.											EPC1,colon,carcinoma,0,1	EPC1	74	.	0			c.C595T						.						72.0	73.0	73.0					10																	32581987		2202	4300	6502	SO:0001587	stop_gained	80314	exon4			CATCTCGCTTCTC	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.595C>T	chr10.hg19:g.32581987G>A	ENSP00000263062:p.Arg199*	92.0	0.0		87.0	33.0	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Nonsense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	G	38	6.729400	0.97796	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	.	.	.	6.08	2.88	0.33553	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8674	16.7515	0.85488	0.0:0.0:0.6531:0.3469	.	.	.	.	X	149;199;199	.	ENSP00000263062:R199X	R	-	1	2	EPC1	32621993	1.000000	0.71417	0.997000	0.53966	0.797000	0.45037	3.544000	0.53640	0.871000	0.35750	-0.230000	0.12252	CGA	.	.		0.338	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1		
ANKRD30A	91074	hgsc.bcm.edu	37	10	37447483	37447483	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:37447483A>G	ENST00000602533.1	+	15	1800	c.1701A>G	c.(1699-1701)ttA>ttG	p.L567L	ANKRD30A_ENST00000361713.1_Silent_p.L567L|ANKRD30A_ENST00000374660.1_Silent_p.L567L			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	623					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CTAAAGCCTTAGAATTGAAGG	0.294																																					p.L567L		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A1701G						.						100.0	92.0	94.0					10																	37447483		1799	4071	5870	SO:0001819	synonymous_variant	91074	exon15			AGCCTTAGAATTG	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1701A>G	chr10.hg19:g.37447483A>G		268.0	0.0		290.0	119.0	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	hg19																																																																																				.	.		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
ALOX5	240	hgsc.bcm.edu	37	10	45924153	45924153	+	Missense_Mutation	SNP	G	G	A	rs28395872		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:45924153G>A	ENST00000374391.2	+	7	975	c.922G>A	c.(922-924)Gct>Act	p.A308T	ALOX5_ENST00000542434.1_Missense_Mutation_p.A308T	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	308	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	GTTCCTGGCCGCTCCCATCTG	0.557																																					p.A308T		Atlas-SNP	.											.	ALOX5	88	.	0			c.G922A						.						118.0	103.0	108.0					10																	45924153		2203	4300	6503	SO:0001583	missense	240	exon7			CTGGCCGCTCCCA	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"""Arachidonate lipoxygenases"""	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.922G>A	chr10.hg19:g.45924153G>A	ENSP00000363512:p.Ala308Thr	142.0	0.0		130.0	43.0	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.045635	0.93685	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	D;D	0.95853	-3.83;-3.83	5.28	5.28	0.74379	Lipoxygenase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.97586	0.9209	M	0.93016	3.37	0.80722	D	1	D;D;D	0.63046	0.985;0.983;0.992	P;P;P	0.54401	0.704;0.751;0.704	D	0.98366	1.0551	10	0.66056	D	0.02	-31.2213	16.4137	0.83727	0.0:0.0:1.0:0.0	.	308;308;308	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	T	308	ENSP00000437634:A308T;ENSP00000363512:A308T	ENSP00000363512:A308T	A	+	1	0	ALOX5	45244159	1.000000	0.71417	0.102000	0.21198	0.903000	0.53119	9.798000	0.99111	2.470000	0.83445	0.655000	0.94253	GCT	.	G|0.973;T|0.027		0.557	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1		
RBP3	5949	hgsc.bcm.edu	37	10	48388542	48388542	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:48388542A>G	ENST00000224600.4	-	1	2449	c.2336T>C	c.(2335-2337)gTg>gCg	p.V779A	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	779	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CAGGTCGATCACCAGCGCAGC	0.622																																					p.V779A		Atlas-SNP	.											.	RBP3	152	.	0			c.T2336C						.						32.0	29.0	30.0					10																	48388542		2201	4300	6501	SO:0001583	missense	5949	exon1			TCGATCACCAGCG	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2336T>C	chr10.hg19:g.48388542A>G	ENSP00000224600:p.Val779Ala	126.0	0.0		110.0	43.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	A	10.71	1.426805	0.25726	.	.	ENSG00000107618	ENST00000224600	T	0.72725	-0.68	5.34	5.34	0.76211	Interphotoreceptor retinol-binding (2);	0.618333	0.14333	N	0.326219	T	0.73297	0.3569	M	0.72894	2.215	0.32287	N	0.566875	P	0.43938	0.822	B	0.42495	0.389	T	0.81147	-0.1065	10	0.87932	D	0	-9.2725	14.5119	0.67794	1.0:0.0:0.0:0.0	.	779	P10745	RET3_HUMAN	A	779	ENSP00000224600:V779A	ENSP00000224600:V779A	V	-	2	0	RBP3	48008548	1.000000	0.71417	0.109000	0.21407	0.030000	0.12068	8.563000	0.90723	2.029000	0.59856	0.533000	0.62120	GTG	.	.		0.622	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
GDF2	2658	hgsc.bcm.edu	37	10	48414329	48414329	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:48414329T>C	ENST00000249598.1	-	2	698	c.539A>G	c.(538-540)gAt>gGt	p.D180G		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	180					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						ATCCCAGGCATCTGTTCCATC	0.537																																					p.D180G		Atlas-SNP	.											.	GDF2	77	.	0			c.A539G						.						79.0	66.0	70.0					10																	48414329		2203	4300	6503	SO:0001583	missense	2658	exon2			CAGGCATCTGTTC	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"""Endogenous ligands"""	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.539A>G	chr10.hg19:g.48414329T>C	ENSP00000249598:p.Asp180Gly	80.0	0.0		96.0	37.0	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	T	9.419	1.082480	0.20309	.	.	ENSG00000128802	ENST00000249598	T	0.64991	-0.13	5.32	0.18	0.15068	Transforming growth factor-beta, N-terminal (1);	0.508313	0.19993	N	0.101504	T	0.53126	0.1777	M	0.63428	1.95	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.41734	-0.9492	10	0.22706	T	0.39	.	10.1783	0.42952	0.0:0.345:0.0:0.655	.	180	Q9UK05	GDF2_HUMAN	G	180	ENSP00000249598:D180G	ENSP00000249598:D180G	D	-	2	0	GDF2	48034335	0.211000	0.23529	0.000000	0.03702	0.845000	0.48019	1.812000	0.38952	-0.212000	0.10109	0.482000	0.46254	GAT	.	.		0.537	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204	
MAPK8	5599	hgsc.bcm.edu	37	10	49628362	49628362	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:49628362C>T	ENST00000374189.1	+	6	796	c.615C>T	c.(613-615)aaC>aaT	p.N205N	MAPK8_ENST00000374174.1_Splice_Site_p.N205N|MAPK8_ENST00000360332.3_Splice_Site_p.N205N|MAPK8_ENST00000395611.3_Splice_Site_p.N205N|MAPK8_ENST00000374182.3_Splice_Site_p.N205N			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	205	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		ACAAGGAAAACGGTCAGCACA	0.393																																					p.N205N		Atlas-SNP	.											.	MAPK8	118	.	0			c.C615T						.						128.0	121.0	123.0					10																	49628362		2203	4300	6503	SO:0001630	splice_region_variant	5599	exon5			GGAAAACGGTCAG	L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6881	protein-coding gene	gene with protein product	"""JUN N-terminal kinase"""	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.616+1C>T	chr10.hg19:g.49628362C>T		108.0	0.0		99.0	7.0	NM_139047	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Silent	SNP	ENST00000374189.1	hg19	CCDS7224.1																																																																																			.	.		0.393	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1		Silent
CHAT	1103	hgsc.bcm.edu	37	10	50854625	50854625	+	Missense_Mutation	SNP	G	G	A	rs536359684		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:50854625G>A	ENST00000337653.2	+	8	1339	c.1186G>A	c.(1186-1188)Gtg>Atg	p.V396M	CHAT_ENST00000395559.2_Missense_Mutation_p.V278M|CHAT_ENST00000351556.3_Missense_Mutation_p.V278M|CHAT_ENST00000339797.1_Missense_Mutation_p.V278M|CHAT_ENST00000455728.2_Missense_Mutation_p.V278M|CHAT_ENST00000395562.2_Missense_Mutation_p.V314M	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	396				V -> L (in Ref. 6; AAB23557). {ECO:0000305}.	adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	GCCAGGAGGCGTGGAGCTCAG	0.632													G|||	1	0.000199681	0.0	0.0	5008	,	,		21243	0.0		0.0	False		,,,				2504	0.001				p.V396M		Atlas-SNP	.											.	CHAT	162	.	0			c.G1186A						.						98.0	87.0	91.0					10																	50854625		2203	4300	6503	SO:0001583	missense	1103	exon8			GGAGGCGTGGAGC	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1186G>A	chr10.hg19:g.50854625G>A	ENSP00000337103:p.Val396Met	149.0	0.0		161.0	76.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	7.773	0.707778	0.15239	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59;-2.59;-2.59	5.27	-0.828	0.10799	.	0.845545	0.10704	N	0.643710	T	0.80979	0.4728	L	0.43646	1.37	0.09310	N	1	B;B	0.22346	0.001;0.068	B;B	0.10450	0.001;0.005	T	0.65327	-0.6195	10	0.33940	T	0.23	-2.3264	5.1433	0.14971	0.2791:0.0:0.476:0.2449	.	278;396	F8W8I2;P28329	.;CLAT_HUMAN	M	278;278;278;396;314;278	ENSP00000343486:V278M;ENSP00000345878:V278M;ENSP00000378926:V278M;ENSP00000337103:V396M;ENSP00000378929:V314M;ENSP00000390521:V278M	ENSP00000337103:V396M	V	+	1	0	CHAT	50524631	0.000000	0.05858	0.045000	0.18777	0.665000	0.39181	-0.417000	0.07088	-0.055000	0.13244	-0.136000	0.14681	GTG	.	.		0.632	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
A1CF	29974	hgsc.bcm.edu	37	10	52587939	52587939	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:52587939A>G	ENST00000373993.1	-	5	765	c.721T>C	c.(721-723)Tct>Cct	p.S241P	A1CF_ENST00000395489.2_Missense_Mutation_p.S234P|A1CF_ENST00000282641.2_Missense_Mutation_p.S241P|A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000374001.2_Missense_Mutation_p.S241P|A1CF_ENST00000373997.3_Missense_Mutation_p.S241P|A1CF_ENST00000395495.1_Intron|A1CF_ENST00000373995.3_Missense_Mutation_p.S249P			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	241	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						TCAGAGGTAGACAGCATAAGA	0.358																																					p.S249P		Atlas-SNP	.											.	A1CF	190	.	0			c.T745C						.						135.0	131.0	132.0					10																	52587939		2203	4300	6503	SO:0001583	missense	29974	exon8			AGGTAGACAGCAT	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.721T>C	chr10.hg19:g.52587939A>G	ENSP00000363105:p.Ser241Pro	58.0	0.0		63.0	20.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.320777	0.41096	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395488;ENST00000395489	T;T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88;2.88	5.48	4.34	0.51931	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.234804	0.44688	N	0.000421	T	0.10594	0.0259	L	0.56199	1.76	0.40079	D	0.976116	B;B;B;B	0.14438	0.01;0.003;0.001;0.005	B;B;B;B	0.17433	0.008;0.008;0.002;0.018	T	0.11060	-1.0603	10	0.45353	T	0.12	.	5.0867	0.14687	0.7553:0.0:0.0856:0.1591	.	234;241;241;249	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	P	241;241;241;249;241;224;234	ENSP00000363113:S241P;ENSP00000363105:S241P;ENSP00000363109:S241P;ENSP00000363107:S249P;ENSP00000282641:S241P;ENSP00000378868:S234P	ENSP00000282641:S241P	S	-	1	0	A1CF	52257945	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.758000	0.55220	0.910000	0.36722	0.460000	0.39030	TCT	.	.		0.358	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
CSTF2T	23283	hgsc.bcm.edu	37	10	53458564	53458564	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:53458564T>A	ENST00000331173.4	-	1	791	c.746A>T	c.(745-747)gAc>gTc	p.D249V	PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000373980.4_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	249					mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		AGGAGGAATGTCCTTCACAGG	0.572																																					p.D249V		Atlas-SNP	.											.	CSTF2T	64	.	0			c.A746T						.						40.0	44.0	43.0					10																	53458564		2203	4300	6503	SO:0001583	missense	23283	exon1			GGAATGTCCTTCA	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"""RNA binding motif (RRM) containing"""	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.746A>T	chr10.hg19:g.53458564T>A	ENSP00000332444:p.Asp249Val	85.0	0.0		65.0	24.0	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	hg19	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.044253	0.55110	.	.	ENSG00000177613	ENST00000331173	T	0.21543	2.0	4.8	3.68	0.42216	.	0.054486	0.64402	D	0.000001	T	0.17746	0.0426	N	0.08118	0	0.58432	D	0.999996	D	0.69078	0.997	P	0.60117	0.869	T	0.03051	-1.1078	10	0.49607	T	0.09	-23.1109	5.4405	0.16507	0.0:0.1872:0.0:0.8128	.	249	Q9H0L4	CSTFT_HUMAN	V	249	ENSP00000332444:D249V	ENSP00000332444:D249V	D	-	2	0	CSTF2T	53128570	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	2.194000	0.42668	2.149000	0.67028	0.533000	0.62120	GAC	.	.		0.572	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235	
SIRT1	23411	hgsc.bcm.edu	37	10	69672422	69672422	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:69672422A>G	ENST00000212015.6	+	8	1602	c.1549A>G	c.(1549-1551)Aca>Gca	p.T517A	SIRT1_ENST00000432464.1_Missense_Mutation_p.T222A|SIRT1_ENST00000406900.1_Missense_Mutation_p.T214A|SIRT1_ENST00000403579.1_Missense_Mutation_p.T214A	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	517	Interaction with CCAR2.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						ACCTCCACGAACACAAAAAGA	0.388																																					p.T517A		Atlas-SNP	.											.	SIRT1	38	.	0			c.A1549G						.						76.0	76.0	76.0					10																	69672422		2203	4300	6503	SO:0001583	missense	23411	exon8			CCACGAACACAAA	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.1549A>G	chr10.hg19:g.69672422A>G	ENSP00000212015:p.Thr517Ala	182.0	0.0		175.0	73.0	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	hg19	CCDS7273.1	.	.	.	.	.	.	.	.	.	.	A	9.115	1.007529	0.19199	.	.	ENSG00000096717	ENST00000212015;ENST00000432464;ENST00000406900;ENST00000403579	T;T;T;T	0.22336	2.53;1.97;1.96;1.96	5.68	0.102	0.14522	.	0.492715	0.20777	N	0.085863	T	0.14270	0.0345	L	0.31476	0.935	0.24340	N	0.994965	B;B	0.15141	0.001;0.012	B;B	0.13407	0.005;0.009	T	0.29792	-1.0000	10	0.09084	T	0.74	-2.3804	16.9373	0.86206	0.3923:0.6077:0.0:0.0	.	214;517	B0QZ35;Q96EB6	.;SIRT1_HUMAN	A	517;222;214;214	ENSP00000212015:T517A;ENSP00000409208:T222A;ENSP00000384508:T214A;ENSP00000384063:T214A	ENSP00000212015:T517A	T	+	1	0	SIRT1	69342428	0.970000	0.33590	0.999000	0.59377	0.995000	0.86356	0.263000	0.18478	0.058000	0.16222	0.528000	0.53228	ACA	.	.		0.388	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1		
SAR1A	56681	hgsc.bcm.edu	37	10	71912317	71912317	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:71912317C>T	ENST00000373242.2	-	8	708	c.512G>A	c.(511-513)cGc>cAc	p.R171H	SAR1A_ENST00000373241.4_Missense_Mutation_p.R171H|SAR1A_ENST00000373238.1_Missense_Mutation_p.R171H|SAR1A_ENST00000431664.2_Missense_Mutation_p.R171H|SAR1A_ENST00000458634.2_Missense_Mutation_p.R128H	NM_001142648.1	NP_001136120.1	Q9NR31	SAR1A_HUMAN	secretion associated, Ras related GTPase 1A	171					intracellular protein transport (GO:0006886)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)	6						TTCCATGGGGCGAGCATTCAG	0.502																																					p.R171H		Atlas-SNP	.											.	SAR1A	19	.	0			c.G512A						.						76.0	66.0	69.0					10																	71912317		2203	4300	6503	SO:0001583	missense	56681	exon7			ATGGGGCGAGCAT		CCDS7298.1	10q22.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000079332	ENSG00000079332			10534	protein-coding gene	gene with protein product		607691	"""SAR1a gene homolog (S. cerevisiae) 1"", ""SAR1a gene homolog 1 (S. cerevisiae)"", ""SAR1 homolog A (S. cerevisiae)"""	SARA1		10871277	Standard	NM_020150		Approved	SAR1, Sara	uc010qji.2	Q9NR31	OTTHUMG00000018400	ENST00000373242.2:c.512G>A	chr10.hg19:g.71912317C>T	ENSP00000362339:p.Arg171His	92.0	0.0		83.0	38.0	NM_020150	B4DQ19	Missense_Mutation	SNP	ENST00000373242.2	hg19	CCDS7298.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432073	0.83776	.	.	ENSG00000079332	ENST00000373241;ENST00000373239;ENST00000373238;ENST00000373242;ENST00000431664;ENST00000458634;ENST00000395026	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	5.61	4.68	0.58851	.	0.051164	0.64402	D	0.000001	T	0.71617	0.3361	M	0.75615	2.305	0.80722	D	1	D	0.60575	0.988	P	0.47075	0.536	T	0.76686	-0.2868	10	0.66056	D	0.02	.	14.8863	0.70572	0.0:0.8556:0.1444:0.0	.	171	Q9NR31	SAR1A_HUMAN	H	171;171;171;171;171;128;90	ENSP00000362338:R171H;ENSP00000362335:R171H;ENSP00000362339:R171H;ENSP00000399698:R171H;ENSP00000437979:R128H	ENSP00000362335:R171H	R	-	2	0	SAR1A	71582323	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	1.316000	0.45131	0.585000	0.79938	CGC	.	.		0.502	SAR1A-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048500.2		
PSAP	5660	hgsc.bcm.edu	37	10	73594212	73594212	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:73594212C>G	ENST00000394936.3	-	2	238	c.91G>C	c.(91-93)Gtg>Ctg	p.V31L	PSAP_ENST00000394934.1_Missense_Mutation_p.V31L			P07602	SAP_HUMAN	prosaposin	31	Saposin A-type 1. {ECO:0000255|PROSITE- ProRule:PRU00414}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TGGCACCACACTGCCGAGCCC	0.582																																					p.V31L		Atlas-SNP	.											.	PSAP	43	.	0			c.G91C						.						47.0	42.0	44.0					10																	73594212		2203	4300	6503	SO:0001583	missense	5660	exon2			ACCACACTGCCGA	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"""Endogenous ligands"""	9498	protein-coding gene	gene with protein product	"""variant Gaucher disease and variant metachromatic leukodystrophy"""	176801	"""sphingolipid activator protein-1"""	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.91G>C	chr10.hg19:g.73594212C>G	ENSP00000378394:p.Val31Leu	99.0	0.0		72.0	28.0	NM_001042466	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Missense_Mutation	SNP	ENST00000394936.3	hg19	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848757	0.91277	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000394929;ENST00000404083	T;T	0.57436	0.4;0.4	5.67	5.67	0.87782	Saposin type A (3);	0.183599	0.48286	D	0.000188	T	0.69396	0.3106	M	0.65975	2.015	0.38631	D	0.951371	D	0.56287	0.975	P	0.62184	0.899	T	0.68685	-0.5343	10	0.37606	T	0.19	-18.5668	18.5336	0.91001	0.0:1.0:0.0:0.0	.	31	P07602	SAP_HUMAN	L	31;31;31;31;31;34	ENSP00000378394:V31L;ENSP00000378392:V31L	ENSP00000350063:V31L	V	-	1	0	PSAP	73264218	0.990000	0.36364	0.960000	0.40013	0.978000	0.69477	2.870000	0.48451	2.680000	0.91292	0.563000	0.77884	GTG	.	.		0.582	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778	
CHST3	9469	hgsc.bcm.edu	37	10	73767711	73767711	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:73767711G>A	ENST00000373115.4	+	3	1359	c.922G>A	c.(922-924)Gcc>Acc	p.A308T		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	308					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						GGCCGTGCTGGCCTCGCGCAT	0.701																																					p.A308T		Atlas-SNP	.											.	CHST3	36	.	0			c.G922A						.						5.0	6.0	6.0					10																	73767711		1903	3753	5656	SO:0001583	missense	9469	exon3			GTGCTGGCCTCGC	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"""Sulfotransferases, membrane-bound"""	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.922G>A	chr10.hg19:g.73767711G>A	ENSP00000362207:p.Ala308Thr	202.0	0.0		195.0	89.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	G	35	5.491125	0.96339	.	.	ENSG00000122863	ENST00000373115	D	0.83163	-1.69	5.55	5.55	0.83447	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.88683	0.6503	M	0.66506	2.035	0.80722	D	1	D	0.56746	0.977	P	0.57425	0.82	D	0.88319	0.2961	10	0.48119	T	0.1	-28.5478	18.5034	0.90889	0.0:0.0:1.0:0.0	.	308	Q7LGC8	CHST3_HUMAN	T	308	ENSP00000362207:A308T	ENSP00000362207:A308T	A	+	1	0	CHST3	73437717	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.855000	0.99526	2.630000	0.89119	0.561000	0.74099	GCC	.	.		0.701	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273	
ZMIZ1	57178	hgsc.bcm.edu	37	10	81065903	81065903	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:81065903C>T	ENST00000334512.5	+	22	3042	c.2470C>T	c.(2470-2472)Ccg>Tcg	p.P824S	ZMIZ1_ENST00000446377.2_5'Flank	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	824					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CAGCTGGCGGCCGGTGCCCAT	0.607																																					p.P824S		Atlas-SNP	.											.	ZMIZ1	101	.	0			c.C2470T						.						69.0	58.0	61.0					10																	81065903		2203	4300	6503	SO:0001583	missense	57178	exon22			TGGCGGCCGGTGC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.2470C>T	chr10.hg19:g.81065903C>T	ENSP00000334474:p.Pro824Ser	51.0	0.0		42.0	14.0	NM_020338	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	hg19	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422601	0.83559	.	.	ENSG00000108175	ENST00000334512;ENST00000360331;ENST00000372347	T	0.39997	1.05	4.6	4.6	0.57074	.	0.000000	0.41396	D	0.000894	T	0.66703	0.2816	M	0.80183	2.485	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.72520	-0.4268	10	0.62326	D	0.03	-7.5952	17.8001	0.88584	0.0:1.0:0.0:0.0	.	824	Q9ULJ6	ZMIZ1_HUMAN	S	824;754;726	ENSP00000334474:P824S	ENSP00000334474:P824S	P	+	1	0	ZMIZ1	80735909	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.458000	0.80787	2.275000	0.75901	0.491000	0.48974	CCG	.	.		0.607	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338	
WAPAL	23063	hgsc.bcm.edu	37	10	88197700	88197700	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:88197700A>T	ENST00000298767.5	-	18	3956	c.3484T>A	c.(3484-3486)Ttt>Att	p.F1162I	WAPAL_ENST00000263070.7_Missense_Mutation_p.F374I|WAPAL_ENST00000484070.1_5'UTR|WAPAL_ENST00000372075.1_Missense_Mutation_p.F374I	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	1162	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						AAACTCAAAAATTTTTTGAGC	0.318																																					p.F1162I		Atlas-SNP	.											.	WAPAL	81	.	0			c.T3484A						.						54.0	61.0	59.0					10																	88197700		2203	4300	6503	SO:0001583	missense	23063	exon18			TCAAAAATTTTTT	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.3484T>A	chr10.hg19:g.88197700A>T	ENSP00000298767:p.Phe1162Ile	497.0	0.0		415.0	133.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	A	35	5.443210	0.96187	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T;T;T	0.40476	1.03;1.03;1.03	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.65760	0.2722	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.87578	0.986;0.998;0.986;0.996	T	0.69826	-0.5040	10	0.87932	D	0	.	16.0204	0.80478	1.0:0.0:0.0:0.0	.	1156;1200;1162;1199	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	I	1247;1162;1247;374;374	ENSP00000298767:F1162I;ENSP00000361145:F374I;ENSP00000263070:F374I	ENSP00000263070:F374I	F	-	1	0	WAPAL	88187680	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.950000	0.93019	2.174000	0.68829	0.533000	0.62120	TTT	.	.		0.318	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	
PANK1	53354	hgsc.bcm.edu	37	10	91371568	91371568	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:91371568C>A	ENST00000307534.4	-	2	1096	c.941G>T	c.(940-942)aGc>aTc	p.S314I	PANK1_ENST00000342512.3_Missense_Mutation_p.S89I|PANK1_ENST00000322191.6_Missense_Mutation_p.S89I|PANK1_ENST00000371774.2_Missense_Mutation_p.S116I	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	314					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell periphery (GO:0071944)|clathrin coat (GO:0030118)|cytosol (GO:0005829)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11						CATAGCACAGCTGGGAAAGCG	0.527																																					p.S314I		Atlas-SNP	.											.	PANK1	35	.	0			c.G941T						.						92.0	79.0	83.0					10																	91371568		2203	4300	6503	SO:0001583	missense	53354	exon2			GCACAGCTGGGAA	AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782			8598	protein-coding gene	gene with protein product		606160	"""pantothenate kinase"""	PANK		11809413	Standard	NM_148977		Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.941G>T	chr10.hg19:g.91371568C>A	ENSP00000302108:p.Ser314Ile	134.0	0.0		128.0	51.0	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Missense_Mutation	SNP	ENST00000307534.4	hg19	CCDS31244.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.011705	0.54468	.	.	ENSG00000152782	ENST00000342512;ENST00000322191;ENST00000371774;ENST00000307534;ENST00000371775	D;D;D;D	0.99503	-6.03;-6.03;-6.03;-6.03	6.11	4.11	0.48088	.	0.133324	0.64402	D	0.000001	D	0.98845	0.9610	L	0.35854	1.095	0.41211	D	0.986442	B;D;B;B	0.58620	0.215;0.983;0.0;0.215	B;P;B;B	0.55923	0.067;0.787;0.003;0.067	D	0.99816	1.1044	10	0.72032	D	0.01	.	16.7682	0.85529	0.0:0.5528:0.4472:0.0	.	116;314;89;89	Q8TE04-4;Q8TE04;Q8TE04-3;Q8TE04-2	.;PANK1_HUMAN;.;.	I	89;89;116;314;177	ENSP00000345118:S89I;ENSP00000318526:S89I;ENSP00000360839:S116I;ENSP00000302108:S314I	ENSP00000302108:S314I	S	-	2	0	PANK1	91361548	0.992000	0.36948	1.000000	0.80357	0.997000	0.91878	1.911000	0.39937	1.459000	0.47892	0.655000	0.94253	AGC	.	.		0.527	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
KIF20B	9585	hgsc.bcm.edu	37	10	91520371	91520371	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:91520371A>T	ENST00000371728.3	+	28	4834	c.4769A>T	c.(4768-4770)gAa>gTa	p.E1590V	KIF20B_ENST00000416354.1_Missense_Mutation_p.E1620V|KIF20B_ENST00000260753.4_Missense_Mutation_p.E1550V|KIF20B_ENST00000394289.2_Missense_Mutation_p.E1590V|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1590	Interaction with PIN1.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						ACAAGTTTTGAAATTTCCAGA	0.353																																					p.E1550V		Atlas-SNP	.											.	KIF20B	191	.	0			c.A4649T						.						56.0	55.0	55.0					10																	91520371		2203	4300	6503	SO:0001583	missense	9585	exon28			GTTTTGAAATTTC	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.4769A>T	chr10.hg19:g.91520371A>T	ENSP00000360793:p.Glu1590Val	307.0	0.0		257.0	97.0	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	13.94	2.386794	0.42308	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	4.7	4.7	0.59300	.	0.132784	0.34178	N	0.004193	T	0.49150	0.1540	L	0.42245	1.32	0.33487	D	0.588244	D;D	0.61697	0.964;0.99	P;P	0.59487	0.601;0.858	T	0.60840	-0.7183	10	0.42905	T	0.14	-10.075	10.7268	0.46072	1.0:0.0:0.0:0.0	.	1590;1550	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	V	1550;1620;1590;1590	ENSP00000260753:E1550V;ENSP00000411545:E1620V;ENSP00000377830:E1590V;ENSP00000360793:E1590V	ENSP00000260753:E1550V	E	+	2	0	KIF20B	91510351	1.000000	0.71417	0.991000	0.47740	0.351000	0.29236	3.735000	0.55044	2.112000	0.64535	0.482000	0.46254	GAA	.	.		0.353	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
ANKRD1	27063	hgsc.bcm.edu	37	10	92675939	92675939	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:92675939C>T	ENST00000371697.3	-	6	888	c.640G>A	c.(640-642)Gcc>Acc	p.A214T		NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	214					cardiac muscle tissue morphogenesis (GO:0055008)|cellular lipid metabolic process (GO:0044255)|cellular response to drug (GO:0035690)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|skeletal muscle cell differentiation (GO:0035914)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I band (GO:0031674)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|p53 binding (GO:0002039)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|titin binding (GO:0031432)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|prostate(3)|skin(1)	27		Colorectal(252;0.0475)				TTATCTCGGGCGCTAATTTTT	0.527																																					p.A214T		Atlas-SNP	.											.	ANKRD1	50	.	0			c.G640A						.						84.0	81.0	82.0					10																	92675939		2203	4300	6503	SO:0001583	missense	27063	exon6			CTCGGGCGCTAAT	X83703	CCDS7412.1	10q23.33	2014-09-17			ENSG00000148677	ENSG00000148677		"""Ankyrin repeat domain containing"""	15819	protein-coding gene	gene with protein product		609599				7730328	Standard	NM_014391		Approved	C-193, ALRP, CARP, CVARP, MCARP	uc001khe.1	Q15327	OTTHUMG00000018734	ENST00000371697.3:c.640G>A	chr10.hg19:g.92675939C>T	ENSP00000360762:p.Ala214Thr	113.0	0.0		76.0	17.0	NM_014391	Q96LE7	Missense_Mutation	SNP	ENST00000371697.3	hg19	CCDS7412.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941171	0.53079	.	.	ENSG00000148677	ENST00000371697	T	0.65364	-0.15	5.35	4.44	0.53790	Ankyrin repeat-containing domain (4);	0.075470	0.56097	D	0.000039	T	0.55768	0.1941	L	0.52573	1.65	0.48135	D	0.999596	B	0.18863	0.031	B	0.21917	0.037	T	0.52555	-0.8560	10	0.30854	T	0.27	.	13.4315	0.61057	0.0:0.9243:0.0:0.0757	.	214	Q15327	ANKR1_HUMAN	T	214	ENSP00000360762:A214T	ENSP00000360762:A214T	A	-	1	0	ANKRD1	92665919	0.868000	0.29978	0.996000	0.52242	0.966000	0.64601	1.646000	0.37249	2.511000	0.84671	0.484000	0.47621	GCC	.	.		0.527	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391	
RRP12	23223	hgsc.bcm.edu	37	10	99131898	99131898	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:99131898C>G	ENST00000370992.4	-	20	2386	c.2275G>C	c.(2275-2277)Gcc>Ccc	p.A759P	RRP12_ENST00000414986.1_Missense_Mutation_p.A698P|RRP12_ENST00000315563.6_Missense_Mutation_p.A659P|RRP12_ENST00000536831.1_Missense_Mutation_p.A477P|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	759						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)		GGAGCCAAGGCCACGACCAGG	0.612																																					p.A759P		Atlas-SNP	.											.	RRP12	97	.	0			c.G2275C						.						85.0	68.0	73.0					10																	99131898		2203	4300	6503	SO:0001583	missense	23223	exon20			CCAAGGCCACGAC		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.2275G>C	chr10.hg19:g.99131898C>G	ENSP00000360031:p.Ala759Pro	75.0	0.0		77.0	17.0	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.917972	0.92249	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24	5.47	5.47	0.80525	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81484	0.4832	M	0.81942	2.565	0.80722	D	1	D;D;D;D	0.89917	0.999;0.996;1.0;0.998	D;D;D;D	0.75020	0.941;0.953;0.985;0.921	D	0.83454	0.0050	10	0.66056	D	0.02	-21.4836	13.5966	0.61994	0.0:0.9258:0.0:0.0742	.	698;659;477;759	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	P	759;659;698;477	ENSP00000360031:A759P;ENSP00000324315:A659P;ENSP00000414863:A698P;ENSP00000446184:A477P	ENSP00000324315:A659P	A	-	1	0	RRP12	99121888	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.492000	0.66893	2.568000	0.86640	0.655000	0.94253	GCC	.	.		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
PKD2L1	9033	hgsc.bcm.edu	37	10	102058491	102058491	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:102058491A>G	ENST00000318222.3	-	4	941	c.559T>C	c.(559-561)Ttc>Ctc	p.F187L	PKD2L1_ENST00000353274.3_Missense_Mutation_p.F187L|PKD2L1_ENST00000338519.3_Missense_Mutation_p.F187L	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	187					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		TAGTAGATGAAGGAGTGGGAG	0.547																																					p.F187L		Atlas-SNP	.											.	PKD2L1	103	.	0			c.T559C						.						83.0	83.0	83.0					10																	102058491		2203	4300	6503	SO:0001583	missense	9033	exon4			AGATGAAGGAGTG	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9011	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 3"""	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.559T>C	chr10.hg19:g.102058491A>G	ENSP00000325296:p.Phe187Leu	130.0	0.0		131.0	35.0	NM_016112	O75972|Q5W039|Q9UP35|Q9UPA2	Missense_Mutation	SNP	ENST00000318222.3	hg19	CCDS7492.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850504	0.71719	.	.	ENSG00000107593	ENST00000338519;ENST00000353274;ENST00000318222;ENST00000339977	T;T;T	0.69040	-0.37;-0.37;-0.37	5.32	5.32	0.75619	Polycystin cation channel, PKD1/PKD2 (1);	0.048691	0.85682	D	0.000000	T	0.58366	0.2117	L	0.41236	1.265	0.50632	D	0.999888	B;B	0.22480	0.07;0.004	B;B	0.26969	0.075;0.029	T	0.53954	-0.8365	10	0.21540	T	0.41	-21.7473	14.4704	0.67512	1.0:0.0:0.0:0.0	.	140;187	Q1L4F0;Q9P0L9	.;PK2L1_HUMAN	L	187	ENSP00000345068:F187L;ENSP00000266049:F187L;ENSP00000325296:F187L	ENSP00000325296:F187L	F	-	1	0	PKD2L1	102048481	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.449000	0.80643	2.015000	0.59207	0.459000	0.35465	TTC	.	.		0.547	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112	
SEMA4G	57715	hgsc.bcm.edu	37	10	102740362	102740362	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:102740362T>A	ENST00000370250.4	+	11	1752	c.1379T>A	c.(1378-1380)gTc>gAc	p.V460D	MRPL43_ENST00000318325.2_Intron|MRPL43_ENST00000370242.4_Intron|RP11-108L7.4_ENST00000447344.1_RNA|MRPL43_ENST00000370241.3_Intron|SEMA4G_ENST00000517724.1_Missense_Mutation_p.V460D|SEMA4G_ENST00000210633.3_Missense_Mutation_p.V460D	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	460	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		AAGGCCGTAGTCCTGGGCTCT	0.507																																					p.V460D		Atlas-SNP	.											.	SEMA4G	55	.	0			c.T1379A						.						119.0	111.0	114.0					10																	102740362		2203	4300	6503	SO:0001583	missense	57715	exon11			CCGTAGTCCTGGG	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.1379T>A	chr10.hg19:g.102740362T>A	ENSP00000359270:p.Val460Asp	108.0	0.0		117.0	43.0	NM_001203244	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	hg19		.	.	.	.	.	.	.	.	.	.	T	13.40	2.226411	0.39300	.	.	ENSG00000095539	ENST00000519649;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T	0.12147	2.71;2.71;2.71;2.71	5.02	5.02	0.67125	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.700209	0.14484	N	0.316768	T	0.13415	0.0325	L	0.37850	1.14	0.58432	D	0.999998	B;B;B	0.27594	0.14;0.182;0.148	B;B;B	0.32533	0.055;0.147;0.039	T	0.09618	-1.0666	10	0.15066	T	0.55	.	13.5579	0.61770	0.0:0.0:0.0:1.0	.	460;460;460	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	D	460	ENSP00000428896:V460D;ENSP00000359270:V460D;ENSP00000430175:V460D;ENSP00000210633:V460D	ENSP00000210633:V460D	V	+	2	0	SEMA4G	102730352	1.000000	0.71417	0.996000	0.52242	0.881000	0.50899	2.782000	0.47758	1.888000	0.54679	0.254000	0.18369	GTC	.	.		0.507	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2		
LDB1	8861	hgsc.bcm.edu	37	10	103870859	103870859	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:103870859A>G	ENST00000425280.1	-	4	558	c.216T>C	c.(214-216)ttT>ttC	p.F72F	LDB1_ENST00000361198.5_Silent_p.F36F|LDB1_ENST00000490751.1_5'UTR	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	72					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		TGTTAAGCTCAAATATTCTGT	0.542																																					p.F72F		Atlas-SNP	.											.	LDB1	61	.	0			c.T216C						.						162.0	160.0	161.0					10																	103870859		2203	4300	6503	SO:0001819	synonymous_variant	8861	exon4			AAGCTCAAATATT	AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"""carboxy terminal LIM domain protein 2"""	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.216T>C	chr10.hg19:g.103870859A>G		71.0	0.0		67.0	37.0	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Silent	SNP	ENST00000425280.1	hg19	CCDS44472.1																																																																																			.	.		0.542	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407	
RPEL1	729020	hgsc.bcm.edu	37	10	105005831	105005831	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:105005831G>A	ENST00000441178.2	+	1	188	c.78G>A	c.(76-78)atG>atA	p.M26I		NM_001143909.1	NP_001137381.1																					GCCTCCAGATGCTAGACTCTG	0.542																																					p.M26I		Atlas-SNP	.											.	.	.	.	0			c.G78A						.						113.0	97.0	102.0					10																	105005831		692	1591	2283	SO:0001583	missense	0	exon1			CCAGATGCTAGAC																												ENST00000441178.2:c.78G>A	chr10.hg19:g.105005831G>A	ENSP00000476672:p.Met26Ile	151.0	0.0		157.0	52.0	NM_001143909		Missense_Mutation	SNP	ENST00000441178.2	hg19																																																																																				.	.		0.542	RP11-332O19.5-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050120.2		
PDCD11	22984	hgsc.bcm.edu	37	10	105182857	105182857	+	Silent	SNP	C	C	A	rs141472462		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:105182857C>A	ENST00000369797.3	+	18	2704	c.2610C>A	c.(2608-2610)ccC>ccA	p.P870P		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	870					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GTCCAGTGCCCGACCTGGTCC	0.572																																					p.P870P		Atlas-SNP	.											.	PDCD11	160	.	0			c.C2610A						.						139.0	120.0	127.0					10																	105182857		2203	4300	6503	SO:0001819	synonymous_variant	22984	exon18			AGTGCCCGACCTG	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.2610C>A	chr10.hg19:g.105182857C>A		158.0	0.0		133.0	58.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	C|1.000;T|0.000		0.572	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
SLK	9748	hgsc.bcm.edu	37	10	105762305	105762305	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:105762305A>T	ENST00000369755.3	+	9	1914	c.1369A>T	c.(1369-1371)Ata>Tta	p.I457L	SLK_ENST00000335753.4_Missense_Mutation_p.I457L	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	457	Glu-rich.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TAATATAATGATAACCTTAGA	0.333																																					p.I457L	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A1369T						.						63.0	71.0	68.0					10																	105762305		2201	4294	6495	SO:0001583	missense	9748	exon9			ATAATGATAACCT		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1369A>T	chr10.hg19:g.105762305A>T	ENSP00000358770:p.Ile457Leu	107.0	0.0		101.0	46.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	5.939	0.357297	0.11239	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.68025	-0.3;-0.3	5.81	-0.969	0.10310	Protein kinase-like domain (1);	0.553031	0.18895	N	0.128204	T	0.51058	0.1652	L	0.36672	1.1	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.13407	0.009;0.002	T	0.34502	-0.9826	10	0.28530	T	0.3	.	10.9001	0.47047	0.5569:0.0:0.4431:0.0	.	457;457	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	L	457	ENSP00000336824:I457L;ENSP00000358770:I457L	ENSP00000336824:I457L	I	+	1	0	SLK	105752295	0.000000	0.05858	0.022000	0.16811	0.947000	0.59692	-0.165000	0.09968	-0.402000	0.07633	0.454000	0.30748	ATA	.	.		0.333	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
ITPRIP	85450	hgsc.bcm.edu	37	10	106075738	106075738	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:106075738C>T	ENST00000337478.1	-	2	243	c.72G>A	c.(70-72)ccG>ccA	p.P24P	RP11-127L20.5_ENST00000472915.2_RNA|ITPRIP_ENST00000278071.2_Silent_p.P24P|ITPRIP_ENST00000358187.2_Silent_p.P24P	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	24						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						CGTTCTCCCGCGGGAACAGCA	0.627																																					p.P24P		Atlas-SNP	.											.	ITPRIP	44	.	0			c.G72A						.						59.0	54.0	56.0					10																	106075738		2203	4300	6503	SO:0001819	synonymous_variant	85450	exon2			CTCCCGCGGGAAC	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"""KIAA1754"", ""inositol 1,4,5-triphosphate receptor interacting protein"""	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.72G>A	chr10.hg19:g.106075738C>T		52.0	0.0		52.0	17.0	NM_001272013	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Silent	SNP	ENST00000337478.1	hg19	CCDS7557.1																																																																																			.	.		0.627	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397	
SMC3	9126	hgsc.bcm.edu	37	10	112337617	112337617	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:112337617C>T	ENST00000361804.4	+	6	421	c.295C>T	c.(295-297)Cga>Tga	p.R99*	snoU13_ENST00000458966.1_RNA|SMC3_ENST00000462899.1_3'UTR	NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	99					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		AGTTTCACTTCGAAGAGTTAT	0.279																																					p.R99X		Atlas-SNP	.											SMC3,NS,carcinoma,0,2	SMC3	103	.	0			c.C295T						.						75.0	79.0	78.0					10																	112337617		2203	4300	6503	SO:0001587	stop_gained	9126	exon6			TCACTTCGAAGAG	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"""Structural maintenance of chromosomes proteins"", ""Proteoglycans / Extracellular Matrix : Other"""	2468	protein-coding gene	gene with protein product	"""bamacan proteoglycan"""	606062	"""chondroitin sulfate proteoglycan 6 (bamacan)"""	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.295C>T	chr10.hg19:g.112337617C>T	ENSP00000354720:p.Arg99*	88.0	0.0		59.0	24.0	NM_005445	A8K156|O60464|Q5T482	Nonsense_Mutation	SNP	ENST00000361804.4	hg19	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	C	37	6.011302	0.97200	.	.	ENSG00000108055	ENST00000361804	.	.	.	5.67	3.75	0.43078	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7855	0.40673	0.25:0.6835:0.0:0.0665	.	.	.	.	X	99	.	ENSP00000354720:R99X	R	+	1	2	SMC3	112327607	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.597000	0.61062	0.687000	0.31509	0.460000	0.39030	CGA	.	.		0.279	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445	
TCF7L2	6934	hgsc.bcm.edu	37	10	114901029	114901029	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:114901029G>A	ENST00000355995.4	+	6	1146	c.639G>A	c.(637-639)ccG>ccA	p.P213P	TCF7L2_ENST00000369395.1_Silent_p.P238P|TCF7L2_ENST00000352065.5_Silent_p.P190P|TCF7L2_ENST00000543371.1_Silent_p.P213P|TCF7L2_ENST00000538897.1_Silent_p.P213P|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000355717.4_Silent_p.P237P|TCF7L2_ENST00000545257.1_Silent_p.P213P|TCF7L2_ENST00000369397.4_Silent_p.P190P|TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000349937.2_Silent_p.P213P|TCF7L2_ENST00000536810.1_Silent_p.P213P|TCF7L2_ENST00000534894.1_Silent_p.P213P			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	213	Mediates interaction with MAD2L2.|Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|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 type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		ACTTCACGCCGGGAAACCCAC	0.587			T	VTI1A	colorectal																																p.P237P		Atlas-SNP	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.G711A						.						157.0	130.0	139.0					10																	114901029		2203	4300	6503	SO:0001819	synonymous_variant	6934	exon6			CACGCCGGGAAAC	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.639G>A	chr10.hg19:g.114901029G>A		138.0	0.0		104.0	32.0	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Silent	SNP	ENST00000355995.4	hg19																																																																																				.	.		0.587	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756	
CCDC172	374355	hgsc.bcm.edu	37	10	118116936	118116936	+	Nonsense_Mutation	SNP	C	C	T	rs201464805		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:118116936C>T	ENST00000333254.3	+	6	744	c.493C>T	c.(493-495)Caa>Taa	p.Q165*		NM_198515.2	NP_940917.1	P0C7W6	CC172_HUMAN	coiled-coil domain containing 172	165																	AAATGAACTTCAAAAACAAAA	0.274																																					p.Q165X		Atlas-SNP	.											.	.	.	.	0			c.C493T						.						41.0	43.0	42.0					10																	118116936		2185	4273	6458	SO:0001587	stop_gained	374355	exon6			GAACTTCAAAAAC	BC044830	CCDS31291.1	10q26.11-q26.12	2012-05-31	2012-05-31	2012-05-31	ENSG00000182645	ENSG00000182645			30524	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 96"""	C10orf96		12477932	Standard	NM_198515		Approved	MGC35062	uc001lck.3	P0C7W6	OTTHUMG00000019098	ENST00000333254.3:c.493C>T	chr10.hg19:g.118116936C>T	ENSP00000329860:p.Gln165*	249.0	0.0		229.0	10.0	NM_198515		Nonsense_Mutation	SNP	ENST00000333254.3	hg19	CCDS31291.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.685066	0.88639	.	.	ENSG00000182645	ENST00000333254	.	.	.	5.6	4.64	0.57946	.	0.215967	0.39407	N	0.001379	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-12.8496	15.2862	0.73831	0.1407:0.8593:0.0:0.0	.	.	.	.	X	165	.	ENSP00000329860:Q165X	Q	+	1	0	C10orf96	118106926	1.000000	0.71417	1.000000	0.80357	0.306000	0.27790	3.429000	0.52800	2.635000	0.89317	0.655000	0.94253	CAA	.	.		0.274	CCDC172-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050516.2	NM_198515	
VAX1	11023	hgsc.bcm.edu	37	10	118896110	118896110	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:118896110T>G	ENST00000369206.5	-	2	301	c.302A>C	c.(301-303)aAg>aCg	p.K101T	VAX1_ENST00000277905.2_Missense_Mutation_p.K101T	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	101					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		GCGCGTCCTCTTAGGCCGGTC	0.657																																					p.K101T		Atlas-SNP	.											.	VAX1	50	.	0			c.A302C						.						52.0	46.0	48.0					10																	118896110		2203	4300	6503	SO:0001583	missense	11023	exon2			GTCCTCTTAGGCC	AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"""Homeoboxes / ANTP class : NKL subclass"""	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.302A>C	chr10.hg19:g.118896110T>G	ENSP00000358207:p.Lys101Thr	109.0	0.0		123.0	59.0	NM_001112704	B1AVW5|Q6ZSX0	Missense_Mutation	SNP	ENST00000369206.5	hg19	CCDS44483.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.144273	0.57044	.	.	ENSG00000148704	ENST00000277905;ENST00000369206	D;D	0.97041	-4.22;-4.22	4.03	4.03	0.46877	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.055699	0.64402	D	0.000001	D	0.98147	0.9388	M	0.90650	3.135	0.58432	D	0.999999	D;D	0.58620	0.983;0.979	P;P	0.57502	0.822;0.801	D	0.98871	1.0766	10	0.87932	D	0	-4.7467	13.1035	0.59233	0.0:0.0:0.0:1.0	.	101;101	Q5SQQ9;Q5SQQ9-2	VAX1_HUMAN;.	T	101	ENSP00000277905:K101T;ENSP00000358207:K101T	ENSP00000277905:K101T	K	-	2	0	VAX1	118886100	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.431000	0.80335	1.691000	0.51100	0.374000	0.22700	AAG	.	.		0.657	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242	
CFAP46	54777	hgsc.bcm.edu	37	10	134628105	134628105	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:134628105G>A	ENST00000368586.5	-	53	7361	c.7261C>T	c.(7261-7263)Cca>Tca	p.P2421S	TTC40_ENST00000263170.5_Missense_Mutation_p.P582S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCCTCGTATGGGTCCACGACG	0.672																																					p.P2421S		Atlas-SNP	.											.	TTC40	100	.	0			c.C7261T						.						8.0	10.0	9.0					10																	134628105		2173	4262	6435	SO:0001583	missense	54777	exon53			CGTATGGGTCCAC																												ENST00000368586.5:c.7261C>T	chr10.hg19:g.134628105G>A	ENSP00000357575:p.Pro2421Ser	180.0	0.0		145.0	12.0	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	hg19	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	G	7.854	0.724657	0.15439	.	.	ENSG00000171811	ENST00000435957;ENST00000368586;ENST00000263170	T;T	0.34275	1.37;1.37	4.6	3.68	0.42216	.	0.000000	0.64402	D	0.000004	T	0.35189	0.0923	M	0.65498	2.005	0.80722	D	1	B	0.14805	0.011	B	0.16722	0.016	T	0.36237	-0.9756	10	0.62326	D	0.03	.	8.9802	0.35961	0.1072:0.0:0.8928:0.0	.	582	Q8IYW2	CJ092_HUMAN	S	4;2421;582	ENSP00000357575:P2421S;ENSP00000263170:P582S	ENSP00000263170:P582S	P	-	1	0	C10orf93	134478095	1.000000	0.71417	0.967000	0.41034	0.103000	0.19146	2.648000	0.46647	2.116000	0.64780	0.591000	0.81541	CCA	.	.		0.672	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
ATHL1	80162	hgsc.bcm.edu	37	11	294325	294325	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:294325A>C	ENST00000409548.2	+	13	1982	c.1867A>C	c.(1867-1869)Agc>Cgc	p.S623R	ATHL1_ENST00000409479.1_Missense_Mutation_p.S650R|ATHL1_ENST00000409655.1_Missense_Mutation_p.S375R	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	623					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)		CTCCAGAGTGAGCGTCTCCGG	0.622																																					p.S623R		Atlas-SNP	.											.	ATHL1	88	.	0			c.A1867C						.						73.0	78.0	76.0					11																	294325		2203	4300	6503	SO:0001583	missense	80162	exon13			AGAGTGAGCGTCT	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.1867A>C	chr11.hg19:g.294325A>C	ENSP00000387185:p.Ser623Arg	101.0	0.0		157.0	71.0	NM_025092	Q658X8|Q8TEG9|Q9H635	Missense_Mutation	SNP	ENST00000409548.2	hg19	CCDS31322.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.91|10.91	1.484496|1.484496	0.26598|0.26598	.|.	.|.	ENSG00000142102|ENSG00000142102	ENST00000397660|ENST00000409548;ENST00000409655;ENST00000409479	.|.	.|.	.|.	4.04|4.04	-8.08|-8.08	0.01094|0.01094	.|Six-hairpin glycosidase-like (1);	.|1.140950	.|0.06247	.|N	.|0.691374	T|T	0.20981|0.20981	0.0505|0.0505	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.15206|0.15206	-1.0445|-1.0445	5|9	.|0.33940	.|T	.|0.23	.|.	3.525|3.525	0.07756|0.07756	0.4002:0.3816:0.0986:0.1195|0.4002:0.3816:0.0986:0.1195	.|.	.|623;375	.|Q32M88;B8ZZ60	.|ATHL1_HUMAN;.	A|R	83|623;375;650	.|.	.|ENSP00000387099:S650R	E|S	+|+	2|1	0|0	ATHL1|ATHL1	284325|284325	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.109000|0.109000	0.19521|0.19521	-2.224000|-2.224000	0.01213|0.01213	-1.656000|-1.656000	0.01495|0.01495	0.379000|0.379000	0.24179|0.24179	GAG|AGC	.	.		0.622	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
LMNTD2	256329	hgsc.bcm.edu	37	11	554999	554999	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:554999T>C	ENST00000329451.3	-	14	1948	c.1886A>G	c.(1885-1887)gAc>gGc	p.D629G	RP11-496I9.1_ENST00000527620.1_RNA	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		629										NS(1)|breast(1)|central_nervous_system(1)|lung(4)|pancreas(1)	8		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;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCGGCAGGTGTCCGCGGTGAC	0.741																																					p.D629G		Atlas-SNP	.											.	C11orf35	22	.	0			c.A1886G						.						6.0	7.0	7.0					11																	554999		1809	3658	5467	SO:0001583	missense	256329	exon14			CAGGTGTCCGCGG																												ENST00000329451.3:c.1886A>G	chr11.hg19:g.554999T>C	ENSP00000331167:p.Asp629Gly	100.0	0.0		104.0	32.0	NM_173573		Missense_Mutation	SNP	ENST00000329451.3	hg19	CCDS7701.1	.	.	.	.	.	.	.	.	.	.	t	17.64	3.438947	0.63067	.	.	ENSG00000185522	ENST00000329451	T	0.52057	0.68	4.64	0.813	0.18749	.	0.379512	0.19440	N	0.114219	T	0.23688	0.0573	N	0.12182	0.205	0.09310	N	1	B	0.21821	0.061	B	0.19666	0.026	T	0.14282	-1.0478	10	0.72032	D	0.01	-14.6999	2.7658	0.05320	0.1906:0.2122:0.0:0.5972	.	629	Q8IXW0	CK035_HUMAN	G	629	ENSP00000331167:D629G	ENSP00000331167:D629G	D	-	2	0	C11orf35	544999	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-0.114000	0.10757	0.210000	0.20664	0.449000	0.29647	GAC	.	.		0.741	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2		
PHRF1	57661	hgsc.bcm.edu	37	11	609548	609548	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:609548G>A	ENST00000264555.5	+	14	4220	c.4092G>A	c.(4090-4092)gcG>gcA	p.A1364A	PHRF1_ENST00000413872.2_Silent_p.A1362A|PHRF1_ENST00000416188.2_Silent_p.A1363A|PHRF1_ENST00000533464.1_Silent_p.A1360A	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1364					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CGGATGTGGCGCCTGCGGGGA	0.692																																					p.A1363A		Atlas-SNP	.											.	PHRF1	188	.	0			c.G4089A						.						17.0	22.0	21.0					11																	609548		2011	4159	6170	SO:0001819	synonymous_variant	57661	exon14			TGTGGCGCCTGCG	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4092G>A	chr11.hg19:g.609548G>A		53.0	0.0		51.0	17.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.		0.692	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
PHRF1	57661	hgsc.bcm.edu	37	11	610607	610607	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:610607C>T	ENST00000264555.5	+	16	4651	c.4523C>T	c.(4522-4524)cCg>cTg	p.P1508L	PHRF1_ENST00000413872.2_Missense_Mutation_p.P1506L|PHRF1_ENST00000416188.2_Missense_Mutation_p.P1507L|PHRF1_ENST00000533464.1_Missense_Mutation_p.P1504L	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1508					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GGGAGCCTGCCGCTAGTGGGC	0.706																																					p.P1507L		Atlas-SNP	.											.	PHRF1	188	.	0			c.C4520T						.						15.0	20.0	19.0					11																	610607		2002	4143	6145	SO:0001583	missense	57661	exon16			GCCTGCCGCTAGT	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.4523C>T	chr11.hg19:g.610607C>T	ENSP00000264555:p.Pro1508Leu	97.0	0.0		111.0	45.0	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	C	12.95	2.090799	0.36855	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	D;D;D;D	0.82344	-1.59;-1.59;-1.6;-1.59	3.82	3.82	0.43975	.	0.000000	0.35555	N	0.003122	D	0.88760	0.6524	L	0.60455	1.87	0.19775	N	0.999955	D;D;D;D	0.76494	0.999;0.996;0.998;0.997	D;P;D;D	0.70935	0.956;0.852;0.971;0.936	T	0.82339	-0.0506	10	0.72032	D	0.01	-25.937	16.2035	0.82105	0.0:1.0:0.0:0.0	.	1504;1506;1507;1508	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	L	1508;1506;1507;1504	ENSP00000264555:P1508L;ENSP00000388589:P1506L;ENSP00000410626:P1507L;ENSP00000431870:P1504L	ENSP00000264555:P1508L	P	+	2	0	PHRF1	600607	0.115000	0.22152	0.010000	0.14722	0.008000	0.06430	3.200000	0.51051	2.074000	0.62210	0.491000	0.48974	CCG	.	.		0.706	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
EPS8L2	64787	hgsc.bcm.edu	37	11	721123	721123	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:721123C>T	ENST00000533256.1	+	9	992	c.617C>T	c.(616-618)gCg>gTg	p.A206V	EPS8L2_ENST00000530636.1_Missense_Mutation_p.A206V|EPS8L2_ENST00000318562.8_Missense_Mutation_p.A206V|EPS8L2_ENST00000526198.1_Missense_Mutation_p.A222V|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	206					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGGCCCGGCGCCCATCCCC	0.736																																					p.A206V		Atlas-SNP	.											.	EPS8L2	42	.	0			c.C617T						.						9.0	10.0	10.0					11																	721123		2067	4079	6146	SO:0001583	missense	64787	exon8			GCCCGGCGCCCAT	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.617C>T	chr11.hg19:g.721123C>T	ENSP00000435585:p.Ala206Val	103.0	0.0		115.0	17.0	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Missense_Mutation	SNP	ENST00000533256.1	hg19	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	c	17.29	3.352367	0.61293	.	.	ENSG00000177106	ENST00000318562;ENST00000533256;ENST00000530636;ENST00000526198	T;T;T;T	0.24723	1.93;1.93;1.93;1.84	3.38	3.38	0.38709	.	0.482476	0.17660	U	0.166358	T	0.23054	0.0557	L	0.53249	1.67	0.45354	D	0.998345	P;D;P	0.54772	0.614;0.968;0.614	B;B;B	0.38106	0.091;0.265;0.091	T	0.17930	-1.0353	10	0.66056	D	0.02	-14.7971	12.1482	0.54036	0.0:1.0:0.0:0.0	.	222;250;206	B7ZKL3;B4DFD2;Q9H6S3	.;.;ES8L2_HUMAN	V	206;206;206;222	ENSP00000320828:A206V;ENSP00000435585:A206V;ENSP00000436035:A206V;ENSP00000436230:A222V	ENSP00000320828:A206V	A	+	2	0	EPS8L2	711123	1.000000	0.71417	0.103000	0.21229	0.137000	0.21094	3.423000	0.52756	1.912000	0.55364	0.556000	0.70494	GCG	.	.		0.736	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
SLC25A22	79751	hgsc.bcm.edu	37	11	792953	792953	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:792953C>T	ENST00000320230.5	-	6	810	c.329G>A	c.(328-330)gGc>gAc	p.G110D	SLC25A22_ENST00000531214.1_Missense_Mutation_p.G110D|CEND1_ENST00000330106.4_5'Flank|CEND1_ENST00000524587.1_5'Flank	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22	110					L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCCCCACAGCCCGCCAGCAT	0.652																																					p.G110D	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	SLC25A22	19	.	0			c.G329A						.						40.0	35.0	37.0					11																	792953		2203	4298	6501	SO:0001583	missense	79751	exon6			CCACAGCCCGCCA	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310	ENST00000320230.5:c.329G>A	chr11.hg19:g.792953C>T	ENSP00000322020:p.Gly110Asp	81.0	0.0		98.0	44.0	NM_001191061	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000320230.5	hg19	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.294378	0.60086	.	.	ENSG00000177542	ENST00000320230;ENST00000531214;ENST00000481290;ENST00000531437;ENST00000533385;ENST00000526152;ENST00000528606;ENST00000527723;ENST00000531514;ENST00000528936	D;D;D;D;D;D;D;D;D;D	0.92249	-3.0;-3.0;-3.0;-3.0;-3.0;-1.88;-1.88;-1.88;-1.88;-1.88	4.14	4.14	0.48551	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.97654	0.9231	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99755	1.1019	10	0.87932	D	0	-22.1587	16.7938	0.85596	0.0:1.0:0.0:0.0	.	110	Q9H936	GHC1_HUMAN	D	110;110;135;106;110;110;110;110;110;110	ENSP00000322020:G110D;ENSP00000437236:G110D;ENSP00000431829:G135D;ENSP00000435862:G106D;ENSP00000434287:G110D;ENSP00000436745:G110D;ENSP00000437045:G110D;ENSP00000434479:G110D;ENSP00000433780:G110D;ENSP00000432817:G110D	ENSP00000322020:G110D	G	-	2	0	SLC25A22	782953	1.000000	0.71417	0.662000	0.29724	0.058000	0.15608	4.732000	0.62029	2.027000	0.59764	0.591000	0.81541	GGC	.	.		0.652	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2		
AP2A2	161	hgsc.bcm.edu	37	11	972110	972110	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:972110C>T	ENST00000448903.2	+	4	469	c.328C>T	c.(328-330)Cgc>Tgc	p.R110C	AP2A2_ENST00000534328.1_Missense_Mutation_p.R110C|AP2A2_ENST00000332231.5_Missense_Mutation_p.R110C	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	110					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGAGCTGATCCGCCTGATCAA	0.557																																					p.R110C		Atlas-SNP	.											.	AP2A2	50	.	0			c.C328T						.						88.0	82.0	84.0					11																	972110		2086	4220	6306	SO:0001583	missense	161	exon4			CTGATCCGCCTGA	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.328C>T	chr11.hg19:g.972110C>T	ENSP00000413234:p.Arg110Cys	51.0	0.0		66.0	30.0	NM_012305	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.412342	0.42817	.	.	ENSG00000183020	ENST00000534328;ENST00000417081;ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310;ENST00000531548;ENST00000534485;ENST00000527024;ENST00000526753;ENST00000530801;ENST00000524559	T;T;T;T;T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74	3.24	2.33	0.28932	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.46718	0.1407	M	0.80332	2.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.971	T	0.42716	-0.9435	10	0.62326	D	0.03	-12.8407	6.6073	0.22731	0.177:0.7279:0.0:0.0951	.	110;110	O94973-2;O94973	.;AP2A2_HUMAN	C	110;110;110;110;110;110;110;116;100;104;34;34;34	ENSP00000436059:R110C;ENSP00000413234:R110C;ENSP00000327694:R110C;ENSP00000433498:R116C;ENSP00000435756:R100C;ENSP00000434563:R104C;ENSP00000435863:R34C;ENSP00000434553:R34C;ENSP00000434432:R34C	ENSP00000327694:R110C	R	+	1	0	AP2A2	962110	1.000000	0.71417	0.983000	0.44433	0.398000	0.30690	3.436000	0.52856	0.957000	0.37930	-0.136000	0.14681	CGC	.	.		0.557	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305	
MUC6	4588	hgsc.bcm.edu	37	11	1015776	1015776	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:1015776G>A	ENST00000421673.2	-	31	7075	c.7025C>T	c.(7024-7026)aCg>aTg	p.T2342M		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2342	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGAGGTGGGCGTAGGTGTCCC	0.627																																					p.T2342M		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	.	0			c.C7025T						.						61.0	69.0	66.0					11																	1015776		2147	4253	6400	SO:0001583	missense	4588	exon31			GTGGGCGTAGGTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.7025C>T	chr11.hg19:g.1015776G>A	ENSP00000406861:p.Thr2342Met	137.0	0.0		190.0	73.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	6.274	0.418687	0.11870	.	.	ENSG00000184956	ENST00000421673	T	0.18810	2.19	3.22	-2.25	0.06888	.	.	.	.	.	T	0.08537	0.0212	N	0.14661	0.345	0.09310	N	1	D	0.56035	0.974	B	0.40134	0.32	T	0.14699	-1.0463	9	0.42905	T	0.14	.	1.3153	0.02106	0.2334:0.1645:0.4348:0.1673	.	2342	Q6W4X9	MUC6_HUMAN	M	2342	ENSP00000406861:T2342M	ENSP00000406861:T2342M	T	-	2	0	MUC6	1005776	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.153000	0.10144	-0.612000	0.05701	0.448000	0.29417	ACG	.	.		0.627	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
CDKN1C	1028	hgsc.bcm.edu	37	11	2905227	2905227	+	Splice_Site	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:2905227A>G	ENST00000414822.3	-	2	1348		c.e2+1		CDKN1C_ENST00000313407.6_Splice_Site|CDKN1C_ENST00000380725.1_Splice_Site|CDKN1C_ENST00000430149.2_Splice_Site|CDKN1C_ENST00000440480.2_Splice_Site	NM_000076.2	NP_000067.1	P49918	CDN1C_HUMAN	cyclin-dependent kinase inhibitor 1C (p57, Kip2)						adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			central_nervous_system(1)|lung(1)	2		all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		CGCTGTACTCACTTGGCTCAC	0.731																																					.	GBM(111;59 1151 2497 5746 16112 18241 29216)	Atlas-SNP	.											.	CDKN1C	4	.	0			c.923+2T>C						.						4.0	6.0	5.0					11																	2905227		2008	4065	6073	SO:0001630	splice_region_variant	1028	exon4			GTACTCACTTGGC	D64137	CCDS7738.1, CCDS44519.1	11p15.5	2014-09-17	2004-02-13		ENSG00000129757	ENSG00000129757			1786	protein-coding gene	gene with protein product		600856	"""Beckwith-Wiedemann syndrome"""	BWCR, BWS		7729684	Standard	NM_000076		Approved	P57, KIP2	uc001lws.4	P49918	OTTHUMG00000010040	ENST00000414822.3:c.948+1T>C	chr11.hg19:g.2905227A>G		178.0	0.0		154.0	67.0	NM_001122630		Splice_Site	SNP	ENST00000414822.3	hg19	CCDS7738.1	.	.	.	.	.	.	.	.	.	.	A	7.253	0.603559	0.14002	.	.	ENSG00000129757	ENST00000380725	.	.	.	2.61	-0.095	0.13643	.	.	.	.	.	.	.	.	.	.	.	0.30522	N	0.768361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3117	0.32075	0.6096:0.3904:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDKN1C	2861803	1.000000	0.71417	0.007000	0.13788	0.418000	0.31294	4.726000	0.61986	-0.021000	0.14009	0.402000	0.26972	.	.	.		0.731	CDKN1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027774.2	NM_000076	Intron
RHOG	391	hgsc.bcm.edu	37	11	3848965	3848965	+	Missense_Mutation	SNP	G	G	A	rs535699358		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:3848965G>A	ENST00000351018.4	-	2	561	c.404C>T	c.(403-405)gCg>gTg	p.A135V	RHOG_ENST00000396978.1_Missense_Mutation_p.A135V|RHOG_ENST00000533217.1_Missense_Mutation_p.A135V|RHOG_ENST00000396979.1_Missense_Mutation_p.A135V	NM_001665.3	NP_001656.2	P84095	RHOG_HUMAN	ras homolog family member G	135					actin cytoskeleton organization (GO:0030036)|activation of Rac GTPase activity (GO:0032863)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|GTP catabolic process (GO:0006184)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of transcription, DNA-templated (GO:0045893)|Rac protein signal transduction (GO:0016601)|regulation of ruffle assembly (GO:1900027)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)	2		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0349)|LUSC - Lung squamous cell carcinoma(625;0.194)		TGTGATGGGCGCCTGGCCCTG	0.642													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19567	0.0		0.0	False		,,,				2504	0.0				p.A135V		Atlas-SNP	.											.	RHOG	13	.	0			c.C404T						.						50.0	46.0	47.0					11																	3848965		2201	4298	6499	SO:0001583	missense	391	exon2			ATGGGCGCCTGGC	X61587	CCDS7748.1	11p15.5-p15.4	2012-02-27	2012-02-27	2004-03-24	ENSG00000177105	ENSG00000177105			672	protein-coding gene	gene with protein product		179505	"""ras homolog gene family, member G (rho G)"""	ARHG		8325658	Standard	NM_001665		Approved	RhoG, MGC125835, MGC125836	uc001lyu.2	P84095	OTTHUMG00000012287	ENST00000351018.4:c.404C>T	chr11.hg19:g.3848965G>A	ENSP00000339467:p.Ala135Val	98.0	0.0		63.0	24.0	NM_001665	P35238|Q8NI04	Missense_Mutation	SNP	ENST00000351018.4	hg19	CCDS7748.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089368	0.36855	.	.	ENSG00000177105	ENST00000351018;ENST00000396979;ENST00000396978;ENST00000533217	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.45	3.58	0.41010	Small GTP-binding protein domain (1);	0.392675	0.30455	N	0.009589	T	0.57066	0.2028	N	0.12182	0.205	0.41724	D	0.989528	B	0.15473	0.013	B	0.08055	0.003	T	0.53704	-0.8401	10	0.46703	T	0.11	.	6.4443	0.21867	0.2747:0.0:0.7253:0.0	.	135	P84095	RHOG_HUMAN	V	135	ENSP00000339467:A135V;ENSP00000380176:A135V;ENSP00000380175:A135V;ENSP00000436932:A135V	ENSP00000339467:A135V	A	-	2	0	RHOG	3805541	0.996000	0.38824	0.970000	0.41538	0.978000	0.69477	2.379000	0.44318	1.285000	0.44548	0.563000	0.77884	GCG	.	.		0.642	RHOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034125.2	NM_001665	
ST5	6764	hgsc.bcm.edu	37	11	8751983	8751983	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:8751983A>G	ENST00000534127.1	-	6	1239	c.854T>C	c.(853-855)aTc>aCc	p.I285T	ST5_ENST00000357665.1_Missense_Mutation_p.I285T|ST5_ENST00000313726.6_Missense_Mutation_p.I285T|ST5_ENST00000526757.1_Intron|ST5_ENST00000530438.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	285					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		AATTTTCTGGATCCGGCTCAG	0.642																																					p.I285T		Atlas-SNP	.											.	ST5	85	.	0			c.T854C						.						42.0	51.0	48.0					11																	8751983		2187	4280	6467	SO:0001583	missense	6764	exon6			TTCTGGATCCGGC	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.854T>C	chr11.hg19:g.8751983A>G	ENSP00000433528:p.Ile285Thr	48.0	0.0		42.0	11.0	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	hg19	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.442880	0.83993	.	.	ENSG00000166444	ENST00000534127;ENST00000313726;ENST00000357665	T;T;T	0.23950	1.88;1.88;1.88	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.63843	1.955	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	T	0.38243	-0.9670	10	0.87932	D	0	-17.9635	16.8222	0.85835	1.0:0.0:0.0:0.0	.	285	P78524	ST5_HUMAN	T	285	ENSP00000433528:I285T;ENSP00000319678:I285T;ENSP00000350294:I285T	ENSP00000319678:I285T	I	-	2	0	ST5	8708559	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.901000	0.92560	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.642	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
DENND5A	23258	hgsc.bcm.edu	37	11	9161225	9161225	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:9161225T>G	ENST00000328194.3	-	23	4177	c.3857A>C	c.(3856-3858)gAc>gCc	p.D1286A	DENND5A_ENST00000527700.1_Missense_Mutation_p.D629A|DENND5A_ENST00000530044.1_3'UTR|SCUBE2_ENST00000534295.1_5'Flank	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	1286					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						AGGTCAGATGTCGATGCCCTT	0.512																																					p.D1286A		Atlas-SNP	.											.	DENND5A	84	.	0			c.A3857C						.						111.0	76.0	88.0					11																	9161225		2201	4296	6497	SO:0001583	missense	23258	exon23			CAGATGTCGATGC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.3857A>C	chr11.hg19:g.9161225T>G	ENSP00000328524:p.Asp1286Ala	30.0	0.0		39.0	13.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.62|14.62	2.588559|2.588559	0.46110|0.46110	.|.	.|.	ENSG00000184014|ENSG00000184014	ENST00000328194;ENST00000527700|ENST00000528725;ENST00000533737	T;T|.	0.20598|.	3.58;2.06|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	0.092310|.	0.85682|.	D|.	0.000000|.	T|T	0.62889|0.62889	0.2465|0.2465	L|L	0.56769|0.56769	1.78|1.78	0.42395|0.42395	D|D	0.992548|0.992548	B|.	0.31790|.	0.34|.	B|.	0.32465|.	0.146|.	T|T	0.62886|0.62886	-0.6759|-0.6759	10|5	0.66056|.	D|.	0.02|.	.|.	10.6809|10.6809	0.45813|0.45813	0.0:0.0747:0.0:0.9253|0.0:0.0747:0.0:0.9253	.|.	1286|.	Q6IQ26|.	DEN5A_HUMAN|.	A|P	1286;629|185;194	ENSP00000328524:D1286A;ENSP00000432549:D629A|.	ENSP00000328524:D1286A|.	D|T	-|-	2|1	0|0	DENND5A|DENND5A	9117801|9117801	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	3.788000|3.788000	0.55446|0.55446	2.064000|2.064000	0.61679|0.61679	0.460000|0.460000	0.39030|0.39030	GAC|ACA	.	.		0.512	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
SPON1	10418	hgsc.bcm.edu	37	11	14264943	14264943	+	RNA	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:14264943G>A	ENST00000310358.7	+	0	1425							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		CTCTCAACGTGTAAGTAACAC	0.488																																					.		Atlas-SNP	.											.	SPON1	65	.	0			c.889+1G>A						.						43.0	49.0	47.0					11																	14264943		2004	4167	6171			10418	exon7			CAACGTGTAAGTA	AB018305	CCDS73262.1	11p15.2	2014-05-06	2004-03-05		ENSG00000152268	ENSG00000262655			11252	protein-coding gene	gene with protein product		604989	"""spondin 1, (f-spondin) extracellular matrix protein"""			9872452	Standard	NM_006108		Approved	KIAA0762, f-spondin	uc001mle.3	Q9HCB6	OTTHUMG00000181576		chr11.hg19:g.14264943G>A		103.0	0.0		56.0	25.0	NM_006108	A8K6W5|O94862|Q8NCD7|Q8WUR5	Splice_Site	SNP	ENST00000310358.7	hg19		.	.	.	.	.	.	.	.	.	.	G	23.4	4.408592	0.83340	.	.	ENSG00000152268	ENST00000310358	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2499	0.66013	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPON1	14221519	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.447000	0.80620	2.422000	0.82143	0.555000	0.69702	.	.	.		0.488	SPON1-201	KNOWN	basic	processed_transcript	processed_transcript		NM_145584	
NAV2	89797	hgsc.bcm.edu	37	11	20119177	20119177	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:20119177G>A	ENST00000396087.3	+	34	6343	c.6244G>A	c.(6244-6246)Gtt>Att	p.V2082I	NAV2_ENST00000533917.1_Missense_Mutation_p.V1087I|NAV2_ENST00000349880.4_Missense_Mutation_p.V2023I|NAV2_ENST00000396085.1_Missense_Mutation_p.V2026I|NAV2_ENST00000527559.2_Missense_Mutation_p.V2011I|NAV2_ENST00000311043.8_Missense_Mutation_p.V1087I|NAV2_ENST00000360655.4_Missense_Mutation_p.V1959I|NAV2_ENST00000540292.1_Missense_Mutation_p.V2013I	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2082					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TTCAGACAGCGTTCTTGGCTA	0.458																																					p.V2082I		Atlas-SNP	.											.	NAV2	255	.	0			c.G6244A						.						109.0	105.0	106.0					11																	20119177		2203	4300	6503	SO:0001583	missense	89797	exon33			GACAGCGTTCTTG	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.6244G>A	chr11.hg19:g.20119177G>A	ENSP00000379396:p.Val2082Ile	126.0	0.0		95.0	33.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	G	5.485	0.274451	0.10403	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000311043	T;T;T;T;T;T;T;T	0.22336	1.99;2.09;2.1;2.07;1.96;1.96;3.62;3.62	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000015	T	0.14657	0.0354	N	0.02286	-0.61	0.80722	D	1	P;P;P;D	0.52996	0.832;0.939;0.782;0.957	B;B;B;P	0.48738	0.252;0.406;0.436;0.588	T	0.33111	-0.9881	9	.	.	.	.	19.9617	0.97254	0.0:0.0:1.0:0.0	.	2026;1087;2023;1959	A7E2D6;Q8IVL1-5;Q8IVL1-3;Q8IVL1-4	.;.;.;.	I	1959;2026;2023;2082;2011;2013;1087;1087	ENSP00000353871:V1959I;ENSP00000379394:V2026I;ENSP00000309577:V2023I;ENSP00000379396:V2082I;ENSP00000435395:V2011I;ENSP00000443489:V2013I;ENSP00000437316:V1087I;ENSP00000312169:V1087I	.	V	+	1	0	NAV2	20075753	1.000000	0.71417	0.157000	0.22605	0.332000	0.28634	6.732000	0.74790	2.894000	0.99253	0.655000	0.94253	GTT	.	.		0.458	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
NELL1	4745	hgsc.bcm.edu	37	11	21135203	21135203	+	Silent	SNP	T	T	C	rs561468649		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:21135203T>C	ENST00000357134.5	+	13	1521	c.1369T>C	c.(1369-1371)Tta>Cta	p.L457L	NELL1_ENST00000532434.1_Silent_p.L457L|NELL1_ENST00000325319.5_Silent_p.L400L|NELL1_ENST00000298925.5_Silent_p.L485L	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	457	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						CCTTCCTGGGTTATATCGCTG	0.393																																					p.L457L		Atlas-SNP	.											.	NELL1	179	.	0			c.T1369C						.						353.0	303.0	320.0					11																	21135203		2203	4300	6503	SO:0001819	synonymous_variant	4745	exon13			CCTGGGTTATATC	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1369T>C	chr11.hg19:g.21135203T>C		148.0	0.0		177.0	71.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	hg19	CCDS7855.1																																																																																			.	.		0.393	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
ARL14EP	120534	hgsc.bcm.edu	37	11	30354502	30354502	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:30354502A>G	ENST00000282032.3	+	3	731	c.516A>G	c.(514-516)aaA>aaG	p.K172K		NM_152316.1	NP_689529.1	Q8N8R7	AL14E_HUMAN	ADP-ribosylation factor-like 14 effector protein	172						cytoplasm (GO:0005737)											AAAGAGAAAAAAGAAGGCTTA	0.408																																					p.K172K		Atlas-SNP	.											.	.	.	.	0			c.A516G						.						68.0	65.0	66.0					11																	30354502		2202	4299	6501	SO:0001819	synonymous_variant	120534	exon3			AGAAAAAAGAAGG	AK096287	CCDS7869.1	11p14.1	2014-09-17	2012-07-09	2012-07-09	ENSG00000152219	ENSG00000152219			26798	protein-coding gene	gene with protein product		612295	"""chromosome 11 open reading frame 46"""	C11orf46		21458045	Standard	XM_005252792		Approved	FLJ38968, ARF7EP	uc001mso.1	Q8N8R7	OTTHUMG00000166154	ENST00000282032.3:c.516A>G	chr11.hg19:g.30354502A>G		64.0	0.0		85.0	37.0	NM_152316	Q5HYH9	Silent	SNP	ENST00000282032.3	hg19	CCDS7869.1																																																																																			.	.		0.408	ARL14EP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388129.1	NM_152316	
MPPED2	744	hgsc.bcm.edu	37	11	30435807	30435807	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:30435807G>A	ENST00000358117.5	-	5	856	c.734C>T	c.(733-735)cCc>cTc	p.P245L	MPPED2_ENST00000524667.1_5'UTR|MPPED2_ENST00000448418.2_Missense_Mutation_p.P245L	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	245					nervous system development (GO:0007399)		hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(15)|skin(2)|upper_aerodigestive_tract(2)	33						ATGGAGCTTGGGCCGGACTCG	0.478																																					p.P245L		Atlas-SNP	.											.	MPPED2	106	.	0			c.C734T						.						122.0	109.0	114.0					11																	30435807		2202	4299	6501	SO:0001583	missense	744	exon5			AGCTTGGGCCGGA	U57911	CCDS7870.1, CCDS44560.1	11p13	2008-07-18	2005-10-10	2005-10-10	ENSG00000066382	ENSG00000066382			1180	protein-coding gene	gene with protein product		600911	"""chromosome 11 open reading frame 8"""	C11orf8		8666403, 9266672	Standard	NM_001584		Approved	239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1	uc001msr.3	Q15777	OTTHUMG00000166159	ENST00000358117.5:c.734C>T	chr11.hg19:g.30435807G>A	ENSP00000350833:p.Pro245Leu	130.0	0.0		102.0	44.0	NM_001584	D3DQZ5|E9PB10|Q59GE6	Missense_Mutation	SNP	ENST00000358117.5	hg19	CCDS7870.1	.	.	.	.	.	.	.	.	.	.	G	34	5.346944	0.95807	.	.	ENSG00000066382	ENST00000448418;ENST00000358117	T;T	0.73575	-0.76;-0.76	5.92	5.92	0.95590	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.88544	0.6465	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	D	0.88708	0.3220	10	0.62326	D	0.03	-8.8258	20.3206	0.98668	0.0:0.0:1.0:0.0	.	245;245	Q15777;E9PB10	MPPD2_HUMAN;.	L	245	ENSP00000388258:P245L;ENSP00000350833:P245L	ENSP00000350833:P245L	P	-	2	0	MPPED2	30392383	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.813000	0.96785	0.561000	0.74099	CCC	.	.		0.478	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584	
PRDM11	56981	hgsc.bcm.edu	37	11	45241211	45241211	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:45241211C>T	ENST00000530656.1	+	6	747	c.747C>T	c.(745-747)atC>atT	p.I249I	CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000424263.2_Silent_p.I215I|PRDM11_ENST00000528980.1_3'UTR|PRDM11_ENST00000263765.4_Silent_p.I249I			Q9NQV5	PRD11_HUMAN	PR domain containing 11	249	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GCAGGGACATCCGGCCTGGGG	0.632																																					p.I215I	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.C645T						.						72.0	58.0	63.0					11																	45241211		2203	4299	6502	SO:0001819	synonymous_variant	56981	exon6			GGACATCCGGCCT	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"""PR-domain containing protein 11"""						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.747C>T	chr11.hg19:g.45241211C>T		90.0	0.0		76.0	24.0	NM_001256695	Q8N9F1	Silent	SNP	ENST00000530656.1	hg19																																																																																				.	.		0.632	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229	
DDB2	1643	hgsc.bcm.edu	37	11	47238524	47238524	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47238524T>C	ENST00000256996.4	+	3	575	c.380T>C	c.(379-381)gTg>gCg	p.V127A	DDB2_ENST00000378600.3_Missense_Mutation_p.V127A|DDB2_ENST00000378601.3_Missense_Mutation_p.V127A|DDB2_ENST00000378603.3_Intron	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	127					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						CCCAGCACTGTGGCTGTGGGT	0.527			"""Mis, N"""			"""skin basal cell, skin squamous cell, melanoma"""		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.V127A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	.	DDB2	31	.	0			c.T380C						.						64.0	59.0	61.0					11																	47238524		2201	4298	6499	SO:0001583	missense	1643	exon3	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GCACTGTGGCTGT		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"""WD repeat domain containing"""	2718	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group E protein"", ""UV-damaged DNA-binding protein 2"", ""DDB p48 subunit"""	600811	"""damage-specific DNA binding protein 2 (48kD)"""			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.380T>C	chr11.hg19:g.47238524T>C	ENSP00000256996:p.Val127Ala	160.0	0.0		145.0	11.0	NM_000107	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Missense_Mutation	SNP	ENST00000256996.4	hg19	CCDS7927.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928234	0.73327	.	.	ENSG00000134574	ENST00000256996;ENST00000378600;ENST00000378601	T;T;T	0.68479	-0.33;-0.16;1.46	5.78	5.78	0.91487	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.295779	0.32518	N	0.005987	T	0.67429	0.2892	M	0.61703	1.905	0.47698	D	0.999497	B;B;P	0.36199	0.287;0.287;0.543	B;B;B	0.37888	0.124;0.167;0.26	T	0.71126	-0.4683	10	0.72032	D	0.01	-16.4465	15.7819	0.78267	0.0:0.0:0.0:1.0	.	127;127;127	Q92466-3;Q92466-2;Q92466	.;.;DDB2_HUMAN	A	127	ENSP00000256996:V127A;ENSP00000367863:V127A;ENSP00000367864:V127A	ENSP00000256996:V127A	V	+	2	0	DDB2	47195100	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	7.331000	0.79192	2.205000	0.71048	0.533000	0.62120	GTG	.	.		0.527	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000107	
SPI1	6688	hgsc.bcm.edu	37	11	47376855	47376855	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47376855T>C	ENST00000378538.3	-	5	958	c.736A>G	c.(736-738)Aag>Gag	p.K246E	MYBPC3_ENST00000256993.4_5'Flank|MYBPC3_ENST00000399249.2_5'Flank|SPI1_ENST00000227163.4_Missense_Mutation_p.K247E|MYBPC3_ENST00000545968.1_5'Flank|SPI1_ENST00000533030.1_3'UTR	NM_001080547.1|NM_003120.2	NP_001074016.1|NP_003111.2	P17947	SPI1_HUMAN	Spi-1 proto-oncogene	246					anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019)	nuclear chromatin (GO:0000790)	core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1)	8				Lung(87;0.0967)		GTGAGCTTCTTCTTCACCTTC	0.692																																					p.K247E		Atlas-SNP	.											.	SPI1	21	.	0			c.A739G						.						73.0	58.0	63.0					11																	47376855		2201	4298	6499	SO:0001583	missense	6688	exon5			GCTTCTTCTTCAC	X52056	CCDS7933.2, CCDS44591.1	11p12-p11.22	2014-06-25	2014-06-25		ENSG00000066336	ENSG00000066336			11241	protein-coding gene	gene with protein product	"""hematopoietic transcription factor PU.1"", ""31 kDa transforming protein"""	165170	"""spleen focus forming virus (SFFV) proviral integration oncogene"""			1693183	Standard	NM_003120		Approved	PU.1, SPI-A, OF, SFPI1, SPI-1	uc001nfb.1	P17947	OTTHUMG00000150150	ENST00000378538.3:c.736A>G	chr11.hg19:g.47376855T>C	ENSP00000367799:p.Lys246Glu	32.0	0.0		42.0	9.0	NM_001080547		Missense_Mutation	SNP	ENST00000378538.3	hg19	CCDS7933.2	.	.	.	.	.	.	.	.	.	.	t	27.8	4.861439	0.91433	.	.	ENSG00000066336	ENST00000378538;ENST00000227163	T;T	0.24538	1.85;1.85	4.11	4.11	0.48088	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.41488	0.1161	M	0.63208	1.945	0.80722	D	1	P;P	0.51449	0.945;0.867	P;P	0.56216	0.794;0.733	T	0.39292	-0.9621	10	0.66056	D	0.02	-26.9315	13.462	0.61233	0.0:0.0:0.0:1.0	.	246;247	P17947;P17947-2	SPI1_HUMAN;.	E	246;247	ENSP00000367799:K246E;ENSP00000227163:K247E	ENSP00000227163:K247E	K	-	1	0	SPI1	47333431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.868000	0.63021	1.639000	0.50556	0.393000	0.25936	AAG	.	.		0.692	SPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316571.1	NM_003120	
C1QTNF4	114900	hgsc.bcm.edu	37	11	47611408	47611408	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47611408C>T	ENST00000302514.3	-	2	1471	c.955G>A	c.(955-957)Gcc>Acc	p.A319T		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	319						extracellular space (GO:0005615)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						cccggcggggcggcgggggcg	0.731																																					p.A319T		Atlas-SNP	.											.	C1QTNF4	19	.	0			c.G955A						.						27.0	35.0	32.0					11																	47611408		1920	3768	5688	SO:0001583	missense	114900	exon2			GCGGGGCGGCGGG	AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247			14346	protein-coding gene	gene with protein product	"""complement-c1q tumor necrosis factor-related protein 4"""	614911				16094384	Standard	NM_031909		Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.955G>A	chr11.hg19:g.47611408C>T	ENSP00000302274:p.Ala319Thr	136.0	0.0		173.0	78.0	NM_031909	Q8IV25	Missense_Mutation	SNP	ENST00000302514.3	hg19	CCDS7942.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243010	0.39697	.	.	ENSG00000172247	ENST00000302514	T	0.74947	-0.89	4.4	1.39	0.22231	.	6.789180	0.01907	U	0.039580	T	0.53174	0.1780	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.12156	0.007	T	0.37934	-0.9684	10	0.21540	T	0.41	.	3.025	0.06087	0.1633:0.5316:0.2005:0.1046	.	319	Q9BXJ3	C1QT4_HUMAN	T	319	ENSP00000302274:A319T	ENSP00000302274:A319T	A	-	1	0	C1QTNF4	47567984	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.304000	0.08199	0.054000	0.16065	-0.258000	0.10820	GCC	.	.		0.731	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391772.1	NM_031909	
OR4C11	219429	hgsc.bcm.edu	37	11	55371494	55371494	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55371494T>A	ENST00000302231.4	-	1	380	c.356A>T	c.(355-357)gAt>gTt	p.D119V		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	119						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						CACATAGCGATCAACAGCCAT	0.433																																					p.D119V		Atlas-SNP	.											.	OR4C11	73	.	0			c.A356T						.						93.0	77.0	83.0					11																	55371494		2179	4007	6186	SO:0001583	missense	219429	exon1			TAGCGATCAACAG	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.356A>T	chr11.hg19:g.55371494T>A	ENSP00000306651:p.Asp119Val	138.0	0.0		155.0	64.0	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	hg19	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.761642	0.49468	.	.	ENSG00000172188	ENST00000302231	T	0.02158	4.42	4.34	4.34	0.51931	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	U	0.000122	T	0.21468	0.0517	H	0.98238	4.18	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.22068	-1.0227	10	0.87932	D	0	.	11.7877	0.52051	0.0:0.0:0.0:1.0	.	119	Q6IEV9	OR4CB_HUMAN	V	119	ENSP00000306651:D119V	ENSP00000306651:D119V	D	-	2	0	OR4C11	55128070	1.000000	0.71417	0.975000	0.42487	0.132000	0.20833	5.063000	0.64332	1.962000	0.57031	0.391000	0.25812	GAT	.	.		0.433	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700	
OR5L1	219437	hgsc.bcm.edu	37	11	55579121	55579121	+	Missense_Mutation	SNP	A	A	T	rs142577076		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55579121A>T	ENST00000333973.2	+	1	268	c.179A>T	c.(178-180)tAc>tTc	p.Y60F		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				ACCCCCATGTACTTTTTCCTC	0.463																																					p.Y60F		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	.	0			c.A179T						.						284.0	253.0	264.0					11																	55579121		2200	4296	6496	SO:0001583	missense	219437	exon1			CCATGTACTTTTT	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.179A>T	chr11.hg19:g.55579121A>T	ENSP00000335529:p.Tyr60Phe	103.0	0.0		153.0	62.0	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	hg19	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	a	15.79	2.938177	0.52972	.	.	ENSG00000186117	ENST00000333973	T	0.14391	2.51	4.32	4.32	0.51571	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44483	D	0.000451	T	0.44808	0.1311	M	0.92317	3.295	0.36280	D	0.855733	D	0.71674	0.998	D	0.72338	0.977	T	0.65134	-0.6242	10	0.87932	D	0	-46.0803	12.3887	0.55347	1.0:0.0:0.0:0.0	.	60	Q8NGL2	OR5L1_HUMAN	F	60	ENSP00000335529:Y60F	ENSP00000335529:Y60F	Y	+	2	0	OR5L1	55335697	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	6.889000	0.75627	1.608000	0.50180	0.358000	0.22013	TAC	.	A|1.000;G|0.000		0.463	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
OR5D16	390144	hgsc.bcm.edu	37	11	55606628	55606628	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55606628A>G	ENST00000378396.1	+	1	401	c.401A>G	c.(400-402)tAc>tGc	p.Y134C		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	134						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				CCTCTGCTCTACACAGTTGCC	0.463																																					p.Y134C		Atlas-SNP	.											.	OR5D16	94	.	0			c.A401G						.						128.0	116.0	120.0					11																	55606628		2201	4296	6497	SO:0001583	missense	390144	exon1			TGCTCTACACAGT	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.401A>G	chr11.hg19:g.55606628A>G	ENSP00000367649:p.Tyr134Cys	106.0	0.0		84.0	37.0	NM_001005496	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	hg19	CCDS31512.1	.	.	.	.	.	.	.	.	.	.	.	11.63	1.695124	0.30052	.	.	ENSG00000205029	ENST00000378396	T	0.33865	1.39	4.47	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.69797	0.3151	H	0.97340	3.985	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59994	-0.7349	9	0.87932	D	0	-24.1127	8.3681	0.32399	0.83:0.0:0.17:0.0	.	134	Q8NGK9	OR5DG_HUMAN	C	134	ENSP00000367649:Y134C	ENSP00000367649:Y134C	Y	+	2	0	OR5D16	55363204	1.000000	0.71417	0.002000	0.10522	0.207000	0.24258	5.675000	0.68123	0.213000	0.20722	-0.528000	0.04320	TAC	.	.		0.463	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
OR8I2	120586	hgsc.bcm.edu	37	11	55860942	55860942	+	Silent	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55860942T>G	ENST00000302124.2	+	1	190	c.159T>G	c.(157-159)tcT>tcG	p.S53S		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GAATGGATTCTCAGCTTCACA	0.368																																					p.S53S		Atlas-SNP	.											.	OR8I2	119	.	0			c.T159G						.						253.0	243.0	247.0					11																	55860942		2201	4296	6497	SO:0001819	synonymous_variant	120586	exon1			GGATTCTCAGCTT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.159T>G	chr11.hg19:g.55860942T>G		72.0	0.0		71.0	36.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Silent	SNP	ENST00000302124.2	hg19	CCDS31517.1																																																																																			.	.		0.368	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
OR8H3	390152	hgsc.bcm.edu	37	11	55890135	55890135	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55890135G>A	ENST00000313472.3	+	1	287	c.287G>A	c.(286-288)gGc>gAc	p.G96D		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	96						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TCCTTCACGGGCTGCTTTGCC	0.443																																					p.G96D		Atlas-SNP	.											.	OR8H3	92	.	0			c.G287A						.						336.0	328.0	331.0					11																	55890135		2201	4296	6497	SO:0001583	missense	390152	exon1			TCACGGGCTGCTT	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.287G>A	chr11.hg19:g.55890135G>A	ENSP00000323928:p.Gly96Asp	99.0	0.0		120.0	7.0	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	hg19	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	G	7.838	0.721222	0.15372	.	.	ENSG00000181761	ENST00000313472	T	0.09723	2.95	3.44	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	0.331079	0.26542	N	0.023795	T	0.12860	0.0312	M	0.64170	1.965	0.26439	N	0.975809	B	0.20368	0.044	B	0.21151	0.033	T	0.14309	-1.0477	10	0.52906	T	0.07	.	10.6985	0.45913	0.0976:0.0:0.9024:0.0	.	96	Q8N146	OR8H3_HUMAN	D	96	ENSP00000323928:G96D	ENSP00000323928:G96D	G	+	2	0	OR8H3	55646711	0.003000	0.15002	0.239000	0.24122	0.272000	0.26649	0.201000	0.17276	0.548000	0.28955	0.173000	0.16961	GGC	.	.		0.443	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
OR5AR1	219493	hgsc.bcm.edu	37	11	56432083	56432083	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:56432083A>G	ENST00000302969.2	+	1	946	c.922A>G	c.(922-924)Aaa>Gaa	p.K308E		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	308						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						AATTGGAAAAAAATCTCAATA	0.343																																					p.K308E		Atlas-SNP	.											.	OR5AR1	68	.	0			c.A922G						.						24.0	25.0	24.0					11																	56432083		2201	4296	6497	SO:0001583	missense	219493	exon1			GGAAAAAAATCTC	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"""GPCR / Class A : Olfactory receptors"""	15260	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AR, member 1"""				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.922A>G	chr11.hg19:g.56432083A>G	ENSP00000302639:p.Lys308Glu	56.0	0.0		56.0	23.0	NM_001004730	Q6IF61	Missense_Mutation	SNP	ENST00000302969.2	hg19	CCDS31535.1	.	.	.	.	.	.	.	.	.	.	A	5.691	0.312126	0.10789	.	.	ENSG00000172459	ENST00000302969	T	0.39406	1.08	4.63	4.63	0.57726	.	1.008850	0.07975	N	0.984696	T	0.37732	0.1014	L	0.43923	1.385	0.09310	N	1	B	0.26081	0.141	B	0.19391	0.025	T	0.20107	-1.0285	10	0.48119	T	0.1	.	10.6087	0.45408	1.0:0.0:0.0:0.0	.	308	Q8NGP9	O5AR1_HUMAN	E	308	ENSP00000302639:K308E	ENSP00000302639:K308E	K	+	1	0	OR5AR1	56188659	0.000000	0.05858	0.021000	0.16686	0.021000	0.10359	0.769000	0.26604	2.074000	0.62210	0.467000	0.42956	AAA	.	.		0.343	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730	
PRG2	5553	hgsc.bcm.edu	37	11	57155302	57155302	+	Missense_Mutation	SNP	G	G	A	rs142359007		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:57155302G>A	ENST00000311862.5	-	5	608	c.535C>T	c.(535-537)Cgc>Tgc	p.R179C	PRG2_ENST00000525955.1_Missense_Mutation_p.R179C|PRG2_ENST00000533605.1_Missense_Mutation_p.R168C	NM_001243245.1|NM_002728.4	NP_001230174.1|NP_002719.3	P13727	PRG2_HUMAN	proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein)	179	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)	p.R179C(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)	10				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)	Sargramostim(DB00020)	AAGTTCCAGCGGCTGCCGTCA	0.637																																					p.R179C		Atlas-SNP	.											PRG2_ENST00000311862,colon,carcinoma,0,1	PRG2	65	.	1	Substitution - Missense(1)	large_intestine(1)	c.C535T						.	G	CYS/ARG	0,4396		0,0,2198	18.0	18.0	18.0		535	-9.9	0.0	11	dbSNP_134	18	1,8581		0,1,4290	no	missense	PRG2	NM_002728.4	180	0,1,6488	AA,AG,GG		0.0117,0.0,0.0077		179/223	57155302	1,12977	2198	4291	6489	SO:0001583	missense	5553	exon5			TCCAGCGGCTGCC	BC005929	CCDS7955.1, CCDS58133.1	11q12	2005-11-25				ENSG00000186652			9362	protein-coding gene	gene with protein product		605601				1565101	Standard	NM_001243245		Approved	MBP, BMPG		P13727		ENST00000311862.5:c.535C>T	chr11.hg19:g.57155302G>A	ENSP00000312134:p.Arg179Cys	202.0	0.0		161.0	65.0	NM_002728	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000311862.5	hg19	CCDS7955.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265585	0.40095	0.0	1.17E-4	ENSG00000186652	ENST00000311862;ENST00000533605;ENST00000525955	T;T;T	0.19669	2.13;2.13;2.13	4.98	-9.95	0.00446	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.531680	0.04767	N	0.427360	T	0.15825	0.0381	L	0.58510	1.815	0.09310	N	1	B;B	0.17852	0.001;0.024	B;B	0.09377	0.002;0.004	T	0.11036	-1.0604	10	0.36615	T	0.2	.	4.9516	0.14017	0.1525:0.4452:0.31:0.0923	.	168;179	A6XMW0;P13727	.;PRG2_HUMAN	C	179;168;179	ENSP00000312134:R179C;ENSP00000433231:R168C;ENSP00000433016:R179C	ENSP00000312134:R179C	R	-	1	0	PRG2	56911878	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.542000	0.00935	-2.572000	0.00467	-0.355000	0.07637	CGC	.	G|1.000;A|0.000		0.637	PRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392468.1	NM_002728	
VPS37C	55048	hgsc.bcm.edu	37	11	60899319	60899319	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:60899319C>T	ENST00000301765.5	-	5	1273	c.1041G>A	c.(1039-1041)ccG>ccA	p.P347P		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	347	Pro-rich.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						CAGGCCCCGGCGGTGGTGGGA	0.697																																					p.P347P		Atlas-SNP	.											.	VPS37C	30	.	0			c.G1041A						.						4.0	4.0	4.0					11																	60899319		1916	3926	5842	SO:0001819	synonymous_variant	55048	exon5			CCCCGGCGGTGGT	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"""vacuolar protein sorting 37C (yeast)"""			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.1041G>A	chr11.hg19:g.60899319C>T		23.0	0.0		33.0	14.0	NM_017966	Q8N3K4	Silent	SNP	ENST00000301765.5	hg19	CCDS31573.1																																																																																			.	.		0.697	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966	
PPP1R32	220004	hgsc.bcm.edu	37	11	61249285	61249285	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:61249285A>T	ENST00000338608.2	+	2	129	c.4A>T	c.(4-6)Atg>Ttg	p.M2L	RP11-286N22.8_ENST00000544880.1_Intron|PPP1R32_ENST00000432063.2_Missense_Mutation_p.M2L|RP11-286N22.8_ENST00000543044.1_3'UTR	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	2							phosphatase binding (GO:0019902)										CAGCATCATGATGGGGAAACT	0.632																																					p.M2L		Atlas-SNP	.											.	.	.	.	0			c.A4T						.						18.0	20.0	20.0					11																	61249285		2201	4298	6499	SO:0001583	missense	220004	exon2			ATCATGATGGGGA	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28869	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 66"""	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.4A>T	chr11.hg19:g.61249285A>T	ENSP00000344140:p.Met2Leu	74.0	0.0		58.0	22.0	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	hg19	CCDS8008.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.934765	0.73442	.	.	ENSG00000256591;ENSG00000162148;ENSG00000162148	ENST00000541135;ENST00000432063;ENST00000338608	T;T;T	0.75589	-0.95;0.37;0.93	4.73	3.57	0.40892	.	0.108731	0.41294	N	0.000906	T	0.73249	0.3563	M	0.72894	2.215	0.80722	D	1	P;P	0.45078	0.85;0.85	B;B	0.43809	0.432;0.432	T	0.73202	-0.4057	10	0.66056	D	0.02	-3.6751	9.2926	0.37795	0.8179:0.1821:0.0:0.0	.	2;2	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	L	154;2;2	ENSP00000443130:M154L;ENSP00000391560:M2L;ENSP00000344140:M2L	ENSP00000344140:M2L	M	+	1	0	C11orf66;RP11-286N22.8	61005861	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.736000	0.38187	0.653000	0.30826	0.329000	0.21502	ATG	.	.		0.632	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017	
FEN1	2237	hgsc.bcm.edu	37	11	61563849	61563849	+	Missense_Mutation	SNP	G	G	A	rs573495657		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:61563849G>A	ENST00000305885.2	+	2	1429	c.1016G>A	c.(1015-1017)cGc>cAc	p.R339H	FADS2_ENST00000574708.1_Intron	NM_004111.5	NP_004102.1			flap structure-specific endonuclease 1											endometrium(1)|large_intestine(4)|lung(1)|ovary(1)	7						ACCCAGGGCCGCCTGGATGAT	0.552								Editing and processing nucleases					G|||	1	0.000199681	0.0	0.0	5008	,	,		17828	0.0		0.0	False		,,,				2504	0.001				p.R339H		Atlas-SNP	.											FEN1,colon,carcinoma,0,1	FEN1	15	.	0			c.G1016A						.						30.0	33.0	32.0					11																	61563849		2202	4299	6501	SO:0001583	missense	2237	exon2			AGGGCCGCCTGGA	L37374	CCDS8010.1	11q12	2013-05-08			ENSG00000168496	ENSG00000168496			3650	protein-coding gene	gene with protein product	"""maturation factor-1"", ""DNase IV"""	600393		RAD2		7774922	Standard	NM_004111		Approved	FEN-1, MF1	uc001nsg.3	P39748	OTTHUMG00000168162	ENST00000305885.2:c.1016G>A	chr11.hg19:g.61563849G>A	ENSP00000305480:p.Arg339His	227.0	0.0		190.0	72.0	NM_004111		Missense_Mutation	SNP	ENST00000305885.2	hg19	CCDS8010.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300983	0.81136	.	.	ENSG00000168496	ENST00000305885	T	0.33654	1.4	5.44	4.54	0.55810	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.000000	0.85682	D	0.000000	T	0.68238	0.2979	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77747	-0.2472	10	0.87932	D	0	-31.7275	14.568	0.68191	0.0703:0.0:0.9297:0.0	.	339	P39748	FEN1_HUMAN	H	339	ENSP00000305480:R339H	ENSP00000305480:R339H	R	+	2	0	FEN1	61320425	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.324000	0.96373	1.446000	0.47643	-0.258000	0.10820	CGC	.	.		0.552	FEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398526.1	NM_004111	
AHNAK	79026	hgsc.bcm.edu	37	11	62303477	62303477	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:62303477C>T	ENST00000378024.4	-	3	368	c.94G>A	c.(94-96)Gtc>Atc	p.V32I	RP11-864I4.3_ENST00000544108.1_RNA|AHNAK_ENST00000257247.7_Missense_Mutation_p.V32I|AHNAK_ENST00000530124.1_Missense_Mutation_p.V32I	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	32	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGCACAAAGACGCCGTCGTCC	0.652																																					p.V32I		Atlas-SNP	.											.	AHNAK	532	.	0			c.G94A						.						61.0	58.0	59.0					11																	62303477		2202	4299	6501	SO:0001583	missense	79026	exon3			CAAAGACGCCGTC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.94G>A	chr11.hg19:g.62303477C>T	ENSP00000367263:p.Val32Ile	45.0	0.0		62.0	33.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	C	9.454	1.091281	0.20471	.	.	ENSG00000124942	ENST00000530124;ENST00000257247;ENST00000533365;ENST00000378024;ENST00000530285;ENST00000528508;ENST00000531324	T;T;T;T;T;T;T	0.41065	1.83;1.83;1.83;1.01;1.83;1.83;1.83	5.36	5.36	0.76844	PDZ/DHR/GLGF (3);	0.127761	0.31427	U	0.007679	T	0.31857	0.0810	N	0.00926	-1.1	0.35379	D	0.78977	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	T	0.37957	-0.9683	10	0.02654	T	1	-29.8375	17.8806	0.88839	0.0:1.0:0.0:0.0	.	32;32	Q09666;A1A586	AHNK_HUMAN;.	I	32	ENSP00000433789:V32I;ENSP00000257247:V32I;ENSP00000433635:V32I;ENSP00000367263:V32I;ENSP00000433286:V32I;ENSP00000435357:V32I;ENSP00000436845:V32I	ENSP00000257247:V32I	V	-	1	0	AHNAK	62060053	0.996000	0.38824	0.955000	0.39395	0.249000	0.25844	3.220000	0.51207	2.512000	0.84698	0.655000	0.94253	GTC	.	.		0.652	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
EML3	256364	hgsc.bcm.edu	37	11	62370721	62370721	+	Splice_Site	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:62370721T>G	ENST00000394773.2	-	20	2565		c.e20-2		EML3_ENST00000531557.1_Splice_Site|EML3_ENST00000529309.1_Splice_Site|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000438258.1_5'Flank|EML3_ENST00000278845.4_Splice_Site|MTA2_ENST00000527204.1_5'Flank|EML3_ENST00000494176.2_Splice_Site|MTA2_ENST00000278823.2_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3							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						CCACGTCCCCTGGGGAGAGGG	0.612																																					.		Atlas-SNP	.											.	EML3	61	.	0			c.2258-2A>C						.						57.0	60.0	59.0					11																	62370721		2202	4299	6501	SO:0001630	splice_region_variant	256364	exon21			GTCCCCTGGGGAG	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.2258-2A>C	chr11.hg19:g.62370721T>G		30.0	0.0		25.0	11.0	NM_153265	Q6ZQW7|Q8NA55	Splice_Site	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	T	17.88	3.498349	0.64186	.	.	ENSG00000149499	ENST00000439994;ENST00000394773;ENST00000394776;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	.	.	.	4.78	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2655	0.54676	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	EML3	62127297	1.000000	0.71417	0.863000	0.33907	0.897000	0.52465	7.717000	0.84732	1.787000	0.52448	0.459000	0.35465	.	.	.		0.612	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	Intron
CHRM1	1128	hgsc.bcm.edu	37	11	62677349	62677349	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:62677349G>A	ENST00000306960.3	-	2	1765	c.1224C>T	c.(1222-1224)taC>taT	p.Y408Y	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	408					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	TGCTGTTGACGTAGCACAGCC	0.582																																					p.Y408Y		Atlas-SNP	.											.	CHRM1	29	.	0			c.C1224T						.						158.0	136.0	143.0					11																	62677349		2201	4298	6499	SO:0001819	synonymous_variant	1128	exon2			GTTGACGTAGCAC	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1950	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 1"""	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1224C>T	chr11.hg19:g.62677349G>A		150.0	0.0		128.0	44.0	NM_000738	Q96RH1	Silent	SNP	ENST00000306960.3	hg19	CCDS8040.1																																																																																			.	.		0.582	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738	
MAP4K2	5871	hgsc.bcm.edu	37	11	64557055	64557055	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64557055G>A	ENST00000294066.2	-	32	2508	c.2417C>T	c.(2416-2418)gCg>gTg	p.A806V	MAP4K2_ENST00000377350.3_Missense_Mutation_p.A798V	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	806					activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						GTTGCTGTGCGCCTCTGGGTT	0.632																																					p.A806V		Atlas-SNP	.											.	MAP4K2	83	.	0			c.C2417T						.						96.0	84.0	88.0					11																	64557055		2201	4297	6498	SO:0001583	missense	5871	exon32			CTGTGCGCCTCTG	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.2417C>T	chr11.hg19:g.64557055G>A	ENSP00000294066:p.Ala806Val	130.0	0.0		114.0	29.0	NM_004579	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	hg19	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117851	0.77323	.	.	ENSG00000168067	ENST00000294066;ENST00000377350	T;T	0.71103	-0.54;-0.5	5.19	5.19	0.71726	.	0.058733	0.64402	D	0.000003	T	0.81754	0.4889	M	0.68952	2.095	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.73380	0.97;0.98	T	0.82812	-0.0272	10	0.56958	D	0.05	.	14.2799	0.66205	0.0:0.0:1.0:0.0	.	798;806	Q86VU3;Q12851	.;M4K2_HUMAN	V	806;798	ENSP00000294066:A806V;ENSP00000366567:A798V	ENSP00000294066:A806V	A	-	2	0	MAP4K2	64313631	1.000000	0.71417	0.877000	0.34402	0.248000	0.25809	8.251000	0.89838	2.446000	0.82766	0.555000	0.69702	GCG	.	.		0.632	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64592001	64592001	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64592001C>T	ENST00000342711.5	-	37	4599	c.4600G>A	c.(4600-4602)Gtc>Atc	p.V1534I		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						CGTTCTGAGACCTGCAGGAGA	0.577																																					p.V1534I		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G4600A						.						42.0	46.0	45.0					11																	64592001		2201	4297	6498	SO:0001630	splice_region_variant	55561	exon37			CTGAGACCTGCAG	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.4600-1G>A	chr11.hg19:g.64592001C>T		347.0	0.0		358.0	138.0	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	hg19	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.081619	0.36758	.	.	ENSG00000171219	ENST00000342711	T	0.66638	-0.22	4.33	3.14	0.36123	.	0.000000	0.34879	N	0.003617	T	0.62768	0.2455	L	0.36672	1.1	0.24694	N	0.993299	P	0.44690	0.841	P	0.58820	0.846	T	0.53085	-0.8488	10	0.10111	T	0.7	.	5.3771	0.16172	0.0:0.8079:0.0:0.1921	.	1534	Q6DT37	MRCKG_HUMAN	I	1534	ENSP00000345133:V1534I	ENSP00000345133:V1534I	V	-	1	0	CDC42BPG	64348577	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	2.275000	0.43399	2.152000	0.67230	0.555000	0.69702	GTC	.	.		0.577	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	Missense_Mutation
EHD1	10938	hgsc.bcm.edu	37	11	64622239	64622239	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64622239C>T	ENST00000320631.3	-	5	1425	c.1171G>A	c.(1171-1173)Gcg>Acg	p.A391T	EHD1_ENST00000488711.1_5'UTR|EHD1_ENST00000359393.2_Missense_Mutation_p.A391T	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	391					blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						ATCAGCCGCGCGATGTCGTTG	0.642																																					p.A391T		Atlas-SNP	.											.	EHD1	31	.	0			c.G1171A						.						215.0	199.0	205.0					11																	64622239		2201	4297	6498	SO:0001583	missense	10938	exon5			GCCGCGCGATGTC	AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"""EF-hand domain containing"""	3242	protein-coding gene	gene with protein product	"""testilin"""	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.1171G>A	chr11.hg19:g.64622239C>T	ENSP00000320516:p.Ala391Thr	32.0	0.0		29.0	10.0	NM_006795	O14611|Q2M3Q4|Q9UNR3	Missense_Mutation	SNP	ENST00000320631.3	hg19	CCDS8084.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.838589	0.71373	.	.	ENSG00000110047	ENST00000320631;ENST00000359393;ENST00000541001;ENST00000421510	T;T;T	0.47177	2.19;2.19;0.85	4.56	4.56	0.56223	.	0.098802	0.64402	D	0.000002	T	0.47655	0.1457	M	0.71581	2.175	0.80722	D	1	B;B	0.27656	0.184;0.184	B;B	0.19391	0.025;0.025	T	0.52253	-0.8600	10	0.52906	T	0.07	.	14.8614	0.70384	0.0:1.0:0.0:0.0	.	391;391	B2R5U3;Q9H4M9	.;EHD1_HUMAN	T	391;391;367;255	ENSP00000320516:A391T;ENSP00000352354:A391T;ENSP00000391429:A255T	ENSP00000320516:A391T	A	-	1	0	EHD1	64378815	1.000000	0.71417	0.649000	0.29536	0.895000	0.52256	7.576000	0.82467	2.381000	0.81170	0.561000	0.74099	GCG	.	.		0.642	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2	NM_006795	
NAALADL1	10004	hgsc.bcm.edu	37	11	64813529	64813529	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:64813529C>T	ENST00000358658.3	-	16	1940	c.1913G>A	c.(1912-1914)cGc>cAc	p.R638H	NAALADL1_ENST00000526799.1_5'UTR|NAALADL1_ENST00000339885.2_3'UTR|NAALADL1_ENST00000355721.3_Missense_Mutation_p.R597H|NAALADL1_ENST00000528884.1_5'UTR|NAALADL1_ENST00000340252.4_Missense_Mutation_p.R689H|NAALADL1_ENST00000355369.2_3'UTR|NAALADL1_ENST00000356632.3_Missense_Mutation_p.R603H	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	638						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						TGTTGATATGCGTTGGCCCAA	0.632																																					p.R638H		Atlas-SNP	.											.	NAALADL1	58	.	0			c.G1913A						.						55.0	51.0	52.0					11																	64813529		2201	4297	6498	SO:0001583	missense	10004	exon16			GATATGCGTTGGC	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"""ileal peptidase I100"""	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.1913G>A	chr11.hg19:g.64813529C>T	ENSP00000351484:p.Arg638His	46.0	0.0		52.0	20.0	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Missense_Mutation	SNP	ENST00000358658.3	hg19	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	C	5.797	0.331378	0.10956	.	.	ENSG00000168060	ENST00000533753;ENST00000358658;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	4.98	-6.83	0.01693	Transferrin receptor-like, dimerisation domain (3);	0.970926	0.08538	N	0.931048	T	0.30166	0.0756	N	0.20610	0.595	0.09310	N	0.999999	B	0.06786	0.001	B	0.10450	0.005	T	0.24225	-1.0166	10	0.26408	T	0.33	-6.1261	8.7798	0.34785	0.1205:0.1896:0.0:0.6899	.	638	Q9UQQ1	NALDL_HUMAN	H	45;638;638;689;597;603	ENSP00000434225:R45H;ENSP00000351484:R638H;ENSP00000344244:R689H;ENSP00000347955:R597H;ENSP00000349045:R603H	ENSP00000344244:R689H	R	-	2	0	NAALADL1	64570105	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.936000	0.01549	-0.899000	0.03901	-0.367000	0.07326	CGC	.	.		0.632	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468	
RELA	5970	hgsc.bcm.edu	37	11	65426225	65426225	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:65426225C>A	ENST00000406246.3	-	7	889	c.628G>T	c.(628-630)Gat>Tat	p.D210Y	RELA_ENST00000308639.9_Missense_Mutation_p.D207Y|RELA_ENST00000525693.1_Missense_Mutation_p.D210Y	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	210	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						AAGATCTCATCCCCACCGAGG	0.567																																					p.D210Y		Atlas-SNP	.											.	RELA	44	.	0			c.G628T						.						140.0	120.0	126.0					11																	65426225		2201	4297	6498	SO:0001583	missense	5970	exon7			TCTCATCCCCACC	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"""	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.628G>T	chr11.hg19:g.65426225C>A	ENSP00000384273:p.Asp210Tyr	78.0	0.0		57.0	38.0	NM_021975	Q6GTV1|Q6SLK1	Missense_Mutation	SNP	ENST00000406246.3	hg19	CCDS31609.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.770269	0.90108	.	.	ENSG00000173039	ENST00000406246;ENST00000525693;ENST00000308639;ENST00000426617;ENST00000545816;ENST00000532999;ENST00000534558;ENST00000527749	T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36	5.13	5.13	0.70059	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.68265	0.2982	M	0.91612	3.225	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	0.998;1.0;1.0;0.999;0.999;0.997	T	0.76688	-0.2867	10	0.87932	D	0	-12.0034	16.0771	0.80976	0.0:1.0:0.0:0.0	.	210;197;207;210;221;210	Q04206-3;Q04206-2;Q04206-4;Q04206;B4E082;Q2TAM5	.;.;.;TF65_HUMAN;.;.	Y	210;210;207;210;221;221;201;179	ENSP00000384273:D210Y;ENSP00000432537:D210Y;ENSP00000311508:D207Y;ENSP00000433526:D221Y;ENSP00000434372:D201Y;ENSP00000436545:D179Y	ENSP00000311508:D207Y	D	-	1	0	RELA	65182801	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.634000	0.83273	2.387000	0.81309	0.655000	0.94253	GAT	.	.		0.567	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975	
RBM4	5936	hgsc.bcm.edu	37	11	66411228	66411228	+	Silent	SNP	C	C	T	rs372104227		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:66411228C>T	ENST00000409406.1	+	2	1497	c.720C>T	c.(718-720)tcC>tcT	p.S240S	RBM4_ENST00000506523.2_Intron|RBM4_ENST00000396053.4_Intron|RBM4_ENST00000408993.2_Silent_p.S240S|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000398692.4_Intron|RBM4_ENST00000514361.3_Silent_p.S215S|RBM4_ENST00000503028.2_Silent_p.S240S|RBM4_ENST00000515838.2_3'UTR|RBM14-RBM4_ENST00000412278.2_Silent_p.S215S|RBM4_ENST00000310092.7_Silent_p.S240S			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	240	Interaction with TNPO3.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		CAGCTGCCTCCGTGTATAATT	0.562																																					p.S240S		Atlas-SNP	.											.	RBM4	34	.	0			c.C720T						.	C	,,,,	1,4091		0,1,2045	37.0	44.0	42.0		,,645,,720	-4.4	1.0	11		42	1,8423		0,1,4211	no	intron,intron,coding-synonymous,intron,coding-synonymous	RBM4,RBM14-RBM4	NM_001198843.1,NM_001198844.1,NM_001198845.1,NM_001198846.1,NM_002896.3	,,,,	0,2,6256	TT,TC,CC		0.0119,0.0244,0.016	,,,,	,,215/340,,240/365	66411228	2,12514	2046	4212	6258	SO:0001819	synonymous_variant	5936	exon3			TGCCTCCGTGTAT	U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.720C>T	chr11.hg19:g.66411228C>T		50.0	0.0		49.0	24.0	NM_002896	B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	Silent	SNP	ENST00000409406.1	hg19	CCDS41676.1																																																																																			.	.		0.562	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	NM_002896	
ANKRD13D	338692	hgsc.bcm.edu	37	11	67069033	67069033	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:67069033C>T	ENST00000447274.2	+	13	2337	c.1162C>T	c.(1162-1164)Cgc>Tgc	p.R388C	SSH3_ENST00000376757.5_5'Flank|ANKRD13D_ENST00000514166.1_Missense_Mutation_p.R388C|ANKRD13D_ENST00000511455.2_Missense_Mutation_p.R475C|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.R388C|ANKRD13D_ENST00000515828.1_Missense_Mutation_p.R125C|ANKRD13D_ENST00000504236.1_3'UTR|SSH3_ENST00000308298.7_5'Flank|SSH3_ENST00000308127.4_5'Flank			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	388						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GGGCATGGAGCGCAACGAGCC	0.662																																					p.R475C		Atlas-SNP	.											.	ANKRD13D	71	.	0			c.C1423T						.						56.0	56.0	56.0					11																	67069033		2200	4294	6494	SO:0001583	missense	338692	exon13			ATGGAGCGCAACG	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"""Ankyrin repeat domain containing"""	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.1162C>T	chr11.hg19:g.67069033C>T	ENSP00000402616:p.Arg388Cys	85.0	0.0		109.0	42.0	NM_207354	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	hg19		.	.	.	.	.	.	.	.	.	.	C	18.05	3.536345	0.65085	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166;ENST00000515828	T;T;T;T;T	0.51071	1.35;1.53;1.35;1.35;0.72	4.71	4.71	0.59529	.	0.379294	0.27591	N	0.018681	T	0.66247	0.2770	M	0.79011	2.435	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70716	0.917;0.97;0.943	T	0.69705	-0.5073	10	0.72032	D	0.01	-28.8024	11.0229	0.47728	0.0:0.9138:0.0:0.0862	.	125;475;388	Q6ZTN6-2;Q6ZTN6-3;Q6ZTN6	.;.;AN13D_HUMAN	C	388;475;388;388;125	ENSP00000402616:R388C;ENSP00000427130:R475C;ENSP00000310874:R388C;ENSP00000444404:R388C;ENSP00000443977:R125C	ENSP00000310874:R388C	R	+	1	0	ANKRD13D	66825609	0.969000	0.33509	1.000000	0.80357	0.546000	0.35178	2.376000	0.44292	2.440000	0.82611	0.561000	0.74099	CGC	.	.		0.662	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354	
MRGPRF	116535	hgsc.bcm.edu	37	11	68772834	68772834	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:68772834C>T	ENST00000309099.6	-	3	1326	c.944G>A	c.(943-945)cGg>cAg	p.R315Q	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Missense_Mutation_p.R315Q	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	315						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGCGCCGTCCCGCAGGGCCCG	0.692																																					p.R315Q		Atlas-SNP	.											.	MRGPRF	22	.	0			c.G944A						.						13.0	11.0	11.0					11																	68772834		2178	4270	6448	SO:0001583	missense	116535	exon3			CCGTCCCGCAGGG	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"""GPCR / Class A : Orphans"""	24828	protein-coding gene	gene with protein product		607233	"""G protein-coupled receptor 168"", ""G protein-coupled receptor 140"""	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.944G>A	chr11.hg19:g.68772834C>T	ENSP00000309782:p.Arg315Gln	47.0	0.0		35.0	12.0	NM_001098515	B3KV43|Q8NBK8	Missense_Mutation	SNP	ENST00000309099.6	hg19	CCDS8188.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490531	0.84962	.	.	ENSG00000172935	ENST00000441623;ENST00000309099;ENST00000421543	T;T	0.04970	3.52;3.52	5.21	4.3	0.51218	.	0.000000	0.34580	N	0.003849	T	0.10551	0.0258	N	0.25332	0.735	0.31714	N	0.639157	D	0.89917	1.0	D	0.76575	0.988	T	0.00964	-1.1498	10	0.05351	T	0.99	-14.2746	11.9025	0.52692	0.0:0.8246:0.1754:0.0	.	315	Q96AM1	MRGRF_HUMAN	Q	315;315;287	ENSP00000403660:R315Q;ENSP00000309782:R315Q	ENSP00000309782:R315Q	R	-	2	0	MRGPRF	68529410	0.022000	0.18835	0.976000	0.42696	0.973000	0.67179	1.490000	0.35573	1.175000	0.42826	0.561000	0.74099	CGG	.	.		0.692	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	
SHANK2	22941	hgsc.bcm.edu	37	11	70332826	70332826	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:70332826G>A	ENST00000423696.2	-	15	2471	c.2435C>T	c.(2434-2436)gCg>gTg	p.A812V	SHANK2_ENST00000409161.1_Missense_Mutation_p.A595V|SHANK2_ENST00000338508.4_Missense_Mutation_p.A1192V|SHANK2_ENST00000449833.2_Missense_Mutation_p.A596V			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	812					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)			GCCGCTGCTCGCGGAGGGCAC	0.706																																					p.A603V		Atlas-SNP	.											.	SHANK2	340	.	0			c.C1808T						.						20.0	26.0	24.0					11																	70332826		2193	4290	6483	SO:0001583	missense	22941	exon10			CTGCTCGCGGAGG	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.2435C>T	chr11.hg19:g.70332826G>A	ENSP00000394536:p.Ala812Val	92.0	0.0		73.0	29.0	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	hg19		.	.	.	.	.	.	.	.	.	.	G	0.402	-0.917591	0.02396	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	3.62	1.21	0.21127	.	1.993000	0.03565	U	0.227639	T	0.29652	0.0740	L	0.29908	0.895	0.37959	D	0.932906	B;B;B	0.21309	0.018;0.054;0.054	B;B;B	0.09377	0.001;0.002;0.004	T	0.13229	-1.0517	10	0.15499	T	0.54	.	6.0032	0.19531	0.0:0.0925:0.1739:0.7336	.	812;1191;596	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	V	596;595;470;1192;812;830;815	ENSP00000399423:A596V;ENSP00000386491:A595V;ENSP00000402944:A470V;ENSP00000345193:A1192V;ENSP00000394536:A812V;ENSP00000294018:A815V	ENSP00000294018:A815V	A	-	2	0	SHANK2	70010474	1.000000	0.71417	0.001000	0.08648	0.001000	0.01503	3.744000	0.55112	-0.046000	0.13446	-0.397000	0.06425	GCG	.	.		0.706	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
DNAJB13	374407	hgsc.bcm.edu	37	11	73675956	73675956	+	Nonsense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:73675956T>A	ENST00000339764.1	+	4	1119	c.368T>A	c.(367-369)tTg>tAg	p.L123*	RP11-167N4.2_ENST00000537019.1_RNA|DNAJB13_ENST00000543947.1_5'Flank|RP11-167N4.2_ENST00000540886.1_RNA|DNAJB13_ENST00000537753.1_5'UTR	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	123					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					GAGGTAGATTTGAACTTTGGG	0.552											OREG0021218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L123X		Atlas-SNP	.											.	DNAJB13	28	.	0			c.T368A						.						47.0	53.0	51.0					11																	73675956		2200	4293	6493	SO:0001587	stop_gained	374407	exon4			TAGATTTGAACTT	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.368T>A	chr11.hg19:g.73675956T>A	ENSP00000344431:p.Leu123*	103.0	0.0	1147	97.0	30.0	NM_153614	B3LEP4|Q8IZW5	Nonsense_Mutation	SNP	ENST00000339764.1	hg19	CCDS8227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	23.8|23.8	4.456187|4.456187	0.84209|0.84209	.|.	.|.	ENSG00000187726|ENSG00000187726	ENST00000542350|ENST00000339764	.|.	.|.	.|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	.|1.310620	.|0.04974	.|N	.|0.464465	T|.	0.37348|.	0.1000|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.16276|.	-1.0408|.	4|.	.|0.07990	.|T	.|0.79	.|.	8.5178|8.5178	0.33257|0.33257	0.0:0.0881:0.0:0.9119|0.0:0.0881:0.0:0.9119	.|.	.|.	.|.	.|.	L|X	23|123	.|.	.|ENSP00000344431:L123X	F|L	+|+	3|2	2|0	DNAJB13|DNAJB13	73353604|73353604	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.765000|0.765000	0.43378|0.43378	1.908000|1.908000	0.39907|0.39907	1.951000|1.951000	0.56629|0.56629	0.369000|0.369000	0.22263|0.22263	TTT|TTG	.	.		0.552	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
C2CD3	26005	hgsc.bcm.edu	37	11	73801915	73801915	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:73801915C>T	ENST00000334126.7	-	20	3810	c.3584G>A	c.(3583-3585)cGa>cAa	p.R1195Q	C2CD3_ENST00000313663.7_Missense_Mutation_p.R1195Q			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1195	C2 1.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GGAAACAGTTCGGGCAGCAAG	0.493																																					p.R1195Q		Atlas-SNP	.											.	C2CD3	288	.	0			c.G3584A						.						131.0	110.0	117.0					11																	73801915		2200	4293	6493	SO:0001583	missense	26005	exon20			ACAGTTCGGGCAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3584G>A	chr11.hg19:g.73801915C>T	ENSP00000334379:p.Arg1195Gln	94.0	0.0		99.0	41.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	15.52	2.859200	0.51376	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.15603	2.9;2.91;2.41	5.7	3.73	0.42828	.	0.520355	0.20720	N	0.086921	T	0.18841	0.0452	N	0.22421	0.69	0.33718	D	0.61657	D	0.76494	0.999	P	0.62649	0.905	T	0.23440	-1.0188	10	0.27082	T	0.32	-8.3216	4.6413	0.12550	0.0:0.6101:0.1746:0.2153	.	1195	Q4AC94-1	.	Q	1195;1195;1195;3	ENSP00000334379:R1195Q;ENSP00000323339:R1195Q;ENSP00000388750:R3Q	ENSP00000323339:R1195Q	R	-	2	0	C2CD3	73479563	0.031000	0.19500	0.993000	0.49108	0.929000	0.56500	0.295000	0.19065	1.434000	0.47414	0.484000	0.47621	CGA	.	.		0.493	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
ARRB1	408	hgsc.bcm.edu	37	11	74984011	74984011	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:74984011C>T	ENST00000420843.2	-	12	1023	c.926G>A	c.(925-927)gGt>gAt	p.G309D	ARRB1_ENST00000393505.4_Missense_Mutation_p.G309D|ARRB1_ENST00000360025.3_Missense_Mutation_p.G309D	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	309					activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						ACGGTTGGCACCTTCCCTCAA	0.612																																					p.G309D		Atlas-SNP	.											.	ARRB1	37	.	0			c.G926A						.						94.0	82.0	86.0					11																	74984011		2200	4293	6493	SO:0001583	missense	408	exon12			TTGGCACCTTCCC	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"""arrestin 2"""	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.926G>A	chr11.hg19:g.74984011C>T	ENSP00000409581:p.Gly309Asp	92.0	0.0		89.0	37.0	NM_020251	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Missense_Mutation	SNP	ENST00000420843.2	hg19	CCDS44684.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.016742	0.75161	.	.	ENSG00000137486	ENST00000420843;ENST00000393505;ENST00000360025	T;T;T	0.10477	2.87;2.87;2.87	5.27	5.27	0.74061	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.072206	0.53938	D	0.000057	T	0.30510	0.0767	M	0.76574	2.34	0.50813	D	0.999892	D;D	0.59357	0.966;0.985	P;P	0.60789	0.692;0.879	T	0.01087	-1.1456	10	0.44086	T	0.13	-13.6043	16.3875	0.83521	0.0:1.0:0.0:0.0	.	309;309	P49407-2;P49407	.;ARRB1_HUMAN	D	309	ENSP00000409581:G309D;ENSP00000377141:G309D;ENSP00000353124:G309D	ENSP00000353124:G309D	G	-	2	0	ARRB1	74661659	1.000000	0.71417	0.948000	0.38648	0.797000	0.45037	5.978000	0.70501	2.471000	0.83476	0.561000	0.74099	GGT	.	.		0.612	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041	
B3GNT6	192134	hgsc.bcm.edu	37	11	76751049	76751049	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:76751049C>T	ENST00000533140.1	+	2	592	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	B3GNT6_ENST00000354301.5_Missense_Mutation_p.R152C|B3GNT6_ENST00000421061.1_Missense_Mutation_p.R63C			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						GCGGCCAGTGCGCCGCCTCTT	0.746																																					p.R152C		Atlas-SNP	.											.	B3GNT6	27	.	0			c.C454T						.						4.0	5.0	5.0					11																	76751049		1612	3616	5228	SO:0001583	missense	192134	exon2			CCAGTGCGCCGCC	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"""Beta 3-glycosyltransferases"""	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.454C>T	chr11.hg19:g.76751049C>T	ENSP00000435352:p.Arg152Cys	23.0	0.0		35.0	10.0	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	hg19	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999444	0.35320	.	.	ENSG00000198488	ENST00000533140;ENST00000354301;ENST00000421061	T;T;T	0.44881	0.91;0.91;0.91	3.28	1.38	0.22167	.	0.203439	0.41001	D	0.000971	T	0.50086	0.1595	H	0.94925	3.6	0.38408	D	0.945851	P	0.41393	0.748	B	0.42138	0.377	T	0.52859	-0.8519	10	0.59425	D	0.04	.	2.7636	0.05314	0.224:0.527:0.0:0.249	.	152	Q6ZMB0	B3GN6_HUMAN	C	152;152;63	ENSP00000435352:R152C;ENSP00000346256:R152C;ENSP00000403463:R63C	ENSP00000346256:R152C	R	+	1	0	B3GNT6	76428697	1.000000	0.71417	0.985000	0.45067	0.179000	0.23085	1.880000	0.39628	0.384000	0.24942	0.462000	0.41574	CGC	.	.		0.746	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706	
MYO7A	4647	hgsc.bcm.edu	37	11	76919769	76919769	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:76919769T>C	ENST00000409709.3	+	44	6244	c.5972T>C	c.(5971-5973)gTg>gCg	p.V1991A	MYO7A_ENST00000409619.2_Missense_Mutation_p.V1942A|MYO7A_ENST00000458637.2_Missense_Mutation_p.V1953A|MYO7A_ENST00000605744.1_3'UTR	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1991	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						ACCTACCAGGTGTTCTTCATG	0.592																																					p.V1991A		Atlas-SNP	.											.	MYO7A	164	.	0			c.T5972C						.						58.0	66.0	63.0					11																	76919769		2083	4207	6290	SO:0001583	missense	4647	exon44			ACCAGGTGTTCTT	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.5972T>C	chr11.hg19:g.76919769T>C	ENSP00000386331:p.Val1991Ala	46.0	0.0		48.0	23.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.517748	0.64634	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	4.37	4.37	0.52481	Band 4.1 domain (1);FERM domain (1);	0.129984	0.51477	D	0.000095	D	0.85487	0.5708	M	0.89095	3.005	0.80722	D	1	D;B	0.54601	0.967;0.108	P;B	0.58013	0.831;0.092	D	0.88713	0.3224	10	0.87932	D	0	.	13.7401	0.62842	0.0:0.0:0.0:1.0	.	1953;1991	F8VUN5;Q13402	.;MYO7A_HUMAN	A	1991;1953;1942;1164;1990;1960;1867;1133;606	ENSP00000386331:V1991A;ENSP00000392185:V1953A;ENSP00000386635:V1942A;ENSP00000417017:V1133A	ENSP00000345075:V1867A	V	+	2	0	MYO7A	76597417	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.503000	0.81632	1.850000	0.53721	0.254000	0.18369	GTG	.	.		0.592	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
GAB2	9846	hgsc.bcm.edu	37	11	77930356	77930356	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:77930356G>A	ENST00000361507.4	-	10	2078	c.1993C>T	c.(1993-1995)Cgg>Tgg	p.R665W	GAB2_ENST00000340149.2_Missense_Mutation_p.R627W	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	665					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GAGGACTGCCGCACGTCTGTC	0.602																																					p.R665W		Atlas-SNP	.											.	GAB2	63	.	0			c.C1993T						.						123.0	99.0	107.0					11																	77930356		2200	4292	6492	SO:0001583	missense	9846	exon10			ACTGCCGCACGTC	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"""Pleckstrin homology (PH) domain containing"""	14458	protein-coding gene	gene with protein product	"""Grb2-associated binder 2"""	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1993C>T	chr11.hg19:g.77930356G>A	ENSP00000354952:p.Arg665Trp	80.0	0.0		73.0	30.0	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Missense_Mutation	SNP	ENST00000361507.4	hg19	CCDS8259.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.007303	0.93287	.	.	ENSG00000033327	ENST00000340149;ENST00000361507	T;T	0.24538	1.85;1.85	5.38	4.46	0.54185	.	0.000000	0.64402	U	0.000001	T	0.56046	0.1959	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65689	-0.6107	10	0.87932	D	0	-16.6452	15.85	0.78924	0.0:0.0:0.8632:0.1368	.	665	Q9UQC2	GAB2_HUMAN	W	627;665	ENSP00000343959:R627W;ENSP00000354952:R665W	ENSP00000343959:R627W	R	-	1	2	GAB2	77608004	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.957000	0.87870	1.384000	0.46424	0.563000	0.77884	CGG	.	.		0.602	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	
CCDC81	60494	hgsc.bcm.edu	37	11	86126223	86126223	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:86126223A>G	ENST00000445632.2	+	13	1831	c.1559A>G	c.(1558-1560)gAa>gGa	p.E520G	CCDC81_ENST00000278487.3_Missense_Mutation_p.E255G|CCDC81_ENST00000528728.1_Missense_Mutation_p.E255G|CCDC81_ENST00000354755.1_Missense_Mutation_p.E430G	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	520										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				CTGATGGTGGAAAAGCAAAAG	0.493																																					p.E520G		Atlas-SNP	.											.	CCDC81	89	.	0			c.A1559G						.						71.0	68.0	69.0					11																	86126223		2202	4299	6501	SO:0001583	missense	60494	exon13			TGGTGGAAAAGCA	AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1559A>G	chr11.hg19:g.86126223A>G	ENSP00000415528:p.Glu520Gly	226.0	0.0		216.0	80.0	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	hg19	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.946835	0.34377	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.46	3.14	0.36123	.	0.431103	0.23365	N	0.048962	T	0.31979	0.0814	L	0.43152	1.355	0.20873	N	0.999833	B;B;B	0.15473	0.003;0.013;0.011	B;B;B	0.11329	0.002;0.006;0.003	T	0.19289	-1.0310	9	.	.	.	-0.3586	9.165	0.37046	0.8474:0.0:0.1526:0.0	.	255;520;430	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	G	430;255;520;255	ENSP00000346800:E430G;ENSP00000278487:E255G;ENSP00000415528:E520G;ENSP00000437165:E255G	.	E	+	2	0	CCDC81	85803871	0.919000	0.31177	0.009000	0.14445	0.009000	0.06853	2.081000	0.41596	0.367000	0.24454	-0.421000	0.06004	GAA	.	.		0.493	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827	
KIAA1731	85459	hgsc.bcm.edu	37	11	93429945	93429945	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:93429945A>G	ENST00000325212.6	+	15	2029	c.1867A>G	c.(1867-1869)Ata>Gta	p.I623V	KIAA1731_ENST00000411936.1_Missense_Mutation_p.I623V|KIAA1731_ENST00000344196.4_5'UTR|KIAA1731_ENST00000531700.1_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	623						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TCCATCATTGATAACTGATTC	0.418																																					p.I623V		Atlas-SNP	.											.	KIAA1731	173	.	0			c.A1867G						.						104.0	81.0	88.0					11																	93429945		692	1591	2283	SO:0001583	missense	85459	exon15			TCATTGATAACTG	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.1867A>G	chr11.hg19:g.93429945A>G	ENSP00000316681:p.Ile623Val	154.0	0.0		122.0	31.0	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	hg19	CCDS44708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.422|4.422	0.078086|0.078086	0.08485|0.08485	.|.	.|.	ENSG00000166004|ENSG00000166004	ENST00000531877|ENST00000325212;ENST00000411936	.|T;T	.|0.10668	.|2.85;2.86	5.23|5.23	-6.08|-6.08	0.02151|0.02151	.|.	.|0.659654	.|0.13269	.|N	.|0.400674	T|T	0.05456|0.05456	0.0144|0.0144	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.10296	.|0.003	.|B	.|0.06405	.|0.002	T|T	0.44544|0.44544	-0.9321|-0.9321	5|10	.|0.10902	.|T	.|0.67	-7.4269|-7.4269	4.5467|4.5467	0.12085|0.12085	0.2239:0.1232:0.5182:0.1347|0.2239:0.1232:0.5182:0.1347	.|.	.|623	.|Q9C0D2	.|K1731_HUMAN	G|V	183|623	.|ENSP00000316681:I623V;ENSP00000406505:I623V	.|ENSP00000316681:I623V	D|I	+|+	2|1	0|0	KIAA1731|KIAA1731	93069593|93069593	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.267000|0.267000	0.26476|0.26476	-0.463000|-0.463000	0.06696|0.06696	-0.604000|-0.604000	0.05760|0.05760	0.482000|0.482000	0.46254|0.46254	GAT|ATA	.	.		0.418	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
GPR83	10888	hgsc.bcm.edu	37	11	94113391	94113391	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:94113391T>C	ENST00000243673.2	-	4	1367	c.1196A>G	c.(1195-1197)aAc>aGc	p.N399S	GPR83_ENST00000539203.2_Missense_Mutation_p.N357S	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	399					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGGCAGGAGGTTATTGGCAAG	0.582																																					p.N399S		Atlas-SNP	.											.	GPR83	47	.	0			c.A1196G						.						75.0	77.0	77.0					11																	94113391		2201	4298	6499	SO:0001583	missense	10888	exon4			AGGAGGTTATTGG	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"""GPCR / Class A : Orphans"""	4523	protein-coding gene	gene with protein product		605569	"""G protein-coupled receptor 72"""	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.1196A>G	chr11.hg19:g.94113391T>C	ENSP00000243673:p.Asn399Ser	154.0	0.0		132.0	47.0	NM_016540	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	hg19	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.092963	0.00364	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.60797	0.16;0.27	5.75	2.17	0.27698	.	0.768897	0.12985	N	0.422940	T	0.28300	0.0699	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20672	-1.0268	10	0.07175	T	0.84	.	1.2577	0.01995	0.1358:0.2417:0.1405:0.482	.	399	Q9NYM4	GPR83_HUMAN	S	399;357	ENSP00000243673:N399S;ENSP00000441550:N357S	ENSP00000243673:N399S	N	-	2	0	GPR83	93753039	0.905000	0.30787	0.001000	0.08648	0.001000	0.01503	0.541000	0.23207	0.120000	0.18254	-0.250000	0.11733	AAC	.	.		0.582	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540	
CEP57	9702	hgsc.bcm.edu	37	11	95562468	95562468	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:95562468A>G	ENST00000325542.5	+	10	1483	c.1245A>G	c.(1243-1245)atA>atG	p.I415M	CEP57_ENST00000541150.1_Missense_Mutation_p.I406M|CEP57_ENST00000325486.5_Missense_Mutation_p.I389M|CEP57_ENST00000537677.1_Missense_Mutation_p.I388M	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	415	Mediates interaction with microtubules. {ECO:0000250}.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CCAACCAAATAACTAAAGTTC	0.363									Mosaic Variegated Aneuploidy Syndrome																												p.I415M		Atlas-SNP	.											.	CEP57	40	.	0			c.A1245G						.						187.0	194.0	191.0					11																	95562468		2201	4298	6499	SO:0001583	missense	9702	exon10	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	CCAAATAACTAAA	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.1245A>G	chr11.hg19:g.95562468A>G	ENSP00000317902:p.Ile415Met	131.0	0.0		157.0	8.0	NM_014679	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	hg19	CCDS8304.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.2|20.2	3.948644|3.948644	0.73787|0.73787	.|.	.|.	ENSG00000166037|ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150|ENST00000535224	T;T;T;T|.	0.56941|.	0.49;0.43;0.43;0.43|.	5.54|5.54	4.35|4.35	0.52113|0.52113	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72326|0.72326	0.3446|0.3446	M|M	0.76838|0.76838	2.35|2.35	0.46874|0.46874	D|D	0.99923|0.99923	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.997;1.0;0.999|.	T|T	0.73642|0.73642	-0.3918|-0.3918	10|5	0.87932|.	D|.	0|.	-26.7924|-26.7924	10.9427|10.9427	0.47283|0.47283	0.6535:0.3465:0.0:0.0|0.6535:0.3465:0.0:0.0	.|.	406;389;415|.	F5H5F7;Q86XR8-2;Q86XR8|.	.;.;CEP57_HUMAN|.	M|D	388;415;389;406|205	ENSP00000441392:I388M;ENSP00000317902:I415M;ENSP00000317487:I389M;ENSP00000443436:I406M|.	ENSP00000317487:I389M|.	I|N	+|+	3|1	3|0	CEP57|CEP57	95202116|95202116	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.297000|2.297000	0.43593|0.43593	2.111000|2.111000	0.64477|0.64477	0.402000|0.402000	0.26972|0.26972	ATA|AAC	.	.		0.363	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679	
MTMR2	8898	hgsc.bcm.edu	37	11	95580973	95580973	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:95580973A>T	ENST00000346299.5	-	10	1424	c.1084T>A	c.(1084-1086)Tca>Aca	p.S362T	MTMR2_ENST00000409459.1_Missense_Mutation_p.S290T|MTMR2_ENST00000393223.3_Missense_Mutation_p.S290T|MTMR2_ENST00000352297.7_Missense_Mutation_p.S290T|MTMR2_ENST00000484818.1_5'Flank	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	362	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTTCGTAATGATTCTCTCATA	0.388																																					p.S362T		Atlas-SNP	.											.	MTMR2	79	.	0			c.T1084A						.						150.0	141.0	144.0					11																	95580973		2201	4298	6499	SO:0001583	missense	8898	exon10			GTAATGATTCTCT	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1084T>A	chr11.hg19:g.95580973A>T	ENSP00000345752:p.Ser362Thr	157.0	0.0		138.0	41.0	NM_016156	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	hg19	CCDS8305.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.131856	0.56828	.	.	ENSG00000087053	ENST00000346299;ENST00000393223;ENST00000409459;ENST00000352297;ENST00000444541	D;D;D;D;D	0.95035	-3.59;-3.59;-3.59;-3.59;-3.59	5.65	5.65	0.86999	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.98074	0.9365	H	0.95224	3.64	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.982	D	0.99376	1.0921	10	0.87932	D	0	.	15.882	0.79211	1.0:0.0:0.0:0.0	.	362;362	A8K5G2;Q13614	.;MTMR2_HUMAN	T	362;290;290;290;290	ENSP00000345752:S362T;ENSP00000376915:S290T;ENSP00000386882:S290T;ENSP00000343737:S290T;ENSP00000396020:S290T	ENSP00000345752:S362T	S	-	1	0	MTMR2	95220621	1.000000	0.71417	0.456000	0.27044	0.201000	0.24016	7.253000	0.78320	2.155000	0.67459	0.533000	0.62120	TCA	.	.		0.388	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
MMP20	9313	hgsc.bcm.edu	37	11	102482511	102482511	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:102482511A>T	ENST00000260228.2	-	3	510	c.498T>A	c.(496-498)gaT>gaA	p.D166E	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	169					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATATCATAATATCCGCTTCTC	0.438																																					p.D166E		Atlas-SNP	.											.	MMP20	52	.	0			c.T498A						.						71.0	70.0	71.0					11																	102482511		2203	4299	6502	SO:0001583	missense	9313	exon3			CATAATATCCGCT	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.498T>A	chr11.hg19:g.102482511A>T	ENSP00000260228:p.Asp166Glu	54.0	0.0		38.0	18.0	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	hg19	CCDS8318.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.113437	0.77210	.	.	ENSG00000137674	ENST00000260228	T	0.33865	1.39	5.35	-2.98	0.05513	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62011	0.2393	M	0.91717	3.235	0.45733	D	0.998637	D	0.76494	0.999	D	0.87578	0.998	T	0.68138	-0.5488	10	0.87932	D	0	.	12.8338	0.57761	0.4615:0.0:0.5385:0.0	.	166	O60882	MMP20_HUMAN	E	166	ENSP00000260228:D166E	ENSP00000260228:D166E	D	-	3	2	MMP20	101987721	0.895000	0.30542	0.422000	0.26621	0.970000	0.65996	0.006000	0.13152	-0.661000	0.05345	-0.250000	0.11733	GAT	.	.		0.438	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
POU2AF1	5450	hgsc.bcm.edu	37	11	111225251	111225251	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:111225251T>C	ENST00000393067.3	-	5	1020	c.506A>G	c.(505-507)gAg>gGg	p.E169G		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	169					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		TGCCTGGTGCTCTGGGCCCTC	0.662			T	BCL6	NHL																																p.E169G		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"""POU domain, class 2, associating factor 1 (OBF1)"""		L	.	POU2AF1	23	.	0			c.A506G						.						26.0	34.0	31.0					11																	111225251		2199	4297	6496	SO:0001583	missense	5450	exon5			TGGTGCTCTGGGC		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"""POU domain class 2, associating factor 1"""			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.506A>G	chr11.hg19:g.111225251T>C	ENSP00000376786:p.Glu169Gly	113.0	0.0		126.0	50.0	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.528384	0.85706	.	.	ENSG00000110777	ENST00000393067	T	0.37411	1.2	4.87	4.87	0.63330	.	0.063541	0.64402	D	0.000009	T	0.52757	0.1754	L	0.54323	1.7	0.40643	D	0.981962	D	0.64830	0.994	D	0.64595	0.927	T	0.56553	-0.7960	10	0.59425	D	0.04	-20.1092	14.3077	0.66395	0.0:0.0:0.0:1.0	.	169	Q16633	OBF1_HUMAN	G	169	ENSP00000376786:E169G	ENSP00000376786:E169G	E	-	2	0	POU2AF1	110730461	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.646000	0.67916	2.043000	0.60533	0.460000	0.39030	GAG	.	.		0.662	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235	
ZW10	9183	hgsc.bcm.edu	37	11	113609090	113609090	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:113609090G>A	ENST00000200135.3	-	13	1924	c.1780C>T	c.(1780-1782)Cgg>Tgg	p.R594W		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	594					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TTCTGTGCCCGCATTTGGGCC	0.388																																					p.R594W		Atlas-SNP	.											.	ZW10	49	.	0			c.C1780T						.						79.0	75.0	76.0					11																	113609090		2201	4296	6497	SO:0001583	missense	9183	exon13			GTGCCCGCATTTG	U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"""ZW10 (Drosophila) homolog, centromere/kinetochore protein"", ""ZW10, kinetochore associated, homolog (Drosophila)"""			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.1780C>T	chr11.hg19:g.113609090G>A	ENSP00000200135:p.Arg594Trp	82.0	0.0		73.0	33.0	NM_004724	A1A528	Missense_Mutation	SNP	ENST00000200135.3	hg19	CCDS8363.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.675261	0.47781	.	.	ENSG00000086827	ENST00000200135	T	0.46819	0.86	5.08	2.96	0.34315	.	0.179894	0.47852	D	0.000203	T	0.44519	0.1297	M	0.66939	2.045	0.41954	D	0.99067	P	0.36712	0.566	B	0.29862	0.108	T	0.57051	-0.7877	10	0.72032	D	0.01	-6.8325	15.292	0.73872	0.0:0.0:0.7337:0.2663	.	594	O43264	ZW10_HUMAN	W	594	ENSP00000200135:R594W	ENSP00000200135:R594W	R	-	1	2	ZW10	113114300	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.086000	0.50159	1.123000	0.41961	0.563000	0.77884	CGG	.	.		0.388	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724	
KMT2A	4297	hgsc.bcm.edu	37	11	118377321	118377321	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:118377321A>G	ENST00000389506.5	+	27	10705	c.10705A>G	c.(10705-10707)Att>Gtt	p.I3569V	KMT2A_ENST00000354520.4_Missense_Mutation_p.I3531V|KMT2A_ENST00000534358.1_Missense_Mutation_p.I3572V			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3569					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TGAAGCACACATTCCAGACCA	0.478																																					p.I3572V		Atlas-SNP	.											.	MLL	548	.	0			c.A10714G						.						98.0	95.0	96.0					11																	118377321		2200	4295	6495	SO:0001583	missense	4297	exon27			GCACACATTCCAG	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10705A>G	chr11.hg19:g.118377321A>G	ENSP00000374157:p.Ile3569Val	151.0	0.0		183.0	81.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.288120	0.23478	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.81078	-1.45;-1.45;-1.42	5.85	1.12	0.20585	.	0.430925	0.25919	N	0.027446	T	0.52500	0.1738	N	0.04508	-0.205	0.24694	N	0.993294	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41034	-0.9531	10	0.06099	T	0.92	.	8.4852	0.33067	0.4573:0.0:0.5427:0.0	.	3572;3569	E9PQG7;Q03164	.;MLL1_HUMAN	V	3572;3569;3531;2479	ENSP00000436786:I3572V;ENSP00000374157:I3569V;ENSP00000346516:I3531V	ENSP00000346516:I3531V	I	+	1	0	MLL	117882531	0.316000	0.24580	1.000000	0.80357	0.998000	0.95712	0.125000	0.15749	0.158000	0.19367	0.477000	0.44152	ATT	.	.		0.478	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
BCL9L	283149	hgsc.bcm.edu	37	11	118779169	118779169	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:118779169G>A	ENST00000334801.3	-	2	1186	c.222C>T	c.(220-222)ggC>ggT	p.G74G	BCL9L_ENST00000526143.1_5'UTR|MIR4492_ENST00000581627.1_RNA	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	74					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		CCGCCCCCACGCCCTTCGAGC	0.587																																					p.G74G		Atlas-SNP	.											.	BCL9L	254	.	0			c.C222T						.						89.0	92.0	91.0					11																	118779169		2200	4295	6495	SO:0001819	synonymous_variant	283149	exon2			CCCCACGCCCTTC	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.222C>T	chr11.hg19:g.118779169G>A		117.0	0.0		100.0	38.0	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	hg19	CCDS8403.1																																																																																			.	.		0.587	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
CBL	867	hgsc.bcm.edu	37	11	119169140	119169140	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:119169140A>T	ENST00000264033.4	+	15	2700	c.2324A>T	c.(2323-2325)gAt>gTt	p.D775V		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	775	Asp/Glu-rich (acidic).|Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		GATGGGTATGATGTCCCAAAG	0.532			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																												p.D775V		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.A2324T						.						97.0	88.0	91.0					11																	119169140		2199	4295	6494	SO:0001583	missense	867	exon15	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	GGTATGATGTCCC	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2324A>T	chr11.hg19:g.119169140A>T	ENSP00000264033:p.Asp775Val	130.0	0.0		156.0	71.0	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	hg19	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807631	0.70797	.	.	ENSG00000110395	ENST00000264033	D	0.84589	-1.87	5.59	5.59	0.84812	.	0.095529	0.64402	D	0.000001	D	0.88969	0.6582	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.90294	0.4325	10	0.87932	D	0	-42.7633	15.777	0.78228	1.0:0.0:0.0:0.0	.	775	P22681	CBL_HUMAN	V	775	ENSP00000264033:D775V	ENSP00000264033:D775V	D	+	2	0	CBL	118674350	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.137000	0.89612	2.120000	0.65058	0.528000	0.53228	GAT	.	.		0.532	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
TECTA	7007	hgsc.bcm.edu	37	11	121039544	121039544	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:121039544C>T	ENST00000392793.1	+	20	6180	c.5909C>T	c.(5908-5910)gCc>gTc	p.A1970V	TECTA_ENST00000264037.2_Missense_Mutation_p.A1970V			O75443	TECTA_HUMAN	tectorin alpha	1970	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GGAGCTGACGCCACACATTTA	0.468																																					p.A1970V		Atlas-SNP	.											.	TECTA	329	.	0			c.C5909T						.						186.0	174.0	178.0					11																	121039544		2203	4299	6502	SO:0001583	missense	7007	exon19			CTGACGCCACACA	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5909C>T	chr11.hg19:g.121039544C>T	ENSP00000376543:p.Ala1970Val	184.0	0.0		156.0	21.0	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558091	0.65538	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.82526	-1.62;-1.62	5.81	5.81	0.92471	Endoglin/CD105 antigen conserved site (1);Zona pellucida sperm-binding protein (3);	0.565601	0.19263	N	0.118624	T	0.75019	0.3793	N	0.12569	0.235	0.27018	N	0.964539	B	0.20887	0.049	B	0.24974	0.057	T	0.67499	-0.5655	10	0.62326	D	0.03	.	20.0812	0.97776	0.0:1.0:0.0:0.0	.	1970	O75443	TECTA_HUMAN	V	1970	ENSP00000376543:A1970V;ENSP00000264037:A1970V	ENSP00000264037:A1970V	A	+	2	0	TECTA	120544754	0.819000	0.29175	0.882000	0.34594	0.941000	0.58515	4.739000	0.62080	2.752000	0.94435	0.557000	0.71058	GCC	.	.		0.468	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
OR8B4	283162	hgsc.bcm.edu	37	11	124294491	124294491	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:124294491A>G	ENST00000356130.3	-	1	298	c.277T>C	c.(277-279)Tat>Cat	p.Y93H		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	93						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(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		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;0.0279)		CATCCCACATAAGAGATGATA	0.383																																					p.Y93H		Atlas-SNP	.											.	OR8B4	60	.	0			c.T277C						.						99.0	97.0	98.0					11																	124294491		2201	4299	6500	SO:0001583	missense	283162	exon1			CCACATAAGAGAT	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.277T>C	chr11.hg19:g.124294491A>G	ENSP00000348449:p.Tyr93His	139.0	0.0		135.0	55.0	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	hg19	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	13.96	2.394406	0.42410	.	.	ENSG00000198657	ENST00000356130	T	0.00397	7.57	4.61	4.61	0.57282	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000199	T	0.00784	0.0026	M	0.80508	2.5	0.28667	N	0.905807	D	0.63880	0.993	P	0.61070	0.883	T	0.36986	-0.9725	10	0.51188	T	0.08	.	10.3205	0.43762	0.8349:0.1651:0.0:0.0	.	93	Q96RC9	OR8B4_HUMAN	H	93	ENSP00000348449:Y93H	ENSP00000348449:Y93H	Y	-	1	0	OR8B4	123799701	0.000000	0.05858	0.872000	0.34217	0.960000	0.62799	1.365000	0.34182	2.070000	0.61991	0.528000	0.53228	TAT	.	.		0.383	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
SIAE	54414	hgsc.bcm.edu	37	11	124509754	124509754	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:124509754C>T	ENST00000263593.3	-	8	1148	c.976G>A	c.(976-978)Gat>Aat	p.D326N	SIAE_ENST00000545756.1_Missense_Mutation_p.D291N			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	326					carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		TTAGACAAATCTGAAGATAAC	0.433																																					p.D326N		Atlas-SNP	.											.	SIAE	37	.	0			c.G976A						.						131.0	122.0	125.0					11																	124509754		2201	4299	6500	SO:0001583	missense	54414	exon8			ACAAATCTGAAGA	AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"""sialic acid-specific acetylesterase II"""	610079	"""Ysg2 homolog (mouse)"""	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.976G>A	chr11.hg19:g.124509754C>T	ENSP00000263593:p.Asp326Asn	56.0	0.0		60.0	20.0	NM_170601	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Missense_Mutation	SNP	ENST00000263593.3	hg19	CCDS8449.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.323895	0.24080	.	.	ENSG00000110013	ENST00000263593;ENST00000545756	D;D	0.94576	-3.46;-3.46	5.4	-2.97	0.05530	Esterase, SGNH hydrolase-type (1);	0.761579	0.12850	N	0.434009	T	0.78253	0.4254	N	0.01048	-1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.70908	-0.4744	10	0.45353	T	0.12	-0.4514	4.7711	0.13157	0.3345:0.4636:0.0773:0.1245	.	326	Q9HAT2	SIAE_HUMAN	N	326;291	ENSP00000263593:D326N;ENSP00000437877:D291N	ENSP00000263593:D326N	D	-	1	0	SIAE	124014964	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-0.675000	0.05227	-0.312000	0.08741	-0.974000	0.02594	GAT	.	.		0.433	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601	
HEPN1	641654	hgsc.bcm.edu	37	11	124791252	124791252	+	IGR	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:124791252C>T	ENST00000408930.5	+	0	1428				HEPACAM_ENST00000298251.4_Missense_Mutation_p.A345T	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN	hepatocellular carcinoma, down-regulated 1							cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|stomach(1)	3	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)		CCGGGCACGGCGGGAGACACG	0.781																																					p.A345T		Atlas-SNP	.											.	HEPACAM	64	.	0			c.G1033A						.						1.0	1.0	1.0					11																	124791252		712	1792	2504	SO:0001628	intergenic_variant	220296	exon7			GCACGGCGGGAGA	BC148521	CCDS41729.1	11q24	2013-07-02	2011-02-11		ENSG00000221932	ENSG00000221932			34400	protein-coding gene	gene with protein product	"""cancer susceptibility gene HEPN1"""	611641	"""HEPACAM opposite strand 1"""			12971969, 23548416	Standard	NM_001037558		Approved		uc001qbj.1	Q6WQI6	OTTHUMG00000165939		chr11.hg19:g.124791252C>T		307.0	0.0		261.0	100.0	NM_152722		Missense_Mutation	SNP	ENST00000408930.5	hg19	CCDS41729.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.359324	0.24598	.	.	ENSG00000165478	ENST00000298251	T	0.44482	0.92	5.46	0.083	0.14431	.	0.361788	0.30809	N	0.008839	T	0.21761	0.0524	N	0.19112	0.55	0.09310	N	1	B	0.25105	0.118	B	0.10450	0.005	T	0.10382	-1.0632	10	0.38643	T	0.18	-6.7065	6.7462	0.23462	0.0:0.2776:0.4516:0.2709	.	345	Q14CZ8	HECAM_HUMAN	T	345	ENSP00000298251:A345T	ENSP00000298251:A345T	A	-	1	0	HEPACAM	124296462	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.153000	0.10144	-0.011000	0.14247	-0.165000	0.13383	GCC	.	.		0.781	HEPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387129.1	NM_001037558	
CHEK1	1111	hgsc.bcm.edu	37	11	125514027	125514027	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:125514027G>A	ENST00000534070.1	+	10	1220	c.965G>A	c.(964-966)cGc>cAc	p.R322H	CHEK1_ENST00000278916.3_Missense_Mutation_p.R322H|CHEK1_ENST00000438015.1_Missense_Mutation_p.R322H|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000524737.1_Missense_Mutation_p.R322H|CHEK1_ENST00000428830.2_Missense_Mutation_p.R322H|CHEK1_ENST00000544373.1_Missense_Mutation_p.R322H|CHEK1_ENST00000427383.2_Missense_Mutation_p.R338H	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	322					cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		CCAGAACCCCGCACAGGTCTT	0.408								Other conserved DNA damage response genes																													p.R322H		Atlas-SNP	.											CHEK1,colon,carcinoma,0,1	CHEK1	44	.	0			c.G965A						.						109.0	107.0	108.0					11																	125514027		2201	4299	6500	SO:0001583	missense	1111	exon10			AACCCCGCACAGG	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"""CHK1 (checkpoint, S.pombe) homolog"", ""CHK1 checkpoint homolog (S. pombe)"""			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.965G>A	chr11.hg19:g.125514027G>A	ENSP00000435371:p.Arg322His	188.0	0.0		152.0	65.0	NM_001244846	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Missense_Mutation	SNP	ENST00000534070.1	hg19	CCDS8459.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.568815	0.45798	.	.	ENSG00000149554	ENST00000438015;ENST00000427383;ENST00000428830;ENST00000544373;ENST00000534070;ENST00000524737;ENST00000278916	T;T;T;T;T;T;T	0.72942	-0.7;-0.38;-0.7;-0.67;-0.7;-0.7;-0.66	5.58	3.69	0.42338	Protein kinase-like domain (1);	0.360905	0.28796	N	0.014119	T	0.59059	0.2166	L	0.43923	1.385	0.41168	D	0.986146	B;B;B;B	0.15719	0.004;0.014;0.012;0.012	B;B;B;B	0.14023	0.003;0.01;0.009;0.009	T	0.52895	-0.8514	10	0.13853	T	0.58	-5.7233	11.7534	0.51862	0.1485:0.0:0.8515:0.0	.	322;338;322;322	F5H7S4;E7EPP6;B5BTY6;O14757	.;.;.;CHK1_HUMAN	H	322;338;322;322;322;322;322	ENSP00000388648:R322H;ENSP00000391090:R338H;ENSP00000412504:R322H;ENSP00000442317:R322H;ENSP00000435371:R322H;ENSP00000432890:R322H;ENSP00000278916:R322H	ENSP00000278916:R322H	R	+	2	0	CHEK1	125019237	0.745000	0.28261	0.985000	0.45067	0.861000	0.49209	2.323000	0.43823	1.370000	0.46153	0.655000	0.94253	CGC	.	.		0.408	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128936699	128936699	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:128936699A>C	ENST00000310343.9	-	6	553	c.554T>G	c.(553-555)cTg>cGg	p.L185R	ARHGAP32_ENST00000524655.1_Missense_Mutation_p.L111R	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	185	PX; atypical.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						ATAAATACACAGATGAAGATG	0.368																																					p.L185R		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.T554G						.						81.0	77.0	79.0					11																	128936699		1566	3578	5144	SO:0001583	missense	9743	exon6			ATACACAGATGAA	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.554T>G	chr11.hg19:g.128936699A>C	ENSP00000310561:p.Leu185Arg	90.0	0.0		95.0	42.0	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	A	7.520	0.656446	0.14580	.	.	ENSG00000134909	ENST00000310343;ENST00000524655;ENST00000457677;ENST00000525234	T;T;T	0.34859	1.34;1.34;1.34	5.05	5.05	0.67936	Phox homologous domain (3);	.	.	.	.	T	0.40886	0.1135	N	0.16656	0.425	0.80722	D	1	B;D	0.89917	0.211;1.0	B;D	0.74023	0.241;0.982	T	0.19353	-1.0308	9	0.21014	T	0.42	.	13.9074	0.63845	1.0:0.0:0.0:0.0	.	119;185	Q86T64;A7KAX9	.;RHG32_HUMAN	R	185;111;119;159	ENSP00000310561:L185R;ENSP00000432468:L111R;ENSP00000432303:L159R	ENSP00000310561:L185R	L	-	2	0	ARHGAP32	128441909	1.000000	0.71417	0.903000	0.35520	0.993000	0.82548	6.763000	0.74955	2.126000	0.65437	0.460000	0.39030	CTG	.	.		0.368	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
NFRKB	4798	hgsc.bcm.edu	37	11	129734929	129734929	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:129734929T>C	ENST00000446488.3	-	25	3809	c.3706A>G	c.(3706-3708)Aat>Gat	p.N1236D	NFRKB_ENST00000304521.5_Missense_Mutation_p.N1236D|NFRKB_ENST00000524746.1_Missense_Mutation_p.N1236D|NFRKB_ENST00000524794.1_Missense_Mutation_p.N1261D	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	1236					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		ACAGGCTTATTGCCAGCAATG	0.532																																					p.N1261D		Atlas-SNP	.											.	NFRKB	101	.	0			c.A3781G						.						122.0	111.0	115.0					11																	129734929		2201	4297	6498	SO:0001583	missense	4798	exon24			GCTTATTGCCAGC		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.3706A>G	chr11.hg19:g.129734929T>C	ENSP00000400476:p.Asn1236Asp	136.0	0.0		126.0	56.0	NM_006165	Q12869|Q15312|Q9H048	Missense_Mutation	SNP	ENST00000446488.3	hg19	CCDS44770.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.978030	0.92982	.	.	ENSG00000170322	ENST00000304521;ENST00000446488;ENST00000524794;ENST00000524746	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.63733	0.2536	N	0.19112	0.55	0.58432	D	0.999993	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.80764	0.968;0.994;0.994	T	0.67070	-0.5763	9	0.51188	T	0.08	-27.296	16.1388	0.81509	0.0:0.0:0.0:1.0	.	1236;1235;1261	Q6P4R8;Q6P4R8-3;Q6P4R8-2	NFRKB_HUMAN;.;.	D	1236;1236;1261;1236	.	ENSP00000303800:N1236D	N	-	1	0	NFRKB	129240139	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	6.101000	0.71479	2.205000	0.71048	0.528000	0.53228	AAT	.	.		0.532	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
SNX19	399979	hgsc.bcm.edu	37	11	130784447	130784447	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:130784447G>A	ENST00000265909.4	-	1	1957	c.1388C>T	c.(1387-1389)gCc>gTc	p.A463V	SNX19_ENST00000530356.1_Intron|SNX19_ENST00000539184.1_Intron|SNX19_ENST00000533318.1_Intron|SNX19_ENST00000533214.1_Missense_Mutation_p.A463V|SNX19_ENST00000528555.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	463					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TGTAACAGAGGCGGTAACATC	0.522																																					p.A463V		Atlas-SNP	.											.	SNX19	84	.	0			c.C1388T						.						106.0	103.0	104.0					11																	130784447		2201	4297	6498	SO:0001583	missense	399979	exon1			ACAGAGGCGGTAA	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1388C>T	chr11.hg19:g.130784447G>A	ENSP00000265909:p.Ala463Val	88.0	0.0		85.0	30.0	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	hg19	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	G	6.076	0.382292	0.11524	.	.	ENSG00000120451	ENST00000265909;ENST00000533214	T;T	0.20738	2.05;2.05	5.1	3.14	0.36123	.	0.996378	0.08150	N	0.990184	T	0.12092	0.0294	N	0.08118	0	0.09310	N	0.999999	B;B	0.20052	0.012;0.041	B;B	0.19391	0.015;0.025	T	0.34976	-0.9807	10	0.31617	T	0.26	.	9.2251	0.37402	0.0:0.1594:0.6751:0.1655	.	463;463	E9PKB9;Q92543	.;SNX19_HUMAN	V	463	ENSP00000265909:A463V;ENSP00000435390:A463V	ENSP00000265909:A463V	A	-	2	0	SNX19	130289657	0.007000	0.16637	0.001000	0.08648	0.143000	0.21401	1.559000	0.36320	0.666000	0.31087	0.650000	0.86243	GCC	.	.		0.522	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
IGSF9B	22997	hgsc.bcm.edu	37	11	133814238	133814238	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:133814238C>T	ENST00000321016.8	-	3	516	c.286G>A	c.(286-288)Gca>Aca	p.A96T	IGSF9B_ENST00000533871.2_Missense_Mutation_p.A96T			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	96	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CGCAGAGATGCCTTATCATGA	0.582																																					p.A96T		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G286A						.						62.0	66.0	64.0					11																	133814238		2020	4186	6206	SO:0001583	missense	22997	exon3			GAGATGCCTTATC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.286G>A	chr11.hg19:g.133814238C>T	ENSP00000317980:p.Ala96Thr	100.0	0.0		60.0	22.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	28.7	4.942764	0.92526	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.27720	1.65;1.65;1.65;1.86	5.69	4.78	0.61160	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.091985	0.41194	D	0.000922	T	0.42966	0.1226	M	0.64676	1.99	0.47737	D	0.999508	P	0.39003	0.654	P	0.46172	0.506	T	0.41016	-0.9532	10	0.59425	D	0.04	.	16.125	0.81386	0.1347:0.8653:0.0:0.0	.	96	Q9UPX0	TUTLB_HUMAN	T	96;96;86;143	ENSP00000317980:A96T;ENSP00000436576:A96T;ENSP00000434026:A86T;ENSP00000435989:A143T	ENSP00000317980:A96T	A	-	1	0	IGSF9B	133319448	1.000000	0.71417	0.949000	0.38748	0.844000	0.47949	5.968000	0.70413	1.392000	0.46585	0.563000	0.77884	GCA	.	.		0.582	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
TEAD4	7004	hgsc.bcm.edu	37	12	3131073	3131073	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:3131073G>A	ENST00000397122.2	+	8	685	c.400G>A	c.(400-402)Gaa>Aaa	p.E134K	TEAD4_ENST00000359864.2_Missense_Mutation_p.E263K|TEAD4_ENST00000358409.2_Missense_Mutation_p.E220K	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	263					gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			CCCCTACCTCGAAGCCGTGGA	0.542																																					p.E263K		Atlas-SNP	.											TEAD4,NS,carcinoma,0,1	TEAD4	45	.	0			c.G787A						.						132.0	130.0	131.0					12																	3131073		2203	4300	6503	SO:0001583	missense	7004	exon10			TACCTCGAAGCCG	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561		ENST00000397122.2:c.400G>A	chr12.hg19:g.3131073G>A	ENSP00000380311:p.Glu134Lys	157.0	0.0		143.0	65.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Missense_Mutation	SNP	ENST00000397122.2	hg19	CCDS41737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.211382|5.211382	0.95069|0.95069	.|.	.|.	ENSG00000197905|ENSG00000197905	ENST00000358409;ENST00000359864;ENST00000397122|ENST00000544666	T;T;T|.	0.35236|.	1.32;1.32;1.32|.	4.19|4.19	4.19|4.19	0.49359|0.49359	.|.	0.196140|.	0.43579|.	D|.	0.000541|.	D|D	0.86151|0.86151	0.5864|0.5864	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	P|.	0.52577|.	0.954|.	B|.	0.41646|.	0.362|.	D|D	0.90541|0.90541	0.4502|0.4502	10|5	0.87932|.	D|.	0|.	-6.5462|-6.5462	15.6724|15.6724	0.77289|0.77289	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	263|.	Q15561|.	TEAD4_HUMAN|.	K|Q	220;263;134|185	ENSP00000351184:E220K;ENSP00000352926:E263K;ENSP00000380311:E134K|.	ENSP00000351184:E220K|.	E|R	+|+	1|2	0|0	TEAD4|TEAD4	3001334|3001334	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.884000|0.884000	0.51177|0.51177	7.770000|7.770000	0.85390|0.85390	2.167000|2.167000	0.68274|0.68274	0.655000|0.655000	0.94253|0.94253	GAA|CGA	.	.		0.542	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213	
VWF	7450	hgsc.bcm.edu	37	12	6128578	6128578	+	Nonsense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:6128578G>A	ENST00000261405.5	-	28	4260	c.4006C>T	c.(4006-4008)Cga>Tga	p.R1336*		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1336	VWFA 1; binding site for platelet glycoprotein Ib. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TCTGACGGTCGCTTCCGGTCC	0.622																																					p.R1336X		Atlas-SNP	.											.	VWF	338	.	0			c.C4006T						.						42.0	41.0	41.0					12																	6128578		2201	4300	6501	SO:0001587	stop_gained	7450	exon28			ACGGTCGCTTCCG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.4006C>T	chr12.hg19:g.6128578G>A	ENSP00000261405:p.Arg1336*	104.0	0.0		86.0	32.0	NM_000552	Q8TCE8|Q99806	Nonsense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	42	9.615016	0.99220	.	.	ENSG00000110799	ENST00000261405	.	.	.	4.98	4.98	0.66077	.	0.189630	0.26086	N	0.026431	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9727	0.47448	0.0:0.0:0.7098:0.2902	.	.	.	.	X	1336	.	ENSP00000261405:R1336X	R	-	1	2	VWF	5998839	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	1.476000	0.35420	2.605000	0.88082	0.555000	0.69702	CGA	.	.		0.622	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562348	6562348	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:6562348C>A	ENST00000266556.7	+	2	345	c.180C>A	c.(178-180)gcC>gcA	p.A60A	CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR|CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000544021.1_Intron	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	60					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GGGCAAGGGCCTCCCTTGTGC	0.632																																					p.A60A		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C180A						.						59.0	48.0	52.0					12																	6562348		2203	4300	6503	SO:0001819	synonymous_variant	55080	exon2			AAGGGCCTCCCTT	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.180C>A	chr12.hg19:g.6562348C>A		146.0	0.0		123.0	43.0	NM_018009	Q9NWB8	Silent	SNP	ENST00000266556.7	hg19	CCDS8546.1																																																																																			.	.		0.632	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
IFFO1	25900	hgsc.bcm.edu	37	12	6657862	6657862	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:6657862C>T	ENST00000396840.2	-	5	1242	c.1201G>A	c.(1201-1203)Gag>Aag	p.E401K	IFFO1_ENST00000465801.1_Missense_Mutation_p.E97K|IFFO1_ENST00000336604.4_Missense_Mutation_p.E404K|IFFO1_ENST00000436152.2_Missense_Mutation_p.E97K|IFFO1_ENST00000356896.4_Missense_Mutation_p.E404K			Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	401						intermediate filament (GO:0005882)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						TGCATCTCCTCGTTGATGCTG	0.692																																					p.E412K		Atlas-SNP	.											.	IFFO1	55	.	0			c.G1234A						.						79.0	74.0	76.0					12																	6657862		2203	4300	6503	SO:0001583	missense	25900	exon6			TCTCCTCGTTGAT	AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295		"""Intermediate filament family orphans"""	24970	protein-coding gene	gene with protein product		610495	"""intermediate filament family orphan"""	IFFO		8771189, 3052284	Standard	NM_001193457		Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000396840.2:c.1201G>A	chr12.hg19:g.6657862C>T	ENSP00000380052:p.Glu401Lys	119.0	0.0		120.0	38.0	NM_001193457	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	Missense_Mutation	SNP	ENST00000396840.2	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.374289	0.95923	.	.	ENSG00000010295	ENST00000436152;ENST00000465801;ENST00000336604;ENST00000396840;ENST00000356896;ENST00000423501	D;D;D;D;D	0.92752	-2.93;-3.1;-2.82;-2.81;-2.88	4.55	4.55	0.56014	.	0.000000	0.64402	D	0.000002	D	0.95027	0.8390	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.995;0.999;0.999;0.999;0.999	D;P;D;D;D;D	0.78314	0.991;0.819;0.991;0.991;0.991;0.941	D	0.95587	0.8651	10	0.66056	D	0.02	-21.5766	17.3158	0.87224	0.0:1.0:0.0:0.0	.	403;96;404;401;404;105	Q0D2I5-7;Q6P593;Q0D2I5-4;Q0D2I5;Q0D2I5-5;B4DQQ1	.;.;.;IFFO1_HUMAN;.;.	K	97;97;404;401;404;41	ENSP00000390721:E97K;ENSP00000436261:E97K;ENSP00000337593:E404K;ENSP00000380052:E401K;ENSP00000349364:E404K	ENSP00000337593:E404K	E	-	1	0	IFFO1	6528123	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.643000	0.83403	2.072000	0.62099	0.655000	0.94253	GAG	.	.		0.692	IFFO1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000280428.1	NM_080730	
PTPN6	5777	hgsc.bcm.edu	37	12	7069305	7069305	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:7069305G>A	ENST00000318974.9	+	13	1728	c.1484G>A	c.(1483-1485)cGc>cAc	p.R495H	PTPN6_ENST00000399448.1_Missense_Mutation_p.R497H|PTPN6_ENST00000456013.1_Missense_Mutation_p.R495H|PTPN6_ENST00000539029.1_3'UTR|PTPN6_ENST00000447931.2_Missense_Mutation_p.R456H	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	495	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						CGGGCGCAGCGCTCGGGCATG	0.592																																					p.R497H		Atlas-SNP	.											.	PTPN6	42	.	0			c.G1490A						.						49.0	57.0	55.0					12																	7069305		2157	4271	6428	SO:0001583	missense	5777	exon13			CGCAGCGCTCGGG		CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.1484G>A	chr12.hg19:g.7069305G>A	ENSP00000326010:p.Arg495His	99.0	0.0		78.0	11.0	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	hg19	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	G	34	5.401697	0.96030	.	.	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24	4.79	4.79	0.61399	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.98479	0.9493	H	0.99764	4.76	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.99737	1.1014	10	0.87932	D	0	.	18.0266	0.89271	0.0:0.0:1.0:0.0	.	483;456;495;495;497	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	H	497;456;495;495	ENSP00000382376:R497H;ENSP00000415979:R456H;ENSP00000326010:R495H;ENSP00000391592:R495H	ENSP00000326010:R495H	R	+	2	0	PTPN6	6939566	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.533000	0.98059	2.497000	0.84241	0.561000	0.74099	CGC	.	.		0.592	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831	
LRP6	4040	hgsc.bcm.edu	37	12	12300444	12300444	+	Missense_Mutation	SNP	G	G	A	rs143966208		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:12300444G>A	ENST00000261349.4	-	15	3329	c.3253C>T	c.(3253-3255)Cgg>Tgg	p.R1085W	LRP6_ENST00000543091.1_Missense_Mutation_p.R1085W	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1085	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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 transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				AAAGCAGCCCGTTCAATTTTA	0.413																																					p.R1085W		Atlas-SNP	.											LRP6,NS,carcinoma,0,1	LRP6	170	.	0			c.C3253T						.	G	TRP/ARG	0,4406		0,0,2203	125.0	132.0	130.0		3253	3.7	1.0	12	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP6	NM_002336.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1085/1614	12300444	1,13005	2203	4300	6503	SO:0001583	missense	4040	exon15			CAGCCCGTTCAAT	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3253C>T	chr12.hg19:g.12300444G>A	ENSP00000261349:p.Arg1085Trp	177.0	1.0		177.0	61.0	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961442	0.74016	0.0	1.16E-4	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.96300	-3.97;-3.97	5.69	3.68	0.42216	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000018	D	0.97823	0.9285	M	0.84156	2.68	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.969;0.996	D	0.98274	1.0505	10	0.87932	D	0	.	12.1502	0.54046	0.0:0.0:0.4196:0.5804	.	1085;1085	F5H7J9;O75581	.;LRP6_HUMAN	W	1085	ENSP00000261349:R1085W;ENSP00000442472:R1085W	ENSP00000261349:R1085W	R	-	1	2	LRP6	12191711	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.110000	0.31147	1.387000	0.46486	0.563000	0.77884	CGG	.	G|1.000;A|0.000		0.413	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
DUSP16	80824	hgsc.bcm.edu	37	12	12633224	12633224	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:12633224G>A	ENST00000228862.2	-	6	1379	c.748C>T	c.(748-750)Cgc>Tgc	p.R250C	DUSP16_ENST00000298573.4_3'UTR|DUSP16_ENST00000545864.1_Intron	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	250	Tyrosine-protein phosphatase.				dephosphorylation (GO:0016311)|inactivation of MAPK activity (GO:0000188)|MAPK export from nucleus (GO:0045204)|MAPK phosphatase export from nucleus, leptomycin B sensitive (GO:0045209)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(7)|kidney(2)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(3)	26		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		GTGGCGGAGCGGGAGATCCCA	0.448																																					p.R250C	Ovarian(158;443 1896 15437 36069 46477)	Atlas-SNP	.											.	DUSP16	64	.	0			c.C748T						.						224.0	207.0	213.0					12																	12633224		2203	4300	6503	SO:0001583	missense	80824	exon6			CGGAGCGGGAGAT	AB052156	CCDS8650.1	12p13	2011-06-09				ENSG00000111266		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	17909	protein-coding gene	gene with protein product	"""MAPK phosphatase-7"""	607175				11359773, 11489891, 15888437	Standard	NM_030640		Approved	MKP-7, KIAA1700, MKP7	uc001rao.2	Q9BY84		ENST00000228862.2:c.748C>T	chr12.hg19:g.12633224G>A	ENSP00000228862:p.Arg250Cys	109.0	0.0		104.0	37.0	NM_030640	Q547C7|Q96QS2|Q9C0G3	Missense_Mutation	SNP	ENST00000228862.2	hg19	CCDS8650.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.449088	0.84101	.	.	ENSG00000111266	ENST00000228862	D	0.98381	-4.9	5.66	5.66	0.87406	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.99459	0.9808	H	0.98487	4.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	D	0.98171	1.0452	10	0.87932	D	0	.	19.7516	0.96271	0.0:0.0:1.0:0.0	.	250;250	Q9BY84;Q96N49	DUS16_HUMAN;.	C	250	ENSP00000228862:R250C	ENSP00000228862:R250C	R	-	1	0	DUSP16	12524491	1.000000	0.71417	0.961000	0.40146	0.809000	0.45718	7.834000	0.86773	2.656000	0.90262	0.655000	0.94253	CGC	.	.		0.448	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	NM_030640	
RERG	85004	hgsc.bcm.edu	37	12	15262428	15262428	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:15262428C>T	ENST00000256953.2	-	5	552	c.216G>A	c.(214-216)ggG>ggA	p.G72G	RERG_ENST00000538313.1_Silent_p.G72G|RERG_ENST00000536465.1_Silent_p.G72G|RERG-IT1_ENST00000539734.1_RNA|RERG_ENST00000546331.1_Silent_p.G53G	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	72					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						ATCGCATGTGCCCCTCCCTCT	0.458																																					p.G72G		Atlas-SNP	.											.	RERG	30	.	0			c.G216A						.						250.0	261.0	257.0					12																	15262428		2203	4300	6503	SO:0001819	synonymous_variant	85004	exon5			CATGTGCCCCTCC	AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.216G>A	chr12.hg19:g.15262428C>T		173.0	0.0		140.0	56.0	NM_032918	B2R9R0|B4DI02	Silent	SNP	ENST00000256953.2	hg19	CCDS8673.1																																																																																			.	.		0.458	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918	
SLCO1B3	28234	hgsc.bcm.edu	37	12	20968682	20968682	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:20968682C>A	ENST00000381545.3	+	3	229	c.10C>A	c.(10-12)Cat>Aat	p.H4N	SLCO1B3_ENST00000553473.1_Missense_Mutation_p.H4N|LST3_ENST00000381541.3_Missense_Mutation_p.H4N|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.H4N|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.H4N|LST3_ENST00000540229.1_Missense_Mutation_p.H4N	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	4					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	AATGGACCAACATCAACATTT	0.308																																					p.H4N		Atlas-SNP	.											.	SLCO1B3	151	.	0			c.C10A						.						53.0	52.0	53.0					12																	20968682		2203	4294	6497	SO:0001583	missense	28234	exon3			GACCAACATCAAC		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.10C>A	chr12.hg19:g.20968682C>A	ENSP00000370956:p.His4Asn	75.0	0.0		56.0	30.0	NM_019844	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	hg19	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.032114	0.00406	.	.	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046;ENSG00000257046;ENSG00000205754	ENST00000540853;ENST00000261196;ENST00000381545;ENST00000553473;ENST00000381541;ENST00000540229;ENST00000554957	T;T;T;T;T;T;T	0.36699	1.24;1.31;1.31;1.32;1.33;1.32;1.33	2.15	-0.511	0.11970	Major facilitator superfamily domain, general substrate transporter (1);	1.405570	0.04707	N	0.416865	T	0.07773	0.0195	N	0.00237	-1.79	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.28396	-1.0045	10	0.07175	T	0.84	.	2.6745	0.05077	0.462:0.2905:0.0:0.2475	.	4;4;4	F5H094;Q5JAR4;Q9NPD5	.;.;SO1B3_HUMAN	N	4	ENSP00000442000:H4N;ENSP00000261196:H4N;ENSP00000370956:H4N;ENSP00000451758:H4N;ENSP00000370952:H4N;ENSP00000441269:H4N;ENSP00000452013:H4N	ENSP00000370952:H4N	H	+	1	0	SLCO1B3;SLCO1B7;RP11-545J16.1	20859949	0.054000	0.20591	0.033000	0.17914	0.278000	0.26855	0.844000	0.27654	-0.109000	0.12044	0.305000	0.20034	CAT	.	.		0.308	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844	
CAPRIN2	65981	hgsc.bcm.edu	37	12	30863317	30863317	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:30863317C>T	ENST00000298892.5	-	17	3503	c.2753G>A	c.(2752-2754)cGt>cAt	p.R918H	CAPRIN2_ENST00000308433.5_Missense_Mutation_p.R634H|CAPRIN2_ENST00000417045.1_3'UTR|CAPRIN2_ENST00000395805.2_3'UTR|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.R968H	NM_023925.3	NP_076414.2			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GGTCATGCTACGGGAGTCTCC	0.522																																					p.R968H		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.G2903A						.						227.0	230.0	229.0					12																	30863317		2203	4300	6503	SO:0001583	missense	65981	exon18			ATGCTACGGGAGT	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"""C1q domain containing 1"""	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000298892.5:c.2753G>A	chr12.hg19:g.30863317C>T	ENSP00000298892:p.Arg918His	89.0	0.0		105.0	43.0	NM_001002259		Missense_Mutation	SNP	ENST00000298892.5	hg19	CCDS8720.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599263	0.87055	.	.	ENSG00000110888	ENST00000298892;ENST00000251071;ENST00000308433	T;T;T	0.76448	-0.67;-0.72;-1.02	5.7	5.7	0.88788	.	0.119796	0.64402	D	0.000019	D	0.82356	0.5019	N	0.24115	0.695	0.50039	D	0.999844	D;D	0.89917	1.0;1.0	D;D	0.77004	0.982;0.989	D	0.84372	0.0544	10	0.72032	D	0.01	-8.6597	19.8253	0.96616	0.0:1.0:0.0:0.0	.	968;918	Q6IMN6;Q6IMN6-2	CAPR2_HUMAN;.	H	918;968;634	ENSP00000298892:R918H;ENSP00000251071:R968H;ENSP00000309785:R634H	ENSP00000251071:R968H	R	-	2	0	CAPRIN2	30754584	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	6.055000	0.71103	2.682000	0.91365	0.655000	0.94253	CGT	.	.		0.522	CAPRIN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402778.1	NM_023925	
FGD4	121512	hgsc.bcm.edu	37	12	32793225	32793225	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:32793225G>A	ENST00000427716.2	+	17	2483	c.2059G>A	c.(2059-2061)Gcc>Acc	p.A687T	FGD4_ENST00000534526.2_Missense_Mutation_p.A824T|FGD4_ENST00000531134.1_Missense_Mutation_p.A772T|FGD4_ENST00000525053.1_Missense_Mutation_p.A799T|FGD4_ENST00000546442.1_Missense_Mutation_p.A594T	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	687	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					CAGAGCCCAGGCCACCATTCC	0.488																																					p.A687T		Atlas-SNP	.											.	FGD4	86	.	0			c.G2059A						.						136.0	131.0	133.0					12																	32793225		2203	4300	6503	SO:0001583	missense	121512	exon17			GCCCAGGCCACCA	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.2059G>A	chr12.hg19:g.32793225G>A	ENSP00000394487:p.Ala687Thr	136.0	0.0		111.0	41.0	NM_139241	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	G	8.819	0.937095	0.18206	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000546442;ENST00000525053	T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65	5.31	4.38	0.52667	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.124137	0.36066	N	0.002809	T	0.11580	0.0282	L	0.38838	1.175	0.80722	D	1	B;B;B	0.14012	0.002;0.001;0.009	B;B;B	0.15484	0.013;0.013;0.011	T	0.09122	-1.0689	10	0.22109	T	0.4	-5.6503	12.5212	0.56060	0.0856:0.0:0.9144:0.0	.	799;772;687	E9PJX4;B7Z493;Q96M96	.;.;FGD4_HUMAN	T	824;772;687;594;799	ENSP00000449273:A824T;ENSP00000431323:A772T;ENSP00000394487:A687T;ENSP00000446695:A594T;ENSP00000433666:A799T	ENSP00000394487:A687T	A	+	1	0	FGD4	32684492	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	3.838000	0.55828	1.143000	0.42306	0.563000	0.77884	GCC	.	.		0.488	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241	
SLC2A13	114134	hgsc.bcm.edu	37	12	40441899	40441899	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:40441899T>G	ENST00000280871.4	-	2	720	c.670A>C	c.(670-672)Agt>Cgt	p.S224R	SLC2A13_ENST00000380858.1_Missense_Mutation_p.S224R	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	224					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				TCAACAACACTTGCAAAGAAC	0.428										HNSCC(50;0.14)																											p.S224R		Atlas-SNP	.											.	SLC2A13	91	.	0			c.A670C						.						169.0	160.0	163.0					12																	40441899		2203	4300	6503	SO:0001583	missense	114134	exon2			CAACACTTGCAAA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"""Solute carriers"""	15956	protein-coding gene	gene with protein product	"""H(+)-myo-inositol symporter"""	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.670A>C	chr12.hg19:g.40441899T>G	ENSP00000280871:p.Ser224Arg	129.0	0.0		86.0	43.0	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669579	0.67814	.	.	ENSG00000151229	ENST00000280871;ENST00000380858	T;T	0.59638	0.25;0.25	5.65	5.65	0.86999	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.080853	0.85682	D	0.000000	T	0.70141	0.3190	M	0.83774	2.66	0.48288	D	0.99962	P;D	0.57257	0.84;0.979	P;P	0.54590	0.673;0.756	T	0.74355	-0.3692	10	0.54805	T	0.06	-27.107	10.2561	0.43399	0.0:0.0735:0.0:0.9265	.	224;224	Q96QE2;E9PE47	MYCT_HUMAN;.	R	224	ENSP00000280871:S224R;ENSP00000370239:S224R	ENSP00000280871:S224R	S	-	1	0	SLC2A13	38728166	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	5.820000	0.69250	2.156000	0.67533	0.533000	0.62120	AGT	.	.		0.428	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2		
IRAK4	51135	hgsc.bcm.edu	37	12	44161948	44161948	+	Missense_Mutation	SNP	C	C	T	rs377584435		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:44161948C>T	ENST00000448290.2	+	2	105	c.34C>T	c.(34-36)Cgc>Tgc	p.R12C	IRAK4_ENST00000551736.1_Missense_Mutation_p.R12C|IRAK4_ENST00000440781.2_Intron|IRAK4_ENST00000431837.1_5'UTR	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	12					cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		AACATATGTGCGCTGCCTCAA	0.343																																					p.R12C		Atlas-SNP	.											IRAK4_ENST00000448290,caecum,carcinoma,0,5	IRAK4	77	.	0			c.C34T						.	C	CYS/ARG,,,,CYS/ARG	0,4406		0,0,2203	78.0	77.0	77.0		34,,,,34	4.6	1.0	12		77	1,8599	1.2+/-3.3	0,1,4299	no	missense,utr-5,utr-5,intron,missense	IRAK4	NM_001114182.2,NM_001145256.1,NM_001145257.1,NM_001145258.1,NM_016123.3	180,,,,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,,,,probably-damaging	12/461,,,,12/461	44161948	1,13005	2203	4300	6503	SO:0001583	missense	51135	exon2			TATGTGCGCTGCC	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.34C>T	chr12.hg19:g.44161948C>T	ENSP00000390651:p.Arg12Cys	213.0	0.0		219.0	38.0	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	hg19	CCDS8744.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.250977	0.80135	0.0	1.16E-4	ENSG00000198001	ENST00000550616;ENST00000448290;ENST00000551736;ENST00000356669	T;T;T	0.78003	-1.14;-1.14;-1.14	5.5	4.56	0.56223	DEATH-like (2);	0.000000	0.85682	D	0.000000	D	0.87669	0.6235	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88359	0.2986	10	0.59425	D	0.04	-10.9971	15.9279	0.79635	0.1352:0.8648:0.0:0.0	.	12	Q9NWZ3	IRAK4_HUMAN	C	12	ENSP00000446571:R12C;ENSP00000390651:R12C;ENSP00000446490:R12C	ENSP00000349096:R12C	R	+	1	0	IRAK4	42448215	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	3.230000	0.51286	2.751000	0.94390	0.650000	0.86243	CGC	.	.		0.343	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
ANO6	196527	hgsc.bcm.edu	37	12	45725118	45725118	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:45725118A>T	ENST00000320560.8	+	3	393	c.191A>T	c.(190-192)gAt>gTt	p.D64V	ANO6_ENST00000425752.2_Missense_Mutation_p.D64V|ANO6_ENST00000435642.1_Missense_Mutation_p.D64V|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000441606.2_Missense_Mutation_p.D46V|ANO6_ENST00000423947.3_Missense_Mutation_p.D85V	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	64					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TTTTTTAATGATGGCCAGCGA	0.294																																					p.D85V		Atlas-SNP	.											.	ANO6	163	.	0			c.A254T						.						67.0	71.0	70.0					12																	45725118		2203	4298	6501	SO:0001583	missense	196527	exon4			TTAATGATGGCCA	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25240	protein-coding gene	gene with protein product		608663	"""transmembrane protein 16F"""	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.191A>T	chr12.hg19:g.45725118A>T	ENSP00000320087:p.Asp64Val	565.0	0.0		527.0	218.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202517	0.79127	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.85461	0.5702	M	0.92412	3.305	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.996;0.997;0.997	D	0.89046	0.3452	10	0.87932	D	0	.	14.69	0.69080	1.0:0.0:0.0:0.0	.	46;85;64;64	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	V	64;85;64;64;46	ENSP00000391417:D64V;ENSP00000409126:D85V;ENSP00000413840:D64V;ENSP00000320087:D64V;ENSP00000413137:D46V	ENSP00000320087:D64V	D	+	2	0	ANO6	44011385	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.235000	0.78143	2.254000	0.74563	0.482000	0.46254	GAT	.	.		0.294	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743	
SLC38A2	54407	hgsc.bcm.edu	37	12	46760702	46760702	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:46760702T>C	ENST00000256689.5	-	7	952	c.508A>G	c.(508-510)Aaa>Gaa	p.K170E	SLC38A2_ENST00000547252.1_5'UTR|SLC38A2_ENST00000551374.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	170					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		AACTCATATTTCACTATGAAG	0.383																																					p.K170E	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A508G						.						87.0	83.0	85.0					12																	46760702		2203	4300	6503	SO:0001583	missense	54407	exon7			CATATTTCACTAT	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"""Solute carriers"""	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.508A>G	chr12.hg19:g.46760702T>C	ENSP00000256689:p.Lys170Glu	72.0	0.0		85.0	34.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Missense_Mutation	SNP	ENST00000256689.5	hg19	CCDS8749.1	.	.	.	.	.	.	.	.	.	.	T	34	5.349087	0.95830	.	.	ENSG00000134294	ENST00000256689	T	0.02323	4.34	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.22166	0.0534	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.02004	-1.1231	10	0.72032	D	0.01	-15.3943	16.8222	0.85835	0.0:0.0:0.0:1.0	.	70;170	Q96QD8-2;Q96QD8	.;S38A2_HUMAN	E	170	ENSP00000256689:K170E	ENSP00000256689:K170E	K	-	1	0	SLC38A2	45046969	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.383	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1		
KMT2D	8085	hgsc.bcm.edu	37	12	49427950	49427950	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:49427950C>T	ENST00000301067.7	-	38	10639	c.10640G>A	c.(10639-10641)cGc>cAc	p.R3547H	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3547	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R3547H(1)|p.R3277H(1)									TTTGGCAGTGCGCTGCTTGGC	0.542																																					p.R3547H		Atlas-SNP	.											MLL2_ENST00000301067,NS,carcinoma,0,4	MLL2	1173	.	2	Substitution - Missense(2)	prostate(2)	c.G10640A						.						83.0	81.0	82.0					12																	49427950		2023	4198	6221	SO:0001583	missense	8085	exon38			GCAGTGCGCTGCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.10640G>A	chr12.hg19:g.49427950C>T	ENSP00000301067:p.Arg3547His	63.0	0.0		47.0	24.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508596	0.44660	.	.	ENSG00000167548	ENST00000301067	T	0.43688	0.94	5.38	5.38	0.77491	.	0.000000	0.36893	N	0.002344	T	0.62048	0.2396	L	0.54323	1.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.63355	-0.6656	10	0.87932	D	0	.	18.2915	0.90131	0.0:1.0:0.0:0.0	.	3547	O14686	MLL2_HUMAN	H	3547	ENSP00000301067:R3547H	ENSP00000301067:R3547H	R	-	2	0	MLL2	47714217	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.818000	0.86416	2.711000	0.92665	0.563000	0.77884	CGC	.	.		0.542	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
AQP6	363	hgsc.bcm.edu	37	12	50367033	50367033	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:50367033C>T	ENST00000315520.5	+	1	414	c.77C>T	c.(76-78)gCg>gTg	p.A26V	AQP6_ENST00000551733.1_Intron	NM_001652.3	NP_001643.2	Q13520	AQP6_HUMAN	aquaporin 6, kidney specific	26					anion transport (GO:0006820)|excretion (GO:0007588)|odontogenesis (GO:0042476)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	integral component of plasma membrane (GO:0005887)|transport vesicle membrane (GO:0030658)	anion channel activity (GO:0005253)|water channel activity (GO:0015250)			endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(2)	13						ATCAGCAGGGCGCTGTTTGCA	0.617																																					p.A26V		Atlas-SNP	.											.	AQP6	25	.	0			c.C77T						.						138.0	118.0	125.0					12																	50367033		2203	4300	6503	SO:0001583	missense	363	exon1			GCAGGGCGCTGTT	AL137716	CCDS31798.1	12q13	2005-09-20			ENSG00000086159	ENSG00000086159		"""Ion channels / Aquaporins"""	639	protein-coding gene	gene with protein product		601383		AQP2L		8812490	Standard	XM_006719375		Approved		uc001rvr.1	Q13520	OTTHUMG00000133548	ENST00000315520.5:c.77C>T	chr12.hg19:g.50367033C>T	ENSP00000320247:p.Ala26Val	91.0	0.0		51.0	13.0	NM_001652		Missense_Mutation	SNP	ENST00000315520.5	hg19	CCDS31798.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251172	0.80135	.	.	ENSG00000086159	ENST00000315520	D	0.86769	-2.17	5.37	4.48	0.54585	Aquaporin-like (2);	0.101360	0.39909	N	0.001228	D	0.94251	0.8154	M	0.92459	3.31	0.50039	D	0.999841	D	0.89917	1.0	D	0.67103	0.949	D	0.95201	0.8317	10	0.87932	D	0	-21.477	13.1013	0.59222	0.1608:0.8392:0.0:0.0	.	26	Q13520	AQP6_HUMAN	V	26	ENSP00000320247:A26V	ENSP00000320247:A26V	A	+	2	0	AQP6	48653300	0.760000	0.28428	0.362000	0.25862	0.707000	0.40811	0.875000	0.28079	1.412000	0.46977	0.561000	0.74099	GCG	.	.		0.617	AQP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257528.2	NM_001652, NM_053286	
AQP6	363	hgsc.bcm.edu	37	12	50368266	50368266	+	Splice_Site	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:50368266G>T	ENST00000315520.5	+	2	898		c.e2+1		AQP6_ENST00000551733.1_Splice_Site	NM_001652.3	NP_001643.2	Q13520	AQP6_HUMAN	aquaporin 6, kidney specific						anion transport (GO:0006820)|excretion (GO:0007588)|odontogenesis (GO:0042476)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	integral component of plasma membrane (GO:0005887)|transport vesicle membrane (GO:0030658)	anion channel activity (GO:0005253)|water channel activity (GO:0015250)			endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(2)	13						CCTCATTGGGGTAAGGAACAG	0.637											OREG0021809	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	AQP6	25	.	0			c.561+1G>T						.						61.0	50.0	53.0					12																	50368266		2203	4300	6503	SO:0001630	splice_region_variant	363	exon2			ATTGGGGTAAGGA	AL137716	CCDS31798.1	12q13	2005-09-20			ENSG00000086159	ENSG00000086159		"""Ion channels / Aquaporins"""	639	protein-coding gene	gene with protein product		601383		AQP2L		8812490	Standard	XM_006719375		Approved		uc001rvr.1	Q13520	OTTHUMG00000133548	ENST00000315520.5:c.561+1G>T	chr12.hg19:g.50368266G>T		46.0	0.0	969	46.0	24.0	NM_001652		Splice_Site	SNP	ENST00000315520.5	hg19	CCDS31798.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819608	0.71028	.	.	ENSG00000086159	ENST00000551733;ENST00000315520	.	.	.	4.18	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8902	0.63733	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AQP6	48654533	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.162000	0.77515	2.344000	0.79699	0.491000	0.48974	.	.	.		0.637	AQP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257528.2	NM_001652, NM_053286	Intron
CERS5	91012	hgsc.bcm.edu	37	12	50537820	50537820	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:50537820G>A	ENST00000317551.6	-	2	342	c.218C>T	c.(217-219)gCa>gTa	p.A73V	CERS5_ENST00000422340.2_Missense_Mutation_p.A15V	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	73					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AATACAGAGTGCACAGGGTTT	0.378																																					p.A73V		Atlas-SNP	.											.	.	.	.	0			c.C218T						.						119.0	117.0	118.0					12																	50537820		2203	4300	6503	SO:0001583	missense	91012	exon2			CAGAGTGCACAGG		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"""Homeoboxes / CERS class"""	23749	protein-coding gene	gene with protein product		615335	"""LAG1 longevity assurance homolog 5 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 5"""	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.218C>T	chr12.hg19:g.50537820G>A	ENSP00000325485:p.Ala73Val	60.0	0.0		76.0	11.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.7|23.7	4.446218|4.446218	0.84101|0.84101	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000317551;ENST00000422340|ENST00000547800	T;T|.	0.22336|.	1.96;2.48|.	4.0|4.0	3.11|3.11	0.35812|0.35812	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73931|0.73931	0.3650|0.3650	M|M	0.79805|0.79805	2.47|2.47	0.58432|0.58432	D|D	0.999999|0.999999	D;P|.	0.71674|.	0.998;0.787|.	D;B|.	0.66847|.	0.947;0.271|.	T|T	0.75858|0.75858	-0.3169|-0.3169	10|5	0.66056|.	D|.	0.02|.	-7.0865|-7.0865	12.6364|12.6364	0.56685|0.56685	0.0826:0.0:0.9174:0.0|0.0826:0.0:0.9174:0.0	.|.	15;73|.	B4DV54;Q8N5B7|.	.;CERS5_HUMAN|.	V|Y	73;15|8	ENSP00000325485:A73V;ENSP00000389050:A15V|.	ENSP00000325485:A73V|.	A|H	-|-	2|1	0|0	CERS5|CERS5	48824087|48824087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.856000|0.856000	0.48823|0.48823	9.046000|9.046000	0.93817|0.93817	1.271000|1.271000	0.44313|0.44313	-0.140000|-0.140000	0.14226|0.14226	GCA|CAC	.	.		0.378	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190	
TFCP2	7024	hgsc.bcm.edu	37	12	51512404	51512404	+	Splice_Site	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:51512404C>A	ENST00000257915.5	-	2	732	c.274G>T	c.(274-276)Gga>Tga	p.G92*	TFCP2_ENST00000549867.1_Splice_Site_p.G92*|TFCP2_ENST00000548115.1_Splice_Site_p.G92*|TFCP2_ENST00000307660.4_Splice_Site_p.G92*	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	92				G -> A (in Ref. 1; M84810/AA sequence). {ECO:0000305}.	regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AGCATCTAACCTTGATTGAGA	0.393																																					p.G92X		Atlas-SNP	.											.	TFCP2	49	.	0			c.G274T						.						160.0	148.0	152.0					12																	51512404		2203	4300	6503	SO:0001630	splice_region_variant	7024	exon2			TCTAACCTTGATT	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.274+1G>T	chr12.hg19:g.51512404C>A		100.0	0.0		89.0	16.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Nonsense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	40	8.060487	0.98635	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115	.	.	.	5.51	4.62	0.57501	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.4074	13.7046	0.62631	0.0:0.9239:0.0:0.0761	.	.	.	.	X	92	.	.	G	-	1	0	TFCP2	49798671	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.731000	0.84895	1.472000	0.48140	0.591000	0.81541	GGA	.	.		0.393	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653	Nonsense_Mutation
SMAGP	57228	hgsc.bcm.edu	37	12	51663059	51663059	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:51663059T>C	ENST00000603798.1	-	2	676	c.4A>G	c.(4-6)Acc>Gcc	p.T2A	SMAGP_ENST00000604188.1_Missense_Mutation_p.T2A|SMAGP_ENST00000603864.1_Missense_Mutation_p.T2A|SMAGP_ENST00000605627.1_5'UTR|SMAGP_ENST00000398453.3_Missense_Mutation_p.T2A|DAZAP2_ENST00000604900.1_Intron|SMAGP_ENST00000603838.1_Missense_Mutation_p.T2A	NM_001031628.1	NP_001026798.1	Q0VAQ4	SMAGP_HUMAN	small cell adhesion glycoprotein	2						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)											AGGAGGCTGGTCATTGTCACT	0.517																																					p.T2A		Atlas-SNP	.											.	SMAGP	7	.	0			c.A4G						.						128.0	131.0	130.0					12																	51663059		1944	4151	6095	SO:0001583	missense	57228	exon2			GGCTGGTCATTGT		CCDS44889.1	12q13.13	2010-02-17			ENSG00000170545	ENSG00000170545			26918	protein-coding gene	gene with protein product	"""small trans-membrane and glycosylated protein"""					15021913	Standard	NM_001031628		Approved	MGC149453, MGC149454, hSMAGP	uc001rye.1	Q0VAQ4		ENST00000603798.1:c.4A>G	chr12.hg19:g.51663059T>C	ENSP00000475068:p.Thr2Ala	104.0	0.0		96.0	35.0	NM_001031628	A6NIL5	Missense_Mutation	SNP	ENST00000603798.1	hg19	CCDS44889.1	.	.	.	.	.	.	.	.	.	.	T	4.081	0.012870	0.07912	.	.	ENSG00000170545	ENST00000380103;ENST00000398453	T	0.40476	1.03	4.38	-0.912	0.10504	.	0.613383	0.11234	U	0.585315	T	0.25121	0.0610	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.18999	-1.0319	9	0.46703	T	0.11	-23.8773	3.2584	0.06840	0.1805:0.3326:0.0:0.4869	.	2	Q0VAQ4	SMAGP_HUMAN	A	2	ENSP00000381471:T2A	ENSP00000369446:T2A	T	-	1	0	SMAGP	49949326	0.625000	0.27111	0.112000	0.21494	0.103000	0.19146	-0.009000	0.12765	-0.144000	0.11314	-0.408000	0.06270	ACC	.	.		0.517	SMAGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469789.1	NM_020467	
NR4A1	3164	hgsc.bcm.edu	37	12	52448156	52448156	+	Missense_Mutation	SNP	C	C	T	rs375396767		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:52448156C>T	ENST00000243050.1	+	3	358	c.44C>T	c.(43-45)cCg>cTg	p.P15L	NR4A1_ENST00000360284.3_Missense_Mutation_p.P28L|NR4A1_ENST00000550082.1_Missense_Mutation_p.P28L|NR4A1_ENST00000547206.1_3'UTR|NR4A1_ENST00000545748.1_Missense_Mutation_p.P69L|NR4A1_ENST00000394824.2_Missense_Mutation_p.P15L|NR4A1_ENST00000548232.1_Missense_Mutation_p.P15L|NR4A1_ENST00000394825.1_Missense_Mutation_p.P15L	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	15					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|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)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		GCACCGAGTCCGGGACCCCGT	0.642																																					p.P28L		Atlas-SNP	.											.	NR4A1	77	.	0			c.C83T						.						52.0	49.0	50.0					12																	52448156		2203	4300	6503	SO:0001583	missense	3164	exon3			CGAGTCCGGGACC	L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358		"""Nuclear hormone receptors"""	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1		2626032	Standard	NM_002135		Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.44C>T	chr12.hg19:g.52448156C>T	ENSP00000243050:p.Pro15Leu	61.0	0.0		72.0	12.0	NM_001202233	B4DML7|Q15627|Q53Y00|Q6IBU8	Missense_Mutation	SNP	ENST00000243050.1	hg19	CCDS8818.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638295	0.47153	.	.	ENSG00000123358	ENST00000360284;ENST00000545748;ENST00000550082;ENST00000243050;ENST00000394825;ENST00000550763;ENST00000394824;ENST00000548232	D;D;D;D;D;T;D;D	0.92699	-3.02;-3.05;-3.02;-3.02;-3.02;0.86;-3.02;-3.09	4.43	4.43	0.53597	.	1.044700	0.07454	N	0.899528	D	0.87653	0.6231	N	0.14661	0.345	0.51012	D	0.999903	P;P;D	0.58620	0.645;0.856;0.983	B;B;P	0.45119	0.089;0.081;0.47	D	0.83674	0.0168	10	0.87932	D	0	.	12.7862	0.57507	0.0:0.8337:0.1663:0.0	.	28;15;15	B4DML7;P22736;Q15627	.;NR4A1_HUMAN;.	L	28;69;28;15;15;15;15;15	ENSP00000353427:P28L;ENSP00000440864:P69L;ENSP00000449539:P28L;ENSP00000243050:P15L;ENSP00000378302:P15L;ENSP00000449858:P15L;ENSP00000378301:P15L;ENSP00000449587:P15L	ENSP00000243050:P15L	P	+	2	0	NR4A1	50734423	0.001000	0.12720	1.000000	0.80357	0.619000	0.37552	1.330000	0.33781	2.451000	0.82905	0.561000	0.74099	CCG	.	.		0.642	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317922.2		
KRT82	3888	hgsc.bcm.edu	37	12	52799999	52799999	+	Silent	SNP	C	C	T	rs558524531		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:52799999C>T	ENST00000257974.2	-	1	140	c.63G>A	c.(61-63)tcG>tcA	p.S21S	RP11-1020M18.10_ENST00000548135.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	21	Head.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GCATGACAGCCGAGTATGAGC	0.632													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18226	0.0		0.0	False		,,,				2504	0.0				p.S21S		Atlas-SNP	.											.	KRT82	45	.	0			c.G63A						.						36.0	32.0	33.0					12																	52799999		2202	4298	6500	SO:0001819	synonymous_variant	3888	exon1			GACAGCCGAGTAT	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.63G>A	chr12.hg19:g.52799999C>T		53.0	0.0		73.0	5.0	NM_033033		Silent	SNP	ENST00000257974.2	hg19	CCDS8826.1																																																																																			.	.		0.632	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
KRT2	3849	hgsc.bcm.edu	37	12	53041638	53041638	+	Splice_Site	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:53041638T>C	ENST00000309680.3	-	6	1145	c.1124A>G	c.(1123-1125)tAt>tGt	p.Y375C		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	375	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)		GAGCTCCTCATACTGATATGG	0.547																																					p.Y375C		Atlas-SNP	.											.	KRT2	94	.	0			c.A1124G						.						62.0	52.0	55.0					12																	53041638		2203	4300	6503	SO:0001630	splice_region_variant	3849	exon6			TCCTCATACTGAT		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.1123-1A>G	chr12.hg19:g.53041638T>C		62.0	0.0		70.0	31.0	NM_000423	Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	hg19	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154708	0.57259	.	.	ENSG00000172867	ENST00000309680	T	0.75367	-0.93	5.03	5.03	0.67393	Filament (1);	.	.	.	.	D	0.84419	0.5468	M	0.72894	2.215	0.47737	D	0.999509	D	0.89917	1.0	D	0.79108	0.992	D	0.84191	0.0445	9	0.38643	T	0.18	.	15.0736	0.72059	0.0:0.0:0.0:1.0	.	375	P35908	K22E_HUMAN	C	375	ENSP00000310861:Y375C	ENSP00000310861:Y375C	Y	-	2	0	KRT2	51327905	0.584000	0.26766	1.000000	0.80357	0.351000	0.29236	0.855000	0.27805	2.046000	0.60703	0.455000	0.32223	TAT	.	.		0.547	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	Missense_Mutation
SMARCC2	6601	hgsc.bcm.edu	37	12	56575357	56575357	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56575357G>A	ENST00000267064.4	-	10	951	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	SMARCC2_ENST00000550164.1_Missense_Mutation_p.R289W|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550859.1_5'Flank|SMARCC2_ENST00000394023.3_Missense_Mutation_p.R289W|SMARCC2_ENST00000347471.4_Missense_Mutation_p.R289W	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	289					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)			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)			TTCTTGTCCCGTCGATCTGAA	0.483																																					p.R289W		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C865T						.						97.0	96.0	97.0					12																	56575357		2203	4300	6503	SO:0001583	missense	6601	exon10			TGTCCCGTCGATC	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.865C>T	chr12.hg19:g.56575357G>A	ENSP00000267064:p.Arg289Trp	156.0	0.0		119.0	46.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.306806	0.60305	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T	0.48836	0.83;0.84;0.8	4.19	2.31	0.28768	.	0.000000	0.85682	D	0.000000	T	0.63307	0.2500	M	0.66939	2.045	0.38593	D	0.950475	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.76575	0.973;0.988;0.973;0.973;0.988	T	0.68221	-0.5466	10	0.87932	D	0	-12.6371	11.4917	0.50385	0.0:0.0:0.5333:0.4667	.	178;289;294;289;289	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	W	289	ENSP00000449396:R289W;ENSP00000302919:R289W;ENSP00000267064:R289W	ENSP00000267064:R289W	R	-	1	2	SMARCC2	54861624	0.995000	0.38212	1.000000	0.80357	0.992000	0.81027	1.236000	0.32683	0.680000	0.31366	-0.314000	0.08810	CGG	.	.		0.483	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
IL23A	51561	hgsc.bcm.edu	37	12	56733288	56733288	+	Nonsense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56733288G>T	ENST00000228534.4	+	2	407	c.241G>T	c.(241-243)Gga>Tga	p.G81*	STAT2_ENST00000556539.1_5'Flank	NM_016584.2	NP_057668.1	Q9NPF7	IL23A_HUMAN	interleukin 23, alpha subunit p19	81					defense response to Gram-negative bacterium (GO:0050829)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|T cell proliferation (GO:0042098)|tissue remodeling (GO:0048771)	interleukin-23 complex (GO:0070743)				kidney(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						TGACCCCCAAGGACTCAGGGA	0.512																																					p.G81X		Atlas-SNP	.											IL23A,NS,carcinoma,0,1	IL23A	12	.	0			c.G241T						.						87.0	74.0	78.0					12																	56733288		2203	4300	6503	SO:0001587	stop_gained	51561	exon2			CCCCAAGGACTCA	AB030000	CCDS8916.1	12q13.13	2011-07-15				ENSG00000110944		"""Interleukins and interleukin receptors"""	15488	protein-coding gene	gene with protein product	"""interleukin-six, G-CSF related factor"""	605580				11114383	Standard	NM_016584		Approved	SGRF, IL23P19, IL-23, IL-23A, P19	uc001sla.3	Q9NPF7		ENST00000228534.4:c.241G>T	chr12.hg19:g.56733288G>T	ENSP00000228534:p.Gly81*	119.0	1.0		103.0	29.0	NM_016584	Q6NZ80|Q6NZ82|Q9H2A5	Nonsense_Mutation	SNP	ENST00000228534.4	hg19	CCDS8916.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.765175	0.90020	.	.	ENSG00000110944	ENST00000228534	.	.	.	5.73	4.83	0.62350	.	0.000000	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.6862	11.2915	0.49252	0.0878:0.0:0.9122:0.0	.	.	.	.	X	81	.	ENSP00000228534:G81X	G	+	1	0	IL23A	55019555	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.243000	0.51392	2.882000	0.98803	0.655000	0.94253	GGA	.	.		0.512	IL23A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_016584	
APOF	319	hgsc.bcm.edu	37	12	56755672	56755672	+	Silent	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56755672A>C	ENST00000398189.3	-	2	395	c.318T>G	c.(316-318)gcT>gcG	p.A106A	STAT2_ENST00000314128.4_5'Flank|STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000557235.1_5'Flank|APOF_ENST00000541105.1_Silent_p.A88A	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	106					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						GTAGCTGTAGAGCCCAAACAT	0.557																																					p.A106A		Atlas-SNP	.											.	APOF	13	.	0			c.T318G						.						62.0	63.0	63.0					12																	56755672		2090	4242	6332	SO:0001819	synonymous_variant	319	exon2			CTGTAGAGCCCAA	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"""Apolipoproteins"""	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.318T>G	chr12.hg19:g.56755672A>C		149.0	0.0		133.0	9.0	NM_001638	Q8TC13	Silent	SNP	ENST00000398189.3	hg19	CCDS44923.1																																																																																			.	.		0.557	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1		
TIMELESS	8914	hgsc.bcm.edu	37	12	56814391	56814391	+	Silent	SNP	A	A	G	rs267603583		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:56814391A>G	ENST00000553532.1	-	26	3340	c.3190T>C	c.(3190-3192)Ttg>Ctg	p.L1064L	TIMELESS_ENST00000229201.4_Silent_p.L1063L|TIMELESS_ENST00000554616.1_Silent_p.L561L					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						AGCTTGCGCAACAGCTGCTGA	0.512																																					p.L1064L		Atlas-SNP	.											.	TIMELESS	107	.	0			c.T3190C						.						133.0	110.0	117.0					12																	56814391		2203	4300	6503	SO:0001819	synonymous_variant	8914	exon26			TGCGCAACAGCTG	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.3190T>C	chr12.hg19:g.56814391A>G		112.0	0.0		107.0	46.0	NM_003920		Silent	SNP	ENST00000553532.1	hg19	CCDS8918.1																																																																																			.	.		0.512	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
DTX3	196403	hgsc.bcm.edu	37	12	58001004	58001004	+	Missense_Mutation	SNP	G	G	A	rs373278710		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:58001004G>A	ENST00000548198.1	+	3	1862	c.358G>A	c.(358-360)Gca>Aca	p.A120T	DTX3_ENST00000548804.1_Missense_Mutation_p.A120T|DTX3_ENST00000337737.3_Missense_Mutation_p.A120T|DTX3_ENST00000551632.1_Missense_Mutation_p.A123T|ARHGEF25_ENST00000333972.7_5'Flank			Q8N9I9	DTX3_HUMAN	deltex 3, E3 ubiquitin ligase	120					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(6)|urinary_tract(1)	12	Melanoma(17;0.122)					GATGCACCGCGCAGGCCCACC	0.687																																					p.A120T		Atlas-SNP	.											.	DTX3	27	.	0			c.G358A						.	G	THR/ALA	0,3736		0,0,1868	14.0	17.0	16.0		358	1.9	1.0	12		16	1,8173		0,1,4086	no	missense	DTX3	NM_178502.2	58	0,1,5954	AA,AG,GG		0.0122,0.0,0.0084	benign	120/348	58001004	1,11909	1868	4087	5955	SO:0001583	missense	196403	exon5			CACCGCGCAGGCC	AK094385	CCDS41800.1, CCDS66410.1	12q13.2	2014-01-28	2014-01-28			ENSG00000178498		"""RING-type (C3HC4) zinc fingers"""	24457	protein-coding gene	gene with protein product		613142	"""deltex 3 homolog (Drosophila)"", ""deltex homolog 3 (Drosophila)"""			12670957	Standard	XM_005268697		Approved	FLJ34766, RNF154	uc001sow.1	Q8N9I9		ENST00000548198.1:c.358G>A	chr12.hg19:g.58001004G>A	ENSP00000447873:p.Ala120Thr	95.0	0.0		67.0	24.0	NM_178502	Q53ZZ2|Q8NAU6|Q8NDS8	Missense_Mutation	SNP	ENST00000548198.1	hg19	CCDS41800.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.682289	0.29872	0.0	1.22E-4	ENSG00000178498	ENST00000548804;ENST00000549583;ENST00000337737;ENST00000548198;ENST00000551632;ENST00000548478	T;T;T;T;T;T	0.43294	1.55;0.95;1.55;1.55;1.55;0.96	4.0	1.94	0.25998	.	0.326263	0.20948	N	0.082808	T	0.19005	0.0456	N	0.08118	0	0.19775	N	0.99996	B	0.26120	0.142	B	0.15052	0.012	T	0.17471	-1.0368	10	0.12766	T	0.61	-4.8237	11.5041	0.50454	0.0:0.6464:0.3536:0.0	.	120	Q8N9I9	DTX3_HUMAN	T	120;123;120;120;123;113	ENSP00000449294:A120T;ENSP00000449688:A123T;ENSP00000338050:A120T;ENSP00000447873:A120T;ENSP00000448696:A123T;ENSP00000448224:A113T	ENSP00000338050:A120T	A	+	1	0	DTX3	56287271	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	0.322000	0.19576	0.805000	0.34159	-0.599000	0.04106	GCA	.	.		0.687	DTX3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407848.1	NM_178502	
USP15	9958	hgsc.bcm.edu	37	12	62785110	62785110	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:62785110T>C	ENST00000280377.5	+	16	2192	c.2134T>C	c.(2134-2136)Ttt>Ctt	p.F712L	USP15_ENST00000353364.3_Missense_Mutation_p.F683L|USP15_ENST00000393654.3_Missense_Mutation_p.F687L	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	712	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AAAACGATTGTTTACATTCCA	0.378																																					p.F712L	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.T2134C						.						116.0	114.0	114.0					12																	62785110		2203	4300	6503	SO:0001583	missense	9958	exon16			CGATTGTTTACAT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2134T>C	chr12.hg19:g.62785110T>C	ENSP00000280377:p.Phe712Leu	269.0	0.0		279.0	105.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	hg19	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.730107	0.89390	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.19938	2.13;2.11;2.12	5.59	5.59	0.84812	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.37812	0.1017	L	0.39633	1.23	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.04467	-1.0949	9	.	.	.	-13.6337	15.7764	0.78224	0.0:0.0:0.0:1.0	.	712;683	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	L	683;712;687	ENSP00000258123:F683L;ENSP00000280377:F712L;ENSP00000377264:F687L	.	F	+	1	0	USP15	61071377	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.447000	0.80620	2.135000	0.66039	0.460000	0.39030	TTT	.	.		0.378	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
MON2	23041	hgsc.bcm.edu	37	12	62938760	62938760	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:62938760A>G	ENST00000393632.2	+	21	2940	c.2549A>G	c.(2548-2550)aAc>aGc	p.N850S	MON2_ENST00000393629.2_Missense_Mutation_p.N850S|MON2_ENST00000546600.1_Missense_Mutation_p.N850S|MON2_ENST00000552115.1_Missense_Mutation_p.N850S|MON2_ENST00000552738.1_Missense_Mutation_p.N827S|MON2_ENST00000280379.6_Missense_Mutation_p.N851S|MON2_ENST00000393630.3_Missense_Mutation_p.N851S|RNU6-399P_ENST00000365164.1_RNA	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	850					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TTAACATTTAACCATGATCCT	0.333																																					p.N850S		Atlas-SNP	.											.	MON2	160	.	0			c.A2549G						.						66.0	65.0	65.0					12																	62938760		2203	4300	6503	SO:0001583	missense	23041	exon21			CATTTAACCATGA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.2549A>G	chr12.hg19:g.62938760A>G	ENSP00000377252:p.Asn850Ser	406.0	0.0		392.0	155.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	A	12.61	1.991003	0.35131	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.54675	0.56;0.57;0.57;0.56;0.56;0.56;1.58	5.59	-4.85	0.03142	.	0.502543	0.22866	N	0.054681	T	0.26666	0.0652	N	0.08118	0	0.09310	N	0.999999	B;B;B;B	0.13145	0.005;0.007;0.002;0.007	B;B;B;B	0.18263	0.021;0.012;0.007;0.02	T	0.11542	-1.0583	9	.	.	.	-0.6927	14.9276	0.70890	0.494:0.0:0.506:0.0	.	850;827;850;850	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	S	850;851;851;850;827;850;850	ENSP00000377252:N850S;ENSP00000377250:N851S;ENSP00000280379:N851S;ENSP00000447407:N850S;ENSP00000449215:N827S;ENSP00000377249:N850S;ENSP00000446635:N850S	.	N	+	2	0	MON2	61225027	0.743000	0.28239	0.520000	0.27837	0.993000	0.82548	0.540000	0.23191	-1.269000	0.02436	-0.261000	0.10672	AAC	.	.		0.333	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
SLC35E3	55508	hgsc.bcm.edu	37	12	69145879	69145879	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:69145879T>C	ENST00000398004.2	+	3	853	c.581T>C	c.(580-582)aTg>aCg	p.M194T		NM_018656.2	NP_061126.2	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	194						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			CAGGCTCCGATGTCATCTGCC	0.463																																					p.M194T		Atlas-SNP	.											.	SLC35E3	23	.	0			c.T581C						.						235.0	225.0	228.0					12																	69145879		2017	4183	6200	SO:0001583	missense	55508	exon3			CTCCGATGTCATC	AF148713, AY358943	CCDS41808.1	12q15	2014-09-04			ENSG00000175782	ENSG00000175782		"""Solute carriers"""	20864	protein-coding gene	gene with protein product						12975309	Standard	XM_005269006		Approved	BLOV1	uc001suh.3	Q7Z769	OTTHUMG00000169282	ENST00000398004.2:c.581T>C	chr12.hg19:g.69145879T>C	ENSP00000381089:p.Met194Thr	123.0	0.0		100.0	42.0	NM_018656	A8K0T0|Q0P5Y5|Q9P0V1	Missense_Mutation	SNP	ENST00000398004.2	hg19	CCDS41808.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.296189	0.60086	.	.	ENSG00000175782	ENST00000398004;ENST00000431174	T;T	0.63744	-0.06;1.29	5.59	5.59	0.84812	Domain of unknown function DUF250 (1);	0.041255	0.85682	D	0.000000	T	0.53706	0.1813	L	0.37630	1.12	0.58432	D	0.999999	B	0.15930	0.015	B	0.23150	0.044	T	0.48068	-0.9067	9	.	.	.	-0.3555	16.0729	0.80948	0.0:0.0:0.0:1.0	.	194	Q7Z769	S35E3_HUMAN	T	194;4	ENSP00000381089:M194T;ENSP00000403769:M4T	.	M	+	2	0	SLC35E3	67432146	1.000000	0.71417	0.994000	0.49952	0.968000	0.65278	7.698000	0.84413	2.266000	0.75297	0.454000	0.30748	ATG	.	.		0.463	SLC35E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403241.1	NM_018656	
RAB3IP	117177	hgsc.bcm.edu	37	12	70188991	70188991	+	Missense_Mutation	SNP	C	C	T	rs575263311	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:70188991C>T	ENST00000247833.7	+	6	1131	c.755C>T	c.(754-756)aCg>aTg	p.T252M	RAB3IP_ENST00000550536.1_Missense_Mutation_p.T268M|RAB3IP_ENST00000483530.2_Missense_Mutation_p.T252M|RAB3IP_ENST00000325555.9_Missense_Mutation_p.T46M|RAB3IP_ENST00000551641.1_Missense_Mutation_p.T46M|RAB3IP_ENST00000553099.1_Missense_Mutation_p.T46M|RAB3IP_ENST00000362025.5_Missense_Mutation_p.T268M|RAB3IP_ENST00000378815.6_Missense_Mutation_p.T252M|RAB3IP_ENST00000550847.1_5'Flank					RAB3A interacting protein											NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			ACATCACCTACGCAGGAGCCT	0.428													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20028	0.0		0.0	False		,,,				2504	0.0				p.T268M		Atlas-SNP	.											.	RAB3IP	48	.	0			c.C803T						.						106.0	103.0	104.0					12																	70188991		2203	4300	6503	SO:0001583	missense	117177	exon6			CACCTACGCAGGA		CCDS8993.1, CCDS8995.1, CCDS8996.1, CCDS41811.1, CCDS44942.1	12q15	2013-01-22	2013-01-22		ENSG00000127328	ENSG00000127328			16508	protein-coding gene	gene with protein product	"""rabin3"""	608686					Standard	NM_175623		Approved	RABIN3	uc001svm.3	Q96QF0	OTTHUMG00000169437	ENST00000247833.7:c.755C>T	chr12.hg19:g.70188991C>T	ENSP00000247833:p.Thr252Met	246.0	0.0		221.0	74.0	NM_175623		Missense_Mutation	SNP	ENST00000247833.7	hg19	CCDS8995.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633427	0.47049	.	.	ENSG00000127328	ENST00000247833;ENST00000378815;ENST00000483530;ENST00000325555;ENST00000550536;ENST00000362025;ENST00000551641;ENST00000553099	T;T;T;T;T	0.47177	0.86;0.9;0.85;0.9;0.9	5.84	3.59	0.41128	.	0.442527	0.27881	N	0.017470	T	0.52853	0.1760	L	0.43152	1.355	0.09310	N	0.999996	P;D;P;D	0.61080	0.929;0.989;0.88;0.972	P;P;P;P	0.56788	0.541;0.806;0.541;0.503	T	0.44997	-0.9291	10	0.44086	T	0.13	.	12.8738	0.57980	0.0:0.8377:0.0:0.1623	.	268;268;252;252	Q96QF0-4;Q96QF0;Q96QF0-3;Q96QF0-7	.;RAB3I_HUMAN;.;.	M	252;252;252;46;268;268;46;46	ENSP00000247833:T252M;ENSP00000323349:T46M;ENSP00000447300:T268M;ENSP00000448773:T46M;ENSP00000448027:T46M	ENSP00000247833:T252M	T	+	2	0	RAB3IP	68475258	0.552000	0.26505	0.066000	0.19879	0.888000	0.51559	2.521000	0.45563	1.386000	0.46466	-0.355000	0.07637	ACG	.	.		0.428	RAB3IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280671.2	NM_022456	
KCNMB4	27345	hgsc.bcm.edu	37	12	70824288	70824288	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:70824288G>A	ENST00000258111.4	+	3	947	c.488G>A	c.(487-489)cGc>cAc	p.R163H		NM_014505.5	NP_055320.4	Q86W47	KCMB4_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 4	163					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of neurotransmitter secretion (GO:0046928)|regulation of vasoconstriction (GO:0019229)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)			kidney(1)|large_intestine(4)|lung(5)	10	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)		Miconazole(DB01110)|Procaine(DB00721)	CTTCTGCATCGCACTCATGAT	0.488																																					p.R163H		Atlas-SNP	.											KCNMB4,caecum,carcinoma,0,3	KCNMB4	27	.	0			c.G488A						.						204.0	188.0	193.0					12																	70824288		2203	4300	6503	SO:0001583	missense	27345	exon3			TGCATCGCACTCA	AF207992	CCDS8997.1	12q15	2006-06-10			ENSG00000135643	ENSG00000135643		"""Potassium channels"""	6289	protein-coding gene	gene with protein product		605223				10692449, 10828459	Standard	NM_014505		Approved		uc001svx.3	Q86W47	OTTHUMG00000167586	ENST00000258111.4:c.488G>A	chr12.hg19:g.70824288G>A	ENSP00000258111:p.Arg163His	68.0	0.0		52.0	21.0	NM_014505	Q8IVR3|Q9NPA4|Q9P0G5	Missense_Mutation	SNP	ENST00000258111.4	hg19	CCDS8997.1	.	.	.	.	.	.	.	.	.	.	G	33	5.268925	0.95429	.	.	ENSG00000135643	ENST00000258111	T	0.15834	2.39	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	M	0.63843	1.955	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	T	0.12682	-1.0538	10	0.66056	D	0.02	-23.5357	20.1653	0.98150	0.0:0.0:1.0:0.0	.	163	Q86W47	KCMB4_HUMAN	H	163	ENSP00000258111:R163H	ENSP00000258111:R163H	R	+	2	0	KCNMB4	69110555	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.440000	0.73435	2.768000	0.95171	0.655000	0.94253	CGC	.	.		0.488	KCNMB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395208.1	NM_014505	
BBS10	79738	hgsc.bcm.edu	37	12	76740856	76740856	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:76740856A>G	ENST00000393262.3	-	2	992	c.909T>C	c.(907-909)agT>agC	p.S303S		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	303					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|regulation of protein complex assembly (GO:0043254)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell projection (GO:0042995)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						TTACATTCTGACTATGTAGAT	0.338									Bardet-Biedl syndrome																												p.S303S		Atlas-SNP	.											.	BBS10	46	.	0			c.T909C						.						118.0	105.0	109.0					12																	76740856		2203	4300	6503	SO:0001819	synonymous_variant	79738	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ATTCTGACTATGT	BC026355	CCDS9014.2	12q21.2	2014-06-17	2006-04-28	2006-04-28	ENSG00000179941	ENSG00000179941		"""Heat Shock Proteins / Chaperonins"""	26291	protein-coding gene	gene with protein product		610148	"""chromosome 12 open reading frame 58"""	C12orf58		16582908	Standard	NM_024685		Approved	FLJ23560	uc001syd.1	Q8TAM1	OTTHUMG00000147352	ENST00000393262.3:c.909T>C	chr12.hg19:g.76740856A>G		75.0	0.0		64.0	24.0	NM_024685	Q96CW2|Q9H5D2	Silent	SNP	ENST00000393262.3	hg19	CCDS9014.2																																																																																			.	.		0.338	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685	
E2F7	144455	hgsc.bcm.edu	37	12	77417817	77417817	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:77417817A>T	ENST00000322886.7	-	13	2949	c.2714T>A	c.(2713-2715)aTc>aAc	p.I905N	E2F7_ENST00000416496.2_3'UTR	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	905					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						GCCGCTGGGGATTTCTAGTCT	0.597																																					p.I905N		Atlas-SNP	.											.	E2F7	201	.	0			c.T2714A						.						102.0	107.0	106.0					12																	77417817		2203	4300	6503	SO:0001583	missense	144455	exon13			CTGGGGATTTCTA	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.2714T>A	chr12.hg19:g.77417817A>T	ENSP00000323246:p.Ile905Asn	84.0	0.0		69.0	32.0	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	hg19	CCDS9016.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.786609	0.49997	.	.	ENSG00000165891	ENST00000322886;ENST00000339887	T	0.24723	1.84	5.91	5.91	0.95273	.	0.128916	0.49916	D	0.000134	T	0.41834	0.1176	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.29882	-0.9997	10	0.87932	D	0	-21.5712	14.0893	0.64980	1.0:0.0:0.0:0.0	.	905	Q96AV8	E2F7_HUMAN	N	905;376	ENSP00000323246:I905N	ENSP00000323246:I905N	I	-	2	0	E2F7	75941948	1.000000	0.71417	0.365000	0.25901	0.009000	0.06853	5.736000	0.68597	2.254000	0.74563	0.533000	0.62120	ATC	.	.		0.597	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
MGAT4C	25834	hgsc.bcm.edu	37	12	86377408	86377408	+	Missense_Mutation	SNP	T	T	C	rs35652293		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:86377408T>C	ENST00000604798.1	-	7	1392	c.188A>G	c.(187-189)cAa>cGa	p.Q63R	MGAT4C_ENST00000548651.1_Missense_Mutation_p.Q63R|MGAT4C_ENST00000552435.2_Missense_Mutation_p.Q63R|MGAT4C_ENST00000549405.2_Missense_Mutation_p.Q63R|MGAT4C_ENST00000332156.1_Missense_Mutation_p.Q63R|MGAT4C_ENST00000552808.2_Missense_Mutation_p.Q63R|MGAT4C_ENST00000393205.2_Missense_Mutation_p.Q92R			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	63					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGAATTCAGTTGATGTGTGGA	0.348																																					p.Q63R		Atlas-SNP	.											.	MGAT4C	110	.	0			c.A188G						.						138.0	137.0	137.0					12																	86377408		2203	4300	6503	SO:0001583	missense	25834	exon6			TTCAGTTGATGTG		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	30871	protein-coding gene	gene with protein product		607385	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"""			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.188A>G	chr12.hg19:g.86377408T>C	ENSP00000474896:p.Gln63Arg	106.0	0.0		91.0	4.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	hg19	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.115001	0.77210	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225;ENST00000552435	T;T;T;T;T;T	0.46063	1.48;1.45;1.48;1.48;1.48;0.88	5.44	5.44	0.79542	.	0.078589	0.53938	D	0.000051	T	0.43188	0.1236	L	0.44542	1.39	0.34850	D	0.741548	P;P	0.47191	0.891;0.891	B;P	0.48368	0.412;0.575	T	0.50980	-0.8763	10	0.18710	T	0.47	4.0E-4	15.502	0.75705	0.0:0.0:0.0:1.0	.	92;63	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	R	63;92;63;63;63;63;63;63	ENSP00000331664:Q63R;ENSP00000376900:Q92R;ENSP00000449022:Q63R;ENSP00000446647:Q63R;ENSP00000447253:Q63R;ENSP00000449172:Q63R	ENSP00000331664:Q63R	Q	-	2	0	MGAT4C	84901539	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	6.104000	0.71498	2.071000	0.62044	0.460000	0.39030	CAA	.	.		0.348	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244	
TMTC3	160418	hgsc.bcm.edu	37	12	88582677	88582677	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:88582677A>G	ENST00000266712.6	+	11	1710	c.1490A>G	c.(1489-1491)aAa>aGa	p.K497R		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	497					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						AATAGAACCAAAGAAGCTGAA	0.299																																					p.K497R		Atlas-SNP	.											.	TMTC3	75	.	0			c.A1490G						.						75.0	81.0	79.0					12																	88582677		2202	4286	6488	SO:0001583	missense	160418	exon11			GAACCAAAGAAGC		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"""Tetratricopeptide (TTC) repeat domain containing"""	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.1490A>G	chr12.hg19:g.88582677A>G	ENSP00000266712:p.Lys497Arg	462.0	0.0		433.0	101.0	NM_181783	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	hg19	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.219074	0.39201	.	.	ENSG00000139324	ENST00000266712	T	0.54479	0.57	5.37	2.75	0.32379	.	0.133494	0.64402	N	0.000002	T	0.41351	0.1155	L	0.42581	1.335	0.36341	D	0.859478	B	0.02656	0.0	B	0.08055	0.003	T	0.34229	-0.9837	10	0.25106	T	0.35	-12.3542	10.5278	0.44958	0.8997:0.0:0.1003:0.0	.	497	Q6ZXV5-2	.	R	497	ENSP00000266712:K497R	ENSP00000266712:K497R	K	+	2	0	TMTC3	87106808	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.051000	0.57412	0.241000	0.21283	0.533000	0.62120	AAA	.	.		0.299	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783	
LUM	4060	hgsc.bcm.edu	37	12	91497984	91497984	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:91497984C>A	ENST00000266718.4	-	3	1429	c.975G>T	c.(973-975)atG>atT	p.M325I	LUM_ENST00000548071.1_5'UTR	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	325					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|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)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						GACATTCATACATATCCGGTG	0.398																																					p.M325I		Atlas-SNP	.											.	LUM	65	.	0			c.G975T						.						117.0	111.0	113.0					12																	91497984		2203	4300	6503	SO:0001583	missense	4060	exon3			TTCATACATATCC	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6724	protein-coding gene	gene with protein product	"""lumican proteoglycan"""	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.975G>T	chr12.hg19:g.91497984C>A	ENSP00000266718:p.Met325Ile	91.0	0.0		125.0	56.0	NM_002345	B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	hg19	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	8.773	0.926379	0.18056	.	.	ENSG00000139329	ENST00000266718	T	0.16897	2.31	5.19	4.29	0.51040	.	0.188883	0.52532	D	0.000064	T	0.12475	0.0303	L	0.31294	0.92	0.44409	D	0.997325	B	0.06786	0.001	B	0.08055	0.003	T	0.09335	-1.0679	10	0.16896	T	0.51	-19.136	13.6563	0.62339	0.0:0.9231:0.0:0.0769	.	325	P51884	LUM_HUMAN	I	325	ENSP00000266718:M325I	ENSP00000266718:M325I	M	-	3	0	LUM	90022115	1.000000	0.71417	0.997000	0.53966	0.547000	0.35210	2.105000	0.41825	2.398000	0.81561	0.591000	0.81541	ATG	.	.		0.398	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345	
ELK3	2004	hgsc.bcm.edu	37	12	96617510	96617510	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:96617510T>C	ENST00000228741.3	+	2	492	c.166T>C	c.(166-168)Tat>Cat	p.Y56H	ELK3_ENST00000552142.1_Missense_Mutation_p.Y56H|RP11-394J1.2_ENST00000551844.1_RNA	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	56					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					AAATATGAACTATGATAAGCT	0.488																																					p.Y56H		Atlas-SNP	.											.	ELK3	36	.	0			c.T166C						.						76.0	72.0	73.0					12																	96617510		2203	4300	6503	SO:0001583	missense	2004	exon2			ATGAACTATGATA	BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.166T>C	chr12.hg19:g.96617510T>C	ENSP00000228741:p.Tyr56His	106.0	0.0		106.0	47.0	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Missense_Mutation	SNP	ENST00000228741.3	hg19	CCDS9060.1	.	.	.	.	.	.	.	.	.	.	t	26.2	4.717535	0.89205	.	.	ENSG00000111145	ENST00000228741;ENST00000552142;ENST00000547860	T;T;T	0.72282	-0.64;-0.64;-0.64	5.48	5.48	0.80851	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (5);	0.000000	0.85682	D	0.000000	D	0.89777	0.6813	H	0.97611	4.04	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.93360	0.6726	10	0.87932	D	0	.	15.5812	0.76445	0.0:0.0:0.0:1.0	.	56	P41970	ELK3_HUMAN	H	56	ENSP00000228741:Y56H;ENSP00000449430:Y56H;ENSP00000447857:Y56H	ENSP00000228741:Y56H	Y	+	1	0	ELK3	95141641	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.036000	0.88901	2.094000	0.63399	0.459000	0.35465	TAT	.	.		0.488	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230	
SCYL2	55681	hgsc.bcm.edu	37	12	100708368	100708368	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:100708368A>G	ENST00000360820.2	+	8	1508	c.1071A>G	c.(1069-1071)ccA>ccG	p.P357P		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	357			P -> L (in dbSNP:rs33968174). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						AAGGACTGCCAAAGGTTCTAC	0.323																																					p.P357P		Atlas-SNP	.											.	SCYL2	99	.	0			c.A1071G						.						65.0	65.0	65.0					12																	100708368		2203	4297	6500	SO:0001819	synonymous_variant	55681	exon8			ACTGCCAAAGGTT	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.1071A>G	chr12.hg19:g.100708368A>G		578.0	0.0		486.0	195.0	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Silent	SNP	ENST00000360820.2	hg19	CCDS9076.1																																																																																			.	.		0.323	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
PMCH	5367	hgsc.bcm.edu	37	12	102591388	102591388	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:102591388G>A	ENST00000329406.4	-	1	235	c.161C>T	c.(160-162)gCa>gTa	p.A54V		NM_002674.2	NP_002665.2	P20382	MCH_HUMAN	pro-melanin-concentrating hormone	54					cell differentiation (GO:0030154)|feeding behavior (GO:0007631)|multicellular organismal development (GO:0007275)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	6						TGATTTTTCTGCAGTGTCTTC	0.358																																					p.A54V		Atlas-SNP	.											.	PMCH	10	.	0			c.C161T						.						112.0	108.0	109.0					12																	102591388		2201	4300	6501	SO:0001583	missense	5367	exon1			TTTTCTGCAGTGT	M57703	CCDS31885.1	12q23.2	2013-02-26			ENSG00000183395	ENSG00000183395		"""Endogenous ligands"""	9109	protein-coding gene	gene with protein product		176795				2149166	Standard	NM_002674		Approved	MCH	uc001tjl.3	P20382	OTTHUMG00000170479	ENST00000329406.4:c.161C>T	chr12.hg19:g.102591388G>A	ENSP00000332225:p.Ala54Val	90.0	0.0		82.0	15.0	NM_002674	Q16044|Q8WVG0	Missense_Mutation	SNP	ENST00000329406.4	hg19	CCDS31885.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710462	0.30322	.	.	ENSG00000183395	ENST00000329406	.	.	.	5.76	2.99	0.34606	.	0.316543	0.30028	N	0.010591	T	0.26268	0.0641	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16424	-1.0403	9	0.46703	T	0.11	.	5.776	0.18279	0.2626:0.0:0.6122:0.1252	.	54	P20382	MCH_HUMAN	V	54	.	ENSP00000332225:A54V	A	-	2	0	PMCH	101115518	0.825000	0.29262	0.981000	0.43875	0.978000	0.69477	2.274000	0.43390	0.378000	0.24764	0.655000	0.94253	GCA	.	.		0.358	PMCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409337.1	NM_002674	
HCFC2	29915	hgsc.bcm.edu	37	12	104476618	104476618	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:104476618T>C	ENST00000229330.4	+	7	1106	c.1002T>C	c.(1000-1002)gaT>gaC	p.D334D		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	334					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						GTGGAAGAGATGGCTACAAAA	0.378																																					p.D334D	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-SNP	.											.	HCFC2	94	.	0			c.T1002C						.						81.0	82.0	82.0					12																	104476618		2203	4300	6503	SO:0001819	synonymous_variant	29915	exon7			AAGAGATGGCTAC	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.1002T>C	chr12.hg19:g.104476618T>C		132.0	0.0		129.0	53.0	NM_013320	B2R8Q5|C0H5X3	Silent	SNP	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.378	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320	
CMKLR1	1240	hgsc.bcm.edu	37	12	108685651	108685651	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:108685651A>G	ENST00000312143.7	-	3	1452	c.1089T>C	c.(1087-1089)acT>acC	p.T363T	CMKLR1_ENST00000397688.2_Silent_p.T361T|CMKLR1_ENST00000550402.1_Silent_p.T363T|CMKLR1_ENST00000552995.1_Silent_p.T361T|CMKLR1_ENST00000412676.1_Silent_p.T363T	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	363					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						CATTCATAGAAGTCCTCTCAT	0.488																																					p.T363T		Atlas-SNP	.											.	CMKLR1	67	.	0			c.T1089C						.						120.0	124.0	123.0					12																	108685651		1922	4136	6058	SO:0001819	synonymous_variant	1240	exon3			CATAGAAGTCCTC	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.1089T>C	chr12.hg19:g.108685651A>G		137.0	0.0		116.0	49.0	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Silent	SNP	ENST00000312143.7	hg19	CCDS44965.1																																																																																			.	.		0.488	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
RBM19	9904	hgsc.bcm.edu	37	12	114397139	114397139	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:114397139G>A	ENST00000545145.2	-	5	527	c.449C>T	c.(448-450)gCg>gTg	p.A150V	RBM19_ENST00000261741.5_Missense_Mutation_p.A150V|RBM19_ENST00000392561.3_Missense_Mutation_p.A150V	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	150					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCCATCATTCGCCCAAGTGGC	0.602																																					p.A150V		Atlas-SNP	.											.	RBM19	117	.	0			c.C449T						.						87.0	81.0	83.0					12																	114397139		2203	4300	6503	SO:0001583	missense	9904	exon5			TCATTCGCCCAAG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.449C>T	chr12.hg19:g.114397139G>A	ENSP00000442053:p.Ala150Val	80.0	0.0		84.0	32.0	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	hg19	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830482	0.32329	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.06849	3.25;3.25;3.25	5.27	4.38	0.52667	.	0.162158	0.56097	D	0.000040	T	0.12561	0.0305	M	0.79926	2.475	0.42178	D	0.991676	B	0.24258	0.1	B	0.17433	0.018	T	0.02190	-1.1198	10	0.46703	T	0.11	-31.3027	9.0416	0.36321	0.0743:0.0:0.7801:0.1456	.	150	Q9Y4C8	RBM19_HUMAN	V	150	ENSP00000442053:A150V;ENSP00000376344:A150V;ENSP00000261741:A150V	ENSP00000261741:A150V	A	-	2	0	RBM19	112881522	1.000000	0.71417	0.837000	0.33122	0.134000	0.20937	4.999000	0.63934	1.230000	0.43646	-0.143000	0.13931	GCG	.	.		0.602	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
MED13L	23389	hgsc.bcm.edu	37	12	116420407	116420407	+	Splice_Site	SNP	C	C	T	rs151181388		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:116420407C>T	ENST00000281928.3	-	22	5163	c.4957G>A	c.(4957-4959)Gtt>Att	p.V1653I		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1653						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CTTTCTGTAACACTGGAGAGA	0.458																																					p.V1653I		Atlas-SNP	.											.	MED13L	193	.	0			c.G4957A						.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	64.0	56.0	58.0		4957	5.0	1.0	12	dbSNP_134	58	0,8600		0,0,4300	no	missense-near-splice	MED13L	NM_015335.4	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	1653/2211	116420407	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	23389	exon22			CTGTAACACTGGA	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.4956-1G>A	chr12.hg19:g.116420407C>T		118.0	0.0		124.0	46.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605349	0.66445	2.27E-4	0.0	ENSG00000123066	ENST00000281928	T	0.74106	-0.81	5.87	4.96	0.65561	.	0.297369	0.38436	N	0.001692	T	0.59321	0.2185	N	0.19112	0.55	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.55496	-0.8132	10	0.44086	T	0.13	.	10.7911	0.46434	0.0:0.7948:0.0:0.2052	.	1653	Q71F56	MD13L_HUMAN	I	1653	ENSP00000281928:V1653I	ENSP00000281928:V1653I	V	-	1	0	MED13L	114904790	0.950000	0.32346	0.999000	0.59377	0.947000	0.59692	0.525000	0.22956	1.427000	0.47276	0.591000	0.81541	GTT	.	C|1.000;T|0.000		0.458	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		Missense_Mutation
SUDS3	64426	hgsc.bcm.edu	37	12	118848915	118848915	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:118848915G>A	ENST00000543473.1	+	11	1153	c.841G>A	c.(841-843)Gac>Aac	p.D281N	SUDS3_ENST00000541280.1_3'UTR|SUDS3_ENST00000397564.2_Missense_Mutation_p.D282N	NM_022491.2	NP_071936.2	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3 homolog (S. cerevisiae)	281					apoptotic process (GO:0006915)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)			breast(1)|lung(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGAGTCAAAGGACAACCAGAA	0.468																																					p.D281N		Atlas-SNP	.											.	SUDS3	26	.	0			c.G841A						.						47.0	44.0	45.0					12																	118848915		1921	4139	6060	SO:0001583	missense	64426	exon11			TCAAAGGACAACC	AK023801	CCDS44993.1	12q24.23	2006-02-13	2006-02-13		ENSG00000111707	ENSG00000111707			29545	protein-coding gene	gene with protein product	"""sin3A-associated protein, 45kDa"""	608250	"""suppressor of defective silencing 3 homolog (SDS3, S. cerevisiae)"""			11909966	Standard	NM_022491		Approved	SDS3, FLJ00052, SAP45	uc001twz.3	Q9H7L9	OTTHUMG00000168884	ENST00000543473.1:c.841G>A	chr12.hg19:g.118848915G>A	ENSP00000443988:p.Asp281Asn	63.0	0.0		71.0	21.0	NM_022491	Q4KMQ5|Q8N6H0|Q9H8D2	Missense_Mutation	SNP	ENST00000543473.1	hg19	CCDS44993.1	.	.	.	.	.	.	.	.	.	.	G	30	5.054496	0.93793	.	.	ENSG00000111707	ENST00000543473;ENST00000397564	.	.	.	5.91	5.91	0.95273	.	0.135771	0.64402	D	0.000002	T	0.61274	0.2334	L	0.46157	1.445	0.80722	D	1	B	0.29531	0.247	B	0.31191	0.125	T	0.60964	-0.7158	9	0.87932	D	0	-19.6053	19.8936	0.96942	0.0:0.0:1.0:0.0	.	281	Q9H7L9	SDS3_HUMAN	N	281;282	.	ENSP00000380695:D282N	D	+	1	0	SUDS3	117333298	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.180000	0.94867	2.793000	0.96121	0.655000	0.94253	GAC	.	.		0.468	SUDS3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401504.1	NM_022491	
CIT	11113	hgsc.bcm.edu	37	12	120151400	120151400	+	Missense_Mutation	SNP	C	C	T	rs370080702		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:120151400C>T	ENST00000261833.7	-	33	4286	c.4234G>A	c.(4234-4236)Ggc>Agc	p.G1412S	CIT_ENST00000392521.2_Missense_Mutation_p.G1454S|CIT_ENST00000537607.1_5'UTR|MIR1178_ENST00000408396.1_RNA	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1412					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.G1440S(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GCAGGCAAGCCGCAGGTGGCT	0.577																																					p.G1454S		Atlas-SNP	.											CIT_ENST00000392521,colon,carcinoma,+1,1	CIT	535	.	1	Substitution - Missense(1)	ovary(1)	c.G4360A						.	C	SER/GLY,SER/GLY	0,4406		0,0,2203	89.0	77.0	81.0		4360,4234	6.1	1.0	12		81	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CIT	NM_001206999.1,NM_007174.2	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1454/2070,1412/2028	120151400	1,13005	2203	4300	6503	SO:0001583	missense	11113	exon34			GCAAGCCGCAGGT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.4234G>A	chr12.hg19:g.120151400C>T	ENSP00000261833:p.Gly1412Ser	96.0	0.0		95.0	35.0	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	35	5.525819	0.96431	0.0	1.16E-4	ENSG00000122966	ENST00000392521;ENST00000261833	D;D	0.84516	-1.86;-1.86	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.93465	0.7915	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	D	0.93270	0.6651	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1454;1412;930	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	S	1454;1412	ENSP00000376306:G1454S;ENSP00000261833:G1412S	ENSP00000261833:G1412S	G	-	1	0	CIT	118635783	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.610000	0.82949	2.884000	0.98904	0.655000	0.94253	GGC	.	.		0.577	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
UNC119B	84747	hgsc.bcm.edu	37	12	121157763	121157763	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:121157763C>A	ENST00000344651.4	+	5	724	c.684C>A	c.(682-684)gaC>gaA	p.D228E	RP11-173P15.5_ENST00000544939.1_RNA	NM_001080533.1	NP_001074002.1	A6NIH7	U119B_HUMAN	unc-119 homolog B (C. elegans)	228					cilium morphogenesis (GO:0060271)|lipoprotein transport (GO:0042953)	ciliary transition zone (GO:0035869)	lipid binding (GO:0008289)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCCGCTCTGACAGCTTCTACT	0.448																																					p.D228E		Atlas-SNP	.											.	UNC119B	21	.	0			c.C684A						.						90.0	83.0	85.0					12																	121157763		2203	4300	6503	SO:0001583	missense	84747	exon5			CTCTGACAGCTTC		CCDS31914.1	12q24	2014-06-16	2001-11-28		ENSG00000175970	ENSG00000175970			16488	protein-coding gene	gene with protein product	"""POC7 centriolar protein homolog B (Chlamydomonas)"""		"""unc119 (C.elegans) homolog B"""				Standard	NM_001080533		Approved	MGC5139, POC7B	uc001tyz.4	A6NIH7	OTTHUMG00000169201	ENST00000344651.4:c.684C>A	chr12.hg19:g.121157763C>A	ENSP00000344942:p.Asp228Glu	77.0	0.0		91.0	40.0	NM_001080533		Missense_Mutation	SNP	ENST00000344651.4	hg19	CCDS31914.1	.	.	.	.	.	.	.	.	.	.	C	36	5.723254	0.96847	.	.	ENSG00000175970	ENST00000344651;ENST00000537794	.	.	.	6.07	6.07	0.98685	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	D	0.90181	0.6931	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92100	0.5687	9	0.87932	D	0	-8.4568	20.6439	0.99570	0.0:1.0:0.0:0.0	.	228	A6NIH7	U119B_HUMAN	E	228	.	ENSP00000344942:D228E	D	+	3	2	UNC119B	119642146	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.792000	0.85828	2.884000	0.98904	0.655000	0.94253	GAC	.	.		0.448	UNC119B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402857.1	NM_001080533	
SETD1B	23067	hgsc.bcm.edu	37	12	122247883	122247883	+	Silent	SNP	C	C	T	rs547856709		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:122247883C>T	ENST00000604567.1	+	6	1100	c.1032C>T	c.(1030-1032)gcC>gcT	p.A344A	SETD1B_ENST00000267197.5_Silent_p.A344A|SETD1B_ENST00000542440.1_Silent_p.A344A			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	344					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						GGGCCACAGCCGCTTTCCGGG	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		13403	0.001		0.0	False		,,,				2504	0.0				p.A344A		Atlas-SNP	.											.	SETD1B	105	.	0			c.C1032T						.						9.0	12.0	11.0					12																	122247883		691	1585	2276	SO:0001819	synonymous_variant	23067	exon5			CACAGCCGCTTTC	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.1032C>T	chr12.hg19:g.122247883C>T		79.0	0.0		78.0	38.0	NM_015048	F6MFW1	Silent	SNP	ENST00000604567.1	hg19																																																																																				.	.		0.647	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
DIABLO	56616	hgsc.bcm.edu	37	12	122693101	122693101	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:122693101C>T	ENST00000443649.3	-	7	1364	c.547G>A	c.(547-549)Gcc>Acc	p.A183T	DIABLO_ENST00000464942.2_Missense_Mutation_p.A130T|DIABLO_ENST00000413918.1_Missense_Mutation_p.A139T|DIABLO_ENST00000353548.6_Missense_Mutation_p.A139T|RP11-512M8.5_ENST00000535844.1_3'UTR|B3GNT4_ENST00000545141.1_3'UTR|B3GNT4_ENST00000546192.1_3'UTR|DIABLO_ENST00000267169.6_Missense_Mutation_p.A130T	NM_019887.4	NP_063940.1	Q9NR28	DBLOH_HUMAN	diablo, IAP-binding mitochondrial protein	183					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)				breast(1)|endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	7	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)		TGATTCCTGGCGGTTATAGAG	0.577																																					p.A183T		Atlas-SNP	.											.	DIABLO	16	.	0			c.G547A						.						65.0	56.0	59.0					12																	122693101		2203	4300	6503	SO:0001583	missense	56616	exon7			TCCTGGCGGTTAT	AF262240	CCDS9228.1, CCDS9229.1, CCDS73541.1	12q24.31	2011-08-02	2011-03-11		ENSG00000184047	ENSG00000184047			21528	protein-coding gene	gene with protein product	"""second mitochondria-derived activator of caspase"""	605219				12749848, 17237824, 21722859	Standard	NM_019887		Approved	SMAC, DIABLO-S, FLJ25049, FLJ10537, DFNA64	uc010tab.2	Q9NR28	OTTHUMG00000157014	ENST00000443649.3:c.547G>A	chr12.hg19:g.122693101C>T	ENSP00000398495:p.Ala183Thr	42.0	0.0		46.0	22.0	NM_019887	B2RDQ0|Q6W3F3|Q96LV0|Q9BT11|Q9HAV6	Missense_Mutation	SNP	ENST00000443649.3	hg19	CCDS9228.1	.	.	.	.	.	.	.	.	.	.	c	21.8	4.203149	0.79127	.	.	ENSG00000184047	ENST00000413918;ENST00000443649;ENST00000353548;ENST00000464942;ENST00000267169;ENST00000541273;ENST00000474004;ENST00000540535;ENST00000541656	T;T;T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.77	4.88	0.63580	Smac/DIABLO-like (1);	0.345133	0.33813	N	0.004534	D	0.82508	0.5052	L	0.60455	1.87	0.29397	N	0.86218	D;D;P	0.71674	0.998;0.994;0.744	P;P;B	0.59703	0.862;0.721;0.262	T	0.79055	-0.1960	10	0.48119	T	0.1	-5.989	11.8481	0.52395	0.0:0.8577:0.0:0.1423	.	139;183;130	Q6W3F3;Q9NR28;Q502X2	.;DBLOH_HUMAN;.	T	139;183;139;130;130;86;110;110;110	ENSP00000411638:A139T;ENSP00000398495:A183T;ENSP00000320343:A139T;ENSP00000442360:A130T;ENSP00000267169:A130T;ENSP00000440971:A86T;ENSP00000442669:A110T;ENSP00000441139:A110T;ENSP00000440653:A110T	ENSP00000267169:A130T	A	-	1	0	DIABLO	121259054	0.875000	0.30112	0.889000	0.34880	0.938000	0.57974	1.671000	0.37513	1.453000	0.47775	-0.127000	0.14921	GCC	.	.		0.577	DIABLO-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347102.2	NM_019887	
GALNT9	50614	hgsc.bcm.edu	37	12	132905784	132905784	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:132905784C>T	ENST00000328957.8	-	1	5	c.6G>A	c.(4-6)gcG>gcA	p.A2A	RP13-895J2.7_ENST00000537720.1_RNA	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	2					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	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)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		TCCTGGCCACCGCCATGAACA	0.682																																					p.A2A	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.G6A						.						16.0	19.0	18.0					12																	132905784		692	1589	2281	SO:0001819	synonymous_variant	50614	exon1			GGCCACCGCCATG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.6G>A	chr12.hg19:g.132905784C>T		114.0	0.0		89.0	38.0	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	hg19																																																																																				.	.		0.682	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
FBRSL1	57666	hgsc.bcm.edu	37	12	133151138	133151138	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:133151138G>A	ENST00000434748.2	+	12	2838	c.1818G>A	c.(1816-1818)caG>caA	p.Q606Q	FBRSL1_ENST00000261673.6_Silent_p.Q533Q	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	606							poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						ACCGTCACCAGCAGAAGATAA	0.647																																					p.Q606Q		Atlas-SNP	.											.	FBRSL1	47	.	0			c.G1818A						.						18.0	20.0	20.0					12																	133151138		692	1590	2282	SO:0001819	synonymous_variant	57666	exon12			TCACCAGCAGAAG		CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787			29308	protein-coding gene	gene with protein product						10997877	Standard	NM_001142641		Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.1818G>A	chr12.hg19:g.133151138G>A		85.0	0.0		65.0	24.0	NM_001142641	Q86XQ1	Silent	SNP	ENST00000434748.2	hg19	CCDS45010.1																																																																																			.	.		0.647	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397404.2		
MIPEP	4285	hgsc.bcm.edu	37	13	24413824	24413824	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:24413824G>A	ENST00000382172.3	-	12	1400	c.1302C>T	c.(1300-1302)taC>taT	p.Y434Y		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	434					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		AAAAATCACAGTAAATGTACC	0.368																																					p.Y434Y		Atlas-SNP	.											.	MIPEP	53	.	0			c.C1302T						.						107.0	105.0	106.0					13																	24413824		2203	4300	6503	SO:0001819	synonymous_variant	4285	exon12			ATCACAGTAAATG		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1302C>T	chr13.hg19:g.24413824G>A		91.0	0.0		56.0	38.0	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Silent	SNP	ENST00000382172.3	hg19	CCDS9303.1																																																																																			.	.		0.368	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
MIPEP	4285	hgsc.bcm.edu	37	13	24413861	24413861	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:24413861A>G	ENST00000382172.3	-	12	1363	c.1265T>C	c.(1264-1266)gTt>gCt	p.V422A		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	422					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		TTCATGAACAACAGCCTAGAA	0.358																																					p.V422A		Atlas-SNP	.											.	MIPEP	53	.	0			c.T1265C						.						75.0	76.0	75.0					13																	24413861		2203	4300	6503	SO:0001583	missense	4285	exon12			TGAACAACAGCCT		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1265T>C	chr13.hg19:g.24413861A>G	ENSP00000371607:p.Val422Ala	63.0	0.0		41.0	25.0	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	hg19	CCDS9303.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321734	0.81580	.	.	ENSG00000027001	ENST00000382172	T	0.24723	1.84	5.2	5.2	0.72013	Metallopeptidase, catalytic domain (1);	0.368225	0.30168	N	0.010244	T	0.52256	0.1723	M	0.77313	2.365	0.58432	D	0.999997	D	0.65815	0.995	D	0.70935	0.971	T	0.57906	-0.7730	10	0.87932	D	0	-1.5937	15.3646	0.74510	1.0:0.0:0.0:0.0	.	422	Q99797	MIPEP_HUMAN	A	422	ENSP00000371607:V422A	ENSP00000371607:V422A	V	-	2	0	MIPEP	23311861	1.000000	0.71417	0.981000	0.43875	0.864000	0.49448	9.146000	0.94640	2.096000	0.63516	0.523000	0.50628	GTT	.	.		0.358	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
SPATA13	221178	hgsc.bcm.edu	37	13	24858385	24858385	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:24858385C>T	ENST00000382095.4	+	4	809	c.402C>T	c.(400-402)ggC>ggT	p.G134G	SPATA13_ENST00000424834.2_Silent_p.G759G|SPATA13_ENST00000399949.2_Silent_p.G56G|SPATA13_ENST00000409126.1_Silent_p.G56G|RP11-307N16.6_ENST00000382141.4_Silent_p.G637G|SPATA13_ENST00000382108.3_Silent_p.G759G|SPATA13_ENST00000343003.6_Silent_p.G78G	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	134	ABR (APC-binding region) domain.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TGCAGCCCGGCGGGGAGCAGC	0.552																																					p.G759G		Atlas-SNP	.											.	SPATA13	92	.	0			c.C2277T						.						41.0	37.0	38.0					13																	24858385		2203	4300	6503	SO:0001819	synonymous_variant	221178	exon5			GCCCGGCGGGGAG	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.402C>T	chr13.hg19:g.24858385C>T		75.0	0.0		33.0	5.0	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	hg19	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	C	9.245	1.039321	0.19669	.	.	ENSG00000182957	ENST00000424834	.	.	.	5.65	-10.2	0.00374	.	.	.	.	.	T	0.33556	0.0867	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40289	-0.9571	4	.	.	.	.	2.3715	0.04331	0.3825:0.1979:0.067:0.3526	.	.	.	.	W	797	.	.	R	+	1	2	SPATA13	23756385	0.010000	0.17322	0.145000	0.22337	0.877000	0.50540	-1.316000	0.02710	-2.009000	0.00954	-0.140000	0.14226	CGG	.	.		0.552	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
NBEA	26960	hgsc.bcm.edu	37	13	35615180	35615180	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:35615180A>T	ENST00000400445.3	+	2	939	c.405A>T	c.(403-405)gaA>gaT	p.E135D	NBEA_ENST00000310336.4_Missense_Mutation_p.E135D|NBEA_ENST00000540320.1_Missense_Mutation_p.E135D|NBEA_ENST00000379939.2_Missense_Mutation_p.E135D	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	135					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)		GTCAAGCAGAAATATGGAGCA	0.383																																					p.E135D		Atlas-SNP	.											.	NBEA	340	.	0			c.A405T						.						126.0	115.0	119.0					13																	35615180		1896	4150	6046	SO:0001583	missense	26960	exon2			AGCAGAAATATGG	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.405A>T	chr13.hg19:g.35615180A>T	ENSP00000383295:p.Glu135Asp	123.0	0.0		54.0	45.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.215312	0.79352	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	5.43	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.65491	0.2696	M	0.80982	2.52	0.80722	D	1	D	0.63880	0.993	D	0.70016	0.967	T	0.65425	-0.6171	10	0.49607	T	0.09	.	8.3159	0.32100	0.8491:0.0:0.1509:0.0	.	135	Q5T321	.	D	135	ENSP00000440951:E135D;ENSP00000383295:E135D;ENSP00000369271:E135D;ENSP00000308534:E135D	ENSP00000308534:E135D	E	+	3	2	NBEA	34513180	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.175000	0.31944	0.910000	0.36722	0.477000	0.44152	GAA	.	.		0.383	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
ENOX1	55068	hgsc.bcm.edu	37	13	43843689	43843689	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:43843689A>C	ENST00000261488.6	-	13	2048	c.1471T>G	c.(1471-1473)Tta>Gta	p.L491V	ENOX1_ENST00000412891.1_Missense_Mutation_p.L491V	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	491					rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TTGTTGTTTAACTCCTCCTGG	0.373																																					p.L491V		Atlas-SNP	.											.	ENOX1	158	.	0			c.T1471G						.						289.0	239.0	256.0					13																	43843689		2203	4300	6503	SO:0001583	missense	55068	exon13			TGTTTAACTCCTC	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"""RNA binding motif (RRM) containing"""	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.1471T>G	chr13.hg19:g.43843689A>C	ENSP00000261488:p.Leu491Val	72.0	0.0		32.0	26.0	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	hg19	CCDS9389.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.404205	0.62288	.	.	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.49139	0.79;0.79	5.95	2.3	0.28687	.	0.000000	0.85682	D	0.000000	T	0.61311	0.2337	M	0.66939	2.045	0.80722	D	1	D	0.63880	0.993	D	0.76071	0.987	T	0.55159	-0.8184	10	0.38643	T	0.18	-8.3657	9.2761	0.37700	0.5578:0.0:0.4422:0.0	.	491	Q8TC92	ENOX1_HUMAN	V	491	ENSP00000261488:L491V;ENSP00000415054:L491V	ENSP00000261488:L491V	L	-	1	2	ENOX1	42741689	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.877000	0.39598	0.064000	0.16427	0.533000	0.62120	TTA	.	.		0.373	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993	
PCDH9	5101	hgsc.bcm.edu	37	13	67799558	67799558	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:67799558C>A	ENST00000377865.2	-	1	3149	c.3015G>T	c.(3013-3015)aaG>aaT	p.K1005N	PCDH9_ENST00000377861.3_Missense_Mutation_p.K1005N|PCDH9_ENST00000328454.5_Missense_Mutation_p.K1005N|PCDH9_ENST00000456367.1_Missense_Mutation_p.K1005N|PCDH9_ENST00000544246.1_Missense_Mutation_p.K1005N			Q9HC56	PCDH9_HUMAN	protocadherin 9	1005					forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GTAAGGGGCCCTTTGTCTTGA	0.478																																					p.K1005N		Atlas-SNP	.											.	PCDH9	252	.	0			c.G3015T						.						111.0	100.0	104.0					13																	67799558		2203	4300	6503	SO:0001583	missense	5101	exon2			GGGGCCCTTTGTC	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.3015G>T	chr13.hg19:g.67799558C>A	ENSP00000367096:p.Lys1005Asn	157.0	0.0		177.0	82.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	C	7.879	0.729818	0.15507	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.54071	0.63;0.63;0.59;0.59;0.59	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	N	0.08118	0	0.58432	D	0.999998	P;P;P;P	0.45902	0.791;0.478;0.868;0.791	B;B;P;B	0.45037	0.277;0.191;0.467;0.277	T	0.15378	-1.0439	10	0.07990	T	0.79	.	12.6988	0.57020	0.0:0.9241:0.0:0.0759	.	1005;1005;1005;1005	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	N	1005	ENSP00000442186:K1005N;ENSP00000367096:K1005N;ENSP00000401699:K1005N;ENSP00000332060:K1005N;ENSP00000367092:K1005N	ENSP00000332060:K1005N	K	-	3	2	PCDH9	66697559	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.595000	0.61048	2.651000	0.90000	0.655000	0.94253	AAG	.	.		0.478	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
DZIP1	22873	hgsc.bcm.edu	37	13	96239850	96239850	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:96239850C>T	ENST00000376829.2	-	20	3012	c.2161G>A	c.(2161-2163)Gcg>Acg	p.A721T	DZIP1_ENST00000347108.3_Missense_Mutation_p.A721T|DZIP1_ENST00000361156.3_Missense_Mutation_p.A702T|DZIP1_ENST00000361396.2_Missense_Mutation_p.A702T	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	721					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)			GTCCCGTCCGCGTCACTTTTC	0.562																																					p.A721T		Atlas-SNP	.											.	DZIP1	195	.	0			c.G2161A						.						173.0	147.0	156.0					13																	96239850		2203	4300	6503	SO:0001583	missense	22873	exon20			CGTCCGCGTCACT	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.2161G>A	chr13.hg19:g.96239850C>T	ENSP00000366025:p.Ala721Thr	102.0	0.0		107.0	43.0	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	C	0.068	-1.207475	0.01568	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.27720	1.65;1.65;1.65;1.65	5.35	2.81	0.32909	.	1.015710	0.07822	N	0.959900	T	0.05364	0.0142	N	0.00119	-2.075	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.41270	-0.9518	10	0.02654	T	1	-7.3955	3.6649	0.08252	0.1635:0.1909:0.0:0.6456	.	702;721	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	T	721;702;702;721	ENSP00000257312:A721T;ENSP00000355018:A702T;ENSP00000355175:A702T;ENSP00000366025:A721T	ENSP00000257312:A721T	A	-	1	0	DZIP1	95037851	0.023000	0.18921	0.932000	0.37286	0.075000	0.17131	0.150000	0.16263	0.877000	0.35895	-0.302000	0.09304	GCG	.	.		0.562	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
DZIP1	22873	hgsc.bcm.edu	37	13	96274617	96274617	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:96274617T>C	ENST00000376829.2	-	9	1941	c.1090A>G	c.(1090-1092)Atg>Gtg	p.M364V	DZIP1_ENST00000347108.3_Missense_Mutation_p.M364V|DZIP1_ENST00000361156.3_Missense_Mutation_p.M364V|DZIP1_ENST00000361396.2_Missense_Mutation_p.M364V	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	364					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)			AGAAGCTGCATGACATTATGG	0.433																																					p.M364V		Atlas-SNP	.											.	DZIP1	195	.	0			c.A1090G						.						215.0	178.0	191.0					13																	96274617		2203	4300	6503	SO:0001583	missense	22873	exon9			GCTGCATGACATT	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.1090A>G	chr13.hg19:g.96274617T>C	ENSP00000366025:p.Met364Val	66.0	0.0		86.0	18.0	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	T	1.642	-0.516340	0.04200	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.03	-0.721	0.11189	.	0.585038	0.20068	N	0.099936	T	0.15998	0.0385	N	0.08118	0	0.23762	N	0.996911	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.25572	-1.0128	10	0.10377	T	0.69	-7.991	6.0699	0.19883	0.0:0.1661:0.4259:0.408	.	364;364	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	V	364	ENSP00000257312:M364V;ENSP00000355018:M364V;ENSP00000355175:M364V;ENSP00000366025:M364V	ENSP00000257312:M364V	M	-	1	0	DZIP1	95072618	0.947000	0.32204	0.998000	0.56505	0.413000	0.31143	0.501000	0.22578	0.030000	0.15379	-1.089000	0.02181	ATG	.	.		0.433	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
CCDC168	643677	hgsc.bcm.edu	37	13	103384583	103384583	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:103384583G>A	ENST00000322527.2	-	1	4576	c.4577C>T	c.(4576-4578)cCt>cTt	p.P1526L		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1526																	GTCAGTGTGAGGTGAACGCAT	0.358																																					p.P6155L		Atlas-SNP	.											.	.	.	.	0			c.C18464T						.						140.0	104.0	115.0					13																	103384583		692	1591	2283	SO:0001583	missense	643677	exon4			GTGTGAGGTGAAC		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.4577C>T	chr13.hg19:g.103384583G>A	ENSP00000320232:p.Pro1526Leu	190.0	0.0		144.0	63.0	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	hg19		.	.	.	.	.	.	.	.	.	.	G	9.248	1.039959	0.19669	.	.	ENSG00000175820	ENST00000322527	T	0.03441	3.93	3.45	0.73	0.18271	.	.	.	.	.	T	0.02193	0.0068	N	0.14661	0.345	0.09310	N	1	B	0.15930	0.015	B	0.11329	0.006	T	0.49293	-0.8955	9	0.20046	T	0.44	.	5.4003	0.16293	0.3839:0.0:0.6161:0.0	.	1526	Q8NDH2	CC168_HUMAN	L	1526	ENSP00000320232:P1526L	ENSP00000320232:P1526L	P	-	2	0	CCDC168	102182584	0.025000	0.19082	0.018000	0.16275	0.011000	0.07611	0.117000	0.15583	0.115000	0.18071	0.557000	0.71058	CCT	.	.		0.358	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
MCF2L	23263	hgsc.bcm.edu	37	13	113718636	113718636	+	Missense_Mutation	SNP	G	G	A	rs563320301		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:113718636G>A	ENST00000375608.3	+	7	656	c.598G>A	c.(598-600)Gta>Ata	p.V200I	MCF2L_ENST00000421756.1_Missense_Mutation_p.V174I|MCF2L_ENST00000535094.2_Missense_Mutation_p.V170I|MCF2L_ENST00000423482.2_Missense_Mutation_p.V168I|MCF2L_ENST00000397030.1_Missense_Mutation_p.V203I|MCF2L_ENST00000375597.4_Missense_Mutation_p.V168I|MCF2L_ENST00000434480.2_Missense_Mutation_p.V176I|MCF2L_ENST00000375604.2_Missense_Mutation_p.V227I|MCF2L_ENST00000442652.2_Missense_Mutation_p.V200I|MCF2L_ENST00000375601.3_Missense_Mutation_p.V174I			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	200	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GCTGAGCTCCGTACCAGACTT	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		18820	0.0		0.0	False		,,,				2504	0.001				p.V170I		Atlas-SNP	.											.	MCF2L	182	.	0			c.G508A						.						168.0	135.0	146.0					13																	113718636		2203	4300	6503	SO:0001583	missense	23263	exon6			AGCTCCGTACCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.598G>A	chr13.hg19:g.113718636G>A	ENSP00000364758:p.Val200Ile	78.0	0.0		62.0	16.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	hg19		.	.	.	.	.	.	.	.	.	.	G	10.63	1.405376	0.25378	.	.	ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000430480;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000423251;ENST00000440749	T;T;T;T;T;T;T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02	5.26	5.26	0.73747	Cellular retinaldehyde-binding/triple function, C-terminal (3);	0.195605	0.45606	D	0.000350	T	0.51975	0.1706	L	0.38838	1.175	0.31522	N	0.662231	P;P;P;P;B;P	0.37466	0.453;0.596;0.453;0.509;0.307;0.509	B;B;B;B;B;B	0.34242	0.064;0.178;0.064;0.129;0.064;0.106	T	0.62854	-0.6766	10	0.44086	T	0.13	.	15.2767	0.73748	0.0:0.1404:0.8596:0.0	.	168;170;227;132;168;200	E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.;.;.;.;.;MCF2L_HUMAN	I	200;200;227;203;170;170;174;174;176;168;168;90;11	ENSP00000364758:V200I;ENSP00000401422:V200I;ENSP00000364754:V227I;ENSP00000380225:V203I;ENSP00000440374:V170I;ENSP00000397285:V174I;ENSP00000364751:V174I;ENSP00000407722:V176I;ENSP00000405639:V168I;ENSP00000364747:V168I;ENSP00000405996:V90I	ENSP00000364747:V168I	V	+	1	0	MCF2L	112766637	0.909000	0.30893	0.906000	0.35671	0.067000	0.16453	1.376000	0.34306	2.456000	0.83038	0.555000	0.69702	GTA	.	.		0.567	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
RASA3	22821	hgsc.bcm.edu	37	13	114784388	114784388	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:114784388G>T	ENST00000334062.7	-	10	914	c.793C>A	c.(793-795)Ctc>Atc	p.L265I	RASA3_ENST00000542651.1_3'UTR|RASA3_ENST00000389544.4_Missense_Mutation_p.L233I	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	265					calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			CGGGGCTGGAGGAAGTACCTG	0.597																																					p.L265I		Atlas-SNP	.											.	RASA3	83	.	0			c.C793A						.						103.0	92.0	96.0					13																	114784388		2203	4300	6503	SO:0001583	missense	22821	exon10			GCTGGAGGAAGTA		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.793C>A	chr13.hg19:g.114784388G>T	ENSP00000335029:p.Leu265Ile	117.0	0.0		102.0	49.0	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	hg19	CCDS32016.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.912115	0.72983	.	.	ENSG00000185989	ENST00000334062;ENST00000389544	T;T	0.81078	-1.45;-1.45	4.62	4.62	0.57501	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.90960	0.7158	M	0.89287	3.02	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.92590	0.6082	9	.	.	.	.	16.2114	0.82164	0.0:0.0:1.0:0.0	.	265	Q14644	RASA3_HUMAN	I	265;233	ENSP00000335029:L265I;ENSP00000374195:L233I	.	L	-	1	0	RASA3	113802490	1.000000	0.71417	0.995000	0.50966	0.300000	0.27592	6.498000	0.73679	2.066000	0.61787	0.467000	0.42956	CTC	.	.		0.597	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
TTC5	91875	hgsc.bcm.edu	37	14	20757848	20757848	+	Nonsense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:20757848T>A	ENST00000258821.3	-	10	1317	c.1261A>T	c.(1261-1263)Aag>Tag	p.K421*	TTC5_ENST00000556592.1_5'Flank	NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	421					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		CCCTGAGGCTTCCCATTCACC	0.527																																					p.K421X		Atlas-SNP	.											.	TTC5	34	.	0			c.A1261T						.						82.0	63.0	69.0					14																	20757848		2203	4300	6503	SO:0001587	stop_gained	91875	exon10			GAGGCTTCCCATT	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"""Tetratricopeptide (TTC) repeat domain containing"""	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.1261A>T	chr14.hg19:g.20757848T>A	ENSP00000258821:p.Lys421*	89.0	0.0		78.0	28.0	NM_138376	A8MQ18|Q96HF9	Nonsense_Mutation	SNP	ENST00000258821.3	hg19	CCDS9546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.8|24.8	4.570075|4.570075	0.86542|0.86542	.|.	.|.	ENSG00000136319|ENSG00000136319	ENST00000423949|ENST00000258821	.|.	.|.	.|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.35653|.	0.0939|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.20107|.	-1.0285|.	4|.	.|0.02654	.|T	.|1	.|.	12.8401|12.8401	0.57797|0.57797	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	V|X	365|421	.|.	.|ENSP00000258821:K421X	E|K	-|-	2|1	0|0	TTC5|TTC5	19827688|19827688	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.786000|0.786000	0.44442|0.44442	5.252000|5.252000	0.65445|0.65445	2.224000|2.224000	0.72417|0.72417	0.528000|0.528000	0.53228|0.53228	GAA|AAG	.	.		0.527	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376	
RNASE7	84659	hgsc.bcm.edu	37	14	21511475	21511475	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:21511475G>A	ENST00000298690.4	+	2	581	c.324G>A	c.(322-324)atG>atA	p.M108I	NDRG2_ENST00000403829.3_Intron	NM_032572.3	NP_115961	Q9H1E1	RNAS7_HUMAN	ribonuclease, RNase A family, 7	108					antibacterial humoral response (GO:0019731)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|membrane disruption in other organism (GO:0051673)|response to bacterium (GO:0009617)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|lipopolysaccharide binding (GO:0001530)|nucleic acid binding (GO:0003676)|peptidoglycan binding (GO:0042834)|ribonuclease activity (GO:0004540)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	6	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;3.42e-11)|Epithelial(56;5.57e-09)|all cancers(55;2.36e-08)	GBM - Glioblastoma multiforme(265;0.0191)		CCCTGACCATGTGTAAGCTCA	0.547																																					p.M108I		Atlas-SNP	.											.	RNASE7	18	.	0			c.G324A						.						113.0	109.0	110.0					14																	21511475		2203	4300	6503	SO:0001583	missense	84659	exon2			GACCATGTGTAAG	AJ131212	CCDS41914.1	14q11.1	2013-02-15			ENSG00000165799	ENSG00000165799		"""Ribonucleases, RNase A"""	19278	protein-coding gene	gene with protein product		612484				12244054, 12527768	Standard	NM_032572		Approved		uc001vzk.4	Q9H1E1	OTTHUMG00000171358	ENST00000298690.4:c.324G>A	chr14.hg19:g.21511475G>A	ENSP00000298690:p.Met108Ile	103.0	0.0		92.0	42.0	NM_032572	P80927|P83685|Q546N3	Missense_Mutation	SNP	ENST00000298690.4	hg19	CCDS41914.1	.	.	.	.	.	.	.	.	.	.	G	7.704	0.693799	0.15039	.	.	ENSG00000165799	ENST00000298690	T	0.12672	2.66	4.94	-1.93	0.07594	Ribonuclease A, domain (4);	3.249820	0.01107	U	0.005496	T	0.09555	0.0235	N	0.25789	0.76	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.25676	-1.0125	10	0.22109	T	0.4	4.1987	5.1682	0.15096	0.344:0.3222:0.3338:0.0	.	108	Q9H1E1	RNAS7_HUMAN	I	108	ENSP00000298690:M108I	ENSP00000298690:M108I	M	+	3	0	RNASE7	20581315	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-1.835000	0.01692	-0.282000	0.09128	-0.150000	0.13652	ATG	.	.		0.547	RNASE7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313936.1	NM_032572	
ZNF219	51222	hgsc.bcm.edu	37	14	21560611	21560611	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:21560611C>A	ENST00000360947.3	-	3	1256	c.845G>T	c.(844-846)aGc>aTc	p.S282I	ZNF219_ENST00000451119.2_Missense_Mutation_p.S282I|ZNF219_ENST00000556101.1_5'Flank|ZNF219_ENST00000421093.2_Missense_Mutation_p.S282I|RP11-998D10.7_ENST00000554733.2_lincRNA	NM_016423.2	NP_057507.2	Q9P2Y4	ZN219_HUMAN	zinc finger protein 219	282					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurotransmitter levels (GO:0001505)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histamine receptor activity (GO:0004969)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(2)	8	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)	GBM - Glioblastoma multiforme(265;0.0191)		CTGTGTAAAGCTCTGGCCGCA	0.657											OREG0022565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S282I		Atlas-SNP	.											.	ZNF219	28	.	0			c.G845T						.						19.0	19.0	19.0					14																	21560611		2179	4273	6452	SO:0001583	missense	51222	exon3			GTAAAGCTCTGGC	AB015427	CCDS9568.1	14q11	2013-01-08			ENSG00000165804	ENSG00000165804		"""Zinc fingers, C2H2-type"""	13011	protein-coding gene	gene with protein product		605036				10819330	Standard	NM_016423		Approved		uc001vzs.2	Q9P2Y4	OTTHUMG00000029647	ENST00000360947.3:c.845G>T	chr14.hg19:g.21560611C>A	ENSP00000354206:p.Ser282Ile	99.0	0.0	749	87.0	34.0	NM_001102454	D3DS16|Q53Y57|Q8IYC1|Q9BW28	Missense_Mutation	SNP	ENST00000360947.3	hg19	CCDS9568.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063011	0.76187	.	.	ENSG00000165804	ENST00000360947;ENST00000451119;ENST00000421093	T;T;T	0.56275	0.47;0.47;0.47	4.65	4.65	0.58169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.053653	0.64402	D	0.000001	T	0.53334	0.1790	L	0.48877	1.53	0.38614	D	0.95097	P	0.49253	0.921	P	0.47251	0.542	T	0.62053	-0.6935	10	0.62326	D	0.03	-25.2119	15.0771	0.72084	0.0:1.0:0.0:0.0	.	282	Q9P2Y4	ZN219_HUMAN	I	282	ENSP00000354206:S282I;ENSP00000388558:S282I;ENSP00000392401:S282I	ENSP00000354206:S282I	S	-	2	0	ZNF219	20630451	0.007000	0.16637	1.000000	0.80357	0.985000	0.73830	0.373000	0.20484	2.414000	0.81942	0.467000	0.42956	AGC	.	.		0.657	ZNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073931.2		
OR4E2	26686	hgsc.bcm.edu	37	14	22133945	22133945	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:22133945T>A	ENST00000408935.1	+	1	649	c.649T>A	c.(649-651)Tcc>Acc	p.S217T		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	217						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(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		CGTGGTCACCTCCTATATGGT	0.512																																					p.S217T		Atlas-SNP	.											.	OR4E2	44	.	0			c.T649A						.						154.0	142.0	146.0					14																	22133945		1973	4159	6132	SO:0001583	missense	26686	exon1			GTCACCTCCTATA		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.649T>A	chr14.hg19:g.22133945T>A	ENSP00000386195:p.Ser217Thr	153.0	0.0		187.0	9.0	NM_001001912	Q6IET6|Q96R62	Missense_Mutation	SNP	ENST00000408935.1	hg19	CCDS41916.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.544075	0.45280	.	.	ENSG00000221977	ENST00000408935	T	0.42900	0.96	5.59	5.59	0.84812	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	U	0.001878	T	0.68732	0.3033	M	0.87827	2.91	0.38657	D	0.951984	D	0.89917	1.0	D	0.87578	0.998	T	0.76997	-0.2751	10	0.87932	D	0	.	13.9921	0.64374	0.0:0.0:0.0:1.0	.	217	Q8NGC2	OR4E2_HUMAN	T	217	ENSP00000386195:S217T	ENSP00000386195:S217T	S	+	1	0	OR4E2	21203785	0.998000	0.40836	0.988000	0.46212	0.120000	0.20174	2.928000	0.48908	2.244000	0.73946	0.482000	0.46254	TCC	.	.		0.512	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1		
MMP14	4323	hgsc.bcm.edu	37	14	23315224	23315224	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:23315224G>A	ENST00000311852.6	+	10	1986	c.1725G>A	c.(1723-1725)caG>caA	p.Q575Q	MMP14_ENST00000548162.1_Intron	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	575					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	TCTACTGCCAGCGTTCCCTGC	0.657																																					p.Q575Q		Atlas-SNP	.											.	MMP14	40	.	0			c.G1725A						.						14.0	14.0	14.0					14																	23315224		2165	4253	6418	SO:0001819	synonymous_variant	4323	exon10			CTGCCAGCGTTCC		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"""membrane type 1 metalloprotease"""	600754	"""matrix metalloproteinase 14 (membrane-inserted)"""			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.1725G>A	chr14.hg19:g.23315224G>A		64.0	0.0		54.0	14.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	hg19	CCDS9577.1																																																																																			.	.		0.657	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
SLC7A8	23428	hgsc.bcm.edu	37	14	23652042	23652042	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:23652042C>G	ENST00000316902.7	-	1	807	c.82G>C	c.(82-84)Ggt>Cgt	p.G28R	C14orf164_ENST00000399910.1_5'Flank|SLC7A8_ENST00000469263.1_Missense_Mutation_p.G28R	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	28					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|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)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	CCTCCGGAACCAGCCTCGGGG	0.592																																					p.G28R		Atlas-SNP	.											.	SLC7A8	54	.	0			c.G82C						.						119.0	118.0	118.0					14																	23652042		2203	4300	6503	SO:0001583	missense	23428	exon1			CGGAACCAGCCTC	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"""Solute carriers"""	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.82G>C	chr14.hg19:g.23652042C>G	ENSP00000320378:p.Gly28Arg	75.0	0.0		70.0	24.0	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	hg19	CCDS9590.1	.	.	.	.	.	.	.	.	.	.	C	9.958	1.221909	0.22457	.	.	ENSG00000092068	ENST00000316902;ENST00000469263;ENST00000524758;ENST00000525062	D;D;D;D	0.94758	-2.66;-3.01;-2.82;-3.51	5.45	3.61	0.41365	.	2.000960	0.02338	N	0.074602	D	0.89364	0.6694	N	0.19112	0.55	0.19300	N	0.999978	B;B	0.25955	0.138;0.037	B;B	0.21917	0.037;0.019	T	0.78150	-0.2316	10	0.17832	T	0.49	.	8.043	0.30532	0.0:0.7462:0.0:0.2538	.	28;28	E9PLV9;Q9UHI5	.;LAT2_HUMAN	R	28	ENSP00000320378:G28R;ENSP00000435114:G28R;ENSP00000434352:G28R;ENSP00000436665:G28R	ENSP00000320378:G28R	G	-	1	0	SLC7A8	22721882	0.002000	0.14202	0.001000	0.08648	0.565000	0.35776	0.845000	0.27668	0.654000	0.30846	0.462000	0.41574	GGT	.	.		0.592	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3		
MYH6	4624	hgsc.bcm.edu	37	14	23863388	23863388	+	Silent	SNP	G	G	A	rs148596692		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:23863388G>A	ENST00000356287.3	-	20	2603	c.2574C>T	c.(2572-2574)ttC>ttT	p.F858F	MYH6_ENST00000405093.3_Silent_p.F858F			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	858					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TGATGCGCCCGAACTCTTCCT	0.572																																					p.F858F		Atlas-SNP	.											MYH6,NS,adenoma,0,1	MYH6	274	.	0			c.C2574T						.	G		1,4405	2.1+/-5.4	0,1,2202	137.0	120.0	126.0		2574	-5.9	0.8	14	dbSNP_134	126	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MYH6	NM_002471.3		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		858/1940	23863388	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon21			GCGCCCGAACTCT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2574C>T	chr14.hg19:g.23863388G>A		111.0	0.0		101.0	51.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	G|1.000;A|0.000		0.572	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
CPNE6	9362	hgsc.bcm.edu	37	14	24542179	24542179	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24542179C>G	ENST00000397016.2	+	3	345	c.34C>G	c.(34-36)Ccc>Gcc	p.P12A	CPNE6_ENST00000216775.2_Missense_Mutation_p.P12A|CPNE6_ENST00000560092.1_Intron|CPNE6_ENST00000537691.1_Missense_Mutation_p.P67A	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	12					lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		GGTGCCTGAGCCCCCAACCAT	0.652																																					p.P12A		Atlas-SNP	.											.	CPNE6	40	.	0			c.C34G						.						36.0	31.0	33.0					14																	24542179		2203	4300	6503	SO:0001583	missense	9362	exon2			CCTGAGCCCCCAA	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.34C>G	chr14.hg19:g.24542179C>G	ENSP00000380211:p.Pro12Ala	51.0	0.0		63.0	23.0	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	hg19	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.952545	0.34471	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.07908	3.15;3.23;3.23	4.58	4.58	0.56647	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.45361	D	0.000375	T	0.03871	0.0109	N	0.02539	-0.55	0.34692	D	0.725858	B;P	0.37141	0.32;0.584	B;B	0.35114	0.119;0.196	T	0.43376	-0.9395	10	0.51188	T	0.08	-12.8409	13.0802	0.59109	0.0:1.0:0.0:0.0	.	67;12	F5GXN1;O95741	.;CPNE6_HUMAN	A	67;12;12	ENSP00000440077:P67A;ENSP00000380211:P12A;ENSP00000216775:P12A	ENSP00000216775:P12A	P	+	1	0	CPNE6	23612019	0.224000	0.23674	1.000000	0.80357	0.998000	0.95712	0.455000	0.21843	2.543000	0.85770	0.563000	0.77884	CCC	.	.		0.652	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
RIPK3	11035	hgsc.bcm.edu	37	14	24806911	24806911	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24806911G>A	ENST00000216274.5	-	7	1108	c.890C>T	c.(889-891)gCt>gTt	p.A297V	RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000396747.3_5'Flank|RP11-934B9.3_ENST00000555591.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000554068.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	297					activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|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)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		CGTGGAGACAGCAGCATTCAT	0.532																																					p.A297V	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C890T						.						152.0	129.0	136.0					14																	24806911		2203	4300	6503	SO:0001583	missense	11035	exon7			GAGACAGCAGCAT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.890C>T	chr14.hg19:g.24806911G>A	ENSP00000216274:p.Ala297Val	130.0	0.0		109.0	37.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523546	0.44866	.	.	ENSG00000129465	ENST00000216274	T	0.79141	-1.24	4.67	4.67	0.58626	Protein kinase-like domain (1);	0.269320	0.26891	N	0.021972	T	0.73521	0.3597	L	0.34521	1.04	0.09310	N	0.999991	D	0.60160	0.987	P	0.49528	0.614	T	0.67624	-0.5623	10	0.48119	T	0.1	-5.7202	13.3819	0.60773	0.0:0.0:1.0:0.0	.	297	Q9Y572	RIPK3_HUMAN	V	297	ENSP00000216274:A297V	ENSP00000216274:A297V	A	-	2	0	RIPK3	23876751	0.048000	0.20356	0.224000	0.23877	0.009000	0.06853	2.340000	0.43974	2.876000	0.98609	0.655000	0.94253	GCT	.	.		0.532	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
NYNRIN	57523	hgsc.bcm.edu	37	14	24877520	24877520	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24877520A>G	ENST00000382554.3	+	3	962	c.644A>G	c.(643-645)cAc>cGc	p.H215R		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	215					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						TCTGACTCCCACTCCGATCCG	0.637																																					p.H215R		Atlas-SNP	.											.	NYNRIN	120	.	0			c.A644G						.						38.0	45.0	43.0					14																	24877520		2080	4221	6301	SO:0001583	missense	57523	exon3			ACTCCCACTCCGA	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.644A>G	chr14.hg19:g.24877520A>G	ENSP00000371994:p.His215Arg	23.0	0.0		38.0	17.0	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.186074	0.00305	.	.	ENSG00000205978	ENST00000382554	T	0.08984	3.03	4.85	-5.98	0.02220	.	2.517910	0.01251	N	0.008885	T	0.02230	0.0069	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	10	0.02654	T	1	.	3.6155	0.08075	0.2548:0.1101:0.4928:0.1423	.	215	Q9P2P1	NYNRI_HUMAN	R	215	ENSP00000371994:H215R	ENSP00000371994:H215R	H	+	2	0	NYNRIN	23947360	0.000000	0.05858	0.000000	0.03702	0.283000	0.27025	-0.224000	0.09164	-0.839000	0.04212	0.533000	0.62120	CAC	.	.		0.637	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
DTD2	112487	hgsc.bcm.edu	37	14	31926576	31926576	+	Silent	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:31926576A>C	ENST00000310850.4	-	1	140	c.24T>G	c.(22-24)ccT>ccG	p.P8P	DTD2_ENST00000356180.4_Silent_p.P8P|RP11-176H8.1_ENST00000547378.1_Silent_p.P8P	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	8					D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)										CCCGGGCCTGAGGAATCCGGC	0.697																																					p.P8P		Atlas-SNP	.											.	.	.	.	0			c.T24G						.						12.0	13.0	13.0					14																	31926576		2189	4279	6468	SO:0001819	synonymous_variant	112487	exon1			GGCCTGAGGAATC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 126"""	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.24T>G	chr14.hg19:g.31926576A>C		223.0	0.0		220.0	88.0	NM_080664	D3DS87	Silent	SNP	ENST00000310850.4	hg19	CCDS9643.1																																																																																			.	.		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664	
PRPF39	55015	hgsc.bcm.edu	37	14	45579384	45579384	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:45579384A>G	ENST00000355765.6	+	9	1434	c.1264A>G	c.(1264-1266)Atg>Gtg	p.M422V	SNORD127_ENST00000458892.1_RNA	NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	422					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AAAGAAACCCATGGTGCATAT	0.403																																					p.M422V		Atlas-SNP	.											.	PRPF39	46	.	0			c.A1264G						.						122.0	119.0	120.0					14																	45579384		2203	4300	6503	SO:0001583	missense	55015	exon9			AAACCCATGGTGC	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.1264A>G	chr14.hg19:g.45579384A>G	ENSP00000348010:p.Met422Val	205.0	0.0		180.0	66.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	11.07	1.530724	0.27387	.	.	ENSG00000185246	ENST00000355765	T	0.32023	1.47	5.53	4.39	0.52855	Tetratricopeptide-like helical (1);	0.238501	0.51477	N	0.000084	T	0.22781	0.0550	L	0.36672	1.1	0.38234	D	0.94111	B;B	0.16802	0.0;0.019	B;B	0.18871	0.001;0.023	T	0.08534	-1.0717	10	0.16420	T	0.52	-1.9165	11.0638	0.47964	0.9263:0.0:0.0737:0.0	.	26;422	Q86UA1-2;Q86UA1	.;PRP39_HUMAN	V	422	ENSP00000348010:M422V	ENSP00000348010:M422V	M	+	1	0	PRPF39	44649134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.239000	0.65371	0.937000	0.37394	0.460000	0.39030	ATG	.	.		0.403	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
SOS2	6655	hgsc.bcm.edu	37	14	50597348	50597348	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:50597348G>A	ENST00000216373.5	-	20	3482	c.3208C>T	c.(3208-3210)Cgg>Tgg	p.R1070W	SOS2_ENST00000543680.1_Missense_Mutation_p.R1037W	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1070					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					TCAGCAATCCGACTAAAGCTT	0.448																																					p.R1070W		Atlas-SNP	.											.	SOS2	195	.	0			c.C3208T						.						191.0	164.0	173.0					14																	50597348		2203	4300	6503	SO:0001583	missense	6655	exon20			CAATCCGACTAAA	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.3208C>T	chr14.hg19:g.50597348G>A	ENSP00000216373:p.Arg1070Trp	206.0	0.0		213.0	90.0	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	hg19	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546139	0.65198	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.80909	-1.43;-1.3	5.62	4.72	0.59763	.	0.046560	0.85682	D	0.000000	D	0.86276	0.5894	L	0.59436	1.845	0.48696	D	0.999699	D;D	0.76494	0.999;0.999	D;D	0.63793	0.918;0.918	D	0.87554	0.2467	10	0.87932	D	0	.	13.7891	0.63128	0.0:0.0:0.6073:0.3927	.	1037;1070	B7ZKT6;Q07890	.;SOS2_HUMAN	W	1070;1037	ENSP00000216373:R1070W;ENSP00000445328:R1037W	ENSP00000216373:R1070W	R	-	1	2	SOS2	49667098	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.776000	0.38594	1.357000	0.45904	0.484000	0.47621	CGG	.	.		0.448	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
PTGER2	5732	hgsc.bcm.edu	37	14	52781730	52781730	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:52781730C>A	ENST00000245457.5	+	1	618	c.464C>A	c.(463-465)gCc>gAc	p.A155D	PTGER2_ENST00000557436.1_Intron	NM_000956.3	NP_000947.2	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	155					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)	GGGGGCCTGGCCGTGCTGCCT	0.657																																					p.A155D		Atlas-SNP	.											.	PTGER2	27	.	0			c.C464A						.						59.0	64.0	62.0					14																	52781730		2203	4300	6503	SO:0001583	missense	5732	exon1			GCCTGGCCGTGCT		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.464C>A	chr14.hg19:g.52781730C>A	ENSP00000245457:p.Ala155Asp	61.0	0.0		54.0	26.0	NM_000956	D3DSC0|Q52LG8	Missense_Mutation	SNP	ENST00000245457.5	hg19	CCDS9708.1	.	.	.	.	.	.	.	.	.	.	C	13.78	2.340399	0.41498	.	.	ENSG00000125384	ENST00000245457	T	0.73681	-0.77	5.23	0.765	0.18470	GPCR, rhodopsin-like superfamily (1);	0.529807	0.21022	N	0.081481	T	0.74749	0.3757	L	0.58810	1.83	0.21719	N	0.999577	P	0.44281	0.831	P	0.52386	0.697	T	0.65245	-0.6215	10	0.66056	D	0.02	-1.6751	6.6937	0.23187	0.0:0.461:0.0:0.539	.	155	P43116	PE2R2_HUMAN	D	155	ENSP00000245457:A155D	ENSP00000245457:A155D	A	+	2	0	PTGER2	51851480	0.001000	0.12720	0.510000	0.27712	0.115000	0.19883	-0.016000	0.12613	0.306000	0.22856	0.563000	0.77884	GCC	.	.		0.657	PTGER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276890.1		
KTN1	3895	hgsc.bcm.edu	37	14	56094630	56094630	+	Splice_Site	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:56094630T>A	ENST00000395314.3	+	6	1032	c.964T>A	c.(964-966)Tca>Aca	p.S322T	KTN1_ENST00000395308.1_Splice_Site_p.S322T|KTN1_ENST00000395309.3_Splice_Site_p.S322T|KTN1_ENST00000416613.1_Splice_Site_p.S322T|KTN1_ENST00000438792.2_Splice_Site_p.S322T|KTN1_ENST00000395311.1_Splice_Site_p.S322T|KTN1_ENST00000413890.2_Splice_Site_p.S322T	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	322					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TCAATTGCAGTCAAGTAAGGG	0.388			T	RET	papillary thryoid																																p.S322T		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.T964A						.						103.0	87.0	92.0					14																	56094630		2203	4300	6503	SO:0001630	splice_region_variant	3895	exon6			TTGCAGTCAAGTA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.964-1T>A	chr14.hg19:g.56094630T>A		142.0	0.0		144.0	56.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.461999	0.26248	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.8	3.28	0.37604	.	0.861201	0.09829	N	0.750471	T	0.29126	0.0724	L	0.29908	0.895	0.29135	N	0.879405	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.24083	-1.0170	9	.	.	.	-0.1021	7.0935	0.25297	0.1172:0.0:0.3281:0.5547	.	322;322;322;322	B4DZ88;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;KTN1_HUMAN	T	322	ENSP00000394992:S322T;ENSP00000378720:S322T;ENSP00000391964:S322T;ENSP00000378725:S322T;ENSP00000378719:S322T;ENSP00000378722:S322T;ENSP00000388807:S322T	.	S	+	1	0	KTN1	55164383	1.000000	0.71417	0.859000	0.33776	0.147000	0.21601	3.031000	0.49728	0.994000	0.38892	0.533000	0.62120	TCA	.	.		0.388	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		Missense_Mutation
TMEM260	54916	hgsc.bcm.edu	37	14	57051736	57051736	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:57051736G>A	ENST00000261556.6	+	2	300	c.178G>A	c.(178-180)Gca>Aca	p.A60T	TMEM260_ENST00000538838.1_Missense_Mutation_p.A60T|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	60						integral component of membrane (GO:0016021)											GATCACAGCCGCACATGAGCT	0.318																																					p.A60T		Atlas-SNP	.											.	.	.	.	0			c.G178A						.						99.0	96.0	97.0					14																	57051736		2203	4298	6501	SO:0001583	missense	0	exon2			ACAGCCGCACATG	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 101"""	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.178G>A	chr14.hg19:g.57051736G>A	ENSP00000261556:p.Ala60Thr	115.0	0.0		90.0	34.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	hg19	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116927	0.77323	.	.	ENSG00000070269	ENST00000556810;ENST00000261556;ENST00000538838	T;T	0.57273	0.98;0.41	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.75882	0.3910	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.79787	-0.1656	10	0.72032	D	0.01	-10.5261	18.8103	0.92056	0.0:0.0:1.0:0.0	.	60	Q9NX78	CN101_HUMAN	T	23;60;60	ENSP00000261556:A60T;ENSP00000441934:A60T	ENSP00000261556:A60T	A	+	1	0	C14orf101	56121489	1.000000	0.71417	0.995000	0.50966	0.933000	0.57130	9.434000	0.97515	2.444000	0.82710	0.650000	0.86243	GCA	.	.		0.318	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799	
AP5M1	55745	hgsc.bcm.edu	37	14	57747061	57747061	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:57747061A>G	ENST00000261558.3	+	3	1275	c.869A>G	c.(868-870)gAc>gGc	p.D290G	AP5M1_ENST00000431972.2_Missense_Mutation_p.D304G|AP5M1_ENST00000556723.1_3'UTR	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	290	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											GCAATGGATGACTCTGCATTT	0.413																																					p.D290G		Atlas-SNP	.											.	.	.	.	0			c.A869G						.						219.0	192.0	201.0					14																	57747061		2203	4300	6503	SO:0001583	missense	55745	exon3			TGGATGACTCTGC	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"""Mu-2 related death-inducing gene"""	614368	"""chromosome 14 open reading frame 108"", ""MU-2/AP1M2 domain containing, death-inducing"""	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.869A>G	chr14.hg19:g.57747061A>G	ENSP00000261558:p.Asp290Gly	144.0	0.0		121.0	60.0	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Missense_Mutation	SNP	ENST00000261558.3	hg19	CCDS9729.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.244038	0.39697	.	.	ENSG00000053770	ENST00000261558;ENST00000431972	T;T	0.19105	2.17;2.17	5.96	5.96	0.96718	Clathrin adaptor, mu subunit, C-terminal (3);	0.044985	0.85682	D	0.000000	T	0.15176	0.0366	N	0.16743	0.435	0.58432	D	0.999997	B	0.02656	0.0	B	0.09377	0.004	T	0.07986	-1.0744	10	0.26408	T	0.33	.	16.4356	0.83874	1.0:0.0:0.0:0.0	.	290	Q9H0R1	MUDEN_HUMAN	G	290;304	ENSP00000261558:D290G;ENSP00000390531:D304G	ENSP00000261558:D290G	D	+	2	0	MUDENG	56816814	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.158000	0.77470	2.280000	0.76307	0.496000	0.49642	GAC	.	.		0.413	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229	
DACT1	51339	hgsc.bcm.edu	37	14	59113492	59113492	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:59113492C>T	ENST00000335867.4	+	4	2175	c.2151C>T	c.(2149-2151)taC>taT	p.Y717Y	DACT1_ENST00000556859.1_Silent_p.Y436Y|DACT1_ENST00000541264.2_Silent_p.Y436Y|DACT1_ENST00000395153.3_Silent_p.Y680Y			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	717					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						CCAGCCCCTACGCCTACGTGG	0.652																																					p.Y717Y		Atlas-SNP	.											DACT1,NS,carcinoma,0,1	DACT1	119	.	0			c.C2151T						.						39.0	41.0	40.0					14																	59113492		2203	4300	6503	SO:0001819	synonymous_variant	51339	exon4			CCCCTACGCCTAC	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.2151C>T	chr14.hg19:g.59113492C>T		94.0	0.0		74.0	24.0	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	hg19	CCDS9736.1																																																																																			.	.		0.652	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950530	59950530	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:59950530T>C	ENST00000247194.4	-	1	618	c.505A>G	c.(505-507)Aca>Gca	p.T169A	JKAMP_ENST00000425728.2_5'Flank|JKAMP_ENST00000356057.5_5'Flank|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000261247.9_5'Flank|L3HYPDH_ENST00000487285.1_5'Flank|JKAMP_ENST00000554271.1_5'Flank|JKAMP_ENST00000556985.1_5'Flank	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	169					metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	CCATTACCTGTGGCCAGCACG	0.647											OREG0022712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T169A		Atlas-SNP	.											.	.	.	.	0			c.A505G						.						8.0	9.0	9.0					14																	59950530		2108	4156	6264	SO:0001583	missense	112849	exon1			TACCTGTGGCCAG	AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"""trans-L-3-hydroxyproline dehydratase"""	614811	"""chromosome 14 open reading frame 149"""	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941	ENST00000247194.4:c.505A>G	chr14.hg19:g.59950530T>C	ENSP00000247194:p.Thr169Ala	40.0	0.0	1042	31.0	16.0	NM_144581	Q96LJ5	Missense_Mutation	SNP	ENST00000247194.4	hg19	CCDS9739.1	.	.	.	.	.	.	.	.	.	.	T	6.818	0.520079	0.13005	.	.	ENSG00000126790	ENST00000247194	T	0.16324	2.35	5.58	0.142	0.14816	.	0.254626	0.45126	N	0.000385	T	0.09730	0.0239	L	0.39692	1.235	0.80722	D	1	B;B	0.15930	0.015;0.001	B;B	0.18561	0.022;0.006	T	0.25745	-1.0123	10	0.08837	T	0.75	.	4.7938	0.13261	0.2711:0.1393:0.0:0.5896	.	169;169	B4DGY8;Q96EM0	.;PRCM_HUMAN	A	169	ENSP00000247194:T169A	ENSP00000247194:T169A	T	-	1	0	C14orf149	59020283	1.000000	0.71417	0.991000	0.47740	0.496000	0.33645	0.769000	0.26604	0.041000	0.15688	-0.379000	0.06801	ACA	.	.		0.647	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581	
MTHFD1	4522	hgsc.bcm.edu	37	14	64921459	64921459	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:64921459A>C	ENST00000545908.1	+	26	2981	c.2752A>C	c.(2752-2754)Atc>Ctc	p.I918L	ZBTB25_ENST00000555220.1_Intron|MTHFD1_ENST00000216605.8_Missense_Mutation_p.I862L|ZBTB25_ENST00000555424.1_Intron|MTHFD1_ENST00000556284.1_3'UTR			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	862	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	GAATCTCCCCATCTGCATGGC	0.517																																					p.I862L	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.A2584C						.						110.0	97.0	102.0					14																	64921459		2203	4300	6503	SO:0001583	missense	4522	exon26			CTCCCCATCTGCA	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2752A>C	chr14.hg19:g.64921459A>C	ENSP00000438588:p.Ile918Leu	101.0	0.0		106.0	26.0	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.19	2.759082	0.49468	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.26810	1.71;1.71;1.71	4.65	3.5	0.40072	.	0.173902	0.51477	D	0.000095	T	0.35913	0.0948	M	0.88181	2.935	0.80722	D	1	B;B	0.22480	0.07;0.052	B;B	0.29716	0.106;0.074	T	0.29212	-1.0019	10	0.66056	D	0.02	-13.5966	7.7201	0.28727	0.8363:0.0:0.1637:0.0	.	918;862	F5H2F4;G3V2B8	.;.	L	918;862;918	ENSP00000438588:I918L;ENSP00000450560:I862L;ENSP00000216605:I918L	ENSP00000216605:I862L	I	+	1	0	MTHFD1	63991212	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	2.805000	0.47939	0.915000	0.36847	0.460000	0.39030	ATC	.	.		0.517	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		
PLEK2	26499	hgsc.bcm.edu	37	14	67864501	67864501	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:67864501G>A	ENST00000216446.4	-	2	225	c.85C>T	c.(85-87)Cgg>Tgg	p.R29W	PLEK2_ENST00000557388.1_5'UTR	NM_016445.1	NP_057529.1	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	29	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	15				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)		GTGTTCTGCCGAAGGATGAAC	0.597																																					p.R29W		Atlas-SNP	.											.	PLEK2	23	.	0			c.C85T						.						58.0	47.0	51.0					14																	67864501		2203	4300	6503	SO:0001583	missense	26499	exon2			TCTGCCGAAGGAT	AF228603	CCDS9782.1	14q23.3	2014-08-12			ENSG00000100558	ENSG00000100558		"""Pleckstrin homology (PH) domain containing"""	19238	protein-coding gene	gene with protein product		608007				11911883, 17658464	Standard	NM_016445		Approved		uc001xjh.1	Q9NYT0	OTTHUMG00000171247	ENST00000216446.4:c.85C>T	chr14.hg19:g.67864501G>A	ENSP00000216446:p.Arg29Trp	118.0	0.0		108.0	47.0	NM_016445	Q96JT0	Missense_Mutation	SNP	ENST00000216446.4	hg19	CCDS9782.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425310	0.62733	.	.	ENSG00000100558	ENST00000216446	T	0.77358	-1.09	5.6	4.59	0.56863	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.507527	0.21430	N	0.074661	T	0.78266	0.4256	M	0.84326	2.69	0.09310	N	1	P	0.51057	0.941	B	0.43360	0.417	T	0.75895	-0.3156	10	0.72032	D	0.01	-11.1157	8.572	0.33576	0.0794:0.0:0.7238:0.1968	.	29	Q9NYT0	PLEK2_HUMAN	W	29	ENSP00000216446:R29W	ENSP00000216446:R29W	R	-	1	2	PLEK2	66934254	0.066000	0.20996	0.985000	0.45067	0.997000	0.91878	1.961000	0.40432	2.793000	0.96121	0.563000	0.77884	CGG	.	.		0.597	PLEK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412547.2		
MAP3K9	4293	hgsc.bcm.edu	37	14	71199865	71199865	+	Missense_Mutation	SNP	G	G	A	rs145221753	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:71199865G>A	ENST00000554752.2	-	11	2220	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	MAP3K9_ENST00000555993.2_Missense_Mutation_p.R755W|MAP3K9_ENST00000553414.1_Missense_Mutation_p.R474W|MAP3K9_ENST00000554146.1_Missense_Mutation_p.R469W|MAP3K9_ENST00000381250.4_Missense_Mutation_p.R718W	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	741					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GCACCGCCCCGCTTGAGGCTG	0.652													G|||	2	0.000399361	0.0015	0.0	5008	,	,		16255	0.0		0.0	False		,,,				2504	0.0				p.R755W	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.C2263T						.	G	TRP/ARG	0,4406		0,0,2203	38.0	43.0	42.0		2263	3.8	1.0	14	dbSNP_134	42	1,8599	1.2+/-3.3	0,1,4299	no	missense	MAP3K9	NM_033141.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	755/1119	71199865	1,13005	2203	4300	6503	SO:0001583	missense	4293	exon12			CGCCCCGCTTGAG	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.2221C>T	chr14.hg19:g.71199865G>A	ENSP00000451612:p.Arg741Trp	92.0	0.0		84.0	15.0	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	hg19		.	.	.	.	.	.	.	.	.	.	G	17.70	3.453363	0.63290	0.0	1.16E-4	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	4.77	3.83	0.44106	.	0.176165	0.47455	D	0.000227	T	0.56217	0.1970	M	0.64997	1.995	0.48511	D	0.999668	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.999;0.999	T	0.60767	-0.7198	10	0.87932	D	0	.	14.5039	0.67741	0.0:0.0:0.8533:0.1467	.	469;741;755;474	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	W	741;755;474;718;469;457	ENSP00000451612:R741W;ENSP00000451038:R474W;ENSP00000370649:R718W;ENSP00000451921:R469W	ENSP00000005198:R755W	R	-	1	2	MAP3K9	70269618	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	2.694000	0.47035	2.478000	0.83669	0.561000	0.74099	CGG	.	G|1.000;A|0.000		0.652	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
ACOT4	122970	hgsc.bcm.edu	37	14	74062092	74062092	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:74062092T>C	ENST00000326303.4	+	3	1254	c.1000T>C	c.(1000-1002)Tat>Cat	p.Y334H		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	334					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		AAGTGAGTTGTATGCCCAAAC	0.507																																					p.Y334H		Atlas-SNP	.											.	ACOT4	25	.	0			c.T1000C						.						88.0	77.0	81.0					14																	74062092		2203	4300	6503	SO:0001583	missense	122970	exon3			GAGTTGTATGCCC	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.1000T>C	chr14.hg19:g.74062092T>C	ENSP00000323071:p.Tyr334His	135.0	0.0		126.0	35.0	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	hg19	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.639304	0.47153	.	.	ENSG00000177465	ENST00000326303	T	0.30182	1.54	5.63	4.47	0.54385	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.669756	0.16037	N	0.232576	T	0.46444	0.1393	L	0.48642	1.525	0.42153	D	0.991568	D	0.89917	1.0	D	0.87578	0.998	T	0.14448	-1.0472	10	0.30078	T	0.28	0.2696	11.6923	0.51523	0.1329:0.0:0.0:0.8671	.	334	Q8N9L9	ACOT4_HUMAN	H	334	ENSP00000323071:Y334H	ENSP00000323071:Y334H	Y	+	1	0	ACOT4	73131845	0.578000	0.26717	0.142000	0.22268	0.749000	0.42624	4.450000	0.60041	0.936000	0.37367	0.459000	0.35465	TAT	.	.		0.507	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876101	74876101	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:74876101G>A	ENST00000554823.1	-	1	408	c.347C>T	c.(346-348)aCc>aTc	p.T116I	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.T116I			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	116					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						AGTCTGGATGGTGACATTCTC	0.587																																					p.T116I		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.C347T						.						85.0	89.0	88.0					14																	74876101		2038	4202	6240	SO:0001583	missense	646658	exon2			TGGATGGTGACAT		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"""caudate-and putamen-enriched sequence"", ""interferon induced transmembrane protein domain containing 4"""	609999	"""transmembrane protein 90A"""	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.347C>T	chr14.hg19:g.74876101G>A	ENSP00000450439:p.Thr116Ile	53.0	0.0		61.0	21.0	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	hg19	CCDS41970.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267015	0.40095	.	.	ENSG00000183379	ENST00000331628;ENST00000554823	D;D	0.95272	-3.66;-3.66	4.63	3.66	0.41972	.	0.524136	0.19671	N	0.108749	D	0.87803	0.6269	N	0.22421	0.69	0.25431	N	0.988183	B	0.23735	0.09	B	0.21360	0.034	T	0.79519	-0.1770	10	0.62326	D	0.03	-9.9873	6.7756	0.23619	0.0:0.1714:0.5472:0.2813	.	116	A6NDD5	SYN1L_HUMAN	I	116	ENSP00000331474:T116I;ENSP00000450439:T116I	ENSP00000331474:T116I	T	-	2	0	SYNDIG1L	73945854	0.998000	0.40836	0.929000	0.37066	0.819000	0.46315	3.050000	0.49877	2.402000	0.81655	0.467000	0.42956	ACC	.	.		0.587	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515	
AREL1	9870	hgsc.bcm.edu	37	14	75130470	75130470	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:75130470G>A	ENST00000356357.4	-	20	2940	c.2425C>T	c.(2425-2427)Ctg>Ttg	p.L809L	AREL1_ENST00000557401.1_Intron	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	809	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GCCAGCTGCAGCATCCTGTGC	0.537																																					p.L809L		Atlas-SNP	.											.	KIAA0317	68	.	0			c.C2425T						.						136.0	142.0	140.0					14																	75130470		2160	4265	6425	SO:0001819	synonymous_variant	9870	exon20			GCTGCAGCATCCT	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"""KIAA0317"""	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.2425C>T	chr14.hg19:g.75130470G>A		95.0	0.0		87.0	41.0	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Silent	SNP	ENST00000356357.4	hg19	CCDS41971.1																																																																																			.	.		0.537	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821	
EIF2B2	8892	hgsc.bcm.edu	37	14	75471454	75471454	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:75471454A>G	ENST00000266126.5	+	4	528	c.448A>G	c.(448-450)Aac>Gac	p.N150D	RP11-950C14.3_ENST00000554430.1_RNA	NM_014239.3	NP_055054.1	P49770	EI2BB_HUMAN	eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa	150					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|central nervous system development (GO:0007417)|gene expression (GO:0010467)|myelination (GO:0042552)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|translation initiation factor activity (GO:0003743)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.00661)		GACAATGGAGAACATTGCAGC	0.373																																					p.N150D		Atlas-SNP	.											.	EIF2B2	22	.	0			c.A448G						.						67.0	64.0	65.0					14																	75471454		2203	4300	6503	SO:0001583	missense	8892	exon4			ATGGAGAACATTG		CCDS9836.1	14q24.3	2008-08-11	2002-08-29			ENSG00000119718			3258	protein-coding gene	gene with protein product		606454	"""eukaryotic translation initiation factor 2B, subunit 2 (beta, 39kD)"""			8887689	Standard	NM_014239		Approved	EIF2B, EIF-2Bbeta	uc001xrc.2	P49770		ENST00000266126.5:c.448A>G	chr14.hg19:g.75471454A>G	ENSP00000266126:p.Asn150Asp	63.0	0.0		43.0	17.0	NM_014239	O43201	Missense_Mutation	SNP	ENST00000266126.5	hg19	CCDS9836.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.062865	0.76187	.	.	ENSG00000119718	ENST00000266126	D	0.92495	-3.05	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.93360	0.7883	L	0.59436	1.845	0.80722	D	1	P	0.37636	0.603	P	0.49528	0.614	D	0.92663	0.6143	10	0.41790	T	0.15	-26.0731	15.827	0.78718	1.0:0.0:0.0:0.0	.	150	P49770	EI2BB_HUMAN	D	150	ENSP00000266126:N150D	ENSP00000266126:N150D	N	+	1	0	EIF2B2	74541207	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	9.065000	0.93941	2.324000	0.78689	0.533000	0.62120	AAC	.	.		0.373	EIF2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414993.1	NM_014239	
CIPC	85457	hgsc.bcm.edu	37	14	77580248	77580248	+	Missense_Mutation	SNP	G	G	A	rs201665496		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:77580248G>A	ENST00000361786.2	+	4	1104	c.787G>A	c.(787-789)Gcc>Acc	p.A263T	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		263					negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		CGCTTCCCCCGCCAGTCCTGT	0.572																																					p.A263T		Atlas-SNP	.											KIAA1737,NS,carcinoma,0,1	KIAA1737	26	.	0			c.G787A						.						86.0	73.0	78.0					14																	77580248		2203	4300	6503	SO:0001583	missense	85457	exon4			TCCCCCGCCAGTC																												ENST00000361786.2:c.787G>A	chr14.hg19:g.77580248G>A	ENSP00000355319:p.Ala263Thr	73.0	0.0		81.0	32.0	NM_033426	B2RCI1|Q8N389|Q8NDZ1	Missense_Mutation	SNP	ENST00000361786.2	hg19	CCDS9855.1	.	.	.	.	.	.	.	.	.	.	G	16.10	3.026280	0.54683	.	.	ENSG00000198894	ENST00000361786	T	0.33216	1.42	5.58	4.63	0.57726	.	0.505693	0.21867	N	0.067941	T	0.34890	0.0913	L	0.51422	1.61	0.39356	D	0.965849	D;D	0.62365	0.991;0.991	P;P	0.52109	0.69;0.69	T	0.02533	-1.1145	10	0.30078	T	0.28	-22.2881	8.9275	0.35650	0.0:0.1491:0.6748:0.1761	.	263;165	Q9C0C6;B3KU75	K1737_HUMAN;.	T	263	ENSP00000355319:A263T	ENSP00000355319:A263T	A	+	1	0	KIAA1737	76650001	0.999000	0.42202	0.996000	0.52242	0.995000	0.86356	2.124000	0.42006	2.792000	0.96026	0.555000	0.69702	GCC	.	G|1.000;C|0.000		0.572	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1		
FLRT2	23768	hgsc.bcm.edu	37	14	86088965	86088965	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:86088965C>A	ENST00000330753.4	+	2	1874	c.1107C>A	c.(1105-1107)ctC>ctA	p.L369L	FLRT2_ENST00000554746.1_Silent_p.L369L	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	369					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GCCTGCCTCTCTTCACCCCAG	0.557																																					p.L369L		Atlas-SNP	.											.	FLRT2	168	.	0			c.C1107A						.						83.0	90.0	88.0					14																	86088965		2203	4300	6503	SO:0001819	synonymous_variant	23768	exon2			GCCTCTCTTCACC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1107C>A	chr14.hg19:g.86088965C>A		69.0	0.0		71.0	26.0	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.		0.557	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
TTC7B	145567	hgsc.bcm.edu	37	14	91155976	91155976	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:91155976C>T	ENST00000328459.6	-	7	979	c.858G>A	c.(856-858)ccG>ccA	p.P286P	TTC7B_ENST00000357056.2_Silent_p.P286P	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	286										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)				GTGACTGGCACGGTGGATCCT	0.527																																					p.P286P		Atlas-SNP	.											.	TTC7B	93	.	0			c.G858A						.						118.0	97.0	104.0					14																	91155976		2203	4300	6503	SO:0001819	synonymous_variant	145567	exon7			CTGGCACGGTGGA	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.858G>A	chr14.hg19:g.91155976C>T		114.0	0.0		131.0	65.0	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	hg19	CCDS32140.1																																																																																			.	.		0.527	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
CHGA	1113	hgsc.bcm.edu	37	14	93397934	93397934	+	Missense_Mutation	SNP	A	A	C	rs71430778		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:93397934A>C	ENST00000216492.5	+	6	975	c.695A>C	c.(694-696)gAg>gCg	p.E232A	CHGA_ENST00000334654.4_Intron|CHGA_ENST00000553866.1_3'UTR	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	232					regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		gaggaggaggaggaggaggag	0.637																																					p.E232A	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.A695C						.						33.0	39.0	37.0					14																	93397934		2203	4300	6503	SO:0001583	missense	1113	exon6			AGGAGGAGGAGGA		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"""vasostatin"", ""pancreastatin"", ""parastatin"""	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.695A>C	chr14.hg19:g.93397934A>C	ENSP00000216492:p.Glu232Ala	174.0	0.0		169.0	69.0	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	hg19	CCDS9906.1	.	.	.	.	.	.	.	.	.	.	A	9.231	1.035830	0.19590	.	.	ENSG00000100604	ENST00000216492	T	0.01584	4.75	4.55	3.4	0.38934	.	0.495175	0.19758	N	0.106736	T	0.04952	0.0133	M	0.64997	1.995	0.80722	D	1	D	0.55605	0.972	P	0.54238	0.746	T	0.34104	-0.9842	10	0.66056	D	0.02	.	7.8352	0.29365	0.9015:0.0:0.0985:0.0	.	232	P10645	CMGA_HUMAN	A	232	ENSP00000216492:E232A	ENSP00000216492:E232A	E	+	2	0	CHGA	92467687	0.962000	0.33011	0.113000	0.21522	0.259000	0.26198	2.363000	0.44178	0.713000	0.32060	0.374000	0.22700	GAG	.	A|0.500;T|0.500		0.637	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275	
BDKRB1	623	hgsc.bcm.edu	37	14	96730967	96730967	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:96730967C>T	ENST00000216629.6	+	3	1554	c.948C>T	c.(946-948)ggC>ggT	p.G316G	RP11-404P21.3_ENST00000553638.1_RNA|BDKRB1_ENST00000553356.1_Silent_p.G250G	NM_000710.3	NP_000701.2	P46663	BKRB1_HUMAN	bradykinin receptor B1	316					cell migration (GO:0016477)|inflammatory response (GO:0006954)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell growth (GO:0030308)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|peptide binding (GO:0042277)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(4)|skin(1)|urinary_tract(1)	16		all_cancers(154;0.0677)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.208)|Epithelial(152;0.226)		TCTTTGTGGGCCGGCTCTTCA	0.453																																					p.G316G		Atlas-SNP	.											.	BDKRB1	41	.	0			c.C948T						.						141.0	149.0	146.0					14																	96730967		2203	4300	6503	SO:0001819	synonymous_variant	623	exon3			TGTGGGCCGGCTC	L42383	CCDS9943.1	14q32.1-q32.2	2012-08-08				ENSG00000100739		"""GPCR / Class A : Bradykinin receptors"""	1029	protein-coding gene	gene with protein product		600337				8808279	Standard	NM_000710		Approved	BKR1, B1BKR, bradyb1	uc001yfh.3	P46663		ENST00000216629.6:c.948C>T	chr14.hg19:g.96730967C>T		111.0	0.0		108.0	44.0	NM_000710	A8K7F5|Q546S7|Q8N0Y8	Silent	SNP	ENST00000216629.6	hg19	CCDS9943.1																																																																																			.	.		0.453	BDKRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413300.1		
ATG2B	55102	hgsc.bcm.edu	37	14	96781801	96781801	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:96781801C>T	ENST00000359933.4	-	22	4374	c.3481G>A	c.(3481-3483)Gat>Aat	p.D1161N		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1161					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)		CCAACTCCATCTGAAGAAGTT	0.418																																					p.D1161N		Atlas-SNP	.											.	ATG2B	169	.	0			c.G3481A						.						59.0	57.0	58.0					14																	96781801		2203	4300	6503	SO:0001583	missense	55102	exon22			CTCCATCTGAAGA	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.3481G>A	chr14.hg19:g.96781801C>T	ENSP00000353010:p.Asp1161Asn	366.0	0.0		377.0	26.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294599	0.40594	.	.	ENSG00000066739	ENST00000359933	T	0.09723	2.95	5.61	5.61	0.85477	.	0.355513	0.22282	U	0.062107	T	0.07188	0.0182	N	0.16478	0.41	0.39419	D	0.966897	B	0.06786	0.001	B	0.06405	0.002	T	0.36672	-0.9738	10	0.15952	T	0.53	.	12.9138	0.58195	0.0:0.9257:0.0:0.0743	.	1161	Q96BY7	ATG2B_HUMAN	N	1161	ENSP00000353010:D1161N	ENSP00000353010:D1161N	D	-	1	0	ATG2B	95851554	1.000000	0.71417	0.980000	0.43619	0.949000	0.60115	3.972000	0.56838	2.654000	0.90174	0.591000	0.81541	GAT	.	.		0.418	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
C14orf177	283598	hgsc.bcm.edu	37	14	99183450	99183450	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:99183450T>C	ENST00000325812.2	+	4	636	c.217T>C	c.(217-219)Ttc>Ctc	p.F73L		NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177	73										endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CTCTACCTGTTTCTGTACAGA	0.488																																					p.F73L		Atlas-SNP	.											.	C14orf177	37	.	0			c.T217C						.						96.0	87.0	90.0					14																	99183450		2203	4300	6503	SO:0001583	missense	283598	exon4			ACCTGTTTCTGTA	AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745	ENST00000325812.2:c.217T>C	chr14.hg19:g.99183450T>C	ENSP00000321360:p.Phe73Leu	92.0	0.0		81.0	29.0	NM_182560	Q8N7D2	Missense_Mutation	SNP	ENST00000325812.2	hg19	CCDS9948.1	.	.	.	.	.	.	.	.	.	.	T	8.607	0.888275	0.17540	.	.	ENSG00000176605	ENST00000325812;ENST00000541516	T;T	0.38722	1.23;1.12	3.23	-0.664	0.11406	.	.	.	.	.	T	0.18882	0.0453	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18967	-1.0320	9	0.87932	D	0	.	2.2474	0.04034	0.4498:0.1553:0.0:0.3949	.	73	Q52M58	CN177_HUMAN	L	73	ENSP00000321360:F73L;ENSP00000440687:F73L	ENSP00000321360:F73L	F	+	1	0	C14orf177	98253203	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.194000	0.17135	-0.132000	0.11557	0.533000	0.62120	TTC	.	.		0.488	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560	
SETD3	84193	hgsc.bcm.edu	37	14	99929899	99929899	+	Silent	SNP	C	C	T	rs146095518		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:99929899C>T	ENST00000331768.5	-	3	279	c.120G>A	c.(118-120)gcG>gcA	p.A40A	SETD3_ENST00000436070.2_Silent_p.A40A|SETD3_ENST00000329331.3_Silent_p.A40A|SETD3_ENST00000453938.1_5'UTR	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	40					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)				CTGGGCCAGGCGCCGGACTGC	0.433																																					p.A40A		Atlas-SNP	.											.	SETD3	56	.	0			c.G120A						.	C	,	0,4406		0,0,2203	70.0	60.0	64.0		120,120	-9.8	0.0	14	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SETD3	NM_032233.2,NM_199123.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	40/595,40/297	99929899	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84193	exon3			GCCAGGCGCCGGA	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.120G>A	chr14.hg19:g.99929899C>T		46.0	0.0		36.0	14.0	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Silent	SNP	ENST00000331768.5	hg19	CCDS9951.1																																																																																			.	C|1.000;T|0.000		0.433	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233	
WDR20	91833	hgsc.bcm.edu	37	14	102675272	102675272	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:102675272C>T	ENST00000342702.3	+	3	796	c.765C>T	c.(763-765)caC>caT	p.H255H	WDR20_ENST00000322340.5_Intron|WDR20_ENST00000556511.2_Silent_p.H194H|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000499851.2_5'UTR|WDR20_ENST00000454394.2_Silent_p.H286H|WDR20_ENST00000545563.1_Silent_p.H82H|WDR20_ENST00000424963.2_Silent_p.H131H|WDR20_ENST00000335263.5_Silent_p.H255H|WDR20_ENST00000556807.1_Silent_p.H194H	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	255										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						TGGAGCTGCACGGTACGATGA	0.557																																					p.H286H		Atlas-SNP	.											.	WDR20	35	.	0			c.C858T						.						78.0	67.0	70.0					14																	102675272		2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			GCTGCACGGTACG	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"""WD repeat domain containing"""	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.765C>T	chr14.hg19:g.102675272C>T		107.0	0.0		113.0	7.0	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000342702.3	hg19	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	C	3.389	-0.124819	0.06795	.	.	ENSG00000140153	ENST00000556511	.	.	.	5.83	3.03	0.35002	.	.	.	.	.	T	0.57315	0.2045	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49652	-0.8917	4	.	.	.	.	7.8045	0.29193	0.0:0.566:0.0:0.434	.	.	.	.	W	186	.	.	R	+	1	2	WDR20	101745025	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	0.617000	0.24359	0.388000	0.25054	0.655000	0.94253	CGG	.	.		0.557	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291	
INF2	64423	hgsc.bcm.edu	37	14	105168020	105168020	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105168020C>T	ENST00000392634.4	+	2	430	c.318C>T	c.(316-318)cgC>cgT	p.R106R	INF2_ENST00000330634.7_Silent_p.R106R|INF2_ENST00000398337.4_Silent_p.R106R	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	106	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		GCTGCGTGCGCGCCGTCATGA	0.706																																					p.R106R		Atlas-SNP	.											.	INF2	148	.	0			c.C318T						.						8.0	11.0	10.0					14																	105168020		2076	4175	6251	SO:0001819	synonymous_variant	64423	exon2			CGTGCGCGCCGTC	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.318C>T	chr14.hg19:g.105168020C>T		66.0	0.0		54.0	13.0	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Silent	SNP	ENST00000392634.4	hg19	CCDS9989.2																																																																																			.	.		0.706	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414171	105414171	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105414171G>T	ENST00000333244.5	-	7	7736	c.7617C>A	c.(7615-7617)gaC>gaA	p.D2539E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2539						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGACCTCCAGGTCAGCGGAAG	0.662																																					p.D2539E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C7617A						.						108.0	121.0	117.0					14																	105414171		1889	4103	5992	SO:0001583	missense	113146	exon7			CTCCAGGTCAGCG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7617C>A	chr14.hg19:g.105414171G>T	ENSP00000353114:p.Asp2539Glu	217.0	0.0		170.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	15.90	2.969777	0.53614	.	.	ENSG00000185567	ENST00000333244	T	0.01139	5.28	3.7	-7.39	0.01402	.	.	.	.	.	T	0.00906	0.0030	L	0.33245	0.995	0.09310	N	1	B	0.19817	0.039	B	0.25140	0.058	T	0.49634	-0.8919	9	0.05833	T	0.94	.	9.9132	0.41419	0.3594:0.5343:0.1063:0.0	.	2539	Q8IVF2	AHNK2_HUMAN	E	2539	ENSP00000353114:D2539E	ENSP00000353114:D2539E	D	-	3	2	AHNAK2	104485216	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-2.249000	0.01188	-1.218000	0.02601	0.306000	0.20318	GAC	.	.		0.662	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414174	105414174	+	Silent	SNP	A	A	G	rs374363751		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105414174A>G	ENST00000333244.5	-	7	7733	c.7614T>C	c.(7612-7614)gcT>gcC	p.A2538A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2538						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCTCCAGGTCAGCGGAAGGGG	0.667																																					p.A2538A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T7614C						.						108.0	121.0	117.0					14																	105414174		1889	4105	5994	SO:0001819	synonymous_variant	113146	exon7			CAGGTCAGCGGAA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7614T>C	chr14.hg19:g.105414174A>G		227.0	0.0		165.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.667	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414177	105414177	+	Silent	SNP	G	G	A	rs368398841	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:105414177G>A	ENST00000333244.5	-	7	7730	c.7611C>T	c.(7609-7611)tcC>tcT	p.S2537S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2537						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCAGGTCAGCGGAAGGGGGCT	0.667													.|||	2	0.000399361	0.0008	0.0	5008	,	,		16640	0.0		0.0	False		,,,				2504	0.001				p.S2537S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C7611T						.	A		4,3784		0,4,1890	110.0	123.0	119.0		7611	-7.4	0.0	14		119	1,8217		0,1,4108	no	coding-synonymous	AHNAK2	NM_138420.2		0,5,5998	AA,AG,GG		0.0122,0.1056,0.0416		2537/5796	105414177	5,12001	1894	4109	6003	SO:0001819	synonymous_variant	113146	exon7			GTCAGCGGAAGGG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7611C>T	chr14.hg19:g.105414177G>A		225.0	0.0		173.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.667	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NIPA2	81614	hgsc.bcm.edu	37	15	23003033	23003033	+	IGR	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:23003033G>A	ENST00000337451.3	-	0	3233				CYFIP1_ENST00000560848.1_Missense_Mutation_p.S1252N|CYFIP1_ENST00000435939.2_Missense_Mutation_p.S821N|CYFIP1_ENST00000313077.7_Missense_Mutation_p.S1252N	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2							early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		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;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		TCCCTCGCCAGCAGCTGAGGG	0.542																																					p.S1252N		Atlas-SNP	.											.	CYFIP1	159	.	0			c.G3755A						.						33.0	30.0	31.0					15																	23003033		2203	4300	6503	SO:0001628	intergenic_variant	23191	exon31			TCGCCAGCAGCTG	AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101		chr15.hg19:g.23003033G>A		120.0	0.0		95.0	41.0	NM_014608	F8W7Y8|Q96F03|Q9BVS2	Missense_Mutation	SNP	ENST00000337451.3	hg19	CCDS10010.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.934067	0.52866	.	.	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.33654	2.19;1.4	6.17	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	L	0.33485	1.01	0.80722	D	1	B;B	0.13145	0.007;0.002	B;B	0.23852	0.049;0.004	T	0.04991	-1.0913	10	0.23891	T	0.37	-27.8302	17.7372	0.88397	0.0:0.1223:0.8776:0.0	.	821;1252	Q7L576-2;Q7L576	.;CYFP1_HUMAN	N	1252;1254;821	ENSP00000324549:S1252N;ENSP00000405956:S821N	ENSP00000324549:S1252N	S	+	2	0	CYFIP1	20554474	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	7.931000	0.87625	1.611000	0.50210	0.655000	0.94253	AGC	.	.		0.542	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922	
NPAP1	23742	hgsc.bcm.edu	37	15	24921255	24921255	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:24921255C>T	ENST00000329468.2	+	1	715	c.241C>T	c.(241-243)Cct>Tct	p.P81S		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	81					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TGCGGCCGCCCCTCTGGGGGT	0.701																																					p.P81S		Atlas-SNP	.											.	.	.	.	0			c.C241T						.						16.0	18.0	17.0					15																	24921255		2117	4170	6287	SO:0001583	missense	23742	exon1			GCCGCCCCTCTGG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.241C>T	chr15.hg19:g.24921255C>T	ENSP00000333735:p.Pro81Ser	109.0	0.0		97.0	42.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	10.85	1.466117	0.26335	.	.	ENSG00000185823	ENST00000329468	T	0.06768	3.26	1.96	-2.28	0.06826	.	1.189390	0.06402	N	0.718990	T	0.05868	0.0153	L	0.38175	1.15	0.09310	N	1	B	0.27166	0.17	B	0.21708	0.036	T	0.40794	-0.9544	10	0.33940	T	0.23	.	2.2894	0.04135	0.2371:0.386:0.0:0.3769	.	81	Q9NZP6	CO002_HUMAN	S	81	ENSP00000333735:P81S	ENSP00000333735:P81S	P	+	1	0	C15orf2	22472348	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.427000	0.06999	-0.577000	0.05967	-0.719000	0.03609	CCT	.	.		0.701	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
APBA2	321	hgsc.bcm.edu	37	15	29406202	29406202	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:29406202T>A	ENST00000558402.1	+	15	2760	c.2161T>A	c.(2161-2163)Tcc>Acc	p.S721T	APBA2_ENST00000561069.1_Missense_Mutation_p.S721T|APBA2_ENST00000411764.1_Missense_Mutation_p.S709T|APBA2_ENST00000558259.1_Missense_Mutation_p.S721T|APBA2_ENST00000558330.1_Missense_Mutation_p.S709T			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	721	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CCAAGCTCTGTCCAACTCGGT	0.637																																					p.S721T		Atlas-SNP	.											.	APBA2	132	.	0			c.T2161A						.						131.0	98.0	109.0					15																	29406202		2203	4300	6503	SO:0001583	missense	321	exon13			GCTCTGTCCAACT	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.2161T>A	chr15.hg19:g.29406202T>A	ENSP00000453293:p.Ser721Thr	94.0	0.0		87.0	37.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490877	0.64074	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.26660	1.72	4.48	4.48	0.54585	PDZ/DHR/GLGF (4);	0.383779	0.22569	N	0.058372	T	0.25901	0.0631	N	0.03891	-0.335	0.80722	D	1	D;B	0.54207	0.965;0.124	D;B	0.70487	0.969;0.078	T	0.29822	-0.9999	10	0.33940	T	0.23	.	12.9729	0.58524	0.0:0.0:0.0:1.0	.	709;721	E9PGI4;Q99767	.;APBA2_HUMAN	T	709;721	ENSP00000409312:S709T	ENSP00000219865:S721T	S	+	1	0	APBA2	27193494	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.842000	0.86851	1.651000	0.50673	0.459000	0.35465	TCC	.	.		0.637	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32908462	32908462	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:32908462C>T	ENST00000361627.3	+	1	772	c.50C>T	c.(49-51)gCc>gTc	p.A17V	ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.A17V|AC123768.4_ENST00000576873.1_lincRNA|ARHGAP11A_ENST00000543522.1_Intron|RP11-1000B6.5_ENST00000500941.2_lincRNA|ARHGAP11A_ENST00000565905.1_Intron|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.A17V	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	17					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(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CATCTGCGGGCCTTCTATGGT	0.547																																					p.A17V	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.C50T						.						77.0	74.0	75.0					15																	32908462		2201	4300	6501	SO:0001583	missense	9824	exon1			TGCGGGCCTTCTA	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.50C>T	chr15.hg19:g.32908462C>T	ENSP00000355090:p.Ala17Val	192.0	0.0		202.0	76.0	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	16.29	3.081246	0.55753	.	.	ENSG00000198826	ENST00000361627	T	0.10005	2.92	3.72	3.72	0.42706	.	0.755248	0.11694	N	0.538556	T	0.07007	0.0178	N	0.24115	0.695	0.80722	D	1	P	0.38617	0.64	B	0.27170	0.077	T	0.42716	-0.9435	10	0.35671	T	0.21	.	12.7189	0.57131	0.0:1.0:0.0:0.0	.	17	Q6P4F7	RHGBA_HUMAN	V	17	ENSP00000355090:A17V	ENSP00000355090:A17V	A	+	2	0	ARHGAP11A	30695754	0.818000	0.29161	0.632000	0.29296	0.965000	0.64279	4.266000	0.58871	2.071000	0.62044	0.478000	0.44815	GCC	.	.		0.547	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
GJD2	57369	hgsc.bcm.edu	37	15	35044813	35044813	+	Missense_Mutation	SNP	G	G	A	rs113904860		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:35044813G>A	ENST00000290374.4	-	2	1308	c.832C>T	c.(832-834)Cgc>Tgc	p.R278C	RP11-814P5.1_ENST00000558707.1_RNA|RP11-814P5.1_ENST00000503496.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	278					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTGATCTTGCGCCATCCCAGG	0.512																																					p.R278C		Atlas-SNP	.											GJD2,NS,carcinoma,+1,1	GJD2	49	.	0			c.C832T						.						130.0	107.0	115.0					15																	35044813		2201	4298	6499	SO:0001583	missense	57369	exon2			TCTTGCGCCATCC	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.832C>T	chr15.hg19:g.35044813G>A	ENSP00000290374:p.Arg278Cys	164.0	0.0		152.0	61.0	NM_020660	Q2M241|Q9P2R0	Missense_Mutation	SNP	ENST00000290374.4	hg19	CCDS10040.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480981	0.63849	.	.	ENSG00000159248	ENST00000290374	D	0.98313	-4.86	5.86	5.86	0.93980	.	0.089867	0.43416	D	0.000568	D	0.97015	0.9025	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	P	0.53689	0.732	D	0.97229	0.9883	10	0.72032	D	0.01	.	14.8465	0.70264	0.0:0.0:0.8224:0.1776	.	278	Q9UKL4	CXD2_HUMAN	C	278	ENSP00000290374:R278C	ENSP00000290374:R278C	R	-	1	0	GJD2	32832105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.960000	0.56752	2.781000	0.95711	0.650000	0.86243	CGC	.	.		0.512	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
THBS1	7057	hgsc.bcm.edu	37	15	39874935	39874935	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:39874935C>T	ENST00000260356.5	+	3	774	c.609C>T	c.(607-609)ggC>ggT	p.G203G		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	203	Laminin G-like.				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)		CAAAGGGGGGCGTCAATGACA	0.557																																					p.G203G		Atlas-SNP	.											.	THBS1	106	.	0			c.C609T						.						38.0	36.0	37.0					15																	39874935		2200	4296	6496	SO:0001819	synonymous_variant	7057	exon3			GGGGGGCGTCAAT		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.609C>T	chr15.hg19:g.39874935C>T		35.0	0.0		33.0	13.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	hg19	CCDS32194.1																																																																																			.	.		0.557	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
THBS1	7057	hgsc.bcm.edu	37	15	39881519	39881519	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:39881519C>T	ENST00000260356.5	+	12	2055	c.1890C>T	c.(1888-1890)ttC>ttT	p.F630F		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	630					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)		CACAGCCCTTCGGCCAGGGTG	0.577																																					p.F630F		Atlas-SNP	.											.	THBS1	106	.	0			c.C1890T						.						68.0	72.0	71.0					15																	39881519		2200	4297	6497	SO:0001819	synonymous_variant	7057	exon12			GCCCTTCGGCCAG		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.1890C>T	chr15.hg19:g.39881519C>T		92.0	0.0		91.0	34.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	1.559	-0.537237	0.04082	.	.	ENSG00000137801	ENST00000397593	.	.	.	5.64	-6.1	0.02138	.	.	.	.	.	T	0.76054	0.3934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79838	-0.1634	5	0.87932	D	0	-13.2719	18.2928	0.90136	0.0:0.2884:0.0:0.7116	.	.	.	.	L	64	.	ENSP00000380721:S64L	S	+	2	0	THBS1	37668811	0.013000	0.17824	0.216000	0.23742	0.063000	0.16089	-0.813000	0.04491	-1.693000	0.01427	-1.731000	0.00696	TCG	.	.		0.577	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
THBS1	7057	hgsc.bcm.edu	37	15	39885371	39885371	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:39885371C>T	ENST00000260356.5	+	18	3103	c.2938C>T	c.(2938-2940)Cgc>Tgc	p.R980C	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	980	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)		CTGGGTTGTACGCCATCAGGG	0.488																																					p.R980C		Atlas-SNP	.											.	THBS1	106	.	0			c.C2938T						.						72.0	63.0	66.0					15																	39885371		2200	4297	6497	SO:0001583	missense	7057	exon18			GTTGTACGCCATC		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.2938C>T	chr15.hg19:g.39885371C>T	ENSP00000260356:p.Arg980Cys	102.0	0.0		89.0	39.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128312	0.77549	.	.	ENSG00000137801	ENST00000260356	D	0.95412	-3.7	5.68	5.68	0.88126	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.36665	N	0.002479	D	0.97318	0.9123	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97222	0.9878	10	0.54805	T	0.06	-28.2234	14.5836	0.68308	0.1461:0.8539:0.0:0.0	.	895;980	B4E3J7;P07996	.;TSP1_HUMAN	C	980	ENSP00000260356:R980C	ENSP00000260356:R980C	R	+	1	0	THBS1	37672663	0.998000	0.40836	0.999000	0.59377	0.999000	0.98932	3.748000	0.55142	2.667000	0.90743	0.655000	0.94253	CGC	.	.		0.488	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
DISP2	85455	hgsc.bcm.edu	37	15	40660890	40660890	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:40660890C>T	ENST00000267889.3	+	8	2664	c.2577C>T	c.(2575-2577)tgC>tgT	p.C859C	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	859					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		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;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		ACCTCTGCTGCGGCCACTCGG	0.667																																					p.C859C		Atlas-SNP	.											.	DISP2	86	.	0			c.C2577T						.						18.0	22.0	21.0					15																	40660890		2201	4299	6500	SO:0001819	synonymous_variant	85455	exon8			CTGCTGCGGCCAC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2577C>T	chr15.hg19:g.40660890C>T		85.0	0.0		75.0	27.0	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	hg19	CCDS10056.1																																																																																			.	.		0.667	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
LTK	4058	hgsc.bcm.edu	37	15	41804450	41804450	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:41804450C>T	ENST00000263800.6	-	4	469	c.373G>A	c.(373-375)Gga>Aga	p.G125R	LTK_ENST00000453182.2_Missense_Mutation_p.G125R|LTK_ENST00000561619.1_Intron|LTK_ENST00000355166.5_Missense_Mutation_p.G125R	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	125					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CCCGCGGCTCCGTAGGCTGAG	0.667										TSP Lung(18;0.14)																											p.G125R		Atlas-SNP	.											.	LTK	117	.	0			c.G373A						.						26.0	32.0	30.0					15																	41804450		2203	4299	6502	SO:0001583	missense	4058	exon4			CGGCTCCGTAGGC	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.373G>A	chr15.hg19:g.41804450C>T	ENSP00000263800:p.Gly125Arg	223.0	0.0		243.0	90.0	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236788	0.95240	.	.	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	D;D;D	0.91945	-2.94;-2.94;-2.94	4.28	4.28	0.50868	.	0.000000	0.34110	U	0.004257	D	0.96531	0.8868	M	0.89163	3.01	0.43084	D	0.994747	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.986;0.999	D	0.97670	1.0166	10	0.87932	D	0	.	16.5404	0.84383	0.0:1.0:0.0:0.0	.	125;125;125	E9PFX4;P29376-4;P29376	.;.;LTK_HUMAN	R	125	ENSP00000347293:G125R;ENSP00000263800:G125R;ENSP00000392196:G125R	ENSP00000263800:G125R	G	-	1	0	LTK	39591742	1.000000	0.71417	0.852000	0.33557	0.988000	0.76386	2.135000	0.42112	2.220000	0.72140	0.561000	0.74099	GGA	.	.		0.667	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
TGM5	9333	hgsc.bcm.edu	37	15	43545733	43545733	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:43545733C>T	ENST00000220420.5	-	5	662	c.655G>A	c.(655-657)Gtc>Atc	p.V219I	TGM5_ENST00000349114.4_Missense_Mutation_p.V137I	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	219					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CTGACGTAGACGGGGCTTCCC	0.607																																					p.V219I		Atlas-SNP	.											.	TGM5	88	.	0			c.G655A						.						72.0	64.0	67.0					15																	43545733		2202	4299	6501	SO:0001583	missense	9333	exon5			CGTAGACGGGGCT	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.655G>A	chr15.hg19:g.43545733C>T	ENSP00000220420:p.Val219Ile	50.0	0.0		46.0	15.0	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	hg19	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.430780	0.43122	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	D;D	0.92249	-3.0;-3.0	5.31	3.42	0.39159	.	0.000000	0.85682	D	0.000000	D	0.89904	0.6850	L	0.39147	1.195	0.33801	D	0.626706	D;D	0.59767	0.986;0.975	P;B	0.54100	0.742;0.41	D	0.88890	0.3345	10	0.17832	T	0.49	-40.1078	9.6247	0.39743	0.0:0.8284:0.0:0.1716	.	137;219	O43548-2;O43548	.;TGM5_HUMAN	I	219;137;218	ENSP00000220420:V219I;ENSP00000220419:V137I	ENSP00000220420:V219I	V	-	1	0	TGM5	41333025	0.174000	0.23070	0.849000	0.33467	0.583000	0.36354	0.776000	0.26704	1.383000	0.46405	-0.137000	0.14449	GTC	.	.		0.607	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
TUBGCP4	27229	hgsc.bcm.edu	37	15	43668752	43668752	+	Missense_Mutation	SNP	C	C	T	rs200951264		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:43668752C>T	ENST00000260383.7	+	3	513	c.259C>T	c.(259-261)Cgg>Tgg	p.R87W	TUBGCP4_ENST00000564079.1_Missense_Mutation_p.R87W|TUBGCP4_ENST00000399460.3_5'UTR|TUBGCP4_ENST00000570081.1_3'UTR			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	87					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		AATCTACCTGCGGGCCTTCTG	0.493											OREG0023088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R87W		Atlas-SNP	.											.	TUBGCP4	48	.	0			c.C259T						.						132.0	126.0	128.0					15																	43668752		1901	4120	6021	SO:0001583	missense	27229	exon3			TACCTGCGGGCCT	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.259C>T	chr15.hg19:g.43668752C>T	ENSP00000260383:p.Arg87Trp	140.0	0.0	918	118.0	42.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	hg19		.	.	.	.	.	.	.	.	.	.	c	21.2	4.112382	0.77210	.	.	ENSG00000137822	ENST00000260383	T	0.09255	3.0	5.38	2.89	0.33648	.	0.000000	0.85682	D	0.000000	T	0.28928	0.0718	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.988	T	0.03608	-1.1020	10	0.72032	D	0.01	-15.6209	12.7941	0.57551	0.5737:0.4263:0.0:0.0	.	87;87	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	W	87	ENSP00000260383:R87W	ENSP00000260383:R87W	R	+	1	2	TUBGCP4	41456044	1.000000	0.71417	0.938000	0.37757	0.991000	0.79684	4.186000	0.58337	0.993000	0.38866	-0.259000	0.10710	CGG	.	C|0.999;A|0.001		0.493	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444	
MAP1A	4130	hgsc.bcm.edu	37	15	43820753	43820753	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:43820753G>A	ENST00000300231.5	+	4	7532	c.7082G>A	c.(7081-7083)gGc>gAc	p.G2361D	MAP1A_ENST00000382031.1_Missense_Mutation_p.G2599D|MAP1A_ENST00000399453.1_Missense_Mutation_p.G2361D			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2361					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GCAGCCAATGGCCCAACTGAA	0.637																																					p.G2361D		Atlas-SNP	.											.	MAP1A	189	.	0			c.G7082A						.						31.0	35.0	33.0					15																	43820753		2002	4155	6157	SO:0001583	missense	4130	exon4			CCAATGGCCCAAC	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.7082G>A	chr15.hg19:g.43820753G>A	ENSP00000300231:p.Gly2361Asp	73.0	0.0		69.0	28.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.251906	0.22880	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01705	4.68;4.68;4.68	4.59	4.59	0.56863	.	0.000000	0.34603	N	0.003828	T	0.04407	0.0121	L	0.36672	1.1	0.42855	D	0.994096	D	0.56521	0.976	P	0.53006	0.715	T	0.51513	-0.8696	10	0.72032	D	0.01	-12.0978	17.5779	0.87956	0.0:0.0:1.0:0.0	.	2361	P78559	MAP1A_HUMAN	D	2599;2361;2361	ENSP00000371462:G2599D;ENSP00000382380:G2361D;ENSP00000300231:G2361D	ENSP00000300231:G2361D	G	+	2	0	MAP1A	41608045	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	4.715000	0.61909	2.392000	0.81423	0.561000	0.74099	GGC	.	.		0.637	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
DUOXA1	90527	hgsc.bcm.edu	37	15	45413420	45413420	+	Splice_Site	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:45413420C>T	ENST00000560572.1	-	3	211		c.e3-1		DUOXA1_ENST00000430224.2_Intron|DUOXA1_ENST00000558996.1_Intron|DUOXA1_ENST00000559014.1_Splice_Site|DUOXA1_ENST00000267803.4_Splice_Site|DUOXA1_ENST00000558422.1_Intron	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1						hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		AAATTCACAGCTGTGGTTGGG	0.493																																					.		Atlas-SNP	.											.	DUOXA1	32	.	0			c.206-1G>A						.						88.0	69.0	76.0					15																	45413420		2198	4298	6496	SO:0001630	splice_region_variant	90527	exon7			TCACAGCTGTGGT	BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.206-1G>A	chr15.hg19:g.45413420C>T		148.0	0.0		131.0	24.0	NM_001276264	Q8N6K9|Q96MI4	Splice_Site	SNP	ENST00000560572.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.2	3.944379	0.73672	.	.	ENSG00000140254	ENST00000267803	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7142	0.88331	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DUOXA1	43200712	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	6.980000	0.76160	2.674000	0.91012	0.650000	0.86243	.	.	.		0.493	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565	Intron
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695622	45695622	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:45695622C>A	ENST00000305560.6	+	1	1094	c.995C>A	c.(994-996)gCc>gAc	p.A332D	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.A332D|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	332						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		CTGGACGGCGCCAGTGGGGAC	0.667																																					p.A332D		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C995A						.						22.0	27.0	25.0					15																	45695622		2194	4287	6481	SO:0001583	missense	79029	exon1			ACGGCGCCAGTGG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.995C>A	chr15.hg19:g.45695622C>A	ENSP00000305494:p.Ala332Asp	121.0	0.0		127.0	63.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	C	10.78	1.446875	0.25987	.	.	ENSG00000171763	ENST00000305560	D	0.94862	-3.54	4.55	2.22	0.28083	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.840508	0.10929	N	0.618658	D	0.92241	0.7539	L	0.50333	1.59	0.09310	N	1	P	0.41080	0.737	B	0.42851	0.4	D	0.84275	0.0491	10	0.87932	D	0	-36.6425	7.7622	0.28959	0.0:0.1833:0.0:0.8167	.	332	Q9BVQ7	SPA5L_HUMAN	D	332	ENSP00000305494:A332D	ENSP00000305494:A332D	A	+	2	0	SPATA5L1	43482914	0.746000	0.28272	0.011000	0.14972	0.041000	0.13682	3.620000	0.54203	0.274000	0.22072	-0.323000	0.08544	GCC	.	.		0.667	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
CEP152	22995	hgsc.bcm.edu	37	15	49030737	49030737	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:49030737G>A	ENST00000380950.2	-	27	5029	c.4842C>T	c.(4840-4842)tcC>tcT	p.S1614S	CEP152_ENST00000399334.3_Silent_p.S1558S	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1614					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		AAAGATAACCGGATGGTGAAA	0.378																																					p.S1614S		Atlas-SNP	.											.	CEP152	145	.	0			c.C4842T						.						100.0	99.0	99.0					15																	49030737		1904	4130	6034	SO:0001819	synonymous_variant	22995	exon27			ATAACCGGATGGT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.4842C>T	chr15.hg19:g.49030737G>A		102.0	0.0		122.0	38.0	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.		0.378	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
GALK2	2585	hgsc.bcm.edu	37	15	49584596	49584596	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:49584596A>T	ENST00000560031.1	+	8	1136	c.829A>T	c.(829-831)Att>Ttt	p.I277F	GALK2_ENST00000396509.2_Missense_Mutation_p.I253F|GALK2_ENST00000559454.1_Missense_Mutation_p.I253F|GALK2_ENST00000544523.1_Missense_Mutation_p.I253F|GALK2_ENST00000543495.1_Missense_Mutation_p.I148F|GALK2_ENST00000561014.1_3'UTR|GALK2_ENST00000327171.3_Missense_Mutation_p.I266F			Q01415	GALK2_HUMAN	galactokinase 2	277					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		TAAACTAGGGATTAGTCTAGA	0.463																																					p.I277F		Atlas-SNP	.											.	GALK2	78	.	0			c.A829T						.						125.0	131.0	129.0					15																	49584596		2196	4295	6491	SO:0001583	missense	2585	exon8			CTAGGGATTAGTC		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.829A>T	chr15.hg19:g.49584596A>T	ENSP00000453129:p.Ile277Phe	121.0	0.0		128.0	44.0	NM_002044	Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	hg19	CCDS42034.1	.	.	.	.	.	.	.	.	.	.	A	5.621	0.299216	0.10622	.	.	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000543495;ENST00000544523	D;T;D	0.85702	-2.02;-0.49;-2.02	5.45	-2.76	0.05896	.	0.416052	0.28653	N	0.014597	T	0.67618	0.2912	L	0.29908	0.895	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.50448	-0.8827	10	0.28530	T	0.3	-32.7812	2.0306	0.03528	0.2066:0.1023:0.4838:0.2072	.	277;266	Q01415;Q7Z4Q4	GALK2_HUMAN;.	F	266;277;148;253	ENSP00000316632:I266F;ENSP00000443220:I148F;ENSP00000440312:I253F	ENSP00000316632:I266F	I	+	1	0	GALK2	47371888	0.639000	0.27234	0.057000	0.19452	0.120000	0.20174	0.644000	0.24766	-0.471000	0.06891	-1.223000	0.01593	ATT	.	.		0.463	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1		
ATP8B4	79895	hgsc.bcm.edu	37	15	50331023	50331023	+	Missense_Mutation	SNP	G	G	A	rs372854928		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:50331023G>A	ENST00000284509.6	-	6	445	c.304C>T	c.(304-306)Cgc>Tgc	p.R102C	ATP8B4_ENST00000558959.1_5'UTR|ATP8B4_ENST00000559829.1_Missense_Mutation_p.R102C	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	102						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		CTCTTGTGGCGAAACTGAAAA	0.363																																					p.R102C		Atlas-SNP	.											.	ATP8B4	173	.	0			c.C304T						.	G	CYS/ARG	0,4392		0,0,2196	132.0	116.0	121.0		304	5.4	1.0	15		121	1,8587	1.2+/-3.3	0,1,4293	no	missense	ATP8B4	NM_024837.2	180	0,1,6489	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	102/1193	50331023	1,12979	2196	4294	6490	SO:0001583	missense	79895	exon6			TGTGGCGAAACTG	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"""ATPases / P-type"""	13536	protein-coding gene	gene with protein product		609123	"""ATPase, Class I, type 8B, member 4"""			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.304C>T	chr15.hg19:g.50331023G>A	ENSP00000284509:p.Arg102Cys	141.0	0.0		94.0	28.0	NM_024837	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	hg19	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348741	0.82132	0.0	1.16E-4	ENSG00000104043	ENST00000284509	D	0.85861	-2.04	5.39	5.39	0.77823	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.95787	0.8629	H	0.99058	4.415	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.97412	1.0003	10	0.87932	D	0	.	17.0049	0.86390	0.0:0.0:1.0:0.0	.	102	Q8TF62	AT8B4_HUMAN	C	102	ENSP00000284509:R102C	ENSP00000284509:R102C	R	-	1	0	ATP8B4	48118315	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.429000	0.80309	2.690000	0.91761	0.655000	0.94253	CGC	.	.		0.363	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837	
TRPM7	54822	hgsc.bcm.edu	37	15	50884115	50884115	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:50884115T>C	ENST00000313478.7	-	26	4598	c.4317A>G	c.(4315-4317)gcA>gcG	p.A1439A	TRPM7_ENST00000560955.1_Silent_p.A1439A	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1439					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TACCTACAAATGCTCCAAATT	0.323																																					p.A1439A		Atlas-SNP	.											.	TRPM7	145	.	0			c.A4317G						.						78.0	73.0	75.0					15																	50884115		1803	4068	5871	SO:0001819	synonymous_variant	54822	exon26			TACAAATGCTCCA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.4317A>G	chr15.hg19:g.50884115T>C		112.0	0.0		94.0	4.0	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Silent	SNP	ENST00000313478.7	hg19	CCDS42035.1																																																																																			.	.		0.323	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	
ADAM10	102	hgsc.bcm.edu	37	15	58936169	58936169	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:58936169A>G	ENST00000260408.3	-	7	1187	c.744T>C	c.(742-744)agT>agC	p.S248S	ADAM10_ENST00000396140.2_Intron|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000402627.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	248	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		CTTTAACATGACTGGATATCT	0.303																																					p.S248S		Atlas-SNP	.											.	ADAM10	59	.	0			c.T744C						.						99.0	99.0	99.0					15																	58936169		2192	4292	6484	SO:0001819	synonymous_variant	102	exon7			AACATGACTGGAT	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	188	protein-coding gene	gene with protein product		602192	"""a disintegrin and metalloproteinase domain 10"""			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.744T>C	chr15.hg19:g.58936169A>G		100.0	0.0		110.0	5.0	NM_001110	B4DU28|Q10742|Q92650	Silent	SNP	ENST00000260408.3	hg19	CCDS10167.1																																																																																			.	.		0.303	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110	
SLTM	79811	hgsc.bcm.edu	37	15	59175873	59175873	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:59175873C>T	ENST00000380516.2	-	20	3035	c.2948G>A	c.(2947-2949)cGa>cAa	p.R983Q	SLTM_ENST00000536328.1_Missense_Mutation_p.R552Q	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	983					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GTCACCCATTCGCCTCGTATC	0.517																																					p.R983Q		Atlas-SNP	.											.	SLTM	90	.	0			c.G2948A						.						217.0	189.0	198.0					15																	59175873		2192	4292	6484	SO:0001583	missense	79811	exon20			CCCATTCGCCTCG	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"""RNA binding motif (RRM) containing"""	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.2948G>A	chr15.hg19:g.59175873C>T	ENSP00000369887:p.Arg983Gln	133.0	0.0		131.0	58.0	NM_024755	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	hg19	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	C	36	5.607455	0.96626	.	.	ENSG00000137776	ENST00000380516;ENST00000432750;ENST00000536328	T	0.28895	1.59	6.02	6.02	0.97574	.	0.000000	0.49305	D	0.000149	T	0.55016	0.1894	L	0.53249	1.67	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.99	T	0.51718	-0.8670	10	0.87932	D	0	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	983;552	Q9NWH9;A8K5V8	SLTM_HUMAN;.	Q	983;549;552	ENSP00000369887:R983Q	ENSP00000369887:R983Q	R	-	2	0	SLTM	56963165	1.000000	0.71417	0.997000	0.53966	0.911000	0.54048	5.987000	0.70571	2.857000	0.98124	0.650000	0.86243	CGA	.	.		0.517	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755	
C2CD4B	388125	hgsc.bcm.edu	37	15	62456187	62456187	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:62456187C>T	ENST00000380392.3	-	2	1125	c.997G>A	c.(997-999)Gcc>Acc	p.A333T		NM_001007595.2	NP_001007596.2	A6NLJ0	C2C4B_HUMAN	C2 calcium-dependent domain containing 4B	333	C2.					focal adhesion (GO:0005925)|nucleolus (GO:0005730)				skin(1)	1						ACGCGAACGGCCAGGCGGCGC	0.706																																					p.A333T		Atlas-SNP	.											.	C2CD4B	4	.	0			c.G997A						.						7.0	8.0	8.0					15																	62456187		2103	4162	6265	SO:0001583	missense	388125	exon2			GAACGGCCAGGCG	BM023530	CCDS32259.1	15q22.2	2009-09-28	2009-09-28	2009-09-28					33628	protein-coding gene	gene with protein product	"""nuclear localized factor 2"""	610344	"""family with sequence similarity 148, member B"""	FAM148B			Standard	NM_001007595		Approved	NLF2	uc002ahg.2	A6NLJ0		ENST00000380392.3:c.997G>A	chr15.hg19:g.62456187C>T	ENSP00000369755:p.Ala333Thr	69.0	0.0		70.0	28.0	NM_001007595		Missense_Mutation	SNP	ENST00000380392.3	hg19	CCDS32259.1	.	.	.	.	.	.	.	.	.	.	C	8.346	0.829853	0.16749	.	.	ENSG00000205502	ENST00000380392	T	0.78003	-1.14	3.57	1.67	0.24075	.	0.405752	0.25332	N	0.031423	T	0.59569	0.2203	L	0.39147	1.195	0.09310	N	1	B	0.26258	0.145	B	0.29176	0.099	T	0.45279	-0.9272	10	0.02654	T	1	.	3.8123	0.08802	0.1827:0.5529:0.0:0.2644	.	333	A6NLJ0	C2C4B_HUMAN	T	333	ENSP00000369755:A333T	ENSP00000369755:A333T	A	-	1	0	C2CD4B	60243479	0.427000	0.25514	0.997000	0.53966	0.054000	0.15201	0.451000	0.21779	0.326000	0.23384	-1.446000	0.01064	GCC	.	.		0.706	C2CD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416117.1	NM_001007595	
TLN2	83660	hgsc.bcm.edu	37	15	63009820	63009820	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:63009820G>A	ENST00000561311.1	+	23	3039	c.2809G>A	c.(2809-2811)Gcc>Acc	p.A937T	TLN2_ENST00000306829.6_Missense_Mutation_p.A937T			Q9Y4G6	TLN2_HUMAN	talin 2	937	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GACCATCGCCGCCTCCCAGAA	0.567																																					p.A937T		Atlas-SNP	.											.	TLN2	253	.	0			c.G2809A						.						30.0	27.0	28.0					15																	63009820		2203	4295	6498	SO:0001583	missense	83660	exon21			ATCGCCGCCTCCC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.2809G>A	chr15.hg19:g.63009820G>A	ENSP00000453508:p.Ala937Thr	236.0	0.0		224.0	81.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	34	5.344071	0.95807	.	.	ENSG00000171914	ENST00000306829	T	0.70869	-0.52	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.86594	0.5970	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85108	0.0961	10	0.35671	T	0.21	-21.3073	19.9855	0.97347	0.0:0.0:1.0:0.0	.	937	Q9Y4G6	TLN2_HUMAN	T	937	ENSP00000303476:A937T	ENSP00000303476:A937T	A	+	1	0	TLN2	60797112	1.000000	0.71417	0.977000	0.42913	0.626000	0.37791	9.751000	0.98889	2.806000	0.96561	0.655000	0.94253	GCC	.	.		0.567	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
PIF1	80119	hgsc.bcm.edu	37	15	65111379	65111379	+	Silent	SNP	C	C	T	rs374363106		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:65111379C>T	ENST00000268043.4	-	9	1471	c.1377G>A	c.(1375-1377)ctG>ctA	p.L459L	PIF1_ENST00000333425.6_Silent_p.L459L|PIF1_ENST00000559239.1_Silent_p.L459L					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GGGTACTGGCCAGCTCAGGGT	0.542																																					p.L459L		Atlas-SNP	.											.	PIF1	43	.	0			c.G1377A						.	C		0,4404		0,0,2202	45.0	41.0	43.0		1377	-5.4	0.3	15		43	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PIF1	NM_025049.2		0,1,6500	TT,TC,CC		0.0116,0.0,0.0077		459/642	65111379	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	80119	exon9			ACTGGCCAGCTCA	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1377G>A	chr15.hg19:g.65111379C>T		221.0	0.0		210.0	91.0	NM_025049		Silent	SNP	ENST00000268043.4	hg19	CCDS10195.2																																																																																			.	.		0.542	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049	
MYO9A	4649	hgsc.bcm.edu	37	15	72338646	72338646	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:72338646T>A	ENST00000356056.5	-	2	731	c.259A>T	c.(259-261)Atg>Ttg	p.M87L	MYO9A_ENST00000444904.1_Missense_Mutation_p.M87L|RNU2-65P_ENST00000410162.1_RNA|MYO9A_ENST00000564571.1_Missense_Mutation_p.M87L|MYO9A_ENST00000424560.1_Missense_Mutation_p.M87L|MYO9A_ENST00000566885.1_Intron|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	87	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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						GGCCACAGCATCATTCGCTGA	0.428																																					p.M87L		Atlas-SNP	.											.	MYO9A	203	.	0			c.A259T						.						85.0	83.0	84.0					15																	72338646		2199	4297	6496	SO:0001583	missense	4649	exon2			ACAGCATCATTCG	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.259A>T	chr15.hg19:g.72338646T>A	ENSP00000348349:p.Met87Leu	95.0	0.0		108.0	45.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	t	10.86	1.469781	0.26423	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448	T;T;T	0.14640	2.49;2.49;2.49	5.33	4.18	0.49190	Ras-association (3);	.	.	.	.	T	0.08358	0.0208	N	0.21097	0.63	0.54753	D	0.999984	B;B;B	0.23316	0.003;0.003;0.083	B;B;B	0.24394	0.002;0.005;0.053	T	0.09143	-1.0688	9	0.02654	T	1	.	12.2501	0.54593	0.0:0.0:0.142:0.858	.	87;87;87	B2RTY4-3;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	L	87	ENSP00000348349:M87L;ENSP00000399162:M87L;ENSP00000398250:M87L	ENSP00000261864:M87L	M	-	1	0	MYO9A	70125700	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.304000	0.51866	0.832000	0.34804	0.372000	0.22366	ATG	.	.		0.428	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
ISLR2	57611	hgsc.bcm.edu	37	15	74426101	74426101	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:74426101G>A	ENST00000361742.3	+	4	1775	c.1006G>A	c.(1006-1008)Gca>Aca	p.A336T	ISLR2_ENST00000419208.1_Missense_Mutation_p.A336T|ISLR2_ENST00000453268.2_Missense_Mutation_p.A336T|ISLR2_ENST00000445793.1_Missense_Mutation_p.A336T|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565159.1_Missense_Mutation_p.A336T|ISLR2_ENST00000435464.1_Missense_Mutation_p.A336T|ISLR2_ENST00000565540.1_Missense_Mutation_p.A336T	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	336	Ig-like.				positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A336P(1)		breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						CCTGGCCCTCGCAAATGGCTC	0.642																																					p.A336T		Atlas-SNP	.											ISLR2,NS,carcinoma,0,1	ISLR2	78	.	1	Substitution - Missense(1)	lung(1)	c.G1006A						.						21.0	22.0	22.0					15																	74426101		2198	4297	6495	SO:0001583	missense	57611	exon4			GCCCTCGCAAATG		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1006G>A	chr15.hg19:g.74426101G>A	ENSP00000355402:p.Ala336Thr	122.0	0.0		113.0	47.0	NM_001130138	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	hg19	CCDS10259.1	.	.	.	.	.	.	.	.	.	.	G	1.031	-0.681696	0.03353	.	.	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000419208	T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7	4.7	0.893	0.19236	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.591333	0.16795	N	0.199204	T	0.11580	0.0282	N	0.21240	0.645	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.25187	-1.0139	10	0.15499	T	0.54	.	1.9626	0.03389	0.3129:0.1302:0.4102:0.1467	.	336	Q6UXK2	ISLR2_HUMAN	T	336	ENSP00000403244:A336T;ENSP00000355402:A336T;ENSP00000411443:A336T;ENSP00000411834:A336T;ENSP00000408872:A336T	ENSP00000355402:A336T	A	+	1	0	ISLR2	72213154	0.000000	0.05858	0.022000	0.16811	0.534000	0.34807	0.182000	0.16900	0.290000	0.22444	0.195000	0.17529	GCA	.	.		0.642	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851	
EDC3	80153	hgsc.bcm.edu	37	15	74932931	74932931	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:74932931A>G	ENST00000315127.4	-	5	1031	c.850T>C	c.(850-852)Tat>Cat	p.Y284H	EDC3_ENST00000426797.3_Missense_Mutation_p.Y284H|EDC3_ENST00000568176.1_Missense_Mutation_p.Y284H	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	284	Required for interaction with DDX6. {ECO:0000250}.|YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				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)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						TGCAGCTCATAGGAAATACTT	0.498																																					p.Y284H		Atlas-SNP	.											.	EDC3	32	.	0			c.T850C						.						88.0	73.0	78.0					15																	74932931		2197	4296	6493	SO:0001583	missense	80153	exon6			GCTCATAGGAAAT	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"""yjeF domain containing (E.coli)"", ""LSM16 homolog (EDC3, S. cerevisiae)"", ""enhancer of mRNA decapping 3 homolog (S. cerevisiae)"""	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.850T>C	chr15.hg19:g.74932931A>G	ENSP00000320503:p.Tyr284His	112.0	0.0		114.0	43.0	NM_001142444	B3KPH0|D3DW61|Q9H797	Missense_Mutation	SNP	ENST00000315127.4	hg19	CCDS10267.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.219139	0.58560	.	.	ENSG00000179151	ENST00000315127;ENST00000426797	T;T	0.42900	0.96;0.96	5.82	5.82	0.92795	YjeF-related protein, N-terminal (2);	0.056460	0.64402	D	0.000001	T	0.41743	0.1172	L	0.38175	1.15	0.80722	D	1	B	0.33940	0.433	B	0.43386	0.418	T	0.18745	-1.0327	10	0.15952	T	0.53	-20.8694	15.3675	0.74535	1.0:0.0:0.0:0.0	.	284	Q96F86	EDC3_HUMAN	H	284	ENSP00000320503:Y284H;ENSP00000401343:Y284H	ENSP00000320503:Y284H	Y	-	1	0	EDC3	72719984	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	8.589000	0.90817	2.225000	0.72522	0.533000	0.62120	TAT	.	.		0.498	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083	
PEAK1	79834	hgsc.bcm.edu	37	15	77471265	77471265	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:77471265C>T	ENST00000560626.2	-	4	3479	c.3004G>A	c.(3004-3006)Gtg>Atg	p.V1002M	PEAK1_ENST00000312493.4_Missense_Mutation_p.V1002M|PEAK1_ENST00000558305.1_Missense_Mutation_p.V1002M			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1002					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTCTGATCCACACTGAGCTGG	0.527																																					p.V1002M		Atlas-SNP	.											.	.	.	.	0			c.G3004A						.						135.0	134.0	135.0					15																	77471265		2118	4233	6351	SO:0001583	missense	0	exon5			GATCCACACTGAG		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3004G>A	chr15.hg19:g.77471265C>T	ENSP00000452796:p.Val1002Met	55.0	0.0		76.0	29.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.709952	0.30322	.	.	ENSG00000173517	ENST00000312493	T	0.70282	-0.47	5.75	2.86	0.33363	.	0.370320	0.24479	N	0.038179	T	0.48589	0.1508	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.40059	-0.9583	10	0.56958	D	0.05	-6.477	5.22	0.15364	0.1309:0.5924:0.0:0.2766	.	1002	Q9H792	PEAK1_HUMAN	M	1002	ENSP00000309230:V1002M	ENSP00000309230:V1002M	V	-	1	0	AC087465.1	75258320	0.000000	0.05858	0.174000	0.22961	0.915000	0.54546	0.023000	0.13533	0.794000	0.33899	0.655000	0.94253	GTG	.	.		0.527	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
AP3B2	8120	hgsc.bcm.edu	37	15	83350208	83350208	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:83350208C>T	ENST00000261722.3	-	5	692	c.485G>A	c.(484-486)cGg>cAg	p.R162Q	AP3B2_ENST00000535359.1_Missense_Mutation_p.R162Q|AP3B2_ENST00000535348.1_Missense_Mutation_p.R130Q|RP11-752G15.3_ENST00000560650.1_RNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	162					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			AGCTGTTTTCCGCACATAGGG	0.582																																					p.R162Q		Atlas-SNP	.											.	AP3B2	103	.	0			c.G485A						.						103.0	105.0	105.0					15																	83350208		2073	4201	6274	SO:0001583	missense	8120	exon5			GTTTTCCGCACAT	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.485G>A	chr15.hg19:g.83350208C>T	ENSP00000261722:p.Arg162Gln	76.0	0.0		80.0	38.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	hg19	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	C	37	6.151902	0.97329	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359;ENST00000541693	T;T;T;T	0.25912	1.77;1.77;1.77;1.77	5.09	5.09	0.68999	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.058253	0.64402	D	0.000002	T	0.68723	0.3032	H	0.97806	4.08	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.994;1.0;1.0	T	0.81824	-0.0755	10	0.87932	D	0	-16.9628	18.6878	0.91571	0.0:1.0:0.0:0.0	.	130;162;162	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	Q	162;130;162;118	ENSP00000261722:R162Q;ENSP00000438721:R130Q;ENSP00000440984:R162Q;ENSP00000441961:R118Q	ENSP00000261722:R162Q	R	-	2	0	AP3B2	81147262	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.627000	0.83176	2.642000	0.89623	0.563000	0.77884	CGG	.	.		0.582	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1		
ALPK3	57538	hgsc.bcm.edu	37	15	85403072	85403072	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:85403072A>G	ENST00000258888.5	+	8	4804	c.4637A>G	c.(4636-4638)tAt>tGt	p.Y1546C		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1546	Ig-like 2.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			TGCGGTGTGTATCGGTGCACC	0.687																																					p.Y1546C		Atlas-SNP	.											.	ALPK3	289	.	0			c.A4637G						.						48.0	45.0	46.0					15																	85403072		2203	4299	6502	SO:0001583	missense	57538	exon8			GTGTGTATCGGTG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4637A>G	chr15.hg19:g.85403072A>G	ENSP00000258888:p.Tyr1546Cys	95.0	0.0		82.0	31.0	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	hg19	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.633489	0.87660	.	.	ENSG00000136383	ENST00000258888	T	0.79247	-1.25	5.52	5.52	0.82312	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.87180	0.6113	M	0.76170	2.325	0.54753	D	0.999987	D	0.89917	1.0	D	0.87578	0.998	D	0.88634	0.3171	10	0.87932	D	0	-8.3972	13.5898	0.61953	1.0:0.0:0.0:0.0	.	1546	Q96L96	ALPK3_HUMAN	C	1546	ENSP00000258888:Y1546C	ENSP00000258888:Y1546C	Y	+	2	0	ALPK3	83204076	1.000000	0.71417	0.853000	0.33588	0.986000	0.74619	6.667000	0.74451	2.101000	0.63845	0.460000	0.39030	TAT	.	.		0.687	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
MFGE8	4240	hgsc.bcm.edu	37	15	89449105	89449105	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:89449105C>T	ENST00000566497.1	-	5	629	c.568G>A	c.(568-570)Gcg>Acg	p.A190T	MFGE8_ENST00000539437.1_Missense_Mutation_p.A182T|MFGE8_ENST00000268151.7_Missense_Mutation_p.A190T|MFGE8_ENST00000268150.8_Missense_Mutation_p.A190T|MFGE8_ENST00000542878.1_Missense_Mutation_p.A146T|MFGE8_ENST00000559997.1_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	190	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					ACATGCACCGCGTTTTTGTTC	0.562																																					p.A190T		Atlas-SNP	.											.	MFGE8	60	.	0			c.G568A						.						136.0	121.0	126.0					15																	89449105		2200	4299	6499	SO:0001583	missense	4240	exon5			GCACCGCGTTTTT	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.568G>A	chr15.hg19:g.89449105C>T	ENSP00000456281:p.Ala190Thr	163.0	0.0		140.0	56.0	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	hg19	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	C	2.803	-0.248735	0.05867	.	.	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437;ENST00000542878	D;D;D;T	0.96685	-4.09;-4.09;-4.09;-1.45	4.97	-0.939	0.10408	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.692542	0.16168	N	0.226449	T	0.77631	0.4159	N	0.00098	-2.145	0.09310	N	1	B;B;B;B;B	0.24258	0.048;0.1;0.036;0.002;0.017	B;B;B;B;B	0.24006	0.018;0.05;0.01;0.004;0.01	T	0.76683	-0.2869	10	0.02654	T	1	-12.7145	10.1991	0.43073	0.0:0.4537:0.0:0.5463	.	182;146;182;190;190	B3KTQ2;F5GZN3;F5H7N9;Q08431-3;Q08431	.;.;.;.;MFGM_HUMAN	T	190;190;182;146	ENSP00000268150:A190T;ENSP00000268151:A190T;ENSP00000442386:A182T;ENSP00000444332:A146T	ENSP00000268150:A190T	A	-	1	0	MFGE8	87250109	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.141000	0.10327	-0.227000	0.09884	-1.093000	0.02169	GCG	.	.		0.562	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
ABHD2	11057	hgsc.bcm.edu	37	15	89698708	89698708	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:89698708A>G	ENST00000352732.5	+	5	1001	c.481A>G	c.(481-483)Aac>Gac	p.N161D	ABHD2_ENST00000565973.1_Missense_Mutation_p.N161D|ABHD2_ENST00000355100.3_Missense_Mutation_p.N161D	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	161					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					CGCCGTGCTGAACCACCTGGG	0.527																																					p.N161D	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	0			c.A481G						.						161.0	133.0	142.0					15																	89698708		2200	4299	6499	SO:0001583	missense	11057	exon9			GTGCTGAACCACC	X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"""Abhydrolase domain containing"""	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.481A>G	chr15.hg19:g.89698708A>G	ENSP00000268129:p.Asn161Asp	143.0	0.0		136.0	68.0	NM_007011	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	hg19	CCDS10348.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.967918	0.92855	.	.	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.25250	1.81;1.81	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.28863	0.0716	L	0.31207	0.915	0.80722	D	1	B	0.31893	0.345	B	0.41813	0.367	T	0.10706	-1.0618	10	0.56958	D	0.05	-1.0008	15.8956	0.79333	1.0:0.0:0.0:0.0	.	161	P08910	ABHD2_HUMAN	D	161	ENSP00000268129:N161D;ENSP00000347217:N161D	ENSP00000268129:N161D	N	+	1	0	ABHD2	87499712	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.183000	0.94887	2.198000	0.70561	0.533000	0.62120	AAC	.	.		0.527	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2		
MESP2	145873	hgsc.bcm.edu	37	15	90320134	90320134	+	Silent	SNP	A	A	G	rs56192595|rs200021459|rs199821487	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:90320134A>G	ENST00000341735.3	+	1	546	c.546A>G	c.(544-546)caA>caG	p.Q182Q	MESP2_ENST00000558723.1_Intron|MESP2_ENST00000560219.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	182	13 X 2 AA tandem repeats of G-Q.				mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q198_G205delQGQGQGQG(1)		kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	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)			ggcaggggcaagggcaggggc	0.786																																					p.Q182Q		Atlas-SNP	.											MESP2,NS,carcinoma,0,1	MESP2	20	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.A546G						.						3.0	3.0	3.0					15																	90320134		1211	2942	4153	SO:0001819	synonymous_variant	145873	exon1			GGGGCAAGGGCAG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"""Basic helix-loop-helix proteins"""	29659	protein-coding gene	gene with protein product		605195	"""mesoderm posterior 2 homolog (mouse)"""			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.546A>G	chr15.hg19:g.90320134A>G		50.0	1.0		20.0	4.0	NM_001039958	Q7RTU2	Silent	SNP	ENST00000341735.3	hg19	CCDS42078.1																																																																																			.	.		0.786	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261	
ASB7	140460	hgsc.bcm.edu	37	15	101152549	101152549	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:101152549G>A	ENST00000332783.7	+	4	913	c.128G>A	c.(127-129)cGa>cAa	p.R43Q	ASB7_ENST00000558747.1_Missense_Mutation_p.R43Q|ASB7_ENST00000343276.4_Missense_Mutation_p.R43Q	NM_198243.2	NP_937886.1	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box containing 7	43					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)	16	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)			CCGAATGGCCGAGATGCGAAT	0.522																																					p.R43Q		Atlas-SNP	.											.	ASB7	32	.	0			c.G128A						.						138.0	135.0	136.0					15																	101152549		2203	4300	6503	SO:0001583	missense	140460	exon4			ATGGCCGAGATGC		CCDS10387.1, CCDS10388.1	15q26.3	2013-01-10	2011-01-25		ENSG00000183475	ENSG00000183475		"""Ankyrin repeat domain containing"""	17182	protein-coding gene	gene with protein product		615052	"""ankyrin repeat and SOCS box-containing 7"""				Standard	NM_024708		Approved		uc002bwk.3	Q9H672	OTTHUMG00000149868	ENST00000332783.7:c.128G>A	chr15.hg19:g.101152549G>A	ENSP00000328327:p.Arg43Gln	149.0	0.0		177.0	76.0	NM_024708	A8K1E5|Q6GSJ6|Q7Z4S3	Missense_Mutation	SNP	ENST00000332783.7	hg19	CCDS10387.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.719202	0.89205	.	.	ENSG00000183475	ENST00000332783;ENST00000343276	T;T	0.65549	-0.16;0.61	5.9	5.9	0.94986	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.70430	0.3223	L	0.28192	0.835	0.80722	D	1	D;B	0.63046	0.992;0.447	D;B	0.70227	0.968;0.018	T	0.68674	-0.5346	10	0.41790	T	0.15	-8.6224	20.2822	0.98520	0.0:0.0:1.0:0.0	.	43;43	Q9H672;Q9H672-2	ASB7_HUMAN;.	Q	43	ENSP00000328327:R43Q;ENSP00000339819:R43Q	ENSP00000328327:R43Q	R	+	2	0	ASB7	98970072	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.296000	0.96104	2.806000	0.96561	0.655000	0.94253	CGA	.	.		0.522	ASB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313617.1	NM_024708	
CAPN15	6650	hgsc.bcm.edu	37	16	599385	599385	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:599385C>T	ENST00000219611.2	+	6	2119	c.1756C>T	c.(1756-1758)Cgg>Tgg	p.R586W	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	586	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTACCAGGTGCGGCTGTGCAA	0.701																																					p.R586W		Atlas-SNP	.											.	SOLH	47	.	0			c.C1756T						.						26.0	18.0	21.0					16																	599385		2171	4272	6443	SO:0001583	missense	6650	exon6			CAGGTGCGGCTGT	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.1756C>T	chr16.hg19:g.599385C>T	ENSP00000219611:p.Arg586Trp	50.0	0.0		56.0	13.0	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	c	21.8	4.205289	0.79127	.	.	ENSG00000103326	ENST00000219611	D	0.89552	-2.53	5.04	5.04	0.67666	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.94748	0.8305	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95469	0.8550	10	0.87932	D	0	.	16.9735	0.86306	0.0:1.0:0.0:0.0	.	586	O75808	CAN15_HUMAN	W	586	ENSP00000219611:R586W	ENSP00000219611:R586W	R	+	1	2	SOLH	539386	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	5.403000	0.66338	2.347000	0.79759	0.556000	0.70494	CGG	.	.		0.701	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
SOX8	30812	hgsc.bcm.edu	37	16	1033875	1033875	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:1033875G>A	ENST00000293894.3	+	2	685	c.570G>A	c.(568-570)gcG>gcA	p.A190A	RP11-161M6.2_ENST00000565467.1_lincRNA	NM_014587.3	NP_055402.2	P57073	SOX8_HUMAN	SRY (sex determining region Y)-box 8	190					adipose tissue development (GO:0060612)|astrocyte fate commitment (GO:0060018)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|enteric nervous system development (GO:0048484)|fat cell differentiation (GO:0045444)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of gliogenesis (GO:0014015)|positive regulation of kidney development (GO:0090184)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone levels (GO:0010817)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|ureter morphogenesis (GO:0072197)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|lung(5)|prostate(2)|skin(1)	10		Hepatocellular(780;0.00308)				ACTCGGGCGCGGAGCTGGGAC	0.682																																					p.A190A		Atlas-SNP	.											.	SOX8	29	.	0			c.G570A						.						26.0	27.0	27.0					16																	1033875		2194	4295	6489	SO:0001819	synonymous_variant	30812	exon2			GGGCGCGGAGCTG	AF164104	CCDS10428.1	16p13.3	2008-05-23			ENSG00000005513	ENSG00000005513		"""SRY (sex determining region Y)-boxes"""	11203	protein-coding gene	gene with protein product		605923				10662550, 10684944	Standard	NM_014587		Approved		uc002ckn.3	P57073	OTTHUMG00000122101	ENST00000293894.3:c.570G>A	chr16.hg19:g.1033875G>A		225.0	0.0		209.0	94.0	NM_014587	Q9NZW2	Silent	SNP	ENST00000293894.3	hg19	CCDS10428.1																																																																																			.	.		0.682	SOX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242867.1		
UNKL	64718	hgsc.bcm.edu	37	16	1464671	1464671	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:1464671C>G	ENST00000389221.4	-	1	21	c.22G>C	c.(22-24)Gcg>Ccg	p.A8P	UNKL_ENST00000397462.1_Missense_Mutation_p.A8P|LA16c-312E8.2_ENST00000568554.1_RNA|UNKL_ENST00000503648.1_5'UTR|UNKL_ENST00000508903.2_Missense_Mutation_p.A8P|UNKL_ENST00000301712.5_Missense_Mutation_p.A8P	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	8	Poly-Ala.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				GCCGCTGCCGCCGCTTTCGAA	0.751																																					p.A8P		Atlas-SNP	.											.	UNKL	46	.	0			c.G22C						.						3.0	4.0	4.0					16																	1464671		1671	3626	5297	SO:0001583	missense	64718	exon1			CTGCCGCCGCTTT	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"""Zinc fingers, CCCH-type domain containing"""	14184	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 28"", ""unkempt homolog (Drosophila)-like"""	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.22G>C	chr16.hg19:g.1464671C>G	ENSP00000373873:p.Ala8Pro	62.0	0.0		81.0	33.0	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Missense_Mutation	SNP	ENST00000389221.4	hg19	CCDS53981.1	.	.	.	.	.	.	.	.	.	.	C	8.247	0.808071	0.16467	.	.	ENSG00000059145	ENST00000389221;ENST00000508903;ENST00000397462;ENST00000301712	T	0.65549	-0.16	2.14	1.14	0.20703	.	0.318901	0.20036	U	0.100605	T	0.49898	0.1584	N	0.08118	0	0.23277	N	0.997991	D	0.62365	0.991	D	0.63703	0.917	T	0.30592	-0.9973	10	0.33940	T	0.23	.	3.8286	0.08865	0.0:0.768:0.0:0.232	.	8	Q9H9P5-5	.	P	8	ENSP00000373873:A8P	ENSP00000301712:A8P	A	-	1	0	UNKL	1404672	0.106000	0.21978	1.000000	0.80357	0.746000	0.42486	0.351000	0.20096	1.133000	0.42147	0.185000	0.17295	GCG	.	.		0.751	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125	
NTHL1	4913	hgsc.bcm.edu	37	16	2093714	2093714	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:2093714T>C	ENST00000219066.1	-	4	581	c.563A>G	c.(562-564)tAc>tGc	p.Y188C	NTHL1_ENST00000562951.1_5'UTR	NM_002528.5	NP_002519.1			nth endonuclease III-like 1 (E. coli)											lung(1)	1						CTGCTTGATGTATTTCACCTT	0.637								Base excision repair (BER), DNA glycosylases																													p.Y188C		Atlas-SNP	.											.	NTHL1	24	.	0			c.A563G						.						93.0	69.0	77.0					16																	2093714		2196	4299	6495	SO:0001583	missense	4913	exon4			TTGATGTATTTCA	U81285	CCDS10457.1	16p13.3	2008-02-05	2001-11-28		ENSG00000065057	ENSG00000065057			8028	protein-coding gene	gene with protein product		602656	"""nth (E.coli endonuclease III)-like 1"""			9045706, 8990169	Standard	NM_002528		Approved	NTH1, OCTS3	uc002col.1	P78549	OTTHUMG00000128744	ENST00000219066.1:c.563A>G	chr16.hg19:g.2093714T>C	ENSP00000219066:p.Tyr188Cys	46.0	0.0		35.0	15.0	NM_002528		Missense_Mutation	SNP	ENST00000219066.1	hg19	CCDS10457.1	.	.	.	.	.	.	.	.	.	.	T	16.58	3.161675	0.57368	.	.	ENSG00000065057	ENST00000219066	D	0.88975	-2.45	5.32	-0.18	0.13295	HhH-GPD domain (2);DNA glycosylase (2);	0.256859	0.40144	N	0.001163	D	0.93301	0.7865	H	0.97587	4.035	0.58432	D	0.999999	P;P	0.39022	0.655;0.655	P;P	0.45428	0.48;0.48	D	0.92323	0.5867	10	0.72032	D	0.01	-8.9262	10.9829	0.47506	0.41:0.0:0.0:0.59	.	188;188	E5KTI5;P78549	.;NTHL1_HUMAN	C	188	ENSP00000219066:Y188C	ENSP00000219066:Y188C	Y	-	2	0	NTHL1	2033715	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	1.346000	0.33964	-0.024000	0.13941	0.402000	0.26972	TAC	.	.		0.637	NTHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250656.1	NM_002528	
SRRM2	23524	hgsc.bcm.edu	37	16	2818134	2818134	+	Silent	SNP	G	G	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:2818134G>C	ENST00000301740.8	+	11	8154	c.7605G>C	c.(7603-7605)tcG>tcC	p.S2535S	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2535	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						GTtcctcctcgtcgtcgtcgt	0.617																																					p.S2535S		Atlas-SNP	.											SRRM2,bladder,carcinoma,+1,1	SRRM2	263	.	0			c.G7605C						.						61.0	54.0	56.0					16																	2818134		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			CTCCTCGTCGTCG	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.7605G>C	chr16.hg19:g.2818134G>C		43.0	0.0		60.0	16.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.617	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
MEFV	4210	hgsc.bcm.edu	37	16	3293875	3293875	+	Missense_Mutation	SNP	C	C	T	rs375665850		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:3293875C>T	ENST00000219596.1	-	9	1816	c.1777G>A	c.(1777-1779)Gct>Act	p.A593T	MEFV_ENST00000339854.4_Missense_Mutation_p.A413T|MEFV_ENST00000536379.1_Missense_Mutation_p.A382T|MEFV_ENST00000541159.1_Missense_Mutation_p.R440H	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	593	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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						TGTGCCTGAGCGCCAATCAGC	0.512																																					p.A593T		Atlas-SNP	.											.	MEFV	170	.	0			c.G1777A						.						48.0	50.0	49.0					16																	3293875		2197	4300	6497	SO:0001583	missense	4210	exon9			CCTGAGCGCCAAT	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.1777G>A	chr16.hg19:g.3293875C>T	ENSP00000219596:p.Ala593Thr	216.0	0.0		194.0	72.0	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Missense_Mutation	SNP	ENST00000219596.1	hg19	CCDS10498.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.47|12.47	1.948409|1.948409	0.34377|0.34377	.|.	.|.	ENSG00000103313|ENSG00000103313	ENST00000545159;ENST00000219596;ENST00000339854;ENST00000536379|ENST00000541159	T;T;T|T	0.64260|0.63417	-0.09;0.34;0.34|-0.04	4.92|4.92	4.92|4.92	0.64577|0.64577	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);|.	0.723385|.	0.12438|.	N|.	0.468915|.	T|T	0.68595|0.68595	0.3018|0.3018	M|M	0.63843|0.63843	1.955|1.955	0.21184|0.21184	N|N	0.999767|0.999767	D|.	0.89917|.	1.0|.	P|.	0.56163|.	0.793|.	T|T	0.60831|0.60831	-0.7185|-0.7185	10|7	0.37606|0.38643	T|T	0.19|0.18	-36.0955|-36.0955	13.8235|13.8235	0.63338|0.63338	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	593|.	O15553|.	MEFV_HUMAN|.	T|H	593;593;413;382|440	ENSP00000219596:A593T;ENSP00000339639:A413T;ENSP00000445079:A382T|ENSP00000438711:R440H	ENSP00000219596:A593T|ENSP00000438711:R440H	A|R	-|-	1|2	0|0	MEFV|MEFV	3233876|3233876	0.805000|0.805000	0.28982|0.28982	0.573000|0.573000	0.28510|0.28510	0.039000|0.039000	0.13416|0.13416	2.355000|2.355000	0.44107|0.44107	2.725000|2.725000	0.93324|0.93324	0.655000|0.655000	0.94253|0.94253	GCT|CGC	.	.		0.512	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
TRAP1	10131	hgsc.bcm.edu	37	16	3712966	3712966	+	Missense_Mutation	SNP	C	C	T	rs549044388	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:3712966C>T	ENST00000246957.5	-	15	1799	c.1711G>A	c.(1711-1713)Gcc>Acc	p.A571T	TRAP1_ENST00000538171.1_Missense_Mutation_p.A518T|DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000575671.1_Missense_Mutation_p.A362T|DNASE1_ENST00000575152.1_3'UTR	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	571					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				AGGCACTCGGCGGCTGCGGAA	0.642													C|||	2	0.000399361	0.0008	0.0	5008	,	,		17870	0.0		0.0	False		,,,				2504	0.001				p.A571T		Atlas-SNP	.											TRAP1,colon,carcinoma,0,1	TRAP1	53	.	0			c.G1711A						.						64.0	49.0	54.0					16																	3712966		2197	4300	6497	SO:0001583	missense	10131	exon15			ACTCGGCGGCTGC	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1711G>A	chr16.hg19:g.3712966C>T	ENSP00000246957:p.Ala571Thr	16.0	0.0		25.0	8.0	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	hg19	CCDS10508.1	.	.	.	.	.	.	.	.	.	.	C	8.864	0.947740	0.18356	.	.	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.14266	2.52;2.52	5.45	-0.454	0.12197	.	0.735859	0.13582	N	0.377261	T	0.04543	0.0124	N	0.04508	-0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.37056	-0.9722	10	0.30854	T	0.27	-0.8126	2.2713	0.04091	0.1244:0.4432:0.1216:0.3109	.	518;571	F5H897;Q12931	.;TRAP1_HUMAN	T	571;518	ENSP00000246957:A571T;ENSP00000442070:A518T	ENSP00000246957:A571T	A	-	1	0	TRAP1	3652967	0.015000	0.18098	0.000000	0.03702	0.003000	0.03518	0.217000	0.17603	0.289000	0.22422	0.650000	0.86243	GCC	.	.		0.642	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
GSPT1	2935	hgsc.bcm.edu	37	16	11981478	11981478	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:11981478A>G	ENST00000563468.1	-	5	518	c.492T>C	c.(490-492)agT>agC	p.S164S	GSPT1_ENST00000420576.2_Silent_p.S164S|GSPT1_ENST00000439887.2_Silent_p.S301S|GSPT1_ENST00000434724.2_Silent_p.S302S|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000564790.1_5'Flank			P15170	ERF3A_HUMAN	G1 to S phase transition 1	164	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						TTGGGACAAAACTCTTGTGGC	0.443																																					p.S302S		Atlas-SNP	.											.	GSPT1	71	.	0			c.T906C						.						149.0	153.0	152.0					16																	11981478		2197	4298	6495	SO:0001819	synonymous_variant	2935	exon7			GACAAAACTCTTG	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000563468.1:c.492T>C	chr16.hg19:g.11981478A>G		212.0	0.0		190.0	78.0	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	hg19	CCDS45414.1																																																																																			.	.		0.443	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094	
ERCC4	2072	hgsc.bcm.edu	37	16	14041629	14041629	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:14041629C>T	ENST00000311895.7	+	11	2185	c.2176C>T	c.(2176-2178)Cgc>Tgc	p.R726C		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	726	ERCC4.|Nuclease.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						GTGCGTGGAGCGCAAGAGTAT	0.498			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R726C		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""		E	.	ERCC4	100	.	0			c.C2176T						.						92.0	89.0	90.0					16																	14041629		2197	4300	6497	SO:0001583	missense	2072	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GTGGAGCGCAAGA	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"""xeroderma pigmentosum, complementation group F"""	133520	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.2176C>T	chr16.hg19:g.14041629C>T	ENSP00000310520:p.Arg726Cys	93.0	0.0		106.0	34.0	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	hg19	CCDS32390.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.423764	0.62733	.	.	ENSG00000175595	ENST00000311895;ENST00000389138	T	0.62941	-0.01	5.58	3.42	0.39159	DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);ERCC4 domain (2);	0.050473	0.85682	D	0.000000	D	0.86083	0.5848	H	0.98901	4.365	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89713	0.3913	10	0.87932	D	0	-21.909	11.3027	0.49316	0.2224:0.6665:0.1111:0.0	.	726	Q92889	XPF_HUMAN	C	726;714	ENSP00000310520:R726C	ENSP00000310520:R726C	R	+	1	0	ERCC4	13949130	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	2.660000	0.46749	1.346000	0.45694	-0.165000	0.13383	CGC	.	.		0.498	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	
PARN	5073	hgsc.bcm.edu	37	16	14721031	14721031	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:14721031A>C	ENST00000437198.2	-	5	400	c.259T>G	c.(259-261)Tca>Gca	p.S87A	PARN_ENST00000566021.1_5'UTR|PARN_ENST00000420015.2_Intron|PARN_ENST00000341484.7_Missense_Mutation_p.S26A|PARN_ENST00000539279.1_Intron	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease	87					female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						AAGTTAAATGACTTCGTTATA	0.363																																					p.S87A		Atlas-SNP	.											.	PARN	72	.	0			c.T259G						.						72.0	68.0	70.0					16																	14721031		1854	4087	5941	SO:0001583	missense	5073	exon5			TAAATGACTTCGT	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"""deadenylation nuclease"""	604212	"""poly(A)-specific ribonuclease (deadenylation nuclease)"""			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.259T>G	chr16.hg19:g.14721031A>C	ENSP00000387911:p.Ser87Ala	142.0	0.0		164.0	61.0	NM_002582	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Missense_Mutation	SNP	ENST00000437198.2	hg19	CCDS45419.1	.	.	.	.	.	.	.	.	.	.	A	11.76	1.734373	0.30774	.	.	ENSG00000140694	ENST00000437198;ENST00000341484	T;T	0.24151	1.87;1.87	5.86	5.86	0.93980	Ribonuclease H-like (1);	0.126644	0.56097	D	0.000030	T	0.18215	0.0437	N	0.16656	0.425	0.80722	D	1	B	0.06786	0.001	B	0.21546	0.035	T	0.08889	-1.0700	10	0.20519	T	0.43	-13.1429	15.448	0.75248	1.0:0.0:0.0:0.0	.	87	O95453	PARN_HUMAN	A	87;26	ENSP00000387911:S87A;ENSP00000345456:S26A	ENSP00000345456:S26A	S	-	1	0	PARN	14628532	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.035000	0.57297	2.240000	0.73641	0.533000	0.62120	TCA	.	.		0.363	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582	
NTAN1	123803	hgsc.bcm.edu	37	16	15131931	15131931	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:15131931T>G	ENST00000287706.3	-	10	982	c.890A>C	c.(889-891)aAt>aCt	p.N297T	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	297					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						GCCATCTTCATTTTTTTTGTA	0.383																																					p.N297T		Atlas-SNP	.											.,1	NTAN1	21	.	0			c.A890C						.						88.0	91.0	90.0					16																	15131931		2197	4299	6496	SO:0001583	missense	123803	exon10			TCTTCATTTTTTT	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.890A>C	chr16.hg19:g.15131931T>G	ENSP00000287706:p.Asn297Thr	145.0	0.0		126.0	10.0	NM_173474	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	hg19	CCDS10558.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.484142	0.44147	.	.	ENSG00000157045	ENST00000287706	T	0.28069	1.63	5.87	5.87	0.94306	.	0.165305	0.56097	D	0.000034	T	0.31606	0.0802	L	0.37630	1.12	0.39621	D	0.970034	P	0.51933	0.949	P	0.46543	0.52	T	0.04078	-1.0979	10	0.32370	T	0.25	-17.8893	15.7569	0.78037	0.0:0.0:0.0:1.0	.	297	Q96AB6	NTAN1_HUMAN	T	297	ENSP00000287706:N297T	ENSP00000287706:N297T	N	-	2	0	NTAN1	15039432	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	2.778000	0.47726	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.383	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
ABCC1	4363	hgsc.bcm.edu	37	16	16177388	16177388	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:16177388A>T	ENST00000399410.3	+	17	2456	c.2281A>T	c.(2281-2283)Att>Ttt	p.I761F	ABCC1_ENST00000349029.5_Intron|ABCC1_ENST00000346370.5_Missense_Mutation_p.I761F|ABCC1_ENST00000399408.2_Missense_Mutation_p.I761F|ABCC1_ENST00000345148.5_Missense_Mutation_p.I761F|ABCC1_ENST00000351154.5_Intron	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	761	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	TCGGACAGAGATTGGCGAGAA	0.537																																					p.I761F		Atlas-SNP	.											.	ABCC1	156	.	0			c.A2281T						.						80.0	82.0	81.0					16																	16177388		2070	4216	6286	SO:0001583	missense	4363	exon17			ACAGAGATTGGCG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2281A>T	chr16.hg19:g.16177388A>T	ENSP00000382342:p.Ile761Phe	161.0	0.0		131.0	27.0	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.647814	0.87958	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000345148;ENST00000536381	D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91	5.38	5.38	0.77491	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.96491	0.8855	M	0.88310	2.945	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.997;0.995	D	0.97228	0.9882	10	0.87932	D	0	-17.4158	14.5874	0.68335	1.0:0.0:0.0:0.0	.	761;761;761;761	P33527-4;P33527-3;P33527;P33527-9	.;.;MRP1_HUMAN;.	F	761;761;761;761;435	ENSP00000382342:I761F;ENSP00000382340:I761F;ENSP00000263019:I761F;ENSP00000263014:I761F	ENSP00000263014:I761F	I	+	1	0	ABCC1	16084889	1.000000	0.71417	0.998000	0.56505	0.828000	0.46876	9.230000	0.95299	2.048000	0.60808	0.460000	0.39030	ATT	.	.		0.537	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
OTOA	146183	hgsc.bcm.edu	37	16	21702950	21702950	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:21702950C>T	ENST00000286149.4	+	8	682	c.681C>T	c.(679-681)tcC>tcT	p.S227S	OTOA_ENST00000388958.3_Silent_p.S227S|OTOA_ENST00000388956.4_Silent_p.S148S			Q7RTW8	OTOAN_HUMAN	otoancorin	227					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CGGCTCATTCCCAGAGAGCTC	0.488																																					p.S227S		Atlas-SNP	.											.	OTOA	144	.	0			c.C681T						.						101.0	91.0	95.0					16																	21702950		2199	4300	6499	SO:0001819	synonymous_variant	146183	exon8			TCATTCCCAGAGA	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.681C>T	chr16.hg19:g.21702950C>T		86.0	0.0		117.0	20.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Silent	SNP	ENST00000286149.4	hg19																																																																																				.	.		0.488	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
OTOA	146183	hgsc.bcm.edu	37	16	21702955	21702955	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:21702955G>A	ENST00000286149.4	+	8	687	c.686G>A	c.(685-687)aGa>aAa	p.R229K	OTOA_ENST00000388958.3_Missense_Mutation_p.R229K|OTOA_ENST00000388956.4_Missense_Mutation_p.R150K			Q7RTW8	OTOAN_HUMAN	otoancorin	229					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CATTCCCAGAGAGCTCTCTAT	0.488																																					p.R229K		Atlas-SNP	.											.	OTOA	144	.	0			c.G686A						.						99.0	90.0	93.0					16																	21702955		2199	4300	6499	SO:0001583	missense	146183	exon8			CCCAGAGAGCTCT	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.686G>A	chr16.hg19:g.21702955G>A	ENSP00000286149:p.Arg229Lys	86.0	0.0		121.0	21.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	hg19		.	.	.	.	.	.	.	.	.	.	G	10.70	1.424300	0.25639	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956	T;T;T	0.12147	2.71;2.71;2.71	5.27	2.23	0.28157	.	0.167421	0.50627	N	0.000103	T	0.10895	0.0266	L	0.52364	1.645	0.80722	D	1	P;P	0.38223	0.623;0.623	B;B	0.36186	0.219;0.219	T	0.18713	-1.0328	10	0.26408	T	0.33	-1.9773	6.27	0.20949	0.1621:0.0:0.6887:0.1492	.	150;229	B3KWU3;E9PF51	.;.	K	229;229;150	ENSP00000373610:R229K;ENSP00000286149:R229K;ENSP00000373608:R150K	ENSP00000286149:R229K	R	+	2	0	OTOA	21610456	1.000000	0.71417	0.757000	0.31301	0.086000	0.17979	1.581000	0.36558	0.225000	0.20959	0.556000	0.70494	AGA	.	.		0.488	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
OTOA	146183	hgsc.bcm.edu	37	16	21721362	21721362	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:21721362G>A	ENST00000286149.4	+	12	1301	c.1300G>A	c.(1300-1302)Gtc>Atc	p.V434I	OTOA_ENST00000388958.3_Missense_Mutation_p.V420I|OTOA_ENST00000388956.4_Missense_Mutation_p.V341I|OTOA_ENST00000388957.3_Missense_Mutation_p.V96I			Q7RTW8	OTOAN_HUMAN	otoancorin	434					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CCTCAACCAGGTCTCAGGTTG	0.522																																					p.V420I		Atlas-SNP	.											.	OTOA	144	.	0			c.G1258A						.						71.0	58.0	63.0					16																	21721362		2199	4300	6499	SO:0001583	missense	146183	exon12			AACCAGGTCTCAG	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.1300G>A	chr16.hg19:g.21721362G>A	ENSP00000286149:p.Val434Ile	120.0	0.0		151.0	49.0	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	hg19		.	.	.	.	.	.	.	.	.	.	G	15.15	2.747220	0.49257	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957	T;T;T;T	0.78364	2.81;2.81;2.81;-1.17	5.21	4.24	0.50183	.	0.215069	0.39544	N	0.001329	T	0.73636	0.3612	M	0.66939	2.045	0.43890	D	0.996512	B;B;B;B	0.29232	0.238;0.238;0.238;0.238	B;B;B;B	0.31495	0.079;0.112;0.131;0.079	T	0.67352	-0.5692	10	0.17832	T	0.49	-17.6608	11.8567	0.52441	0.0869:0.0:0.9131:0.0	.	434;341;96;420	Q7RTW8;B3KWU3;Q7RTW8-2;E9PF51	OTOAN_HUMAN;.;.;.	I	420;434;341;96	ENSP00000373610:V420I;ENSP00000286149:V434I;ENSP00000373608:V341I;ENSP00000373609:V96I	ENSP00000286149:V434I	V	+	1	0	OTOA	21628863	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.330000	0.65899	1.143000	0.42306	0.643000	0.83706	GTC	.	.		0.522	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
KIAA0556	23247	hgsc.bcm.edu	37	16	27752080	27752080	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:27752080A>G	ENST00000261588.4	+	15	2481	c.2462A>G	c.(2461-2463)aAc>aGc	p.N821S		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	821						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CGGAGTGTCAACACCAAGGAG	0.602																																					p.N821S		Atlas-SNP	.											.	KIAA0556	348	.	0			c.A2462G						.						45.0	48.0	47.0					16																	27752080		2197	4300	6497	SO:0001583	missense	23247	exon15			GTGTCAACACCAA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2462A>G	chr16.hg19:g.27752080A>G	ENSP00000261588:p.Asn821Ser	133.0	0.0		143.0	53.0	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.467670	0.26335	.	.	ENSG00000047578	ENST00000261588	T	0.09723	2.95	5.15	0.0363	0.14191	.	0.307133	0.33290	N	0.005065	T	0.05410	0.0143	N	0.19112	0.55	0.09310	N	1	B	0.19817	0.039	B	0.18871	0.023	T	0.28459	-1.0043	10	0.49607	T	0.09	-22.8944	3.1277	0.06413	0.3324:0.3125:0.0:0.3551	.	821	O60303	K0556_HUMAN	S	821	ENSP00000261588:N821S	ENSP00000261588:N821S	N	+	2	0	KIAA0556	27659581	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.029000	0.13666	0.006000	0.14734	-0.527000	0.04329	AAC	.	.		0.602	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
MVP	9961	hgsc.bcm.edu	37	16	29848108	29848108	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:29848108G>A	ENST00000357402.5	+	7	876	c.738G>A	c.(736-738)ggG>ggA	p.G246G	MVP_ENST00000395353.1_Silent_p.G246G|MVP_ENST00000452209.2_Missense_Mutation_p.G61R	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	246					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						GCCGCACTGGGGAGGAGTGGC	0.642																																					p.G246G		Atlas-SNP	.											.	MVP	80	.	0			c.G738A						.						47.0	46.0	46.0					16																	29848108		2197	4300	6497	SO:0001819	synonymous_variant	9961	exon7			CACTGGGGAGGAG	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.738G>A	chr16.hg19:g.29848108G>A		106.0	0.0		119.0	45.0	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Silent	SNP	ENST00000357402.5	hg19	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835504	0.50951	.	.	ENSG00000013364	ENST00000452209	T	0.64438	-0.1	5.47	1.12	0.20585	.	0.000000	0.85682	D	0.000000	T	0.56441	0.1985	.	.	.	0.23162	N	0.998194	.	.	.	.	.	.	T	0.52320	-0.8591	7	0.87932	D	0	-13.119	5.0154	0.14333	0.3406:0.1497:0.5098:0.0	.	.	.	.	R	61	ENSP00000387916:G61R	ENSP00000387916:G61R	G	+	1	0	MVP	29755609	0.972000	0.33761	0.999000	0.59377	0.954000	0.61252	-0.046000	0.11983	0.321000	0.23259	0.462000	0.41574	GGA	.	.		0.642	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
SRCAP	10847	hgsc.bcm.edu	37	16	30727435	30727435	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:30727435C>T	ENST00000262518.4	+	17	2927	c.2542C>T	c.(2542-2544)Cag>Tag	p.Q848*	SRCAP_ENST00000395059.2_Nonsense_Mutation_p.Q848*|SRCAP_ENST00000344771.4_Nonsense_Mutation_p.Q848*	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	848					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TGTTGAGAAGCAGATGCCCAA	0.498																																					p.Q848X		Atlas-SNP	.											.	SRCAP	298	.	0			c.C2542T						.						148.0	126.0	133.0					16																	30727435		2197	4300	6497	SO:0001587	stop_gained	10847	exon17			GAGAAGCAGATGC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.2542C>T	chr16.hg19:g.30727435C>T	ENSP00000262518:p.Gln848*	95.0	0.0		87.0	29.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Nonsense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	39	7.810078	0.98501	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	.	.	.	5.25	5.25	0.73442	.	0.000000	0.51477	D	0.000082	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.6405	17.783	0.88529	0.0:1.0:0.0:0.0	.	.	.	.	X	848	.	ENSP00000262518:Q848X	Q	+	1	0	SRCAP	30634936	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.500000	0.81588	2.726000	0.93360	0.561000	0.74099	CAG	.	.		0.498	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
SRCAP	10847	hgsc.bcm.edu	37	16	30734920	30734920	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:30734920C>A	ENST00000262518.4	+	25	4560	c.4175C>A	c.(4174-4176)gCt>gAt	p.A1392D	SRCAP_ENST00000395059.2_Missense_Mutation_p.A1330D|SRCAP_ENST00000344771.4_Missense_Mutation_p.A1234D	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1392	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GCCCCCGGAGCTGCCCCCTTG	0.572																																					p.A1392D		Atlas-SNP	.											.	SRCAP	298	.	0			c.C4175A						.						141.0	134.0	136.0					16																	30734920		2197	4300	6497	SO:0001583	missense	10847	exon25			CCGGAGCTGCCCC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4175C>A	chr16.hg19:g.30734920C>A	ENSP00000262518:p.Ala1392Asp	73.0	0.0		82.0	30.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	2.967	-0.213287	0.06140	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91577	-2.78;-2.87;-2.86	5.65	4.69	0.59074	.	0.370343	0.23429	N	0.048274	T	0.80314	0.4600	N	0.08118	0	0.18873	N	0.999983	B;B;B	0.30361	0.096;0.277;0.181	B;B;B	0.28638	0.092;0.092;0.042	T	0.74748	-0.3560	10	0.87932	D	0	-1.8765	11.6028	0.51012	0.0:0.9144:0.0:0.0856	.	1234;1330;1392	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	D	1392;1330;1234	ENSP00000262518:A1392D;ENSP00000378499:A1330D;ENSP00000343042:A1234D	ENSP00000262518:A1392D	A	+	2	0	SRCAP	30642421	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	2.044000	0.41241	2.658000	0.90341	0.555000	0.69702	GCT	.	.		0.572	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
STX1B	112755	hgsc.bcm.edu	37	16	31008338	31008338	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:31008338A>T	ENST00000215095.5	-	6	628	c.397T>A	c.(397-399)Tat>Aat	p.Y133N	STX1B_ENST00000565419.1_Missense_Mutation_p.Y133N	NM_052874.3	NP_443106.1	P61266	STX1B_HUMAN	syntaxin 1B	133					intracellular protein transport (GO:0006886)|neurotransmitter transport (GO:0006836)|regulation of exocytosis (GO:0017157)|regulation of gene expression (GO:0010468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|large_intestine(5)|lung(5)	13						GTCGCGTTATATTCGGTCATT	0.627																																					p.Y133N		Atlas-SNP	.											.	STX1B	26	.	0			c.T397A						.						44.0	41.0	42.0					16																	31008338		2197	4300	6497	SO:0001583	missense	112755	exon6			CGTTATATTCGGT	AY028792	CCDS10699.1	16p12-p11	2008-02-05	2007-06-20	2007-06-20	ENSG00000099365	ENSG00000099365			18539	protein-coding gene	gene with protein product		601485	"""syntaxin 1B1"", ""syntaxin 1B2"""	STX1B1, STX1B2			Standard	NM_052874		Approved		uc010cad.2	P61266	OTTHUMG00000132391	ENST00000215095.5:c.397T>A	chr16.hg19:g.31008338A>T	ENSP00000215095:p.Tyr133Asn	64.0	0.0		74.0	25.0	NM_052874	Q15531|Q2VPS2	Missense_Mutation	SNP	ENST00000215095.5	hg19	CCDS10699.1	.	.	.	.	.	.	.	.	.	.	A	35	5.572248	0.96553	.	.	ENSG00000099365	ENST00000215095	T	0.31769	1.48	4.86	4.86	0.63082	t-SNARE (1);Syntaxin, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.63920	0.2552	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73799	-0.3869	10	0.87932	D	0	.	13.5675	0.61826	1.0:0.0:0.0:0.0	.	133;133	Q2VPS2;P61266	.;STX1B_HUMAN	N	133	ENSP00000215095:Y133N	ENSP00000215095:Y133N	Y	-	1	0	STX1B	30915839	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.139000	0.94554	2.051000	0.60960	0.454000	0.30748	TAT	.	.		0.627	STX1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255521.2		
FUS	2521	hgsc.bcm.edu	37	16	31196408	31196408	+	Silent	SNP	C	C	T	rs533399799	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:31196408C>T	ENST00000254108.7	+	6	777	c.672C>T	c.(670-672)ggC>ggT	p.G224G	RP11-388M20.6_ENST00000564743.1_RNA|FUS_ENST00000380244.3_Silent_p.G223G|FUS_ENST00000568685.1_Silent_p.G224G	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	224	Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		gtggtggcggcggcggcggcg	0.672			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""								C|||	4	0.000798722	0.0015	0.0	5008	,	,		10664	0.001		0.0	False		,,,				2504	0.001				p.G224G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	FUS	52	.	0			c.C672T						.						20.0	19.0	19.0					16																	31196408		2193	4291	6484	SO:0001819	synonymous_variant	2521	exon6			TGGCGGCGGCGGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.672C>T	chr16.hg19:g.31196408C>T		72.0	0.0		73.0	29.0	NM_004960	Q9H4A8	Silent	SNP	ENST00000254108.7	hg19	CCDS10707.1																																																																																			.	.		0.672	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
SALL1	6299	hgsc.bcm.edu	37	16	51173443	51173443	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:51173443A>G	ENST00000251020.4	-	2	2723	c.2690T>C	c.(2689-2691)gTc>gCc	p.V897A	SALL1_ENST00000440970.1_Missense_Mutation_p.V800A|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	897					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ATTGGTCAGGACATCCCCCTC	0.542																																					p.V897A	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.T2690C						.						98.0	77.0	84.0					16																	51173443		2198	4300	6498	SO:0001583	missense	6299	exon2			GTCAGGACATCCC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2690T>C	chr16.hg19:g.51173443A>G	ENSP00000251020:p.Val897Ala	82.0	0.0		110.0	49.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.531823	0.00951	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.80824	-1.42;-1.42	5.5	4.34	0.51931	.	0.305299	0.36338	N	0.002655	T	0.67335	0.2882	L	0.29908	0.895	0.23473	N	0.997601	B	0.24317	0.101	B	0.21360	0.034	T	0.51228	-0.8732	10	0.16420	T	0.52	.	11.2091	0.48786	0.7174:0.2826:0.0:0.0	.	897	Q9NSC2	SALL1_HUMAN	A	897;800;861	ENSP00000251020:V897A;ENSP00000407914:V800A	ENSP00000251020:V897A	V	-	2	0	SALL1	49730944	0.301000	0.24444	1.000000	0.80357	0.057000	0.15508	2.369000	0.44231	2.085000	0.62840	0.455000	0.32223	GTC	.	.		0.542	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
CPNE2	221184	hgsc.bcm.edu	37	16	57144691	57144691	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57144691G>A	ENST00000535318.2	+	3	398	c.37G>A	c.(37-39)Ggg>Agg	p.G13R	CPNE2_ENST00000290776.8_Missense_Mutation_p.G13R|CPNE2_ENST00000537605.1_5'UTR|CPNE2_ENST00000565874.1_Missense_Mutation_p.G13R			Q96FN4	CPNE2_HUMAN	copine II	13	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				CCCAGCAGCGGGGGCAGCCCC	0.647																																					p.G13R		Atlas-SNP	.											.	CPNE2	48	.	0			c.G37A						.						33.0	30.0	31.0					16																	57144691		2198	4299	6497	SO:0001583	missense	221184	exon2			GCAGCGGGGGCAG		CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.37G>A	chr16.hg19:g.57144691G>A	ENSP00000439018:p.Gly13Arg	156.0	0.0		124.0	50.0	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	hg19	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.764349	0.69878	.	.	ENSG00000140848	ENST00000290776;ENST00000535318	T;T	0.04706	3.57;3.57	4.22	4.22	0.49857	C2 calcium/lipid-binding domain, CaLB (1);	0.547211	0.19070	N	0.123526	T	0.03477	0.0100	N	0.08118	0	0.80722	D	1	B;B	0.12630	0.006;0.001	B;B	0.06405	0.002;0.001	T	0.50734	-0.8793	10	0.54805	T	0.06	-1.0409	14.5079	0.67764	0.0:0.1478:0.8522:0.0	.	13;13	A8K8A4;Q96FN4	.;CPNE2_HUMAN	R	13	ENSP00000290776:G13R;ENSP00000439018:G13R	ENSP00000290776:G13R	G	+	1	0	CPNE2	55702192	0.998000	0.40836	0.873000	0.34254	0.279000	0.26890	2.742000	0.47434	2.655000	0.90218	0.650000	0.86243	GGG	.	.		0.647	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727	
KIFC3	3801	hgsc.bcm.edu	37	16	57794959	57794959	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57794959G>A	ENST00000379655.4	-	15	2254	c.1997C>T	c.(1996-1998)aCc>aTc	p.T666I	KIFC3_ENST00000543930.1_Missense_Mutation_p.T524I|KIFC3_ENST00000541240.1_Missense_Mutation_p.T688I|KIFC3_ENST00000445690.2_Missense_Mutation_p.T666I|KIFC3_ENST00000465878.2_Missense_Mutation_p.T527I|KIFC3_ENST00000540079.2_Missense_Mutation_p.T564I|KIFC3_ENST00000421376.2_Missense_Mutation_p.T527I|KIFC3_ENST00000539578.1_Missense_Mutation_p.T608I|KIFC3_ENST00000562903.1_Missense_Mutation_p.T527I	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	666	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				CTCACCCGTGGTGCGGAGGCC	0.672																																					p.T666I		Atlas-SNP	.											.	KIFC3	55	.	0			c.C1997T						.						57.0	52.0	53.0					16																	57794959		2198	4299	6497	SO:0001583	missense	3801	exon15			CCCGTGGTGCGGA	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"""Kinesins"""	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.1997C>T	chr16.hg19:g.57794959G>A	ENSP00000368976:p.Thr666Ile	40.0	0.0		29.0	11.0	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	hg19	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972637	0.53614	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94;-0.94;-0.94	5.21	5.21	0.72293	Kinesin, motor domain (4);	0.103125	0.64402	D	0.000003	T	0.76737	0.4029	L	0.41356	1.27	0.80722	D	1	P;D;P;B;P;P	0.54601	0.953;0.967;0.751;0.324;0.866;0.84	P;P;B;B;P;B	0.52823	0.71;0.455;0.267;0.064;0.62;0.274	T	0.78518	-0.2173	10	0.54805	T	0.06	.	17.7443	0.88415	0.0:0.0:1.0:0.0	.	688;608;524;564;666;527	B7Z484;F5H4I9;B7Z896;F5H3M2;Q9BVG8;A8K6S2	.;.;.;.;KIFC3_HUMAN;.	I	666;666;527;688;564;524;608	ENSP00000368976:T666I;ENSP00000401696:T666I;ENSP00000396399:T527I;ENSP00000442008:T688I;ENSP00000438805:T564I;ENSP00000444012:T524I;ENSP00000444884:T608I	ENSP00000368976:T666I	T	-	2	0	KIFC3	56352460	1.000000	0.71417	1.000000	0.80357	0.239000	0.25481	9.498000	0.97972	2.460000	0.83146	0.205000	0.17691	ACC	.	.		0.672	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550	
CNGB1	1258	hgsc.bcm.edu	37	16	57937813	57937813	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57937813A>G	ENST00000251102.8	-	27	2767	c.2707T>C	c.(2707-2709)Tac>Cac	p.Y903H	CNGB1_ENST00000564448.1_Missense_Mutation_p.Y897H	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	903					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						AAATTCATGTACTTCACCGTG	0.572																																					p.Y903H	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.T2707C						.						131.0	139.0	136.0					16																	57937813		2086	4197	6283	SO:0001583	missense	1258	exon27			TCATGTACTTCAC	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2707T>C	chr16.hg19:g.57937813A>G	ENSP00000251102:p.Tyr903His	71.0	0.0		72.0	30.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.319897	0.81469	.	.	ENSG00000070729	ENST00000251102	D	0.97731	-4.51	4.82	3.69	0.42338	Cyclic nucleotide-binding-like (1);	0.076454	0.53938	D	0.000046	D	0.98573	0.9523	M	0.87269	2.87	0.80722	D	1	D;P	0.89917	1.0;0.784	D;P	0.91635	0.999;0.686	D	0.98532	1.0628	10	0.66056	D	0.02	.	10.7068	0.45960	0.8395:0.1605:0.0:0.0	.	275;903	Q14028-2;Q14028	.;CNGB1_HUMAN	H	903	ENSP00000251102:Y903H	ENSP00000251102:Y903H	Y	-	1	0	CNGB1	56495314	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.336000	0.96533	0.656000	0.30886	0.460000	0.39030	TAC	.	.		0.572	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
C16orf70	80262	hgsc.bcm.edu	37	16	67184217	67184217	+	IGR	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67184217A>G	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Silent_p.L58L	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		GCGTCGGGTAACTGGAACGCG	0.756																																					p.L58L		Atlas-SNP	.											.	B3GNT9	25	.	0			c.T172C						.						7.0	9.0	8.0					16																	67184217		1763	3973	5736	SO:0001628	intergenic_variant	84752	exon2			CGGGTAACTGGAA	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 6"""	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		chr16.hg19:g.67184217A>G		138.0	0.0		108.0	39.0	NM_033309	Q9HA86	Silent	SNP	ENST00000219139.3	hg19	CCDS10828.1																																																																																			.	.		0.756	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187	
RLTPR	146206	hgsc.bcm.edu	37	16	67683180	67683180	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67683180A>G	ENST00000334583.6	+	19	2040	c.1712A>G	c.(1711-1713)cAc>cGc	p.H571R	RLTPR_ENST00000545661.1_Missense_Mutation_p.H535R	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	571					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)		GACGTCCTGCACCGGATTGTC	0.627																																					p.H571R		Atlas-SNP	.											.	RLTPR	124	.	0			c.A1712G						.						57.0	64.0	61.0					16																	67683180		2017	4164	6181	SO:0001583	missense	146206	exon19			TCCTGCACCGGAT	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.1712A>G	chr16.hg19:g.67683180A>G	ENSP00000334958:p.His571Arg	59.0	0.0		48.0	19.0	NM_001013838	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	hg19	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.399064	0.83120	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.51574	0.7;0.7	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.54532	0.1864	L	0.38838	1.175	0.43417	D	0.995569	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.991	T	0.47459	-0.9116	10	0.16420	T	0.52	-16.3245	12.6465	0.56738	1.0:0.0:0.0:0.0	.	535;571	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	R	571;535	ENSP00000334958:H571R;ENSP00000441481:H535R	ENSP00000334958:H571R	H	+	2	0	RLTPR	66240681	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.386000	0.66238	1.817000	0.53016	0.459000	0.35465	CAC	.	.		0.627	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
RANBP10	57610	hgsc.bcm.edu	37	16	67765413	67765413	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67765413G>A	ENST00000317506.3	-	7	966	c.851C>T	c.(850-852)cCg>cTg	p.P284L	RANBP10_ENST00000602677.1_Missense_Mutation_p.P284L|RANBP10_ENST00000411657.2_Missense_Mutation_p.P167L|RANBP10_ENST00000448631.2_Missense_Mutation_p.P228L|RANBP10_ENST00000536251.1_Missense_Mutation_p.P55L|RANBP10_ENST00000425512.2_Missense_Mutation_p.P152L	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	284	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.P284Q(1)		endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		TTCCTGAATCGGGGTTTCAGT	0.478																																					p.P284L		Atlas-SNP	.											RANBP10,NS,lymphoid_neoplasm,0,1	RANBP10	56	.	1	Substitution - Missense(1)	lung(1)	c.C851T						.						147.0	134.0	138.0					16																	67765413		2198	4300	6498	SO:0001583	missense	57610	exon7			TGAATCGGGGTTT	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.851C>T	chr16.hg19:g.67765413G>A	ENSP00000316589:p.Pro284Leu	169.0	0.0		117.0	49.0	NM_020850	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Missense_Mutation	SNP	ENST00000317506.3	hg19	CCDS32469.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.825099	0.50739	.	.	ENSG00000141084	ENST00000317506;ENST00000448631;ENST00000536251;ENST00000411657;ENST00000425512	D	0.88046	-2.33	5.78	5.78	0.91487	LisH dimerisation motif (2);	0.297907	0.35096	N	0.003442	T	0.80788	0.4690	N	0.19112	0.55	0.46849	D	0.999229	B;B;B;B;B	0.11235	0.004;0.003;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.001	T	0.73219	-0.4052	10	0.33141	T	0.24	-20.3522	19.6088	0.95594	0.0:0.0:1.0:0.0	.	152;284;167;228;284	B4DHL9;B4E1Y2;B4DID0;B4DQH9;Q6VN20	.;.;.;.;RBP10_HUMAN	L	284;228;55;167;152	ENSP00000410617:P152L	ENSP00000316589:P284L	P	-	2	0	RANBP10	66322914	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.274000	0.65569	2.734000	0.93682	0.563000	0.77884	CCG	.	.		0.478	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850	
PSKH1	5681	hgsc.bcm.edu	37	16	67943147	67943147	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67943147G>T	ENST00000291041.5	+	2	665	c.495G>T	c.(493-495)caG>caT	p.Q165H		NM_006742.2	NP_006733.1	P11801	KPSH1_HUMAN	protein serine kinase H1	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|large_intestine(1)|lung(7)|pancreas(1)	12		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)		TCGAGACACAGGAGCGGGTGT	0.632																																					p.Q165H		Atlas-SNP	.											.	PSKH1	28	.	0			c.G495T						.						109.0	102.0	105.0					16																	67943147		2198	4300	6498	SO:0001583	missense	5681	exon2			GACACAGGAGCGG	M14504	CCDS10851.1	16q22.1	2008-02-05			ENSG00000159792	ENSG00000159792			9529	protein-coding gene	gene with protein product		177015				8268911	Standard	NM_006742		Approved		uc002euv.3	P11801	OTTHUMG00000137548	ENST00000291041.5:c.495G>T	chr16.hg19:g.67943147G>T	ENSP00000291041:p.Gln165His	129.0	0.0		115.0	37.0	NM_006742	Q9NY19	Missense_Mutation	SNP	ENST00000291041.5	hg19	CCDS10851.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.293653	0.40594	.	.	ENSG00000159792	ENST00000291041	T	0.39592	1.07	5.21	3.25	0.37280	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113455	0.64402	D	0.000010	T	0.28234	0.0697	N	0.17674	0.51	0.42502	D	0.992931	B	0.22800	0.075	B	0.25759	0.063	T	0.11817	-1.0572	10	0.51188	T	0.08	-21.6908	10.6928	0.45882	0.1565:0.0:0.8435:0.0	.	165	P11801	KPSH1_HUMAN	H	165	ENSP00000291041:Q165H	ENSP00000291041:Q165H	Q	+	3	2	PSKH1	66500648	1.000000	0.71417	0.997000	0.53966	0.467000	0.32768	0.821000	0.27338	1.222000	0.43521	0.655000	0.94253	CAG	.	.		0.632	PSKH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268882.3	NM_006742	
TERF2	7014	hgsc.bcm.edu	37	16	69418537	69418537	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:69418537T>A	ENST00000254942.3	-	3	568	c.552A>T	c.(550-552)gaA>gaT	p.E184D	TERF2_ENST00000567296.2_Missense_Mutation_p.E184D|TERF2_ENST00000569611.2_5'UTR|TERF2_ENST00000603068.1_Missense_Mutation_p.E142D	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	184	TRFH dimerization.				age-dependent telomere shortening (GO:0001309)|cell cycle (GO:0007049)|cellular senescence (GO:0090398)|in utero embryonic development (GO:0001701)|negative regulation of telomere maintenance (GO:0032205)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|positive regulation of telomere maintenance (GO:0032206)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)|telomeric loop formation (GO:0031627)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded telomeric DNA binding (GO:0003691)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			NS(2)|breast(1)|large_intestine(3)|lung(1)	7		Ovarian(137;0.101)				TCAGTGTAAATTCCGTTTTAA	0.398																																					p.E184D	Ovarian(13;63 524 30420 31710 34037)	Atlas-SNP	.											.	TERF2	24	.	0			c.A552T						.						111.0	105.0	107.0					16																	69418537		2198	4300	6498	SO:0001583	missense	7014	exon3			TGTAAATTCCGTT		CCDS10879.1, CCDS10879.2	16q22.1	2008-02-05			ENSG00000132604	ENSG00000132604			11729	protein-coding gene	gene with protein product		602027		TRBF2		9326950, 10226653	Standard	NM_005652		Approved	TRF2	uc002exd.4	Q15554	OTTHUMG00000137566	ENST00000254942.3:c.552A>T	chr16.hg19:g.69418537T>A	ENSP00000254942:p.Glu184Asp	91.0	0.0		98.0	39.0	NM_005652		Missense_Mutation	SNP	ENST00000254942.3	hg19		.	.	.	.	.	.	.	.	.	.	T	18.71	3.681753	0.68042	.	.	ENSG00000132604	ENST00000254942	.	.	.	5.48	1.15	0.20763	Telomere repeat-binding factor, dimerisation domain (4);	0.148438	0.50627	D	0.000107	T	0.49898	0.1584	N	0.16656	0.425	0.44677	D	0.997668	B;D	0.58620	0.046;0.983	B;D	0.72982	0.069;0.979	T	0.38373	-0.9664	9	0.33940	T	0.23	-16.4594	8.5205	0.33273	0.0:0.5361:0.0:0.4639	.	142;142	Q15554-2;Q15554	.;TERF2_HUMAN	D	142	.	ENSP00000254942:E142D	E	-	3	2	TERF2	67976038	0.997000	0.39634	0.994000	0.49952	0.881000	0.50899	0.104000	0.15313	0.242000	0.21303	0.477000	0.44152	GAA	.	.		0.398	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2		
MTSS1L	92154	hgsc.bcm.edu	37	16	70708260	70708260	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:70708260G>A	ENST00000338779.6	-	11	1276	c.1002C>T	c.(1000-1002)gaC>gaT	p.D334D		NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	334	Ser-rich.				filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						AGTAGGTGGCGTCCTGGGAGA	0.642																																					p.D334D		Atlas-SNP	.											.	MTSS1L	22	.	0			c.C1002T						.						70.0	71.0	71.0					16																	70708260		2198	4300	6498	SO:0001819	synonymous_variant	92154	exon11			GGTGGCGTCCTGG		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"""actin-bundling protein with BAIAP2 homology"""					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.1002C>T	chr16.hg19:g.70708260G>A		123.0	0.0		102.0	42.0	NM_138383	A6NJI7|Q9BUA8	Silent	SNP	ENST00000338779.6	hg19	CCDS32476.1																																																																																			.	.		0.642	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383	
ZNF19	7567	hgsc.bcm.edu	37	16	71509598	71509598	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:71509598A>G	ENST00000288177.5	-	6	1107	c.852T>C	c.(850-852)ggT>ggC	p.G284G	ZNF19_ENST00000567225.1_Intron|ZNF19_ENST00000565637.1_Silent_p.G242G|ZNF19_ENST00000564230.1_Silent_p.G284G|ZNF19_ENST00000565100.2_Silent_p.G214G|AC010547.9_ENST00000561908.1_Intron	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	284					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(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		GGGGTGAATTACCAACAAAAG	0.443																																					p.G284G		Atlas-SNP	.											.	ZNF19	46	.	0			c.T852C						.						93.0	91.0	92.0					16																	71509598		2198	4300	6498	SO:0001819	synonymous_variant	7567	exon6			TGAATTACCAACA	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"""Zinc fingers, C2H2-type"", ""-"""	12981	protein-coding gene	gene with protein product		194525	"""zinc finger protein 19 (KOX 12)"""			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.852T>C	chr16.hg19:g.71509598A>G		110.0	0.0		111.0	45.0	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Silent	SNP	ENST00000288177.5	hg19	CCDS10901.1																																																																																			.	.		0.443	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961	
PMFBP1	83449	hgsc.bcm.edu	37	16	72157448	72157448	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:72157448T>C	ENST00000537792.1	-	2	187	c.188A>G	c.(187-189)cAg>cGg	p.Q63R	PMFBP1_ENST00000237353.10_Missense_Mutation_p.Q897R|PMFBP1_ENST00000355636.6_Missense_Mutation_p.Q752R|PMFBP1_ENST00000537465.1_Missense_Mutation_p.Q902R			Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	902						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TACTCACTTCTGCTGTTTTGC	0.562																																					p.Q897R		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A2690G						.						117.0	99.0	105.0					16																	72157448		2198	4300	6498	SO:0001583	missense	83449	exon18			CACTTCTGCTGTT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000537792.1:c.188A>G	chr16.hg19:g.72157448T>C	ENSP00000443366:p.Gln63Arg	81.0	0.0		99.0	32.0	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000537792.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.52	3.641325	0.67244	.	.	ENSG00000118557	ENST00000537792;ENST00000537465;ENST00000237353;ENST00000355636	T;T;T;T	0.62498	0.02;1.46;1.45;1.52	4.95	4.95	0.65309	.	0.000000	0.46145	D	0.000309	T	0.74366	0.3707	M	0.72118	2.19	0.45883	D	0.998739	D;D;D	0.67145	0.989;0.996;0.981	D;D;D	0.78314	0.979;0.991;0.969	T	0.72124	-0.4385	10	0.25751	T	0.34	.	10.9428	0.47283	0.0:0.0:0.0:1.0	.	902;897;902	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	R	63;902;897;752	ENSP00000443366:Q63R;ENSP00000443817:Q902R;ENSP00000237353:Q897R;ENSP00000347854:Q752R	ENSP00000237353:Q897R	Q	-	2	0	PMFBP1	70714949	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	3.432000	0.52824	2.088000	0.63022	0.528000	0.53228	CAG	.	.		0.562	PMFBP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396523.1	NM_031293	
ZNRF1	84937	hgsc.bcm.edu	37	16	75033861	75033861	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:75033861G>A	ENST00000335325.4	+	1	934	c.292G>A	c.(292-294)Gcc>Acc	p.A98T	ZNRF1_ENST00000567962.1_Missense_Mutation_p.A98T|ZNRF1_ENST00000320619.6_Missense_Mutation_p.A98T|ZNRF1_ENST00000566250.1_Missense_Mutation_p.A98T|WDR59_ENST00000562331.1_5'Flank	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase	98					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						CTCCACCTATGCCCATGGCAA	0.701																																					p.A98T		Atlas-SNP	.											.	ZNRF1	6	.	0			c.G292A						.						20.0	19.0	19.0					16																	75033861		2189	4283	6472	SO:0001583	missense	84937	exon1			ACCTATGCCCATG	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"""RING-type (C3HC4) zinc fingers"""	18452	protein-coding gene	gene with protein product		612060	"""zinc and ring finger 1"""				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606	ENST00000335325.4:c.292G>A	chr16.hg19:g.75033861G>A	ENSP00000335091:p.Ala98Thr	93.0	0.0		74.0	21.0	NM_032268	D3DUJ9|Q9H083	Missense_Mutation	SNP	ENST00000335325.4	hg19	CCDS10912.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.962988	0.53507	.	.	ENSG00000186187	ENST00000320619;ENST00000335325	.	.	.	4.93	4.93	0.64822	.	0.429360	0.23752	N	0.044919	T	0.25975	0.0633	N	0.08118	0	0.38241	D	0.94133	B;P;B	0.39311	0.002;0.667;0.001	B;B;B	0.33254	0.001;0.16;0.0	T	0.18304	-1.0341	9	0.23302	T	0.38	-10.6251	15.3624	0.74487	0.0:0.0:1.0:0.0	.	98;98;98	B4DG67;Q8ND25-2;Q8ND25	.;.;ZNRF1_HUMAN	T	98	.	ENSP00000323362:A98T	A	+	1	0	ZNRF1	73591362	0.928000	0.31464	1.000000	0.80357	0.996000	0.88848	0.593000	0.23999	2.701000	0.92244	0.650000	0.86243	GCC	.	.		0.701	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2		
GAN	8139	hgsc.bcm.edu	37	16	81411036	81411036	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:81411036C>T	ENST00000568107.2	+	11	1791	c.1629C>T	c.(1627-1629)taC>taT	p.Y543Y		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	543					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				ATTACGACTACGTGCGTGAGT	0.468																																					p.Y543Y	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.C1629T						.						173.0	157.0	163.0					16																	81411036		2201	4300	6501	SO:0001819	synonymous_variant	8139	exon11			CGACTACGTGCGT	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"""Kelch-like"", ""BTB/POZ domain containing"""	4137	protein-coding gene	gene with protein product	"""kelch-like family member 16"""	605379	"""giant axonal neuropathy (gigaxonin)"""			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.1629C>T	chr16.hg19:g.81411036C>T		113.0	0.0		136.0	11.0	NM_022041		Silent	SNP	ENST00000568107.2	hg19	CCDS10935.1																																																																																			.	.		0.468	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3		
PIEZO1	9780	hgsc.bcm.edu	37	16	88779224	88779224	+	IGR	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:88779224G>A	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Silent_p.P216P|CTU2_ENST00000567949.1_Silent_p.P287P|CTU2_ENST00000312060.5_Silent_p.P216P|CTU2_ENST00000378384.3_Silent_p.P129P	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						TGGCAAGACCGCCTGCCCCTG	0.672																																					p.P216P		Atlas-SNP	.											.	CTU2	66	.	0			c.G648A						.						19.0	22.0	21.0					16																	88779224		2184	4283	6467	SO:0001628	intergenic_variant	348180	exon7			AAGACCGCCTGCC	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		chr16.hg19:g.88779224G>A		128.0	0.0		120.0	44.0	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	hg19	CCDS54058.1																																																																																			.	.		0.672	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
PIEZO1	9780	hgsc.bcm.edu	37	16	88793275	88793275	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:88793275T>C	ENST00000301015.9	-	25	3793	c.3547A>G	c.(3547-3549)Agc>Ggc	p.S1183G		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1183					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						CCGAAGATGCTGATGCGGGTG	0.647																																					p.S1183G		Atlas-SNP	.											.	PIEZO1	79	.	0			c.A3547G						.						53.0	68.0	64.0					16																	88793275		692	1590	2282	SO:0001583	missense	9780	exon25			AGATGCTGATGCG	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.3547A>G	chr16.hg19:g.88793275T>C	ENSP00000301015:p.Ser1183Gly	163.0	0.0		175.0	52.0	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	hg19	CCDS54058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.91|15.91	2.973451|2.973451	0.53614|0.53614	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015	.|T	.|0.20598	.|2.06	4.43|4.43	3.3|3.3	0.37823|0.37823	.|.	.|0.562910	.|0.21462	.|N	.|0.074153	T|T	0.46268|0.46268	0.1384|0.1384	M|M	0.83384|0.83384	2.64|2.64	0.80722|0.80722	D|D	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.77557	.|0.99	T|T	0.43212|0.43212	-0.9405|-0.9405	5|10	.|0.62326	.|D	.|0.03	-36.4888|-36.4888	10.0646|10.0646	0.42295|0.42295	0.0:0.0:0.1697:0.8303|0.0:0.0:0.1697:0.8303	.|.	.|1183	.|Q92508	.|PIEZ1_HUMAN	R|G	1128|1183	.|ENSP00000301015:S1183G	.|ENSP00000301015:S1183G	Q|S	-|-	2|1	0|0	FAM38A|FAM38A	87320776|87320776	1.000000|1.000000	0.71417|0.71417	0.804000|0.804000	0.32291|0.32291	0.549000|0.549000	0.35272|0.35272	5.471000|5.471000	0.66762|0.66762	0.706000|0.706000	0.31912|0.31912	0.260000|0.260000	0.18958|0.18958	CAG|AGC	.	.		0.647	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
ZNF276	92822	hgsc.bcm.edu	37	16	89804261	89804261	+	Missense_Mutation	SNP	C	C	T	rs149209309		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:89804261C>T	ENST00000443381.2	+	10	1619	c.1522C>T	c.(1522-1524)Cgg>Tgg	p.R508W	FANCA_ENST00000389301.3_3'UTR|ZNF276_ENST00000446326.2_Missense_Mutation_p.R294W|ZNF276_ENST00000568064.1_Missense_Mutation_p.R416W|ZNF276_ENST00000289816.5_Missense_Mutation_p.R433W	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	508					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CTTCAAGCAGCGGAAGCACCT	0.587																																					p.R508W		Atlas-SNP	.											.	ZNF276	70	.	0			c.C1522T						.						137.0	122.0	127.0					16																	89804261		2198	4300	6498	SO:0001583	missense	92822	exon10			AAGCAGCGGAAGC	AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"""Zinc fingers, C2H2-type"""	23330	protein-coding gene	gene with protein product	"""centromere protein Z"", ""zinc finger, AD-type"""	608460	"""zinc finger protein 276 homolog (mouse)"""	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.1522C>T	chr16.hg19:g.89804261C>T	ENSP00000415836:p.Arg508Trp	156.0	0.0		166.0	7.0	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Missense_Mutation	SNP	ENST00000443381.2	hg19	CCDS45554.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561125	0.65538	.	.	ENSG00000158805	ENST00000446326;ENST00000289816;ENST00000443381	T;T;T	0.52754	0.65;0.65;0.65	5.62	4.66	0.58398	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.63331	0.2502	L	0.49640	1.575	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	T	0.66881	-0.5811	10	0.87932	D	0	-37.2611	14.9466	0.71035	0.144:0.856:0.0:0.0	.	346;508;294;433	B4DIT3;Q8N554;A8K186;Q8N554-2	.;ZN276_HUMAN;.;.	W	294;433;508	ENSP00000415999:R294W;ENSP00000289816:R433W;ENSP00000415836:R508W	ENSP00000289816:R433W	R	+	1	2	ZNF276	88331762	1.000000	0.71417	1.000000	0.80357	0.652000	0.38707	1.591000	0.36665	1.352000	0.45808	0.555000	0.69702	CGG	.	C|1.000;G|0.000		0.587	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
CENPBD1	92806	hgsc.bcm.edu	37	16	90037950	90037950	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:90037950G>A	ENST00000314994.3	-	1	992	c.381C>T	c.(379-381)ggC>ggT	p.G127G	CENPBD1_ENST00000567035.1_Intron|RP11-566K11.5_ENST00000565150.1_RNA|AFG3L1P_ENST00000437774.1_RNA	NM_145039.3	NP_659476.2	B2RD01	CENP1_HUMAN	CENPB DNA-binding domains containing 1	127	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(2)	3						gagaaccttcgccatgttcac	0.532																																					p.G127G		Atlas-SNP	.											.	CENPBD1	18	.	0			c.C381T						.						84.0	85.0	85.0					16																	90037950		1858	3692	5550	SO:0001819	synonymous_variant	92806	exon1			ACCTTCGCCATGT	AK056131	CCDS45556.1	16q24.3	2009-08-26			ENSG00000177946	ENSG00000177946			28272	protein-coding gene	gene with protein product							Standard	NM_145039		Approved	MGC16385	uc002fpr.3	B2RD01		ENST00000314994.3:c.381C>T	chr16.hg19:g.90037950G>A		215.0	0.0		188.0	67.0	NM_145039		Silent	SNP	ENST00000314994.3	hg19	CCDS45556.1																																																																																			.	.		0.532	CENPBD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421897.1	NM_145039	
SRR	63826	hgsc.bcm.edu	37	17	2227123	2227123	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:2227123A>G	ENST00000344595.5	+	8	1297	c.979A>G	c.(979-981)Aag>Gag	p.K327E	TSR1_ENST00000301364.5_3'UTR|SRR_ENST00000576848.1_Missense_Mutation_p.K101E	NM_021947.1	NP_068766.1	Q9GZT4	SRR_HUMAN	serine racemase	327					aging (GO:0007568)|brain development (GO:0007420)|D-serine biosynthetic process (GO:0070179)|D-serine metabolic process (GO:0070178)|L-serine metabolic process (GO:0006563)|protein homotetramerization (GO:0051289)|pyruvate biosynthetic process (GO:0042866)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|serine family amino acid metabolic process (GO:0009069)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|D-serine ammonia-lyase activity (GO:0008721)|glycine binding (GO:0016594)|L-serine ammonia-lyase activity (GO:0003941)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|serine racemase activity (GO:0030378)|threonine racemase activity (GO:0018114)			NS(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)	AACTTGGGTGAAGCAGGCTGA	0.393																																					p.K327E		Atlas-SNP	.											.	SRR	21	.	0			c.A979G						.						75.0	71.0	72.0					17																	2227123		2203	4300	6503	SO:0001583	missense	63826	exon8			TGGGTGAAGCAGG	AF169974	CCDS11017.1	17p13	2007-01-18			ENSG00000167720	ENSG00000167720			14398	protein-coding gene	gene with protein product		606477				17067558, 15953485, 15193426	Standard	NM_021947		Approved	ILV1, ISO1	uc002fue.1	Q9GZT4	OTTHUMG00000090583	ENST00000344595.5:c.979A>G	chr17.hg19:g.2227123A>G	ENSP00000339435:p.Lys327Glu	99.0	0.0		67.0	6.0	NM_021947	D3DTI5|Q6IA55	Missense_Mutation	SNP	ENST00000344595.5	hg19	CCDS11017.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.397930	0.25205	.	.	ENSG00000167720	ENST00000344595	D	0.99376	-5.79	5.26	1.7	0.24286	.	0.396760	0.31071	N	0.008311	D	0.94729	0.8299	N	0.08118	0	0.53688	D	0.999973	B	0.06786	0.001	B	0.04013	0.001	D	0.89397	0.3693	10	0.07813	T	0.8	0.8681	8.5224	0.33285	0.7649:0.0:0.2351:0.0	.	327	Q9GZT4	SRR_HUMAN	E	327	ENSP00000339435:K327E	ENSP00000339435:K327E	K	+	1	0	SRR	2173873	1.000000	0.71417	0.922000	0.36590	0.496000	0.33645	3.305000	0.51873	0.310000	0.22990	0.455000	0.32223	AAG	.	.		0.393	SRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207129.2	NM_021947	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2911342	2911342	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:2911342A>G	ENST00000254695.8	+	17	1487	c.1397A>G	c.(1396-1398)gAt>gGt	p.D466G	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.D451G|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.D466G|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.D447G	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	466					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						AACCTTCACGATGAGCTCCAC	0.597																																					p.D466G		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.A1397G						.						61.0	67.0	65.0					17																	2911342		2077	4202	6279	SO:0001583	missense	23108	exon17			TTCACGATGAGCT	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1397A>G	chr17.hg19:g.2911342A>G	ENSP00000254695:p.Asp466Gly	116.0	0.0		52.0	42.0	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	hg19	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.411652	0.62399	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.95573	0.8561	M	0.73598	2.24	0.80722	D	1	D;D	0.63046	0.992;0.986	P;P	0.60286	0.872;0.731	D	0.95599	0.8661	10	0.54805	T	0.06	-6.186	14.0619	0.64804	1.0:0.0:0.0:0.0	.	451;466	Q684P5-2;Q684P5	.;RPGP2_HUMAN	G	466;451;447;466	ENSP00000254695:D466G;ENSP00000389824:D451G;ENSP00000439688:D447G;ENSP00000444890:D466G	ENSP00000254695:D466G	D	+	2	0	RAP1GAP2	2858092	1.000000	0.71417	0.929000	0.37066	0.939000	0.58152	9.339000	0.96797	1.909000	0.55274	0.379000	0.24179	GAT	.	.		0.597	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
OR1A1	8383	hgsc.bcm.edu	37	17	3119841	3119841	+	Silent	SNP	G	G	A	rs142898585		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:3119841G>A	ENST00000304094.1	+	1	927	c.927G>A	c.(925-927)tcG>tcA	p.S309S		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						GAATCTCCTCGTAACCAATGT	0.473													G|||	1	0.000199681	0.0	0.0	5008	,	,		19470	0.0		0.001	False		,,,				2504	0.0				p.S309S		Atlas-SNP	.											.	OR1A1	54	.	0			c.G927A						.	G		0,4406		0,0,2203	61.0	59.0	60.0		927	-1.8	0.0	17	dbSNP_134	60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR1A1	NM_014565.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		309/310	3119841	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8383	exon1			CTCCTCGTAACCA	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"""GPCR / Class A : Olfactory receptors"""	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.927G>A	chr17.hg19:g.3119841G>A		72.0	0.0		28.0	18.0	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Silent	SNP	ENST00000304094.1	hg19	CCDS11022.1																																																																																			.	G|1.000;A|0.000		0.473	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565	
TM4SF5	9032	hgsc.bcm.edu	37	17	4686302	4686302	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:4686302T>C	ENST00000270560.3	+	4	580	c.549T>C	c.(547-549)ggT>ggC	p.G183G		NM_003963.2	NP_003954.2	O14894	T4S5_HUMAN	transmembrane 4 L six family member 5	183						integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(3)|ovary(1)	6						CGACCATTGGTGTCTTCTGCG	0.562																																					p.G183G		Atlas-SNP	.											.	TM4SF5	26	.	0			c.T549C						.						144.0	118.0	127.0					17																	4686302		2203	4300	6503	SO:0001819	synonymous_variant	9032	exon4			CATTGGTGTCTTC	AF027204	CCDS11054.1	17p13.3	2007-01-06	2005-03-21		ENSG00000142484	ENSG00000142484			11857	protein-coding gene	gene with protein product		604657	"""transmembrane 4 superfamily member 5"""			9479038	Standard	NM_003963		Approved		uc002fyw.1	O14894	OTTHUMG00000090776	ENST00000270560.3:c.549T>C	chr17.hg19:g.4686302T>C		197.0	0.0		95.0	28.0	NM_003963	Q17RW9|Q6IB79	Silent	SNP	ENST00000270560.3	hg19	CCDS11054.1																																																																																			.	.		0.562	TM4SF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207558.2		
DVL2	1856	hgsc.bcm.edu	37	17	7130768	7130768	+	Missense_Mutation	SNP	G	G	A	rs372746877		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:7130768G>A	ENST00000005340.5	-	12	1600	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W	DVL2_ENST00000575458.1_Missense_Mutation_p.R434W|DVL2_ENST00000574642.1_5'Flank	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	440	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						ATGCGGTCCCGGACTTCCAGT	0.612																																					p.R440W		Atlas-SNP	.											.	DVL2	49	.	0			c.C1318T						.	G	TRP/ARG	0,4406		0,0,2203	68.0	71.0	70.0		1318	4.8	1.0	17		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	DVL2	NM_004422.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	440/737	7130768	1,13005	2203	4300	6503	SO:0001583	missense	1856	exon12			GGTCCCGGACTTC	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.1318C>T	chr17.hg19:g.7130768G>A	ENSP00000005340:p.Arg440Trp	105.0	0.0		51.0	39.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.302374	0.81136	0.0	1.16E-4	ENSG00000004975	ENST00000005340	T	0.17370	2.28	4.76	4.76	0.60689	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.60125	-0.7324	10	0.87932	D	0	-12.4618	15.2834	0.73806	0.0:0.0:1.0:0.0	.	434;440	B4DLQ0;O14641	.;DVL2_HUMAN	W	440	ENSP00000005340:R440W	ENSP00000005340:R440W	R	-	1	2	DVL2	7071492	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.475000	0.53136	2.482000	0.83794	0.655000	0.94253	CGG	.	.		0.612	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
DNAH2	146754	hgsc.bcm.edu	37	17	7667529	7667529	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:7667529A>T	ENST00000572933.1	+	20	4734	c.3274A>T	c.(3274-3276)Atc>Ttc	p.I1092F	DNAH2_ENST00000389173.2_Missense_Mutation_p.I1092F			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1092	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GGAGACTCAGATCCCTCCCAT	0.552																																					p.I1092F		Atlas-SNP	.											.	DNAH2	498	.	0			c.A3274T						.						198.0	177.0	184.0					17																	7667529		2203	4300	6503	SO:0001583	missense	146754	exon19			ACTCAGATCCCTC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.3274A>T	chr17.hg19:g.7667529A>T	ENSP00000458355:p.Ile1092Phe	408.0	0.0		219.0	149.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	4.310	0.056889	0.08339	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.22336	1.96	4.66	4.66	0.58398	.	0.000000	0.64402	D	0.000002	T	0.08088	0.0202	N	0.03948	-0.315	0.80722	D	1	B	0.09022	0.002	B	0.13407	0.009	T	0.14364	-1.0475	10	0.02654	T	1	.	11.6042	0.51022	1.0:0.0:0.0:0.0	.	1092	Q9P225	DYH2_HUMAN	F	1092	ENSP00000373825:I1092F	ENSP00000353818:I1092F	I	+	1	0	DNAH2	7608254	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	8.156000	0.89645	1.732000	0.51606	0.454000	0.30748	ATC	.	.		0.552	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
C17orf59	54785	hgsc.bcm.edu	37	17	8092992	8092992	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:8092992C>T	ENST00000389017.4	-	1	572	c.467G>A	c.(466-468)gGc>gAc	p.G156D	MIR3676_ENST00000579470.1_RNA	NM_017622.2	NP_060092.2	Q96GS4	CQ059_HUMAN	chromosome 17 open reading frame 59	156										large_intestine(2)|lung(3)|urinary_tract(1)	6						GAACGAGCGGCCGGCTCTGCT	0.726																																					p.G156D		Atlas-SNP	.											.	C17orf59	19	.	0			c.G467A						.						11.0	15.0	13.0					17																	8092992		2086	4132	6218	SO:0001583	missense	54785	exon1			GAGCGGCCGGCTC	BC018880	CCDS11133.2	17p13.1	2005-12-16			ENSG00000196544	ENSG00000196544			25939	protein-coding gene	gene with protein product						12477932	Standard	NM_017622		Approved	FLJ20014	uc010vut.2	Q96GS4	OTTHUMG00000153930	ENST00000389017.4:c.467G>A	chr17.hg19:g.8092992C>T	ENSP00000373669:p.Gly156Asp	30.0	0.0		23.0	10.0	NM_017622	Q53HS4|Q9NXW8	Missense_Mutation	SNP	ENST00000389017.4	hg19	CCDS11133.2	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298762	0.40694	.	.	ENSG00000196544	ENST00000389017	.	.	.	4.83	3.87	0.44632	.	0.672971	0.13547	N	0.379765	T	0.27098	0.0664	L	0.29908	0.895	0.18873	N	0.999984	P	0.40602	0.723	B	0.38562	0.276	T	0.11690	-1.0577	9	0.72032	D	0.01	-7.7334	8.7548	0.34639	0.0:0.8981:0.0:0.1019	.	156	Q96GS4	CQ059_HUMAN	D	156	.	ENSP00000373669:G156D	G	-	2	0	C17orf59	8033717	0.127000	0.22367	0.229000	0.23960	0.071000	0.16799	1.524000	0.35942	1.281000	0.44480	0.561000	0.74099	GGC	.	.		0.726	C17orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333072.1	NM_017622	
MYH1	4619	hgsc.bcm.edu	37	17	10408257	10408257	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:10408257G>A	ENST00000226207.5	-	22	2655	c.2561C>T	c.(2560-2562)gCc>gTc	p.A854V	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	854					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTTCATGTTGGCCATCTCCTT	0.443																																					p.A854V		Atlas-SNP	.											.	MYH1	403	.	0			c.C2561T						.						155.0	144.0	148.0					17																	10408257		2203	4300	6503	SO:0001583	missense	4619	exon22			ATGTTGGCCATCT		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2561C>T	chr17.hg19:g.10408257G>A	ENSP00000226207:p.Ala854Val	114.0	0.0		166.0	43.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953120	0.73902	.	.	ENSG00000109061	ENST00000226207	D	0.93488	-3.23	5.48	5.48	0.80851	.	0.000000	0.42964	U	0.000638	D	0.94152	0.8124	M	0.87456	2.885	0.38141	D	0.938453	B	0.30511	0.282	B	0.34038	0.174	D	0.94392	0.7615	10	0.66056	D	0.02	.	14.5454	0.68027	0.0:0.0:0.8537:0.1463	.	854	P12882	MYH1_HUMAN	V	854	ENSP00000226207:A854V	ENSP00000226207:A854V	A	-	2	0	MYH1	10348982	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.396000	0.66297	2.749000	0.94314	0.655000	0.94253	GCC	.	.		0.443	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
ELAC2	60528	hgsc.bcm.edu	37	17	12906873	12906873	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:12906873A>G	ENST00000338034.4	-	12	1241	c.1002T>C	c.(1000-1002)gaT>gaC	p.D334D	ELAC2_ENST00000426905.3_Silent_p.D294D|ELAC2_ENST00000609345.1_5'UTR|ELAC2_ENST00000395962.2_Silent_p.D315D	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	334					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						CCACGGGGGCATCTGCCTTTC	0.597											OREG0024189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D334D		Atlas-SNP	.											.	ELAC2	48	.	0			c.T1002C						.						117.0	95.0	102.0					17																	12906873		2203	4300	6503	SO:0001819	synonymous_variant	60528	exon12			GGGGGCATCTGCC	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.1002T>C	chr17.hg19:g.12906873A>G		59.0	0.0	683	65.0	23.0	NM_173717	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	A	7.391	0.630710	0.14322	.	.	ENSG00000006744	ENST00000446899	.	.	.	5.19	-10.4	0.00318	.	.	.	.	.	T	0.14830	0.0358	.	.	.	0.23765	N	0.996904	.	.	.	.	.	.	T	0.10823	-1.0613	4	.	.	.	-5.6271	2.4027	0.04405	0.1234:0.3613:0.2621:0.2532	.	.	.	.	R	114	.	.	C	-	1	0	ELAC2	12847598	0.000000	0.05858	0.000000	0.03702	0.867000	0.49689	-0.464000	0.06688	-2.343000	0.00623	0.533000	0.62120	TGC	.	.		0.597	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
ELAC2	60528	hgsc.bcm.edu	37	17	12919138	12919138	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:12919138T>C	ENST00000338034.4	-	4	618	c.379A>G	c.(379-381)Act>Gct	p.T127A	ELAC2_ENST00000426905.3_Missense_Mutation_p.T127A|ELAC2_ENST00000609345.1_5'UTR|ELAC2_ENST00000395962.2_Missense_Mutation_p.T108A|ELAC2_ENST00000578071.1_Missense_Mutation_p.T127A	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	127					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						TCCTTTAAAGTAAGAATCATT	0.398																																					p.T127A		Atlas-SNP	.											.	ELAC2	48	.	0			c.A379G						.						106.0	109.0	108.0					17																	12919138		2203	4300	6503	SO:0001583	missense	60528	exon4			TTAAAGTAAGAAT	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.379A>G	chr17.hg19:g.12919138T>C	ENSP00000337445:p.Thr127Ala	123.0	0.0		132.0	17.0	NM_001165962	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284565	0.40394	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962	T;T;T	0.55234	0.53;0.53;0.53	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.66177	0.2763	M	0.77103	2.36	0.80722	D	1	P;D;D;P	0.59357	0.866;0.985;0.982;0.866	B;P;P;B	0.56278	0.341;0.786;0.795;0.414	T	0.71467	-0.4584	10	0.72032	D	0.01	-19.2318	11.7192	0.51672	0.0:0.0:0.0:1.0	.	127;110;108;127	B4DPL9;E9PGJ0;G5E9D5;Q9BQ52	.;.;.;RNZ2_HUMAN	A	127;127;108	ENSP00000405223:T127A;ENSP00000337445:T127A;ENSP00000379291:T108A	ENSP00000337445:T127A	T	-	1	0	ELAC2	12859863	1.000000	0.71417	0.786000	0.31890	0.997000	0.91878	6.774000	0.75012	1.855000	0.53841	0.528000	0.53228	ACT	.	.		0.398	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
ELAC2	60528	hgsc.bcm.edu	37	17	12921261	12921261	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:12921261A>G	ENST00000338034.4	-	1	243	c.4T>C	c.(4-6)Tgg>Cgg	p.W2R	ELAC2_ENST00000426905.3_Missense_Mutation_p.W2R|ELAC2_ENST00000609345.1_5'Flank|ELAC2_ENST00000395962.2_Missense_Mutation_p.W2R|ELAC2_ENST00000578071.1_Missense_Mutation_p.W2R	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	2					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						CAAAGCGCCCACATGCGCCCG	0.697																																					p.W2R		Atlas-SNP	.											.	ELAC2	48	.	0			c.T4C						.						3.0	3.0	3.0					17																	12921261		1663	3368	5031	SO:0001583	missense	60528	exon1			GCGCCCACATGCG	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.4T>C	chr17.hg19:g.12921261A>G	ENSP00000337445:p.Trp2Arg	72.0	0.0		46.0	8.0	NM_001165962	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Missense_Mutation	SNP	ENST00000338034.4	hg19	CCDS11164.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.392730	0.83011	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962	T;T;T	0.65178	0.3;-0.08;-0.14	4.88	4.88	0.63580	.	0.063071	0.64402	D	0.000002	T	0.60090	0.2242	N	0.08118	0	0.35694	D	0.815067	D;D;D;D	0.71674	0.997;0.997;0.998;0.997	D;D;D;D	0.70935	0.936;0.936;0.971;0.936	T	0.71797	-0.4484	10	0.54805	T	0.06	-13.2928	12.7538	0.57323	1.0:0.0:0.0:0.0	.	2;2;2;2	B4DPL9;E9PGJ0;G5E9D5;Q9BQ52	.;.;.;RNZ2_HUMAN	R	2	ENSP00000405223:W2R;ENSP00000337445:W2R;ENSP00000379291:W2R	ENSP00000337445:W2R	W	-	1	0	ELAC2	12861986	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	1.763000	0.38461	2.164000	0.68074	0.533000	0.62120	TGG	.	.		0.697	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
LLGL1	3996	hgsc.bcm.edu	37	17	18138832	18138832	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:18138832C>T	ENST00000316843.4	+	11	1429	c.1333C>T	c.(1333-1335)Cga>Tga	p.R445*		NM_004140.3	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1 (Drosophila)	445					axonogenesis (GO:0007409)|cortical actin cytoskeleton organization (GO:0030866)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|maintenance of apical/basal cell polarity (GO:0035090)|positive regulation of Rab GTPase activity (GO:0032851)|protein complex assembly (GO:0006461)	cell projection (GO:0042995)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome membrane (GO:0031901)|Golgi cis cisterna (GO:0000137)|myelin sheath abaxonal region (GO:0035748)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)|structural molecule activity (GO:0005198)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_neural(463;0.228)					GCCGTCACAGCGAGGGCTGCT	0.637																																					p.R445X		Atlas-SNP	.											.	LLGL1	61	.	0			c.C1333T						.						87.0	78.0	81.0					17																	18138832		2203	4300	6503	SO:0001587	stop_gained	3996	exon11			TCACAGCGAGGGC		CCDS32586.1	17p11.2	2013-01-10	2001-11-28		ENSG00000131899	ENSG00000131899		"""WD repeat domain containing"""	6628	protein-coding gene	gene with protein product		600966	"""lethal giant larvae (Drosophila) homolog 1"""	DLG4, LLGL, HUGL, HUGL-1		7542763, 8565641	Standard	XM_005256643		Approved		uc002gsp.3	Q15334	OTTHUMG00000059396	ENST00000316843.4:c.1333C>T	chr17.hg19:g.18138832C>T	ENSP00000321537:p.Arg445*	55.0	0.0		83.0	34.0	NM_004140	A7MBM7|O00188|Q58F11|Q86UK6	Nonsense_Mutation	SNP	ENST00000316843.4	hg19	CCDS32586.1	.	.	.	.	.	.	.	.	.	.	C	37	6.043830	0.97231	.	.	ENSG00000131899	ENST00000316843	.	.	.	5.19	1.91	0.25777	.	0.244039	0.40385	N	0.001113	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.1751	7.7692	0.28997	0.3714:0.5498:0.0:0.0788	.	.	.	.	X	445	.	ENSP00000321537:R445X	R	+	1	2	LLGL1	18079557	0.997000	0.39634	0.989000	0.46669	0.483000	0.33249	0.819000	0.27308	0.883000	0.36040	0.650000	0.86243	CGA	.	.		0.637	LLGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132067.3		
MAPK7	5598	hgsc.bcm.edu	37	17	19284128	19284128	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:19284128T>C	ENST00000308406.5	+	4	992	c.606T>C	c.(604-606)ggT>ggC	p.G202G	MAPK7_ENST00000571657.1_Intron|MFAP4_ENST00000574313.2_5'Flank|B9D1_ENST00000468679.3_5'Flank|MAPK7_ENST00000395604.3_Silent_p.G202G|MAPK7_ENST00000299612.7_Silent_p.G63G|B9D1_ENST00000477478.2_5'Flank|B9D1_ENST00000575403.1_5'Flank|MAPK7_ENST00000395602.4_Silent_p.G202G	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	202	Necessary for oligomerization. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					GTGACTTTGGTATGGCTCGTG	0.557																																					p.G202G		Atlas-SNP	.											.	MAPK7	72	.	0			c.T606C						.						128.0	107.0	114.0					17																	19284128		2203	4300	6503	SO:0001819	synonymous_variant	5598	exon4			CTTTGGTATGGCT	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"""Mitogen-activated protein kinase cascade / Kinases"""	6880	protein-coding gene	gene with protein product	"""BMK1 kinase"", ""extracellular-signal-regulated kinase 5"""	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.606T>C	chr17.hg19:g.19284128T>C		108.0	0.0		128.0	61.0	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Silent	SNP	ENST00000308406.5	hg19	CCDS11206.1																																																																																			.	.		0.557	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033	
C17orf51	339263	hgsc.bcm.edu	37	17	21438727	21438727	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:21438727G>T	ENST00000391411.5	-	2	757	c.500C>A	c.(499-501)gCc>gAc	p.A167D	RP11-822E23.2_ENST00000579239.1_RNA|C17orf51_ENST00000412778.3_3'UTR|RP11-822E23.8_ENST00000426261.2_RNA|C17orf51_ENST00000535846.1_5'UTR	NM_001113434.3	NP_001106905.1	A8MQB3	CQ051_HUMAN	chromosome 17 open reading frame 51	167										endometrium(1)	1						TTTTTCTGGGGCACTTCTCCC	0.502																																					p.A167D		Atlas-SNP	.											.	C17orf51	24	.	0			c.C500A						.						94.0	79.0	84.0					17																	21438727		692	1591	2283	SO:0001583	missense	339263	exon2			TCTGGGGCACTTC	BC010612	CCDS45629.1	17p11.2	2012-10-11			ENSG00000212719	ENSG00000212719			27904	protein-coding gene	gene with protein product							Standard	XM_005256621		Approved	FLJ12977, FLJ31874, FLJ33618	uc002gyw.4	A8MQB3	OTTHUMG00000132832	ENST00000391411.5:c.500C>A	chr17.hg19:g.21438727G>T	ENSP00000384286:p.Ala167Asp	67.0	0.0		54.0	23.0	NM_001113434	B2RN29|B5MCL4	Missense_Mutation	SNP	ENST00000391411.5	hg19	CCDS45629.1	.	.	.	.	.	.	.	.	.	.	G	8.637	0.895006	0.17613	.	.	ENSG00000212719	ENST00000391411	.	.	.	1.11	0.0786	0.14413	.	.	.	.	.	T	0.26919	0.0659	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	D	0.68483	0.958	T	0.11867	-1.0570	8	0.87932	D	0	.	3.395	0.07303	0.293:0.0:0.707:0.0	.	167	A8MQB3	CQ051_HUMAN	D	167	.	ENSP00000384286:A167D	A	-	2	0	C17orf51	21379320	0.537000	0.26386	0.026000	0.17262	0.074000	0.17049	1.655000	0.37345	0.026000	0.15269	-0.218000	0.12543	GCC	.	.		0.502	C17orf51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256298.3	NM_001113434	
NOS2	4843	hgsc.bcm.edu	37	17	26096024	26096024	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:26096024G>T	ENST00000313735.6	-	17	2246	c.2013C>A	c.(2011-2013)agC>agA	p.S671R		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	671	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GCACGGCCCAGCTGCGGAAGG	0.612																																					p.S671R		Atlas-SNP	.											.	NOS2	113	.	0			c.C2013A						.						51.0	45.0	47.0					17																	26096024		2203	4299	6502	SO:0001583	missense	4843	exon17			GGCCCAGCTGCGG	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2013C>A	chr17.hg19:g.26096024G>T	ENSP00000327251:p.Ser671Arg	27.0	0.0		34.0	15.0	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.788330	0.49997	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.59224	0.28	5.16	5.16	0.70880	Flavodoxin/nitric oxide synthase (2);	0.332353	0.32884	N	0.005540	T	0.50718	0.1632	L	0.31526	0.94	0.42957	D	0.994392	B;P	0.38129	0.032;0.619	B;B	0.43123	0.075;0.409	T	0.48703	-0.9012	10	0.30078	T	0.28	.	14.2421	0.65963	0.0:0.0:0.8507:0.1493	.	636;671	F8WEM3;P35228	.;NOS2_HUMAN	R	671;632;636	ENSP00000327251:S671R	ENSP00000305638:S636R	S	-	3	2	NOS2	23120151	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.442000	0.44873	2.397000	0.81536	0.462000	0.41574	AGC	.	.		0.612	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
SLC46A1	113235	hgsc.bcm.edu	37	17	26731651	26731651	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:26731651G>A	ENST00000440501.1	-	2	1159	c.1064C>T	c.(1063-1065)aCg>aTg	p.T355M	SLC46A1_ENST00000321666.5_Missense_Mutation_p.T355M|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	355					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	CATGAGAGGCGTGATAGTGGC	0.592																																					p.T355M		Atlas-SNP	.											.	SLC46A1	17	.	0			c.C1064T						.						41.0	40.0	40.0					17																	26731651		2006	4178	6184	SO:0001583	missense	113235	exon2			AGAGGCGTGATAG	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.1064C>T	chr17.hg19:g.26731651G>A	ENSP00000395653:p.Thr355Met	96.0	0.0		99.0	45.0	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	hg19		.	.	.	.	.	.	.	.	.	.	G	19.74	3.883402	0.72410	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	T;T	0.57752	0.38;0.38	5.11	5.11	0.69529	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.72969	0.3527	.	.	.	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	T	0.72899	-0.4152	9	0.39692	T	0.17	-6.3156	18.5385	0.91019	0.0:0.0:1.0:0.0	.	355;355;355	B4DJ17;Q96NT5-2;Q96NT5	.;.;PCFT_HUMAN	M	355	ENSP00000395653:T355M;ENSP00000318828:T355M	ENSP00000318828:T355M	T	-	2	0	SLC46A1	23755778	1.000000	0.71417	0.997000	0.53966	0.702000	0.40608	9.444000	0.97578	2.360000	0.80028	0.563000	0.77884	ACG	.	.		0.592	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669	
SLC46A1	113235	hgsc.bcm.edu	37	17	26732401	26732401	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:26732401C>T	ENST00000440501.1	-	2	409	c.314G>A	c.(313-315)gGa>gAa	p.G105E	SLC46A1_ENST00000321666.5_Missense_Mutation_p.G105E|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	105					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	GCTCCAAGCTCCCAGCAGGGT	0.642																																					p.G105E		Atlas-SNP	.											.	SLC46A1	17	.	0			c.G314A						.						11.0	15.0	14.0					17																	26732401		2027	4173	6200	SO:0001583	missense	113235	exon2			CAAGCTCCCAGCA	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.314G>A	chr17.hg19:g.26732401C>T	ENSP00000395653:p.Gly105Glu	180.0	0.0		182.0	72.0	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	hg19		.	.	.	.	.	.	.	.	.	.	c	16.21	3.059212	0.55325	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	T;T	0.73469	-0.75;-0.75	5.38	5.38	0.77491	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.87430	0.6175	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.998;1.0	D	0.88579	0.3135	9	0.87932	D	0	-8.5213	19.0886	0.93217	0.0:1.0:0.0:0.0	.	105;105;105	B4DJ17;Q96NT5-2;Q96NT5	.;.;PCFT_HUMAN	E	105	ENSP00000395653:G105E;ENSP00000318828:G105E	ENSP00000318828:G105E	G	-	2	0	SLC46A1	23756528	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	7.391000	0.79828	2.685000	0.91497	0.556000	0.70494	GGA	.	.		0.642	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669	
NEK8	284086	hgsc.bcm.edu	37	17	27061037	27061037	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:27061037G>T	ENST00000268766.6	+	2	118	c.84G>T	c.(82-84)aaG>aaT	p.K28N	AC010761.6_ENST00000584779.1_RNA|NEK8_ENST00000593261.1_3'UTR	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	28	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					CTGACCAGAAGCTGGTGATCA	0.572																																					p.K28N	NSCLC(6;19 293 14866 25253 49845)	Atlas-SNP	.											.	NEK8	76	.	0			c.G84T						.						94.0	84.0	88.0					17																	27061037		2203	4300	6503	SO:0001583	missense	284086	exon2			CCAGAAGCTGGTG	AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"""NIMA (never in mitosis gene a)- related kinase 8"""			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.84G>T	chr17.hg19:g.27061037G>T	ENSP00000268766:p.Lys28Asn	89.0	0.0		90.0	24.0	NM_178170	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Missense_Mutation	SNP	ENST00000268766.6	hg19	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.360634	0.41801	.	.	ENSG00000160602	ENST00000543014;ENST00000268766	T;T	0.67698	-0.28;-0.28	4.92	3.93	0.45458	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.107611	0.64402	D	0.000006	T	0.59376	0.2189	L	0.39467	1.215	0.43321	D	0.995347	B	0.23128	0.08	B	0.29942	0.109	T	0.61964	-0.6954	10	0.56958	D	0.05	.	12.7217	0.57146	0.0814:0.0:0.9186:0.0	.	28	Q86SG6	NEK8_HUMAN	N	28	ENSP00000465859:K28N;ENSP00000268766:K28N	ENSP00000268766:K28N	K	+	3	2	NEK8	24085164	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.319000	0.33655	2.267000	0.75376	0.313000	0.20887	AAG	.	.		0.572	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2		
EFCAB5	374786	hgsc.bcm.edu	37	17	28419089	28419089	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:28419089C>T	ENST00000394835.3	+	21	4330	c.4138C>T	c.(4138-4140)Cgt>Tgt	p.R1380C	RP11-1148O4.2_ENST00000582938.1_RNA|EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Missense_Mutation_p.R1256C	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1380							calcium ion binding (GO:0005509)	p.R1380C(1)		breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GAAACTAGTGCGTGACATCCT	0.388																																					p.R1380C		Atlas-SNP	.											EFCAB5,NS,carcinoma,0,1	EFCAB5	122	.	1	Substitution - Missense(1)	lung(1)	c.C4138T						.						85.0	86.0	86.0					17																	28419089		1906	4126	6032	SO:0001583	missense	374786	exon21			CTAGTGCGTGACA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.4138C>T	chr17.hg19:g.28419089C>T	ENSP00000378312:p.Arg1380Cys	163.0	0.0		143.0	43.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980031	0.53827	.	.	ENSG00000176927	ENST00000394835;ENST00000320856;ENST00000419434	T;T;T	0.10477	2.87;2.87;2.88	5.75	5.75	0.90469	.	0.521011	0.21036	N	0.081252	T	0.08758	0.0217	N	0.08118	0	0.80722	D	1	D;D	0.57257	0.979;0.979	B;B	0.43123	0.409;0.409	T	0.24083	-1.0170	10	0.87932	D	0	-0.1214	18.943	0.92611	0.0:1.0:0.0:0.0	.	1256;1380	E7EVS9;A4FU69	.;EFCB5_HUMAN	C	1380;1256;1062	ENSP00000378312:R1380C;ENSP00000322003:R1256C;ENSP00000417009:R1062C	ENSP00000322003:R1256C	R	+	1	0	EFCAB5	25443215	0.063000	0.20901	0.011000	0.14972	0.025000	0.11179	2.608000	0.46308	2.714000	0.92807	0.655000	0.94253	CGT	.	.		0.388	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
PSMD11	5717	hgsc.bcm.edu	37	17	30806365	30806365	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:30806365C>T	ENST00000261712.3	+	10	1272	c.1009C>T	c.(1009-1011)Cga>Tga	p.R337*	PSMD11_ENST00000457654.2_Nonsense_Mutation_p.R337*	NM_001270482.1|NM_002815.3	NP_001257411.1|NP_002806.2	O00231	PSD11_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	337	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome assembly (GO:0043248)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stem cell differentiation (GO:0048863)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			GAATCTGATCCGAGTCATTGA	0.517																																					p.R337X	Ovarian(130;1038 1716 9294 11987 19279)	Atlas-SNP	.											.	PSMD11	41	.	0			c.C1009T						.						136.0	131.0	132.0					17																	30806365		2203	4300	6503	SO:0001587	stop_gained	5717	exon10			CTGATCCGAGTCA	AB003102	CCDS11272.1	17q12	2008-05-22			ENSG00000108671	ENSG00000108671		"""Proteasome (prosome, macropain) subunits"""	9556	protein-coding gene	gene with protein product		604449				9426256, 9119060	Standard	NM_001270482		Approved	S9, p44.5, MGC3844, Rpn6	uc010cta.2	O00231	OTTHUMG00000132811	ENST00000261712.3:c.1009C>T	chr17.hg19:g.30806365C>T	ENSP00000261712:p.Arg337*	136.0	0.0		93.0	36.0	NM_002815	A8K3I7|E1P663|O00495|Q53FT5	Nonsense_Mutation	SNP	ENST00000261712.3	hg19	CCDS11272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.459853|5.459853	0.96240|0.96240	.|.	.|.	ENSG00000108671|ENSG00000108671	ENST00000457654|ENST00000261712	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.43875|.	0.1267|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.36504|.	-0.9745|.	3|.	.|0.02654	.|T	.|1	-2.6927|-2.6927	16.7464|16.7464	0.85473|0.85473	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	L|X	74|337	.|.	.|ENSP00000261712:R337X	P|R	+|+	2|1	0|2	PSMD11|PSMD11	27830478|27830478	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	1.912000|1.912000	0.39946|0.39946	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	CCG|CGA	.	.		0.517	PSMD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256252.2	NM_002815	
LIG3	3980	hgsc.bcm.edu	37	17	33325644	33325644	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:33325644C>T	ENST00000378526.4	+	14	2144	c.2011C>T	c.(2011-2013)Cgg>Tgg	p.R671W	LIG3_ENST00000262327.5_Missense_Mutation_p.R671W	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	671					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)	GCCTGGGAAGCGGCACTGGCT	0.532								Other BER factors			OREG0024326	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R671W		Atlas-SNP	.											.	LIG3	164	.	0			c.C2011T						.						119.0	128.0	125.0					17																	33325644		2203	4300	6503	SO:0001583	missense	3980	exon14			GGGAAGCGGCACT		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.2011C>T	chr17.hg19:g.33325644C>T	ENSP00000367787:p.Arg671Trp	84.0	0.0	839	83.0	33.0	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	C	27.5	4.841329	0.91197	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	D;D	0.87334	-2.24;-2.24	5.27	4.29	0.51040	DNA ligase, ATP-dependent, central (2);DNA ligase, ATP-dependent, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96207	0.8763	H	0.98901	4.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97697	1.0182	10	0.87932	D	0	-8.4847	14.4308	0.67249	0.1483:0.8517:0.0:0.0	.	671;671	P49916;E5KLB6	DNLI3_HUMAN;.	W	671	ENSP00000367787:R671W;ENSP00000262327:R671W	ENSP00000262327:R671W	R	+	1	2	LIG3	30349757	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.745000	0.68672	1.426000	0.47256	0.655000	0.94253	CGG	.	.		0.532	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975	
LIG3	3980	hgsc.bcm.edu	37	17	33329755	33329755	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:33329755G>T	ENST00000378526.4	+	19	2876	c.2743G>T	c.(2743-2745)Gtg>Ttg	p.V915L	RP5-837J1.2_ENST00000578488.1_RNA|LIG3_ENST00000262327.5_Missense_Mutation_p.V915L	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	915					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)	GTCTTCTCCAGTGAAAGTAGG	0.552								Other BER factors																													p.V915L		Atlas-SNP	.											.	LIG3	164	.	0			c.G2743T						.						66.0	54.0	58.0					17																	33329755		2203	4300	6503	SO:0001583	missense	3980	exon19			TCTCCAGTGAAAG		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.2743G>T	chr17.hg19:g.33329755G>T	ENSP00000367787:p.Val915Leu	234.0	0.0		224.0	89.0	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	G	9.380	1.072830	0.20147	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	T;T	0.61742	0.22;0.08	3.51	2.52	0.30459	.	0.704560	0.13672	N	0.370811	T	0.43897	0.1268	L	0.43152	1.355	0.24286	N	0.995189	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.25502	-1.0130	10	0.13470	T	0.59	-6.2242	8.27	0.31838	0.0:0.0:0.7635:0.2365	.	915;915	P49916;E5KLB6	DNLI3_HUMAN;.	L	915	ENSP00000367787:V915L;ENSP00000262327:V915L	ENSP00000262327:V915L	V	+	1	0	LIG3	30353868	.	.	0.285000	0.24819	0.753000	0.42808	.	.	1.033000	0.39918	0.563000	0.77884	GTG	.	.		0.552	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975	
CCL15	6359	hgsc.bcm.edu	37	17	34324830	34324830	+	Missense_Mutation	SNP	C	C	T	rs551984257	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:34324830C>T	ENST00000354059.4	-	4	867	c.315G>A	c.(313-315)atG>atA	p.M105I	CCL14_ENST00000536149.1_5'UTR|CCL15-CCL14_ENST00000481427.2_Missense_Mutation_p.M105I	NM_032965.4	NP_116741.1	Q16663	CCL15_HUMAN	chemokine (C-C motif) ligand 15	105					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|immune response (GO:0006955)|positive chemotaxis (GO:0050918)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)|receptor binding (GO:0005102)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCAGCTTTTTCATGCAATCCT	0.468													C|||	2	0.000399361	0.0	0.0	5008	,	,		16643	0.0		0.0	False		,,,				2504	0.002				p.M105I		Atlas-SNP	.											.	CCL15	15	.	0			c.G315A						.						78.0	74.0	76.0					17																	34324830		2203	4300	6503	SO:0001583	missense	6359	exon4			CTTTTTCATGCAA	AF031587	CCDS11304.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000267596	ENSG00000275718		"""Chemokine ligands"", ""Endogenous ligands"""	10613	protein-coding gene	gene with protein product	"""leukotactin 1"", ""CC chemokine 3"", ""macrophage inflammatory protein 5"", ""chemokine CC-2"", ""MIP-1 delta"""	601393	"""small inducible cytokine subfamily A (Cys-Cys), member 15"""	SCYA15		8661057	Standard	NM_032965		Approved	HCC-2, NCC-3, SCYL3, MIP-5, Lkn-1, MIP-1d, HMRP-2B	uc010wcu.2	Q16663	OTTHUMG00000188406	ENST00000354059.4:c.315G>A	chr17.hg19:g.34324830C>T	ENSP00000293276:p.Met105Ile	76.0	0.0		103.0	7.0	NM_032965	B2RU34|E1P651|Q9UM74	Missense_Mutation	SNP	ENST00000354059.4	hg19	CCDS11304.1	.	.	.	.	.	.	.	.	.	.	C	0.230	-1.022123	0.02061	.	.	ENSG00000161574	ENST00000354059	T	0.04194	3.68	4.72	-3.32	0.04973	Chemokine interleukin-8-like domain (3);	1.213440	0.06406	N	0.719711	T	0.01800	0.0057	N	0.05534	-0.03	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.43925	-0.9361	10	0.06099	T	0.92	.	0.8665	0.01205	0.1487:0.2889:0.2735:0.289	.	105	Q16663	CCL15_HUMAN	I	105	ENSP00000293276:M105I	ENSP00000293276:M105I	M	-	3	0	CCL15	31348943	0.033000	0.19621	0.050000	0.19076	0.009000	0.06853	-0.032000	0.12266	-0.640000	0.05495	-0.469000	0.05056	ATG	.	.		0.468	CCL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256584.2	NM_004167	
AATF	26574	hgsc.bcm.edu	37	17	35310201	35310201	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:35310201A>G	ENST00000225402.5	+	3	550	c.299A>G	c.(298-300)gAt>gGt	p.D100G		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	100	Glu-rich.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				GAAATATCTGATGAGGAAGGG	0.453																																					p.D100G	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.A299G						.						77.0	80.0	79.0					17																	35310201		2203	4300	6503	SO:0001583	missense	26574	exon3			TATCTGATGAGGA	AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.299A>G	chr17.hg19:g.35310201A>G	ENSP00000225402:p.Asp100Gly	156.0	0.0		165.0	55.0	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Missense_Mutation	SNP	ENST00000225402.5	hg19	CCDS32632.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.782088	0.31502	.	.	ENSG00000108270	ENST00000225402	T	0.31247	1.5	5.84	4.75	0.60458	.	0.147974	0.64402	D	0.000016	T	0.32194	0.0821	M	0.64997	1.995	0.45554	D	0.998507	P	0.39060	0.657	B	0.37650	0.255	T	0.07616	-1.0763	10	0.52906	T	0.07	-2.2421	11.5879	0.50929	0.8509:0.1491:0.0:0.0	.	100	Q9NY61	AATF_HUMAN	G	100	ENSP00000225402:D100G	ENSP00000225402:D100G	D	+	2	0	AATF	32384314	1.000000	0.71417	0.379000	0.26080	0.006000	0.05464	4.056000	0.57448	1.003000	0.39130	0.533000	0.62120	GAT	.	.		0.453	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138	
AATF	26574	hgsc.bcm.edu	37	17	35346611	35346611	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:35346611A>T	ENST00000225402.5	+	7	1466	c.1215A>T	c.(1213-1215)agA>agT	p.R405S		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	405	RB1 and SP1 binding.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				ACAAAGAGAGATTACTTCGAA	0.493																																					p.R405S	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.A1215T						.						279.0	270.0	273.0					17																	35346611		2203	4300	6503	SO:0001583	missense	26574	exon7			AGAGAGATTACTT	AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.1215A>T	chr17.hg19:g.35346611A>T	ENSP00000225402:p.Arg405Ser	89.0	0.0		73.0	25.0	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Missense_Mutation	SNP	ENST00000225402.5	hg19	CCDS32632.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.980851	0.74474	.	.	ENSG00000108270	ENST00000225402	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.80303	0.4598	M	0.88105	2.93	0.54753	D	0.999985	D	0.89917	1.0	D	0.76071	0.987	T	0.83111	-0.0123	9	0.62326	D	0.03	-15.7616	10.3345	0.43841	0.8532:0.0:0.0:0.1467	.	405	Q9NY61	AATF_HUMAN	S	405	.	ENSP00000225402:R405S	R	+	3	2	AATF	32420724	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	1.316000	0.33620	1.963000	0.57068	0.383000	0.25322	AGA	.	.		0.493	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138	
ACACA	31	hgsc.bcm.edu	37	17	35620662	35620662	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:35620662G>A	ENST00000394406.2	-	11	1334	c.1144C>T	c.(1144-1146)Cgc>Tgc	p.R382C	ACACA_ENST00000353139.5_Missense_Mutation_p.R419C|ACACA_ENST00000335166.5_Missense_Mutation_p.R304C|ACACA_ENST00000360679.3_Missense_Mutation_p.R324C	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	382	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TGATGCCTGCGTTGTACAGAG	0.418																																					p.R419C	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											ACACA_ENST00000353139,NS,malignant_melanoma,0,2	ACACA	395	.	0			c.C1255T						.						259.0	235.0	243.0					17																	35620662		2203	4300	6503	SO:0001583	missense	31	exon11			GCCTGCGTTGTAC	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1144C>T	chr17.hg19:g.35620662G>A	ENSP00000377928:p.Arg382Cys	123.0	0.0		142.0	62.0	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930444	0.92389	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	D;D;D;D	0.97924	-4.61;-4.61;-4.61;-4.61	5.78	4.78	0.61160	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.85682	D	0.000000	D	0.99390	0.9785	H	0.99689	4.705	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	D	0.97936	1.0323	10	0.87932	D	0	-10.3882	16.221	0.82258	0.0:0.0:0.8665:0.1335	.	419;382;324	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	C	419;324;382;406;304	ENSP00000344789:R419C;ENSP00000353898:R324C;ENSP00000377928:R382C;ENSP00000335323:R304C	ENSP00000335323:R304C	R	-	1	0	ACACA	32694775	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	6.744000	0.74854	2.722000	0.93159	0.655000	0.94253	CGC	.	.		0.418	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
MED1	5469	hgsc.bcm.edu	37	17	37584012	37584012	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:37584012A>G	ENST00000394287.3	-	10	886	c.681T>C	c.(679-681)tcT>tcC	p.S227S	MED1_ENST00000300651.6_Silent_p.S227S			O95243	MBD4_HUMAN	mediator complex subunit 1	112					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		GGTCAGAAGGAGAGACATAGT	0.318										HNSCC(31;0.082)																											p.S227S	Pancreas(21;279 768 2492 4877 24026)	Atlas-SNP	.											.	MED1	123	.	0			c.T681C						.						96.0	95.0	96.0					17																	37584012		2203	4300	6503	SO:0001819	synonymous_variant	5469	exon10			AGAAGGAGAGACA	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"""PPAR binding protein"""	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000394287.3:c.681T>C	chr17.hg19:g.37584012A>G		88.0	0.0		96.0	36.0	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Silent	SNP	ENST00000394287.3	hg19																																																																																				.	.		0.318	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000256944.1	NM_004774	
MED24	9862	hgsc.bcm.edu	37	17	38183700	38183700	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:38183700C>T	ENST00000394128.2	-	16	1547	c.1466G>A	c.(1465-1467)cGg>cAg	p.R489Q	MED24_ENST00000394127.2_Missense_Mutation_p.R476Q|MED24_ENST00000501516.3_Missense_Mutation_p.R508Q|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000394126.1_Missense_Mutation_p.R514Q|MED24_ENST00000356271.3_Missense_Mutation_p.R476Q	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	489					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R489L(1)		autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CAGCAGGGCCCGGACGGAGGC	0.647											OREG0024386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R489Q		Atlas-SNP	.											MED24,NS,carcinoma,0,1	MED24	89	.	1	Substitution - Missense(1)	lung(1)	c.G1466A						.						33.0	32.0	33.0					17																	38183700		2203	4300	6503	SO:0001583	missense	9862	exon16			AGGGCCCGGACGG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1466G>A	chr17.hg19:g.38183700C>T	ENSP00000377686:p.Arg489Gln	167.0	0.0	876	112.0	53.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527162	0.64860	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	T;T;T	0.61980	0.06;0.06;0.06	4.89	4.89	0.63831	Mediator complex, subunit Med24, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.78855	0.4349	M	0.72894	2.215	0.80722	D	1	P;D;D;D;D;D	0.89917	0.953;0.998;1.0;0.998;0.998;1.0	P;P;D;D;D;D	0.81914	0.543;0.845;0.995;0.986;0.992;0.995	T	0.81230	-0.1027	10	0.72032	D	0.01	-6.9283	18.2773	0.90087	0.0:1.0:0.0:0.0	.	430;439;399;476;489;431	B4DSQ6;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;MED24_HUMAN;.	Q	489;489;489;439;476;431;399	ENSP00000377686:R489Q;ENSP00000443344:R439Q;ENSP00000377685:R476Q	ENSP00000348610:R489Q	R	-	2	0	MED24	35437226	1.000000	0.71417	0.097000	0.21041	0.175000	0.22909	4.792000	0.62467	2.534000	0.85438	0.655000	0.94253	CGG	.	.		0.647	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
KRT20	54474	hgsc.bcm.edu	37	17	39034421	39034421	+	Missense_Mutation	SNP	C	C	T	rs377652428		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39034421C>T	ENST00000167588.3	-	6	1156	c.1115G>A	c.(1114-1116)cGc>cAc	p.R372H		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	372	Coil 2.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				TTCCAGAAGGCGGCGGTAAGT	0.418																																					p.R372H		Atlas-SNP	.											.	KRT20	38	.	0			c.G1115A						.	C	HIS/ARG	0,4406		0,0,2203	241.0	210.0	220.0		1115	0.9	0.9	17		220	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT20	NM_019010.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	372/425	39034421	1,13005	2203	4300	6503	SO:0001583	missense	54474	exon6			AGAAGGCGGCGGT	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.1115G>A	chr17.hg19:g.39034421C>T	ENSP00000167588:p.Arg372His	97.0	0.0		90.0	39.0	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	hg19	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.854326	0.71719	0.0	1.16E-4	ENSG00000171431	ENST00000167588	D	0.89810	-2.57	5.27	0.929	0.19449	Filament (1);Intermediate filament protein, conserved site (1);	0.195280	0.36591	N	0.002513	D	0.91043	0.7182	M	0.66939	2.045	0.23309	N	0.997932	D	0.89917	1.0	D	0.72625	0.978	T	0.82210	-0.0570	10	0.54805	T	0.06	.	5.4275	0.16433	0.1237:0.5308:0.0:0.3456	.	372	P35900	K1C20_HUMAN	H	372	ENSP00000167588:R372H	ENSP00000167588:R372H	R	-	2	0	KRT20	36287947	0.413000	0.25400	0.908000	0.35775	0.997000	0.91878	0.893000	0.28336	-0.029000	0.13827	0.591000	0.81541	CGC	.	.		0.418	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
KRT20	54474	hgsc.bcm.edu	37	17	39041125	39041125	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39041125A>C	ENST00000167588.3	-	1	354	c.313T>G	c.(313-315)Tgg>Ggg	p.W105G		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	105	Coil 1A.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				GTTTCGTACCACTGCTTGATT	0.502																																					p.W105G		Atlas-SNP	.											.	KRT20	38	.	0			c.T313G						.						114.0	102.0	106.0					17																	39041125		2203	4300	6503	SO:0001583	missense	54474	exon1			CGTACCACTGCTT	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.313T>G	chr17.hg19:g.39041125A>C	ENSP00000167588:p.Trp105Gly	117.0	0.0		122.0	6.0	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	hg19	CCDS11379.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800851	0.50315	.	.	ENSG00000171431	ENST00000167588	D	0.88975	-2.45	5.65	5.65	0.86999	Filament (1);	0.000000	0.56097	D	0.000035	D	0.95338	0.8487	M	0.89601	3.045	0.46478	D	0.999069	D	0.76494	0.999	D	0.72338	0.977	D	0.96110	0.9076	10	0.72032	D	0.01	.	15.8704	0.79115	1.0:0.0:0.0:0.0	.	105	P35900	K1C20_HUMAN	G	105	ENSP00000167588:W105G	ENSP00000167588:W105G	W	-	1	0	KRT20	36294651	1.000000	0.71417	1.000000	0.80357	0.106000	0.19336	7.257000	0.78362	2.141000	0.66446	0.533000	0.62120	TGG	.	.		0.502	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
KRT31	3881	hgsc.bcm.edu	37	17	39551555	39551555	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39551555A>T	ENST00000251645.2	-	5	870	c.818T>A	c.(817-819)aTc>aAc	p.I273N		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	273	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				TCTCAGCTCGATGATCTCCGC	0.582																																					p.I273N		Atlas-SNP	.											.	KRT31	158	.	0			c.T818A						.						123.0	112.0	115.0					17																	39551555		2203	4300	6503	SO:0001583	missense	3881	exon5			AGCTCGATGATCT	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6448	protein-coding gene	gene with protein product	"""hard keratin type I 1"""	601077	"""keratin, hair, acidic, 1"""	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.818T>A	chr17.hg19:g.39551555A>T	ENSP00000251645:p.Ile273Asn	107.0	0.0		105.0	42.0	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	hg19	CCDS11391.1	.	.	.	.	.	.	.	.	.	.	a	16.02	3.005161	0.54254	.	.	ENSG00000094796	ENST00000251645	T	0.75938	-0.98	5.36	4.27	0.50696	Filament (1);	0.000000	0.64402	D	0.000006	T	0.75496	0.3857	L	0.33339	1.005	0.35822	D	0.824646	D	0.67145	0.996	D	0.67900	0.954	T	0.79577	-0.1746	10	0.87932	D	0	.	6.6752	0.23090	0.739:0.0:0.261:0.0	.	273	Q15323	K1H1_HUMAN	N	273	ENSP00000251645:I273N	ENSP00000251645:I273N	I	-	2	0	KRT31	36805081	1.000000	0.71417	0.977000	0.42913	0.679000	0.39708	3.951000	0.56684	0.853000	0.35312	0.456000	0.33151	ATC	.	.		0.582	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277	
NT5C3B	115024	hgsc.bcm.edu	37	17	39983842	39983842	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:39983842T>C	ENST00000435506.2	-	8	673	c.604A>G	c.(604-606)Aca>Gca	p.T202A	NT5C3B_ENST00000269534.8_Missense_Mutation_p.T194A|NT5C3B_ENST00000521789.1_Intron			Q969T7	5NT3B_HUMAN	5'-nucleotidase, cytosolic IIIB	202					nucleotide metabolic process (GO:0009117)	cytoplasm (GO:0005737)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										TTGTTGTATGTGTGTATGAGC	0.502																																					p.T202A		Atlas-SNP	.											.	.	.	.	0			c.A604G						.						155.0	147.0	150.0					17																	39983842		2203	4300	6503	SO:0001583	missense	115024	exon8			TGTATGTGTGTAT		CCDS11410.1, CCDS11410.2	17q21.2	2013-01-31	2013-01-31	2013-01-31	ENSG00000141698	ENSG00000141698	3.1.3.5		28300	protein-coding gene	gene with protein product			"""5'-nucleotidase, cytosolic III-like"""	NT5C3L		23223233	Standard	NM_052935		Approved	MGC20781	uc021txo.1	Q969T7	OTTHUMG00000133499	ENST00000435506.2:c.604A>G	chr17.hg19:g.39983842T>C	ENSP00000389948:p.Thr202Ala	209.0	0.0		184.0	60.0	NM_052935	A8MWB9|C9JKC4|Q7L3B7	Missense_Mutation	SNP	ENST00000435506.2	hg19	CCDS11410.2	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320204	0.60634	.	.	ENSG00000141698	ENST00000269534;ENST00000393911;ENST00000435506;ENST00000415460	D;D;D	0.82619	-1.63;-1.63;-1.63	5.07	5.07	0.68467	HAD-like domain (2);	0.104097	0.64402	D	0.000004	D	0.83903	0.5355	M	0.67625	2.065	0.46849	D	0.999222	P;P	0.40144	0.704;0.704	P;P	0.45071	0.468;0.468	T	0.82147	-0.0601	10	0.26408	T	0.33	1.7022	14.6635	0.68891	0.0:0.0:0.0:1.0	.	202;194	C9JKC4;Q969T7	.;5NT3L_HUMAN	A	194;236;202;172	ENSP00000269534:T194A;ENSP00000389948:T202A;ENSP00000397742:T172A	ENSP00000269534:T194A	T	-	1	0	NT5C3L	37237368	1.000000	0.71417	0.994000	0.49952	0.969000	0.65631	3.282000	0.51693	2.131000	0.65755	0.379000	0.24179	ACA	.	.		0.502	NT5C3B-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257430.2	NM_052935	
DHX58	79132	hgsc.bcm.edu	37	17	40263791	40263791	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:40263791C>A	ENST00000251642.3	-	3	342	c.120G>T	c.(118-120)cgG>cgT	p.R40R		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	40	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		TCTCTAGGTGCCGCTTGGCCA	0.597																																					p.R40R		Atlas-SNP	.											.	DHX58	39	.	0			c.G120T						.						127.0	114.0	118.0					17																	40263791		2203	4300	6503	SO:0001819	synonymous_variant	79132	exon3			TAGGTGCCGCTTG	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.120G>T	chr17.hg19:g.40263791C>A		87.0	0.0		108.0	29.0	NM_024119	Q9HAM6	Silent	SNP	ENST00000251642.3	hg19	CCDS11416.1																																																																																			.	.		0.597	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119	
VPS25	84313	hgsc.bcm.edu	37	17	40928326	40928326	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:40928326A>G	ENST00000253794.2	+	5	446	c.406A>G	c.(406-408)Aca>Gca	p.T136A		NM_032353.2	NP_115729.1	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25 homolog (S. cerevisiae)	136					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)	5		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TGGGGAAGACACAGAGGATGA	0.423																																					p.T136A		Atlas-SNP	.											.	VPS25	11	.	0			c.A406G						.						97.0	92.0	94.0					17																	40928326		2203	4300	6503	SO:0001583	missense	84313	exon5			GAAGACACAGAGG	AB014763	CCDS11438.1	17q21.31	2014-02-12	2006-04-04		ENSG00000131475	ENSG00000131475			28122	protein-coding gene	gene with protein product		610907	"""vacuolar protein sorting 25 (yeast)"""			15511219	Standard	NM_032353		Approved	MGC10540, EAP20, DERP9	uc002ibi.3	Q9BRG1		ENST00000253794.2:c.406A>G	chr17.hg19:g.40928326A>G	ENSP00000253794:p.Thr136Ala	153.0	0.0		145.0	52.0	NM_032353	B2R581	Missense_Mutation	SNP	ENST00000253794.2	hg19	CCDS11438.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377327	0.61735	.	.	ENSG00000131475	ENST00000253794	T	0.51325	0.71	5.4	5.4	0.78164	ESCRT-II complex, Vps25 subunit, C-terminal winged helix (1);	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	M	0.65498	2.005	0.80722	D	1	P	0.42518	0.782	B	0.40101	0.319	T	0.52472	-0.8571	10	0.42905	T	0.14	-3.3437	15.0877	0.72167	1.0:0.0:0.0:0.0	.	136	Q9BRG1	VPS25_HUMAN	A	136	ENSP00000253794:T136A	ENSP00000253794:T136A	T	+	1	0	VPS25	38181852	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	8.931000	0.92884	2.050000	0.60909	0.454000	0.30748	ACA	.	.		0.423	VPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452383.1	NM_032353	
MPP3	4356	hgsc.bcm.edu	37	17	41907454	41907454	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:41907454C>T	ENST00000398389.4	-	6	409	c.244G>A	c.(244-246)Gcc>Acc	p.A82T	MPP3_ENST00000398393.1_Missense_Mutation_p.A107T	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	82	L27 2. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		TGCACGGAGGCGGCCTGCAAC	0.622																																					p.A82T		Atlas-SNP	.											.	MPP3	42	.	0			c.G244A						.						34.0	43.0	40.0					17																	41907454		2149	4260	6409	SO:0001583	missense	4356	exon6			CGGAGGCGGCCTG		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.244G>A	chr17.hg19:g.41907454C>T	ENSP00000381425:p.Ala82Thr	37.0	0.0		47.0	25.0	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Missense_Mutation	SNP	ENST00000398389.4	hg19	CCDS42344.1	.	.	.	.	.	.	.	.	.	.	C	9.185	1.024601	0.19433	.	.	ENSG00000161647	ENST00000398393;ENST00000398389;ENST00000356492	T;T	0.15834	2.39;2.4	4.78	3.81	0.43845	L27, C-terminal (1);L27 (2);	0.256058	0.39475	N	0.001349	T	0.10981	0.0268	N	0.05306	-0.075	0.37641	D	0.92203	D;B;B	0.63046	0.992;0.006;0.011	P;B;B	0.51324	0.666;0.014;0.014	T	0.25710	-1.0124	10	0.15952	T	0.53	.	8.9554	0.35814	0.0:0.8296:0.0:0.1704	.	107;82;107	B4DS20;Q13368;D3DX46	.;MPP3_HUMAN;.	T	107;82;107	ENSP00000381430:A107T;ENSP00000381425:A82T	ENSP00000348885:A107T	A	-	1	0	MPP3	39262980	0.984000	0.35163	0.998000	0.56505	0.899000	0.52679	1.249000	0.32839	1.231000	0.43661	0.462000	0.41574	GCC	.	.		0.622	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932	
TMEM101	84336	hgsc.bcm.edu	37	17	42089395	42089395	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:42089395C>A	ENST00000589334.1	-	5	990	c.675G>T	c.(673-675)tgG>tgT	p.W225C	TMEM101_ENST00000206380.3_Missense_Mutation_p.W225C|TMEM101_ENST00000542039.1_Missense_Mutation_p.W167C			Q96IK0	TM101_HUMAN	transmembrane protein 101	225					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCGTGTTGTGCCAGTAAGCAA	0.562																																					p.W225C		Atlas-SNP	.											.	TMEM101	18	.	0			c.G675T						.						115.0	91.0	99.0					17																	42089395		2203	4300	6503	SO:0001583	missense	84336	exon4			GTTGTGCCAGTAA	AK172826	CCDS11474.1	17q21.31	2005-12-16							28653	protein-coding gene	gene with protein product						12761501	Standard	NM_032376		Approved	MGC4251, FLJ23987	uc002ieu.3	Q96IK0		ENST00000589334.1:c.675G>T	chr17.hg19:g.42089395C>A	ENSP00000468025:p.Trp225Cys	81.0	0.0		88.0	40.0	NM_032376	B2R9N6	Missense_Mutation	SNP	ENST00000589334.1	hg19	CCDS11474.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.412091	0.83340	.	.	ENSG00000091947	ENST00000206380;ENST00000542039	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70680	-0.4805	9	0.87932	D	0	-5.1077	17.0298	0.86458	0.0:1.0:0.0:0.0	.	225	Q96IK0	TM101_HUMAN	C	225;167	.	ENSP00000206380:W225C	W	-	3	0	TMEM101	39444921	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.707000	0.84623	2.615000	0.88500	0.484000	0.47621	TGG	.	.		0.562	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376	
HDAC5	10014	hgsc.bcm.edu	37	17	42171119	42171119	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:42171119G>A	ENST00000393622.2	-	4	509	c.178C>T	c.(178-180)Cgg>Tgg	p.R60W	HDAC5_ENST00000225983.6_Missense_Mutation_p.R61W|HDAC5_ENST00000586802.1_Missense_Mutation_p.R60W|HDAC5_ENST00000336057.5_Missense_Mutation_p.R60W	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	60					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		AGAGCCCCCCGTAGCTCCACA	0.667																																					p.R61W		Atlas-SNP	.											HDAC5,NS,carcinoma,0,1	HDAC5	67	.	0			c.C181T						.						13.0	15.0	15.0					17																	42171119		2197	4295	6492	SO:0001583	missense	10014	exon4			CCCCCCGTAGCTC	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.178C>T	chr17.hg19:g.42171119G>A	ENSP00000377244:p.Arg60Trp	118.0	0.0		143.0	58.0	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	hg19	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.604577	0.66445	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.50001	0.78;0.78;0.76	4.14	4.14	0.48551	.	0.240511	0.26859	N	0.022121	T	0.56891	0.2016	L	0.32530	0.975	0.42561	D	0.993142	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.69654	0.965;0.924;0.965;0.924	T	0.63189	-0.6693	10	0.87932	D	0	-23.2017	15.156	0.72743	0.0:0.0:1.0:0.0	.	60;60;61;60	Q9UQL6-2;B4DGT4;Q9UQL6-3;Q9UQL6	.;.;.;HDAC5_HUMAN	W	61;60;60	ENSP00000225983:R61W;ENSP00000377244:R60W;ENSP00000337290:R60W	ENSP00000225983:R61W	R	-	1	2	HDAC5	39526645	0.996000	0.38824	0.992000	0.48379	0.875000	0.50365	3.362000	0.52314	1.858000	0.53909	0.462000	0.41574	CGG	.	.		0.667	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053	
NMT1	4836	hgsc.bcm.edu	37	17	43171104	43171104	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:43171104G>A	ENST00000592782.1	+	5	568	c.437G>A	c.(436-438)cGc>cAc	p.R146H	NMT1_ENST00000258960.2_Missense_Mutation_p.R146H|NMT1_ENST00000590114.1_3'UTR			P30419	NMT1_HUMAN	N-myristoyltransferase 1	146					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				GACAATATCCGCCAGGAGCCC	0.627																																					p.R146H		Atlas-SNP	.											.	NMT1	31	.	0			c.G437A						.						69.0	61.0	64.0					17																	43171104		2203	4300	6503	SO:0001583	missense	4836	exon4			ATATCCGCCAGGA		CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"""alternative, short form NMT-S"", ""myristoyl-CoA:protein N-myristoyltransferase"", ""long form, NMT-L"""	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.437G>A	chr17.hg19:g.43171104G>A	ENSP00000468424:p.Arg146His	66.0	0.0		71.0	26.0	NM_021079	A8K7C1|Q9UE09	Missense_Mutation	SNP	ENST00000592782.1	hg19	CCDS11494.1	.	.	.	.	.	.	.	.	.	.	G	35	5.542206	0.96474	.	.	ENSG00000136448	ENST00000258960	T	0.49720	0.77	5.02	5.02	0.67125	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, N-terminal (1);	0.048417	0.85682	N	0.000000	T	0.79082	0.4386	H	0.95187	3.635	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.85347	0.1099	10	0.87932	D	0	-15.1227	18.8925	0.92410	0.0:0.0:1.0:0.0	.	146	P30419	NMT1_HUMAN	H	146	ENSP00000258960:R146H	ENSP00000258960:R146H	R	+	2	0	NMT1	40526630	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.601000	0.98297	2.767000	0.95098	0.655000	0.94253	CGC	.	.		0.627	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
KANSL1	284058	hgsc.bcm.edu	37	17	44108889	44108889	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:44108889G>A	ENST00000262419.6	-	15	3741	c.3271C>T	c.(3271-3273)Cgg>Tgg	p.R1091W	KANSL1_ENST00000575318.1_Missense_Mutation_p.R1027W|KANSL1_ENST00000574590.1_Missense_Mutation_p.R1091W|KANSL1_ENST00000432791.1_Missense_Mutation_p.R1091W|KANSL1_ENST00000393476.3_Missense_Mutation_p.R385W|KANSL1_ENST00000572904.1_Missense_Mutation_p.R1091W	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1091	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R1091W(1)									ACCAGATGCCGACTCTTGAGG	0.612																																					p.R1091W		Atlas-SNP	.											KIAA1267,face,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	skin(1)	c.C3271T						.						25.0	23.0	24.0					17																	44108889		2203	4300	6503	SO:0001583	missense	284058	exon15			GATGCCGACTCTT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3271C>T	chr17.hg19:g.44108889G>A	ENSP00000262419:p.Arg1091Trp	98.0	0.0		88.0	30.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.445331	0.63178	.	.	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.28255	2.43;2.43;1.62	5.72	3.53	0.40419	.	0.000000	0.51477	D	0.000086	T	0.33585	0.0868	N	0.19112	0.55	0.39056	D	0.960425	D;D;D;D	0.71674	0.994;0.994;0.998;0.998	P;P;P;P	0.59546	0.629;0.629;0.859;0.859	T	0.29852	-0.9998	10	0.66056	D	0.02	-3.8111	11.5213	0.50553	0.0:0.1263:0.7277:0.146	.	359;422;1091;1091	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	W	1091;1091;385	ENSP00000262419:R1091W;ENSP00000387393:R1091W;ENSP00000377117:R385W	ENSP00000262419:R1091W	R	-	1	2	KIAA1267	41464736	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	4.125000	0.57931	1.414000	0.47017	0.561000	0.74099	CGG	.	.		0.612	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
ITGB3	3690	hgsc.bcm.edu	37	17	45363766	45363766	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:45363766T>C	ENST00000559488.1	+	5	771	c.755T>C	c.(754-756)aTc>aCc	p.I252T	ITGB3_ENST00000560629.1_Silent_p.H240H|ITGB3_ENST00000571680.1_Missense_Mutation_p.I252T|ITGB3_ENST00000435993.2_Missense_Mutation_p.I205T	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	252	VWFA.				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)	tttgatgccaTCATGCAGGCT	0.532																																					p.I252T		Atlas-SNP	.											.	ITGB3	157	.	0			c.T755C						.						101.0	84.0	90.0					17																	45363766		2203	4300	6503	SO:0001583	missense	3690	exon5			ATGCCATCATGCA		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.755T>C	chr17.hg19:g.45363766T>C	ENSP00000452786:p.Ile252Thr	79.0	0.0		88.0	32.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.528815	0.85706	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.98296	-4.85	5.01	5.01	0.66863	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.048416	0.85682	D	0.000000	D	0.99020	0.9665	M	0.89968	3.075	0.80722	D	1	P;D	0.58268	0.701;0.982	P;D	0.74348	0.694;0.983	D	0.99589	1.0975	10	0.87932	D	0	.	13.9843	0.64324	0.0:0.0:0.0:1.0	.	252;252	P05106;Q2YFE1	ITB3_HUMAN;.	T	252;205	ENSP00000407801:I205T	ENSP00000262017:I252T	I	+	2	0	C17orf57	42718765	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.997000	0.88414	2.006000	0.58801	0.459000	0.35465	ATC	.	.		0.532	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
OSBPL7	114881	hgsc.bcm.edu	37	17	45895948	45895948	+	Missense_Mutation	SNP	G	G	A	rs368110786		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:45895948G>A	ENST00000007414.3	-	6	595	c.404C>T	c.(403-405)gCg>gTg	p.A135V	OSBPL7_ENST00000392507.3_Missense_Mutation_p.A135V	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	135	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						ACGCAGCTGCGCCACCCAGCT	0.617																																					p.A135V		Atlas-SNP	.											.	OSBPL7	65	.	0			c.C404T						.	G	VAL/ALA	0,4404		0,0,2202	27.0	31.0	30.0		404	6.0	1.0	17		30	1,8595		0,1,4297	no	missense	OSBPL7	NM_145798.2	64	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	benign	135/843	45895948	1,12999	2202	4298	6500	SO:0001583	missense	114881	exon6			AGCTGCGCCACCC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.404C>T	chr17.hg19:g.45895948G>A	ENSP00000007414:p.Ala135Val	72.0	0.0		81.0	36.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	G	19.59	3.856095	0.71834	0.0	1.16E-4	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.17854	2.25;2.25	5.97	5.97	0.96955	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.344395	0.34110	N	0.004253	T	0.13543	0.0328	N	0.20483	0.58	0.42564	D	0.993156	B	0.25743	0.133	B	0.25140	0.058	T	0.12041	-1.0563	10	0.27785	T	0.31	-9.7525	17.3447	0.87307	0.0:0.0:1.0:0.0	.	135	Q9BZF2	OSBL7_HUMAN	V	135	ENSP00000007414:A135V;ENSP00000376295:A135V	ENSP00000007414:A135V	A	-	2	0	OSBPL7	43250947	0.998000	0.40836	0.997000	0.53966	0.993000	0.82548	3.929000	0.56514	2.837000	0.97791	0.655000	0.94253	GCG	.	.		0.617	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
OSBPL7	114881	hgsc.bcm.edu	37	17	45896429	45896429	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:45896429G>A	ENST00000007414.3	-	5	483	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	OSBPL7_ENST00000392507.3_Missense_Mutation_p.R98W	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	98	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						ACCGACAGCCGGACATCGATG	0.552																																					p.R98W		Atlas-SNP	.											.	OSBPL7	65	.	0			c.C292T						.						154.0	122.0	133.0					17																	45896429		2203	4300	6503	SO:0001583	missense	114881	exon5			ACAGCCGGACATC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.292C>T	chr17.hg19:g.45896429G>A	ENSP00000007414:p.Arg98Trp	110.0	0.0		102.0	35.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.104875	0.37145	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.19250	2.16;2.16	5.35	5.35	0.76521	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.105384	0.64402	D	0.000004	T	0.42359	0.1199	L	0.55213	1.73	0.41193	D	0.986315	D	0.89917	1.0	D	0.73708	0.981	T	0.26883	-1.0090	10	0.72032	D	0.01	-23.0732	15.9951	0.80234	0.0:0.0:1.0:0.0	.	98	Q9BZF2	OSBL7_HUMAN	W	98	ENSP00000007414:R98W;ENSP00000376295:R98W	ENSP00000007414:R98W	R	-	1	2	OSBPL7	43251428	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	0.914000	0.28624	2.504000	0.84457	0.655000	0.94253	CGG	.	.		0.552	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
HOXB7	3217	hgsc.bcm.edu	37	17	46687954	46687954	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:46687954G>A	ENST00000239165.7	-	1	425	c.327C>T	c.(325-327)ggC>ggT	p.G109G	HOXB7_ENST00000567101.2_Intron	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	109					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						GCTCCTTGGCGCCCGCCGCCT	0.657																																					p.G109G		Atlas-SNP	.											.	HOXB7	15	.	0			c.C327T						.						7.0	7.0	7.0					17																	46687954		2098	4146	6244	SO:0001819	synonymous_variant	3217	exon1			CTTGGCGCCCGCC		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"""Homeoboxes / ANTP class : HOXL subclass"""	5118	protein-coding gene	gene with protein product		142962	"""homeo box B7"""	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.327C>T	chr17.hg19:g.46687954G>A		198.0	0.0		199.0	83.0	NM_004502	A8K3N8|Q15957|Q53FN3|Q96BQ6	Silent	SNP	ENST00000239165.7	hg19	CCDS11532.1																																																																																			.	.		0.657	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3		
HOXB13	10481	hgsc.bcm.edu	37	17	46805444	46805444	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:46805444G>T	ENST00000290295.7	-	1	1096	c.512C>A	c.(511-513)tCt>tAt	p.S171Y	PRAC2_ENST00000422730.2_RNA	NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	171					angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						GAGAGCCCAAGACTGGTAACT	0.567																																					p.S171Y		Atlas-SNP	.											.	HOXB13	28	.	0			c.C512A						.						77.0	73.0	74.0					17																	46805444		2203	4300	6503	SO:0001583	missense	10481	exon1			GCCCAAGACTGGT	U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184		"""Homeoboxes / ANTP class : HOXL subclass"""	5112	protein-coding gene	gene with protein product		604607	"""homeo box B13"""			8756292, 9665387	Standard	NM_006361		Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.512C>A	chr17.hg19:g.46805444G>T	ENSP00000290295:p.Ser171Tyr	112.0	0.0		146.0	71.0	NM_006361	B2R878|Q96QM4|Q99810	Missense_Mutation	SNP	ENST00000290295.7	hg19	CCDS11536.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.110888	0.56398	.	.	ENSG00000159184	ENST00000290295	D	0.91740	-2.9	4.79	4.79	0.61399	.	0.118436	0.64402	D	0.000015	D	0.87700	0.6243	L	0.29908	0.895	0.39184	D	0.962838	B	0.16802	0.019	B	0.04013	0.001	D	0.85599	0.1251	10	0.72032	D	0.01	.	16.5918	0.84767	0.0:0.0:1.0:0.0	.	171	Q92826	HXB13_HUMAN	Y	171	ENSP00000290295:S171Y	ENSP00000290295:S171Y	S	-	2	0	HOXB13	44160443	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	5.167000	0.64972	2.498000	0.84270	0.561000	0.74099	TCT	.	.		0.567	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358087.3	NM_006361	
ZNF652	22834	hgsc.bcm.edu	37	17	47389292	47389292	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:47389292G>A	ENST00000362063.2	-	4	1479	c.1161C>T	c.(1159-1161)tgC>tgT	p.C387C	ZNF652_ENST00000430262.2_Silent_p.C387C	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			TCCTTACCTCGCATCTAAAGG	0.512																																					p.C387C		Atlas-SNP	.											ZNF652,colon,carcinoma,0,1	ZNF652	54	.	0			c.C1161T						.						163.0	130.0	141.0					17																	47389292		2203	4300	6503	SO:0001819	synonymous_variant	22834	exon4			TACCTCGCATCTA	AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"""Zinc fingers, C2H2-type"""	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.1161C>T	chr17.hg19:g.47389292G>A		121.0	0.0		116.0	31.0	NM_001145365	A4QPD9|Q5H9Q0	Silent	SNP	ENST00000362063.2	hg19	CCDS32677.1																																																																																			.	.		0.512	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897	
SAMD14	201191	hgsc.bcm.edu	37	17	48191303	48191303	+	Silent	SNP	G	G	A	rs367685385		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:48191303G>A	ENST00000330175.4	-	9	1400	c.1083C>T	c.(1081-1083)gaC>gaT	p.D361D	SAMD14_ENST00000503734.1_5'Flank|SAMD14_ENST00000503131.1_Silent_p.D389D	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	361	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						GTTTGCTTCCGTCCAGCTGCA	0.572																																					p.D389D		Atlas-SNP	.											.	SAMD14	36	.	0			c.C1167T						.	G		0,4406		0,0,2203	50.0	49.0	49.0		1167	-6.4	0.9	17		49	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SAMD14	NM_174920.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		389/446	48191303	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	201191	exon10			GCTTCCGTCCAGC		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"""Sterile alpha motif (SAM) domain containing"""	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.1083C>T	chr17.hg19:g.48191303G>A		154.0	0.0		167.0	79.0	NM_174920	A5D8V1|Q8N2X0	Silent	SNP	ENST00000330175.4	hg19	CCDS58562.1																																																																																			.	.		0.572	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920	
EME1	146956	hgsc.bcm.edu	37	17	48452870	48452870	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:48452870A>G	ENST00000338165.4	+	2	383	c.301A>G	c.(301-303)Aca>Gca	p.T101A	MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000507088.1_5'Flank|MRPL27_ENST00000442592.3_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.T101A|EME1_ENST00000393271.2_Missense_Mutation_p.T101A|MRPL27_ENST00000225969.4_5'Flank	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	101					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TCAAAGGCTTACATGTAAGTT	0.428								Direct reversal of damage;Homologous recombination																													p.T101A		Atlas-SNP	.											.	EME1	39	.	0			c.A301G						.						82.0	85.0	84.0					17																	48452870		2203	4300	6503	SO:0001583	missense	146956	exon2			AGGCTTACATGTA	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.301A>G	chr17.hg19:g.48452870A>G	ENSP00000339897:p.Thr101Ala	180.0	0.0		156.0	71.0	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	hg19	CCDS11565.1	.	.	.	.	.	.	.	.	.	.	A	0.684	-0.797025	0.02862	.	.	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511519;ENST00000511648	T;T;T;T	0.18502	2.92;2.91;2.21;2.91	4.84	-0.259	0.12971	.	1.055010	0.07445	N	0.897984	T	0.11410	0.0278	L	0.29908	0.895	0.09310	N	1	B;B	0.23937	0.034;0.094	B;B	0.21708	0.036;0.026	T	0.38415	-0.9662	10	0.30078	T	0.28	.	5.3177	0.15864	0.5715:0.2784:0.15:0.0	.	101;101	Q96AY2-2;Q96AY2	.;EME1_HUMAN	A	101	ENSP00000339897:T101A;ENSP00000376952:T101A;ENSP00000423029:T101A;ENSP00000421700:T101A	ENSP00000339897:T101A	T	+	1	0	EME1	45807869	0.001000	0.12720	0.000000	0.03702	0.018000	0.09664	1.178000	0.31981	0.037000	0.15575	-0.912000	0.02778	ACA	.	.		0.428	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
NME1	4830	hgsc.bcm.edu	37	17	49233116	49233116	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:49233116G>A	ENST00000393196.3	+	2	232	c.101G>A	c.(100-102)cGc>cAc	p.R34H	NME2_ENST00000555572.1_Missense_Mutation_p.R59H|NME2_ENST00000376392.6_Missense_Mutation_p.R34H|NME1_ENST00000336097.3_Missense_Mutation_p.R59H|NME1-NME2_ENST00000608447.1_Missense_Mutation_p.R59H|NME1_ENST00000511355.1_Missense_Mutation_p.R34H|NME1_ENST00000480143.1_Missense_Mutation_p.R59H|NME1-NME2_ENST00000393198.3_Missense_Mutation_p.R34H|NME1_ENST00000013034.3_Missense_Mutation_p.R59H|NME2_ENST00000393193.2_Missense_Mutation_p.R34H	NM_000269.2	NP_000260.1	P15531	NDKA_HUMAN	NME/NM23 nucleoside diphosphate kinase 1	34					cellular response to drug (GO:0035690)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|CTP biosynthetic process (GO:0006241)|DNA catabolic process (GO:0006308)|endocytosis (GO:0006897)|GTP biosynthetic process (GO:0006183)|hippocampus development (GO:0021766)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amine (GO:0014075)|response to cAMP (GO:0051591)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|deoxyribonuclease activity (GO:0004536)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|nucleoside diphosphate kinase activity (GO:0004550)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|single-stranded DNA binding (GO:0003697)			endometrium(1)|large_intestine(1)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)		Adefovir Dipivoxil(DB00718)|Lamivudine(DB00709)|Tenofovir(DB00300)	AAAGGATTCCGCCTTGTTGGT	0.458																																					p.R59H	GBM(176;1298 2890 6639 30062)	Atlas-SNP	.											.	NME1	12	.	0			c.G176A						.						211.0	181.0	191.0					17																	49233116		2203	4300	6503	SO:0001583	missense	4830	exon3			GATTCCGCCTTGT	AL360191, X17620	CCDS11578.1, CCDS11579.1	17q21.33	2013-04-29	2012-05-18		ENSG00000239672	ENSG00000239672			7849	protein-coding gene	gene with protein product		156490	"""non-metastatic cells 1, protein (NM23A) expressed in"""			8270257, 19852809	Standard	NM_000269		Approved	NM23, NM23-H1, NDPKA		P15531	OTTHUMG00000137474	ENST00000393196.3:c.101G>A	chr17.hg19:g.49233116G>A	ENSP00000376892:p.Arg34His	138.0	0.0		139.0	32.0	NM_198175	Q6FGK3|Q86XQ2|Q9UDJ6	Missense_Mutation	SNP	ENST00000393196.3	hg19	CCDS11579.1	.	.	.	.	.	.	.	.	.	.	G	9.471	1.095664	0.20471	.	.	ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000239672;ENSG00000011052;ENSG00000011052;ENSG00000243678;ENSG00000243678	ENST00000393196;ENST00000336097;ENST00000480143;ENST00000511355;ENST00000013034;ENST00000456492;ENST00000376392;ENST00000555572;ENST00000393193;ENST00000393198	T;T;T;T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48;0.48	4.93	-2.4	0.06583	.	.	.	.	.	T	0.37128	0.0992	L	0.41824	1.3	0.09310	N	1	B;B;B;B	0.26120	0.142;0.018;0.033;0.1	B;B;B;B	0.23018	0.043;0.002;0.018;0.025	T	0.29181	-1.0020	9	0.54805	T	0.06	.	5.2607	0.15571	0.4413:0.0:0.3435:0.2152	.	59;59;34;59	E7ERL0;Q32Q12;P15531;P15531-2	.;.;NDKA_HUMAN;.	H	34;59;59;34;59;59;34;59;34;59	ENSP00000376892:R34H;ENSP00000337060:R59H;ENSP00000429318:R59H;ENSP00000428553:R34H;ENSP00000013034:R59H;ENSP00000387682:R59H;ENSP00000365572:R34H;ENSP00000451932:R59H;ENSP00000376889:R34H	ENSP00000013034:R59H	R	+	2	0	NME2;NME1-NME2;NME1	46588115	0.001000	0.12720	0.112000	0.21494	0.045000	0.14185	0.033000	0.13754	-0.407000	0.07576	-0.749000	0.03505	CGC	.	.		0.458	NME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268662.2	NM_000269	
PPM1D	8493	hgsc.bcm.edu	37	17	58740416	58740416	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:58740416C>T	ENST00000305921.3	+	6	1553	c.1321C>T	c.(1321-1323)Cgt>Tgt	p.R441C	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	441					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			TGCCCTGGTTCGTAGCAATGC	0.408											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R441C		Atlas-SNP	.											PPM1D,colon,carcinoma,0,1	PPM1D	50	.	0			c.C1321T						.						109.0	109.0	109.0					17																	58740416		2203	4300	6503	SO:0001583	missense	8493	exon6			CTGGTTCGTAGCA	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9277	protein-coding gene	gene with protein product	"""wild-type p53-induced phosphatase 1"", ""protein phosphatase 2C, delta isoform"""	605100	"""protein phosphatase 1D magnesium-dependent, delta isoform"""			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1321C>T	chr17.hg19:g.58740416C>T	ENSP00000306682:p.Arg441Cys	148.0	0.0	1033	160.0	65.0	NM_003620	Q53XP4|Q6P991|Q8IVR6	Missense_Mutation	SNP	ENST00000305921.3	hg19	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.170723	0.78452	.	.	ENSG00000170836	ENST00000305921	T	0.55413	0.52	5.78	4.75	0.60458	.	0.103267	0.64402	D	0.000005	T	0.56455	0.1986	L	0.29908	0.895	0.54753	D	0.999989	D	0.89917	1.0	P	0.57846	0.828	T	0.56529	-0.7964	10	0.51188	T	0.08	-6.7846	15.9796	0.80097	0.1353:0.8647:0.0:0.0	.	441	O15297	PPM1D_HUMAN	C	441	ENSP00000306682:R441C	ENSP00000306682:R441C	R	+	1	0	PPM1D	56095198	0.980000	0.34600	1.000000	0.80357	0.913000	0.54294	2.592000	0.46171	2.894000	0.99253	0.591000	0.81541	CGT	.	.		0.408	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620	
CD79B	974	hgsc.bcm.edu	37	17	62007735	62007735	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:62007735A>G	ENST00000006750.3	-	3	221	c.129T>C	c.(127-129)tgT>tgC	p.C43C	CD79B_ENST00000349817.2_Intron|CD79B_ENST00000392795.3_Silent_p.C44C	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	43	Ig-like V-type.				B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						AGATCCGCGAACAAGCACTAC	0.612			"""Mis, O"""		DLBCL																																p.C44C		Atlas-SNP	.		Dom	yes		17	17q23	974	"""CD79b molecule, immunoglobulin-associated beta"""		L	.	CD79B	38	.	0			c.T132C						.						41.0	34.0	36.0					17																	62007735		2203	4300	6503	SO:0001819	synonymous_variant	974	exon3			CCGCGAACAAGCA	L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1699	protein-coding gene	gene with protein product		147245	"""CD79B antigen (immunoglobulin-associated beta)"""	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.129T>C	chr17.hg19:g.62007735A>G		62.0	0.0		81.0	28.0	NM_001039933	Q53FS2|Q9BU06	Silent	SNP	ENST00000006750.3	hg19	CCDS11655.1																																																																																			.	.		0.612	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1		
BPTF	2186	hgsc.bcm.edu	37	17	65862621	65862621	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:65862621A>G	ENST00000321892.4	+	3	1539	c.1478A>G	c.(1477-1479)tAt>tGt	p.Y493C	BPTF_ENST00000424123.3_Missense_Mutation_p.Y354C|BPTF_ENST00000306378.6_Missense_Mutation_p.Y493C|BPTF_ENST00000335221.5_Missense_Mutation_p.Y493C			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	493					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAAATTTGGTATTACAGCACA	0.333																																					p.Y493C		Atlas-SNP	.											.	BPTF	415	.	0			c.A1478G						.						81.0	93.0	89.0					17																	65862621		2203	4300	6503	SO:0001583	missense	2186	exon3			TTTGGTATTACAG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.1478A>G	chr17.hg19:g.65862621A>G	ENSP00000315454:p.Tyr493Cys	175.0	0.0		152.0	71.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.44	3.123571	0.56613	.	.	ENSG00000171634	ENST00000544491;ENST00000306378;ENST00000335221;ENST00000321892;ENST00000544778	T;T;T;D	0.86769	-1.26;-1.37;-1.31;-2.17	5.84	5.84	0.93424	.	.	.	.	.	D	0.94082	0.8103	M	0.84846	2.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	D	0.94854	0.8016	9	0.87932	D	0	.	16.2302	0.82332	1.0:0.0:0.0:0.0	.	493;493;493	Q12830;Q12830-2;Q12830-4	BPTF_HUMAN;.;.	C	398;493;493;493;354	ENSP00000307208:Y493C;ENSP00000334351:Y493C;ENSP00000315454:Y493C;ENSP00000440854:Y354C	ENSP00000307208:Y493C	Y	+	2	0	BPTF	63293083	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.095000	0.89535	2.228000	0.72767	0.533000	0.62120	TAT	.	.		0.333	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
ABCA9	10350	hgsc.bcm.edu	37	17	66972304	66972304	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:66972304T>C	ENST00000340001.4	-	38	4959	c.4748A>G	c.(4747-4749)tAc>tGc	p.Y1583C	ABCA9_ENST00000453985.2_Missense_Mutation_p.Y1545C|ABCA9_ENST00000370732.2_3'UTR	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1583					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					TGAGAGGCTGTACTCCTCCAG	0.393																																					p.Y1583C		Atlas-SNP	.											.	ABCA9	192	.	0			c.A4748G						.						97.0	89.0	92.0					17																	66972304		2203	4300	6503	SO:0001583	missense	10350	exon38			AGGCTGTACTCCT	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4748A>G	chr17.hg19:g.66972304T>C	ENSP00000342216:p.Tyr1583Cys	197.0	0.0		217.0	59.0	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Missense_Mutation	SNP	ENST00000340001.4	hg19	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.915024	0.52546	.	.	ENSG00000154258	ENST00000340001;ENST00000453985	D	0.89343	-2.5	4.92	4.92	0.64577	.	0.000000	0.42682	D	0.000666	D	0.96396	0.8824	H	0.97240	3.965	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97625	1.0138	10	0.87932	D	0	.	13.7627	0.62977	0.0:0.0:0.0:1.0	.	1583	Q8IUA7	ABCA9_HUMAN	C	1583;1528	ENSP00000342216:Y1583C	ENSP00000342216:Y1583C	Y	-	2	0	ABCA9	64483899	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	5.261000	0.65496	1.854000	0.53819	0.496000	0.49642	TAC	.	.		0.393	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
GRIN2C	2905	hgsc.bcm.edu	37	17	72840513	72840513	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:72840513C>T	ENST00000293190.5	-	12	2631	c.2485G>A	c.(2485-2487)Gcc>Acc	p.A829T	GRIN2C_ENST00000347612.4_Missense_Mutation_p.A829T	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	829					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACCAGCAGGGCCAGCCCCATG	0.597																																					p.A829T		Atlas-SNP	.											.	GRIN2C	144	.	0			c.G2485A						.						114.0	103.0	107.0					17																	72840513		2203	4300	6503	SO:0001583	missense	2905	exon12			GCAGGGCCAGCCC		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.2485G>A	chr17.hg19:g.72840513C>T	ENSP00000293190:p.Ala829Thr	135.0	0.0		133.0	52.0	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	hg19	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.543653	0.45280	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.44083	0.93	4.79	3.74	0.42951	.	0.119523	0.53938	D	0.000047	T	0.21387	0.0515	N	0.08118	0	0.44380	D	0.997289	B;B	0.32573	0.376;0.273	B;B	0.36666	0.214;0.23	T	0.09100	-1.0690	10	0.87932	D	0	.	3.2291	0.06742	0.223:0.5647:0.0:0.2124	.	863;829	Q8IW23;Q14957	.;NMDE3_HUMAN	T	829;863	ENSP00000293190:A829T	ENSP00000293190:A829T	A	-	1	0	GRIN2C	70352108	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.903000	0.63272	2.360000	0.80028	0.561000	0.74099	GCC	.	.		0.597	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
KIAA0195	9772	hgsc.bcm.edu	37	17	73490855	73490855	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73490855T>C	ENST00000314256.7	+	19	2949	c.2555T>C	c.(2554-2556)gTc>gCc	p.V852A	KIAA0195_ENST00000375248.5_Missense_Mutation_p.V862A|KIAA0195_ENST00000579208.1_Missense_Mutation_p.V503A|AC100787.1_ENST00000579379.1_RNA	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	852						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			ATCCGCTTTGTCTACTTCTCT	0.567																																					p.V852A		Atlas-SNP	.											.	KIAA0195	102	.	0			c.T2555C						.						102.0	93.0	96.0					17																	73490855		2203	4300	6503	SO:0001583	missense	9772	exon19			GCTTTGTCTACTT		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.2555T>C	chr17.hg19:g.73490855T>C	ENSP00000313885:p.Val852Ala	116.0	0.0		127.0	46.0	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	hg19	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088382	0.55968	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.69685	-0.42;-0.42	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.82655	0.5084	M	0.81341	2.54	0.80722	D	1	D;D;D	0.71674	0.993;0.998;0.997	D;D;D	0.77557	0.967;0.99;0.978	D	0.85196	0.1012	10	0.87932	D	0	-42.2554	16.1298	0.81418	0.0:0.0:0.0:1.0	.	862;862;852	B4DGC6;C9JL75;Q12767	.;.;K0195_HUMAN	A	852;862	ENSP00000313885:V852A;ENSP00000364397:V862A	ENSP00000313885:V852A	V	+	2	0	KIAA0195	71002450	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.954000	0.87848	2.208000	0.71279	0.482000	0.46254	GTC	.	.		0.567	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
GALK1	2584	hgsc.bcm.edu	37	17	73754367	73754367	+	Missense_Mutation	SNP	G	G	A	rs371517491		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73754367G>A	ENST00000588479.1	-	7	1605	c.1031C>T	c.(1030-1032)aCg>aTg	p.T344M	GALK1_ENST00000225614.2_Missense_Mutation_p.T344M|GALK1_ENST00000437911.1_Missense_Mutation_p.T374M			P51570	GALK1_HUMAN	galactokinase 1	344					carbohydrate metabolic process (GO:0005975)|galactitol metabolic process (GO:0019402)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|galactose binding (GO:0005534)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	5	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCACCGCCCGTCATGCGGCT	0.672																																					p.T344M		Atlas-SNP	.											.	GALK1	17	.	0			c.C1031T	GRCh37	CM993835	GALK1	M		.	G	MET/THR	0,4354		0,0,2177	14.0	17.0	16.0		1031	4.5	0.9	17		16	1,8555		0,1,4277	no	missense	GALK1	NM_000154.1	81	0,1,6454	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	344/393	73754367	1,12909	2177	4278	6455	SO:0001583	missense	2584	exon7			CCGCCCGTCATGC		CCDS11728.1	17q25.1	2013-09-19			ENSG00000108479	ENSG00000108479	2.7.1.6		4118	protein-coding gene	gene with protein product		604313		GALK		7670469	Standard	NM_000154		Approved		uc002jpk.3	P51570	OTTHUMG00000179832	ENST00000588479.1:c.1031C>T	chr17.hg19:g.73754367G>A	ENSP00000465930:p.Thr344Met	90.0	0.0		94.0	32.0	NM_000154	B2RC07|B4E1G6	Missense_Mutation	SNP	ENST00000588479.1	hg19	CCDS11728.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.847209	0.91277	0.0	1.17E-4	ENSG00000108479	ENST00000225614;ENST00000437911	D;D	0.91631	-2.88;-2.88	4.46	4.46	0.54185	GHMP kinase, C-terminal (1);	.	.	.	.	D	0.95749	0.8617	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96383	0.9283	9	0.87932	D	0	-11.08	17.3028	0.87187	0.0:0.0:1.0:0.0	.	344	P51570	GALK1_HUMAN	M	344;374	ENSP00000225614:T344M;ENSP00000406305:T374M	ENSP00000225614:T344M	T	-	2	0	GALK1	71265962	1.000000	0.71417	0.946000	0.38457	0.973000	0.67179	9.060000	0.93907	2.317000	0.78254	0.563000	0.77884	ACG	.	.		0.672	GALK1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448430.1		
FBF1	85302	hgsc.bcm.edu	37	17	73910972	73910972	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73910972G>A	ENST00000586717.1	-	24	2901	c.2628C>T	c.(2626-2628)tgC>tgT	p.C876C	RP11-552F3.12_ENST00000587556.1_5'Flank|FBF1_ENST00000389570.4_Silent_p.C876C|FBF1_ENST00000319129.5_Silent_p.C875C			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	876					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						GCTCCTCCCCGCACTTGAGCA	0.677																																					p.C875C		Atlas-SNP	.											.	FBF1	48	.	0			c.C2625T						.						24.0	29.0	27.0					17																	73910972		2102	4209	6311	SO:0001819	synonymous_variant	85302	exon24			CTCCCCGCACTTG	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.2628C>T	chr17.hg19:g.73910972G>A		75.0	0.0		81.0	28.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	hg19																																																																																				.	.		0.677	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
GALR2	8811	hgsc.bcm.edu	37	17	74072920	74072920	+	Missense_Mutation	SNP	C	C	A	rs534747980		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:74072920C>A	ENST00000329003.3	+	2	662	c.572C>A	c.(571-573)aCc>aAc	p.T191N	ZACN_ENST00000334586.5_5'Flank|ZACN_ENST00000392503.2_5'Flank	NM_003857.2	NP_003848.1	O43603	GALR2_HUMAN	galanin receptor 2	191					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell surface receptor signaling pathway (GO:0007166)|digestion (GO:0007586)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|negative regulation of adenylate cyclase activity (GO:0007194)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of large conductance calcium-activated potassium channel activity (GO:1902608)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|peptide hormone binding (GO:0017046)			cervix(1)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						GACATCTGCACCTTCGTCTTC	0.697																																					p.T191N		Atlas-SNP	.											.	GALR2	17	.	0			c.C572A						.						45.0	32.0	36.0					17																	74072920		2200	4299	6499	SO:0001583	missense	8811	exon2			TCTGCACCTTCGT	AF040630	CCDS11739.1	17q25.3	2012-08-08			ENSG00000182687	ENSG00000182687		"""GPCR / Class A : Galanin receptors"""	4133	protein-coding gene	gene with protein product		603691				9685625, 9832121	Standard	NM_003857		Approved	GALNR2	uc002jqm.1	O43603	OTTHUMG00000167479	ENST00000329003.3:c.572C>A	chr17.hg19:g.74072920C>A	ENSP00000329684:p.Thr191Asn	51.0	0.0		52.0	21.0	NM_003857	A5JUU4|Q32MN8	Missense_Mutation	SNP	ENST00000329003.3	hg19	CCDS11739.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165023	0.94727	.	.	ENSG00000182687	ENST00000329003	T	0.72505	-0.66	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81922	0.4925	L	0.60012	1.86	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82161	-0.0594	10	0.46703	T	0.11	.	17.8276	0.88671	0.0:1.0:0.0:0.0	.	191	O43603	GALR2_HUMAN	N	191	ENSP00000329684:T191N	ENSP00000329684:T191N	T	+	2	0	GALR2	71584515	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	7.706000	0.84615	2.308000	0.77769	0.462000	0.41574	ACC	.	.		0.697	GALR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394760.1		
ENGASE	64772	hgsc.bcm.edu	37	17	77081342	77081342	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:77081342C>T	ENST00000579016.1	+	12	1618	c.1618C>T	c.(1618-1620)Cga>Tga	p.R540*		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	540						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						ACACAGCCTCCGACCCCTCCG	0.607																																					p.R540X		Atlas-SNP	.											.	ENGASE	55	.	0			c.C1618T						.						31.0	35.0	34.0					17																	77081342		1945	4141	6086	SO:0001587	stop_gained	64772	exon12			AGCCTCCGACCCC	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.1618C>T	chr17.hg19:g.77081342C>T	ENSP00000462333:p.Arg540*	502.0	1.0		262.0	198.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Nonsense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	C	37	6.587067	0.97684	.	.	ENSG00000167280	ENST00000545583	.	.	.	5.03	1.63	0.23807	.	1.128810	0.06486	N	0.733791	.	.	.	.	.	.	0.20638	N	0.999875	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-21.8065	6.45	0.21898	0.4837:0.4293:0.0:0.087	.	.	.	.	X	540	.	ENSP00000438577:R540X	R	+	1	2	ENGASE	74592937	0.000000	0.05858	0.121000	0.21740	0.843000	0.47879	0.106000	0.15354	0.449000	0.26747	0.561000	0.74099	CGA	.	.		0.607	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
ANAPC11	51529	hgsc.bcm.edu	37	17	79857927	79857927	+	Nonsense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:79857927A>T	ENST00000575195.2	+	2	421	c.241A>T	c.(241-243)Aag>Tag	p.K81*	ANAPC11_ENST00000574924.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000571874.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000571024.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000578544.1_3'UTR|ANAPC11_ENST00000357385.3_Missense_Mutation_p.E181V|ANAPC11_ENST00000583839.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000572851.2_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000344877.5_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000572639.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000579978.1_Nonsense_Mutation_p.K81*|NPB_ENST00000573081.1_5'Flank|ANAPC11_ENST00000392376.3_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000578550.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000577747.1_Nonsense_Mutation_p.K81*|ANAPC11_ENST00000577425.1_3'UTR|ANAPC11_ENST00000579133.1_3'UTR|ANAPC11_ENST00000571570.1_Nonsense_Mutation_p.K81*|NPB_ENST00000333383.7_5'Flank			Q9NYG5	APC11_HUMAN	anaphase promoting complex subunit 11	81					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CCAGGAATGGAAGTTCAAGGA	0.642																																					p.K81X		Atlas-SNP	.											.	ANAPC11	1	.	0			c.A241T						.						61.0	50.0	54.0					17																	79857927		2200	4300	6500	SO:0001587	stop_gained	51529	exon3			GAATGGAAGTTCA	AF247565	CCDS11789.1, CCDS32769.1, CCDS74180.1	17q25.3	2011-06-15	2008-10-30			ENSG00000141552		"""Anaphase promoting complex subunits"""	14452	protein-coding gene	gene with protein product		614534	"""anaphase promoting complex subunit 11 (yeast APC11 homolog)"""			10922056	Standard	NM_001002245		Approved	HSPC214, APC11, Apc11p, MGC882	uc002kby.1	Q9NYG5		ENST00000575195.2:c.241A>T	chr17.hg19:g.79857927A>T	ENSP00000458515:p.Lys81*	97.0	0.0		50.0	34.0	NM_001002247	A8MTT2|B7ZW64|Q502X9|Q9BW64|Q9P0R2	Nonsense_Mutation	SNP	ENST00000575195.2	hg19	CCDS11789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	36|36	5.807083|5.807083	0.96967|0.96967	.|.	.|.	ENSG00000141552|ENSG00000141552	ENST00000357385|ENST00000344877;ENST00000392376	.|.	.|.	.|.	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	0.291843|.	0.25958|.	U|.	0.027215|.	T|.	0.27866|.	0.0686|.	.|.	.|.	.|.	0.28144|0.28144	N|N	0.929673|0.929673	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|.	0.09292|.	-1.0681|.	8|.	0.87932|0.07482	D|T	0|0.82	.|.	14.9859|14.9859	0.71348|0.71348	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	181|.	Q9NYG5-2|.	.|.	V|X	181|81	.|.	ENSP00000349957:E181V|ENSP00000339695:K81X	E|K	+|+	2|1	0|0	ANAPC11|ANAPC11	77451219|77451219	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	8.187000|8.187000	0.89708|0.89708	1.954000|1.954000	0.56735|0.56735	0.460000|0.460000	0.39030|0.39030	GAA|AAG	.	.		0.642	ANAPC11-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440106.2	NM_016476	
ENOSF1	55556	hgsc.bcm.edu	37	18	675343	675343	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:675343C>T	ENST00000251101.7	-	15	1296	c.1208G>A	c.(1207-1209)cGg>cAg	p.R403Q	ENOSF1_ENST00000383578.3_Missense_Mutation_p.R321Q|ENOSF1_ENST00000340116.7_Missense_Mutation_p.R410Q|ENOSF1_ENST00000583973.1_5'UTR|ENOSF1_ENST00000580982.1_Missense_Mutation_p.R327Q|ENOSF1_ENST00000319815.6_Missense_Mutation_p.R173Q	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	403					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						GTAGGAAGCCCGCTGGATCAT	0.557																																					p.R410Q		Atlas-SNP	.											.	ENOSF1	44	.	0			c.G1229A						.						83.0	69.0	74.0					18																	675343		2203	4300	6503	SO:0001583	missense	55556	exon14			GAAGCCCGCTGGA	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.1208G>A	chr18.hg19:g.675343C>T	ENSP00000251101:p.Arg403Gln	103.0	0.0		126.0	57.0	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Missense_Mutation	SNP	ENST00000251101.7	hg19	CCDS11822.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.693600	0.30052	.	.	ENSG00000132199	ENST00000383578;ENST00000319815;ENST00000251101;ENST00000340116	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.97	4.83	0.62350	.	0.521550	0.23296	N	0.049728	T	0.27169	0.0666	N	0.20685	0.6	0.80722	D	1	B;B;B;B;B	0.16802	0.01;0.0;0.019;0.001;0.0	B;B;B;B;B	0.11329	0.004;0.001;0.006;0.003;0.001	T	0.06075	-1.0847	10	0.51188	T	0.08	.	8.0276	0.30446	0.0:0.1621:0.0:0.8379	.	410;222;434;403;321	A6NMP3;B3KXE4;Q6ZS08;Q7L5Y1;Q7L5Y1-2	.;.;.;ENOF1_HUMAN;.	Q	321;173;403;410	ENSP00000373072:R321Q;ENSP00000313346:R173Q;ENSP00000251101:R403Q;ENSP00000345974:R410Q	ENSP00000251101:R403Q	R	-	2	0	ENOSF1	665343	0.970000	0.33590	0.907000	0.35723	0.756000	0.42949	1.955000	0.40372	1.088000	0.41272	-0.312000	0.09012	CGG	.	.		0.557	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
CHMP1B	57132	hgsc.bcm.edu	37	18	11851635	11851635	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:11851635A>C	ENST00000526991.2	+	1	241	c.125A>C	c.(124-126)aAg>aCg	p.K42T	GNAL_ENST00000334049.6_Intron|GNAL_ENST00000423027.3_Intron|GNAL_ENST00000269162.5_Intron|RP11-78A19.3_ENST00000586474.1_RNA|GNAL_ENST00000535121.1_Intron	NM_020412.4	NP_065145.2	Q7LBR1	CHM1B_HUMAN	charged multivesicular body protein 1B	42					cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|protein transport (GO:0015031)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|lung(1)|urinary_tract(1)	3						GCCATTCAGAAGGGCAACATG	0.488																																					p.K42T		Atlas-SNP	.											.	CHMP1B	16	.	0			c.A125C						.						57.0	58.0	58.0					18																	11851635		2022	4186	6208	SO:0001583	missense	57132	exon1			TTCAGAAGGGCAA	AF306520	CCDS54180.1	18p11.21	2011-09-21	2011-09-21		ENSG00000255112	ENSG00000255112		"""Charged multivesicular body proteins"""	24287	protein-coding gene	gene with protein product		606486	"""chromatin modifying protein 1B"""			15537668	Standard	NM_020412		Approved	CHMP1.5, C18orf2, Vps46B	uc002kqe.3	Q7LBR1	OTTHUMG00000165820	ENST00000526991.2:c.125A>C	chr18.hg19:g.11851635A>C	ENSP00000432279:p.Lys42Thr	91.0	0.0		107.0	6.0	NM_020412	Q96E89|Q9HD41	Missense_Mutation	SNP	ENST00000526991.2	hg19	CCDS54180.1	.	.	.	.	.	.	.	.	.	.	A	31	5.078484	0.94000	.	.	ENSG00000255112	ENST00000526991	T	0.73469	-0.75	5.54	5.54	0.83059	.	.	.	.	.	D	0.88448	0.6439	H	0.94385	3.53	0.80722	D	1	D	0.57571	0.98	P	0.60541	0.876	D	0.91445	0.5177	9	0.87932	D	0	.	13.9287	0.63981	1.0:0.0:0.0:0.0	.	42	Q7LBR1	CHM1B_HUMAN	T	42	ENSP00000432279:K42T	ENSP00000432279:K42T	K	+	2	0	CHMP1B	11841635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.155000	0.77445	2.235000	0.73313	0.533000	0.62120	AAG	.	.		0.488	CHMP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386375.2	NM_020412	
ROCK1	6093	hgsc.bcm.edu	37	18	18625320	18625320	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:18625320C>T	ENST00000399799.2	-	5	1463	c.523G>A	c.(523-525)Gca>Aca	p.A175T		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TAGAATCGTGCCCATTTTTCA	0.373																																					p.A175T		Atlas-SNP	.											.	ROCK1	162	.	0			c.G523A						.						128.0	117.0	121.0					18																	18625320		2203	4300	6503	SO:0001583	missense	6093	exon5			ATCGTGCCCATTT		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.523G>A	chr18.hg19:g.18625320C>T	ENSP00000382697:p.Ala175Thr	52.0	0.0		69.0	23.0	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	hg19	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	C	36	5.730189	0.96856	.	.	ENSG00000067900	ENST00000399799	T	0.68025	-0.3	5.36	5.36	0.76844	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	0.85682	D	0.000000	T	0.77811	0.4186	L	0.45137	1.4	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.79024	-0.1972	10	0.87932	D	0	.	19.2924	0.94105	0.0:1.0:0.0:0.0	.	175	Q13464	ROCK1_HUMAN	T	175	ENSP00000382697:A175T	ENSP00000382697:A175T	A	-	1	0	ROCK1	16879318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.559000	0.82265	2.783000	0.95769	0.655000	0.94253	GCA	.	.		0.373	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406	
NPC1	4864	hgsc.bcm.edu	37	18	21136382	21136382	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:21136382G>A	ENST00000269228.5	-	8	1705	c.1151C>T	c.(1150-1152)cCc>cTc	p.P384L	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Missense_Mutation_p.P134L	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	384					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CTGGCTGCTGGGGGCTGACCA	0.557																																					p.P384L		Atlas-SNP	.											.	NPC1	114	.	0			c.C1151T						.						48.0	49.0	48.0					18																	21136382		2203	4300	6503	SO:0001583	missense	4864	exon8			CTGCTGGGGGCTG	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1151C>T	chr18.hg19:g.21136382G>A	ENSP00000269228:p.Pro384Leu	175.0	0.0		182.0	84.0	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	hg19	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321058	0.81580	.	.	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.97404	-4.37;-4.37	5.97	5.97	0.96955	.	0.099552	0.64402	D	0.000001	D	0.98213	0.9409	M	0.87097	2.86	0.80722	D	1	P;P	0.50369	0.934;0.837	P;P	0.52710	0.707;0.707	D	0.98669	1.0687	10	0.87932	D	0	-19.4693	20.428	0.99075	0.0:0.0:1.0:0.0	.	395;384	Q59GR1;O15118	.;NPC1_HUMAN	L	384;134;229	ENSP00000269228:P384L;ENSP00000408606:P134L	ENSP00000269228:P384L	P	-	2	0	NPC1	19390380	1.000000	0.71417	0.310000	0.25168	0.226000	0.24999	9.863000	0.99569	2.837000	0.97791	0.655000	0.94253	CCC	.	.		0.557	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
DSC3	1825	hgsc.bcm.edu	37	18	28584133	28584133	+	Silent	SNP	T	T	A	rs527772600		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:28584133T>A	ENST00000360428.4	-	13	2168	c.2088A>T	c.(2086-2088)atA>atT	p.I696I	DSC3_ENST00000434452.1_Silent_p.I696I	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	696					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TACCCAGTAATATTGCAAGGA	0.333																																					p.I696I		Atlas-SNP	.											.	DSC3	225	.	0			c.A2088T						.						98.0	92.0	94.0					18																	28584133		2203	4300	6503	SO:0001819	synonymous_variant	1825	exon13			CAGTAATATTGCA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.2088A>T	chr18.hg19:g.28584133T>A		115.0	0.0		115.0	41.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	hg19	CCDS32810.1																																																																																			.	.		0.333	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
SETBP1	26040	hgsc.bcm.edu	37	18	42532195	42532195	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:42532195T>C	ENST00000282030.5	+	4	3186	c.2890T>C	c.(2890-2892)Ttc>Ctc	p.F964L		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	964						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AATCACCAAGTTCCAAGTGTT	0.483									Schinzel-Giedion syndrome																												p.F964L		Atlas-SNP	.											.	SETBP1	577	.	0			c.T2890C						.						84.0	82.0	82.0					18																	42532195		2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ACCAAGTTCCAAG	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.2890T>C	chr18.hg19:g.42532195T>C	ENSP00000282030:p.Phe964Leu	176.0	0.0		150.0	11.0	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	T	8.737	0.917947	0.17982	.	.	ENSG00000152217	ENST00000282030	T	0.80994	-1.44	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.56819	0.2011	N	0.03608	-0.345	0.38853	D	0.956315	B	0.33022	0.394	B	0.27796	0.083	T	0.64702	-0.6345	10	0.02654	T	1	.	16.3512	0.83208	0.0:0.0:0.0:1.0	.	964	Q9Y6X0	SETBP_HUMAN	L	964	ENSP00000282030:F964L	ENSP00000282030:F964L	F	+	1	0	SETBP1	40786193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.107000	0.57811	2.266000	0.75297	0.533000	0.62120	TTC	.	.		0.483	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
LOXHD1	125336	hgsc.bcm.edu	37	18	44098132	44098132	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:44098132C>T	ENST00000398722.4	-	27	4524	c.4525G>A	c.(4525-4527)Ggg>Agg	p.G1509R	LOXHD1_ENST00000441551.2_Missense_Mutation_p.G1581R|LOXHD1_ENST00000398686.4_Missense_Mutation_p.G26R|LOXHD1_ENST00000536736.1_Missense_Mutation_p.G1725R|LOXHD1_ENST00000582408.1_Missense_Mutation_p.G614R|LOXHD1_ENST00000441893.2_Missense_Mutation_p.G658R|LOXHD1_ENST00000300591.6_Missense_Mutation_p.G676R|LOXHD1_ENST00000398705.2_Missense_Mutation_p.G26R|LOXHD1_ENST00000579038.1_Missense_Mutation_p.G580R			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1509	PLAT 11. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						TCTGTGCTCCCGTTGATGCCG	0.592																																					p.G1725R		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G5173A						.						118.0	111.0	113.0					18																	44098132		692	1591	2283	SO:0001583	missense	125336	exon33			TGCTCCCGTTGAT	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.4525G>A	chr18.hg19:g.44098132C>T	ENSP00000381707:p.Gly1509Arg	108.0	0.0		87.0	42.0	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	hg19		.	.	.	.	.	.	.	.	.	.	C	15.98	2.993671	0.54041	.	.	ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000398705;ENST00000536736;ENST00000441893;ENST00000398686;ENST00000414184;ENST00000335730;ENST00000452425	T;T;T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84;0.84;0.84	5.3	5.3	0.74995	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	0.058818	0.64402	D	0.000003	T	0.75895	0.3912	M	0.90145	3.09	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.934;1.0;1.0;0.973	T	0.81540	-0.0886	10	0.87932	D	0	.	18.9527	0.92646	0.0:1.0:0.0:0.0	.	1725;658;1447;1509	F5GZB4;F8WA52;Q8IVV2-2;Q8IVV2	.;.;.;LOXH1_HUMAN	R	676;1509;26;1725;658;26;26;1447;43	ENSP00000300591:G676R;ENSP00000381707:G1509R;ENSP00000381692:G26R;ENSP00000444586:G1725R;ENSP00000409062:G658R;ENSP00000381676:G26R;ENSP00000392440:G26R;ENSP00000414278:G43R	ENSP00000300591:G676R	G	-	1	0	LOXHD1	42352130	1.000000	0.71417	0.985000	0.45067	0.943000	0.58893	7.296000	0.78790	2.488000	0.83962	0.455000	0.32223	GGG	.	.		0.592	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
TCF4	6925	hgsc.bcm.edu	37	18	52895534	52895534	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:52895534G>A	ENST00000356073.4	-	19	2537	c.1926C>T	c.(1924-1926)tcC>tcT	p.S642S	TCF4_ENST00000457482.3_Silent_p.S486S|TCF4_ENST00000564228.1_Silent_p.S571S|TCF4_ENST00000354452.3_Silent_p.S646S|TCF4_ENST00000540999.1_Silent_p.S618S|TCF4_ENST00000537856.3_Silent_p.S512S|TCF4_ENST00000570177.2_Silent_p.S512S|TCF4_ENST00000564999.1_Silent_p.S642S|TCF4_ENST00000570287.2_Silent_p.S482S|TCF4_ENST00000564403.2_Silent_p.S652S|TCF4_ENST00000398339.1_Silent_p.S748S|TCF4_ENST00000543082.1_Silent_p.S600S|TCF4_ENST00000566279.1_Silent_p.S586S|TCF4_ENST00000561831.3_Silent_p.S482S|TCF4_ENST00000537578.1_Silent_p.S622S|TCF4_ENST00000568740.1_Silent_p.S617S|TCF4_ENST00000567880.1_Silent_p.S582S|TCF4_ENST00000544241.2_Silent_p.S575S|TCF4_ENST00000568673.1_Silent_p.S622S|TCF4_ENST00000566286.1_Silent_p.S639S|TCF4_ENST00000561992.1_Silent_p.S512S|TCF4_ENST00000565018.2_Silent_p.S646S	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	642	Class A specific domain.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GAGGCTCTGAGGACACCTTCT	0.507																																					p.S748S		Atlas-SNP	.											.	TCF4	178	.	0			c.C2244T						.						127.0	118.0	121.0					18																	52895534		2203	4300	6503	SO:0001819	synonymous_variant	6925	exon20			CTCTGAGGACACC	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1926C>T	chr18.hg19:g.52895534G>A		65.0	0.0		74.0	15.0	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	hg19	CCDS11960.1																																																																																			.	.		0.507	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
ST8SIA3	51046	hgsc.bcm.edu	37	18	55024435	55024435	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:55024435A>G	ENST00000324000.3	+	3	2628	c.594A>G	c.(592-594)caA>caG	p.Q198Q		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	198					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		AGGCTTTCCAAAGAGATGTTG	0.413																																					p.Q198Q		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A594G						.						72.0	76.0	75.0					18																	55024435		2203	4300	6503	SO:0001819	synonymous_variant	51046	exon3			TTTCCAAAGAGAT	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"""Sialyltransferases"""	14269	protein-coding gene	gene with protein product	"""ST8Sia III"""	609478	"""sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"""	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.594A>G	chr18.hg19:g.55024435A>G		158.0	0.0		151.0	47.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Silent	SNP	ENST00000324000.3	hg19	CCDS32834.1																																																																																			.	.		0.413	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879	
VPS4B	9525	hgsc.bcm.edu	37	18	61071042	61071042	+	Nonsense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:61071042G>A	ENST00000238497.5	-	5	585	c.382C>T	c.(382-384)Cga>Tga	p.R128*	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	128					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						ACATTTGGTCGTTCTATAACA	0.348																																					p.R128X		Atlas-SNP	.											.	VPS4B	33	.	0			c.C382T						.						69.0	62.0	64.0					18																	61071042		2203	4300	6503	SO:0001587	stop_gained	9525	exon5			TTGGTCGTTCTAT	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"""ATPases / AAA-type"""	10895	protein-coding gene	gene with protein product		609983	"""suppressor of K+ transport defect 1"", ""vacuolar protein sorting 4B (yeast)"""	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.382C>T	chr18.hg19:g.61071042G>A	ENSP00000238497:p.Arg128*	66.0	0.0		67.0	25.0	NM_004869	Q69HW4|Q9GZS7	Nonsense_Mutation	SNP	ENST00000238497.5	hg19	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	G	38	6.963087	0.97967	.	.	ENSG00000119541	ENST00000238497	.	.	.	5.69	3.83	0.44106	.	0.137128	0.52532	D	0.000068	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-12.3543	14.618	0.68562	0.0:0.0:0.5113:0.4887	.	.	.	.	X	128	.	ENSP00000238497:R128X	R	-	1	2	VPS4B	59222022	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.386000	0.44380	1.394000	0.46624	0.650000	0.86243	CGA	.	.		0.348	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869	
TMX3	54495	hgsc.bcm.edu	37	18	66377257	66377257	+	Splice_Site	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:66377257C>G	ENST00000299608.2	-	4	582		c.e4+1		TMX3_ENST00000443099.2_Splice_Site|TMX3_ENST00000562706.1_Splice_Site	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3						cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TGAAGGCTTACTAGAATAGGA	0.358																																					.		Atlas-SNP	.											.	TMX3	44	.	0			c.265+1G>C						.						105.0	99.0	101.0					18																	66377257		2203	4300	6503	SO:0001630	splice_region_variant	54495	exon5			GGCTTACTAGAAT	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"""Protein disulfide isomerases"""	24718	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 13"""		"""thioredoxin domain containing 10"""	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.265+1G>C	chr18.hg19:g.66377257C>G		96.0	0.0		90.0	17.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Splice_Site	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.393874	0.83011	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1057	0.89519	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMX3	64528237	1.000000	0.71417	0.988000	0.46212	0.980000	0.70556	7.407000	0.80029	2.619000	0.88677	0.563000	0.77884	.	.	.		0.358	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	Intron
CD226	10666	hgsc.bcm.edu	37	18	67614087	67614087	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:67614087T>C	ENST00000280200.4	-	3	533	c.265A>G	c.(265-267)Aat>Gat	p.N89D	CD226_ENST00000582621.1_Missense_Mutation_p.N89D|CD226_ENST00000581982.1_Intron|CD226_ENST00000577287.1_Intron	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	89	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				GTCATGTTATTGGAAGCCATC	0.448																																					p.N89D	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											.	CD226	51	.	0			c.A265G						.						115.0	101.0	106.0					18																	67614087		2203	4300	6503	SO:0001583	missense	10666	exon3			TGTTATTGGAAGC	U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	16961	protein-coding gene	gene with protein product		605397	"""CD226 antigen"""			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.265A>G	chr18.hg19:g.67614087T>C	ENSP00000280200:p.Asn89Asp	245.0	0.0		210.0	18.0	NM_006566	B2R818	Missense_Mutation	SNP	ENST00000280200.4	hg19	CCDS11997.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.693802	0.48202	.	.	ENSG00000150637	ENST00000280200	T	0.02737	4.18	5.51	2.68	0.31781	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.533834	0.22044	N	0.065415	T	0.05777	0.0151	L	0.56769	1.78	0.09310	N	1	P	0.48589	0.912	P	0.47603	0.551	T	0.19647	-1.0299	10	0.44086	T	0.13	.	10.551	0.45087	0.0:0.0:0.4514:0.5486	.	89	Q15762	CD226_HUMAN	D	89	ENSP00000280200:N89D	ENSP00000280200:N89D	N	-	1	0	CD226	65765067	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-0.187000	0.09656	0.269000	0.21961	0.533000	0.62120	AAT	.	.		0.448	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566	
CTDP1	9150	hgsc.bcm.edu	37	18	77488909	77488909	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:77488909C>T	ENST00000299543.7	+	11	2567	c.2420C>T	c.(2419-2421)gCg>gTg	p.A807V	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	807					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)		CCTTTCAGAGCGGTTCCGCCA	0.552																																					p.A807V		Atlas-SNP	.											CTDP1,NS,carcinoma,0,1	CTDP1	67	.	0			c.C2420T						.						158.0	179.0	172.0					18																	77488909		2203	4300	6503	SO:0001583	missense	9150	exon11			TCAGAGCGGTTCC	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.2420C>T	chr18.hg19:g.77488909C>T	ENSP00000299543:p.Ala807Val	67.0	0.0		53.0	9.0	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	hg19	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	C	4.726	0.135042	0.09032	.	.	ENSG00000060069	ENST00000299543	T	0.46451	0.87	5.01	-0.0294	0.13918	FCP1-like phosphatase, C-terminal (1);	1.078290	0.07078	N	0.836606	T	0.20495	0.0493	N	0.04043	-0.29	0.80722	D	1	B;B	0.17667	0.023;0.006	B;B	0.10450	0.003;0.005	T	0.12319	-1.0552	10	0.19147	T	0.46	-0.0228	9.0808	0.36550	0.0:0.1879:0.0:0.8121	.	688;807	Q9Y5B0-3;Q9Y5B0	.;CTDP1_HUMAN	V	807	ENSP00000299543:A807V	ENSP00000299543:A807V	A	+	2	0	CTDP1	75589897	1.000000	0.71417	0.356000	0.25785	0.053000	0.15095	1.891000	0.39738	-0.263000	0.09378	-0.199000	0.12753	GCG	.	.		0.552	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
ADNP2	22850	hgsc.bcm.edu	37	18	77895803	77895803	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:77895803A>T	ENST00000262198.4	+	4	2962	c.2507A>T	c.(2506-2508)gAg>gTg	p.E836V		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	836					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|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(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		AAGCTTGGGGAGCGGGAAGTC	0.527																																					p.E836V		Atlas-SNP	.											.	ADNP2	102	.	0			c.A2507T						.						66.0	66.0	66.0					18																	77895803		2203	4300	6503	SO:0001583	missense	22850	exon4			TTGGGGAGCGGGA	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	23803	protein-coding gene	gene with protein product			"""zinc finger protein 508"""	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2507A>T	chr18.hg19:g.77895803A>T	ENSP00000262198:p.Glu836Val	48.0	0.0		49.0	13.0	NM_014913	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	hg19	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.425753	0.83667	.	.	ENSG00000101544	ENST00000262198	.	.	.	5.18	5.18	0.71444	.	0.241133	0.35378	N	0.003259	T	0.73682	0.3618	M	0.62723	1.935	0.49130	D	0.999754	D	0.63046	0.992	P	0.61800	0.894	T	0.74153	-0.3757	8	.	.	.	-27.8706	15.1957	0.73084	1.0:0.0:0.0:0.0	.	836	Q6IQ32	ADNP2_HUMAN	V	836	.	.	E	+	2	0	ADNP2	75996794	1.000000	0.71417	0.988000	0.46212	0.940000	0.58332	4.082000	0.57635	2.171000	0.68590	0.533000	0.62120	GAG	.	.		0.527	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913	
SHC2	25759	hgsc.bcm.edu	37	19	438994	438994	+	Silent	SNP	G	G	A	rs372414911		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:438994G>A	ENST00000264554.6	-	3	575	c.576C>T	c.(574-576)ggC>ggT	p.G192G		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	192	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)		ATCCCCGGACGCCAGGCACGG	0.672																																					p.G192G		Atlas-SNP	.											.	SHC2	47	.	0			c.C576T						.	G		0,3714		0,0,1857	22.0	23.0	23.0		576	-2.2	0.9	19		23	2,8158		0,2,4078	no	coding-synonymous	SHC2	NM_012435.2		0,2,5935	AA,AG,GG		0.0245,0.0,0.0168		192/583	438994	2,11872	1857	4080	5937	SO:0001819	synonymous_variant	25759	exon3			CCGGACGCCAGGC	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.576C>T	chr19.hg19:g.438994G>A		244.0	0.0		145.0	95.0	NM_012435	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	hg19	CCDS45891.1																																																																																			.	.		0.672	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3		
PTBP1	5725	hgsc.bcm.edu	37	19	804698	804698	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:804698A>G	ENST00000349038.4	+	6	675	c.602A>G	c.(601-603)cAc>cGc	p.H201R	PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000356948.6_Missense_Mutation_p.H201R|PTBP1_ENST00000394601.4_Missense_Mutation_p.H201R|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	201	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		GATGTGCTGCACCAGGTGAGG	0.687																																					p.H201R		Atlas-SNP	.											.	PTBP1	43	.	0			c.A602G						.						58.0	56.0	57.0					19																	804698		2203	4300	6503	SO:0001583	missense	5725	exon6			TGCTGCACCAGGT	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.602A>G	chr19.hg19:g.804698A>G	ENSP00000014112:p.His201Arg	68.0	0.0		32.0	19.0	NM_031990	Q9BUQ0	Missense_Mutation	SNP	ENST00000349038.4	hg19	CCDS32859.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.009406	0.54361	.	.	ENSG00000011304	ENST00000356948;ENST00000394601;ENST00000349038	T;T;T	0.53640	0.61;0.67;1.01	4.65	4.65	0.58169	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.051377	0.85682	D	0.000000	T	0.47469	0.1447	L	0.47716	1.5	0.80722	D	1	P;B;B	0.34815	0.47;0.038;0.051	B;B;B	0.40702	0.338;0.078;0.17	T	0.53294	-0.8459	10	0.87932	D	0	-48.146	13.2834	0.60228	1.0:0.0:0.0:0.0	.	201;201;201	P26599;P26599-2;Q9BUQ0	PTBP1_HUMAN;.;.	R	201	ENSP00000349428:H201R;ENSP00000408096:H201R;ENSP00000014112:H201R	ENSP00000014112:H201R	H	+	2	0	PTBP1	755698	1.000000	0.71417	0.996000	0.52242	0.495000	0.33615	7.186000	0.77722	1.739000	0.51704	0.533000	0.62120	CAC	.	.		0.687	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
STK11	6794	hgsc.bcm.edu	37	19	1218439	1218439	+	Nonsense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1218439T>G	ENST00000326873.7	+	2	1487	c.314T>G	c.(313-315)tTa>tGa	p.L105*	STK11_ENST00000585748.1_3'UTR	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGAGGAGGTTACGGCACAAA	0.547		14	"""D, Mis, N, F, S"""		"""NSCLC, pancreatic"""	"""jejunal harmartoma, ovarian, testicular, pancreatic"""			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.L105X		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"""E, M, O"""	.	STK11	410	.	23	Whole gene deletion(20)|Unknown(2)|Deletion - Frameshift(1)	cervix(15)|lung(4)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.T314G						.						167.0	173.0	171.0					19																	1218439		2010	4168	6178	SO:0001587	stop_gained	6794	exon2	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	GGAGGTTACGGCA	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"""polarization-related protein LKB1"""	602216	"""serine/threonine kinase 11 (Peutz-Jeghers syndrome)"""			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.314T>G	chr19.hg19:g.1218439T>G	ENSP00000324856:p.Leu105*	94.0	0.0		70.0	31.0	NM_000455	B2RBX7|E7EW76	Nonsense_Mutation	SNP	ENST00000326873.7	hg19	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	T	46	12.840858	0.99700	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	.	.	.	4.1	4.1	0.47936	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.0596	12.2854	0.54789	0.0:0.0:0.0:1.0	.	.	.	.	X	105	.	ENSP00000324856:L105X	L	+	2	0	STK11	1169439	0.999000	0.42202	0.117000	0.21633	0.785000	0.44390	7.837000	0.86796	1.506000	0.48736	0.402000	0.26972	TTA	.	.		0.547	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455	
ADAMTSL5	339366	hgsc.bcm.edu	37	19	1510710	1510710	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1510710G>A	ENST00000413997.2	-	3	148	c.149C>T	c.(148-150)cCg>cTg	p.P50L	CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000330475.4_Missense_Mutation_p.P40L|ADAMTSL5_ENST00000395467.2_5'UTR|ADAMTSL5_ENST00000590562.1_5'UTR			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	50	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)		GGACACCCACGGGGTCCACTC	0.716																																					p.P40L		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.C119T						.						5.0	5.0	5.0					19																	1510710		2002	3897	5899	SO:0001583	missense	339366	exon3			ACCCACGGGGTCC	BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain containing 6"""	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.149C>T	chr19.hg19:g.1510710G>A	ENSP00000399364:p.Pro50Leu	206.0	0.0		84.0	52.0	NM_213604	B4DXK7|Q8IW95	Missense_Mutation	SNP	ENST00000413997.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.35	1.325261	0.24080	.	.	ENSG00000185761	ENST00000413997;ENST00000330475	T;T	0.54479	0.57;0.57	3.43	1.18	0.20946	.	0.682392	0.14384	N	0.322928	T	0.40862	0.1134	L	0.45581	1.43	0.23113	N	0.998277	B;B	0.18863	0.031;0.031	B;B	0.14578	0.011;0.011	T	0.27434	-1.0074	10	0.38643	T	0.18	.	6.6092	0.22741	0.2373:0.0:0.7627:0.0	.	50;40	B4DXK7;Q6ZMM2	.;ATL5_HUMAN	L	50;40	ENSP00000399364:P50L;ENSP00000327608:P40L	ENSP00000327608:P40L	P	-	2	0	ADAMTSL5	1461710	0.015000	0.18098	0.014000	0.15608	0.647000	0.38526	1.583000	0.36579	0.156000	0.19299	0.456000	0.33151	CCG	.	.		0.716	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919	
TCF3	6929	hgsc.bcm.edu	37	19	1625583	1625583	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1625583C>T	ENST00000262965.5	-	7	835	c.491G>A	c.(490-492)gGc>gAc	p.G164D	TCF3_ENST00000588136.1_Missense_Mutation_p.G164D|TCF3_ENST00000453954.2_Missense_Mutation_p.G80D|TCF3_ENST00000395423.3_Missense_Mutation_p.G113D|TCF3_ENST00000344749.5_Missense_Mutation_p.G164D	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		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)		ACCTAGGCTGCCGTCTGCCGC	0.697			T	"""PBX1, HLF, TFPT"""	pre B-ALL																																p.G164D		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.G491A						.						9.0	11.0	10.0					19																	1625583		2163	4269	6432	SO:0001583	missense	6929	exon7			AGGCTGCCGTCTG	M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"""Basic helix-loop-helix proteins"""	11633	protein-coding gene	gene with protein product	"""transcription factor E2-alpha"", ""immunoglobulin transcription factor 1"", ""kappa-E2-binding factor"", ""E2A immunoglobulin enhancer-binding factor E12/E47"", ""VDR interacting repressor"""	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.491G>A	chr19.hg19:g.1625583C>T	ENSP00000262965:p.Gly164Asp	169.0	0.0		127.0	87.0	NM_003200	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000262965.5	hg19	CCDS12074.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505246	0.26949	.	.	ENSG00000071564	ENST00000262965;ENST00000344749;ENST00000453954;ENST00000395423	T;T;T	0.40476	1.03;1.03;1.03	4.52	4.52	0.55395	.	0.476605	0.22677	N	0.056981	T	0.36331	0.0963	N	0.16790	0.44	0.19945	N	0.999948	D;P;B	0.61697	0.99;0.954;0.016	P;B;B	0.53861	0.736;0.356;0.003	T	0.16600	-1.0397	10	0.11182	T	0.66	-2.4508	13.9503	0.64113	0.0:1.0:0.0:0.0	.	164;164;113	P15923-2;P15923;Q2TB39	.;TFE2_HUMAN;.	D	164;164;164;113	ENSP00000262965:G164D;ENSP00000344375:G164D;ENSP00000378813:G113D	ENSP00000262965:G164D	G	-	2	0	TCF3	1576583	0.058000	0.20735	0.009000	0.14445	0.017000	0.09413	3.330000	0.52068	2.049000	0.60858	0.561000	0.74099	GGC	.	.		0.697	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200	
REXO1	57455	hgsc.bcm.edu	37	19	1827184	1827184	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1827184A>G	ENST00000170168.4	-	2	1698	c.1604T>C	c.(1603-1605)gTg>gCg	p.V535A	CTB-31O20.4_ENST00000587741.1_RNA|REXO1_ENST00000587524.1_5'Flank|CTB-31O20.4_ENST00000593201.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	535	Interacts with TCEB3.					nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		CACGCTCGGCACCCCTGGCCC	0.716																																					p.V535A		Atlas-SNP	.											.	REXO1	55	.	0			c.T1604C						.						6.0	6.0	6.0					19																	1827184		1997	3963	5960	SO:0001583	missense	57455	exon2			CTCGGCACCCCTG	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1604T>C	chr19.hg19:g.1827184A>G	ENSP00000170168:p.Val535Ala	61.0	0.0		28.0	18.0	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	hg19	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.240958	0.00274	.	.	ENSG00000079313	ENST00000170168	T	0.10668	2.85	3.93	0.408	0.16377	.	591.051000	0.00687	N	0.000710	T	0.03564	0.0102	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32955	-0.9887	10	0.07644	T	0.81	-3.1855	1.9791	0.03422	0.12:0.1999:0.4747:0.2054	.	535	Q8N1G1	REXO1_HUMAN	A	535	ENSP00000170168:V535A	ENSP00000170168:V535A	V	-	2	0	REXO1	1778184	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.065000	0.11617	-0.008000	0.14320	-0.475000	0.04921	GTG	.	.		0.716	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
DOT1L	84444	hgsc.bcm.edu	37	19	2193778	2193778	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:2193778C>T	ENST00000398665.3	+	6	620	c.584C>T	c.(583-585)gCg>gTg	p.A195V		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	195	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		GCCAAGTATGCGGAGGTGAGC	0.607																																					p.A195V		Atlas-SNP	.											.	DOT1L	205	.	0			c.C584T						.						87.0	90.0	89.0					19																	2193778		2179	4268	6447	SO:0001583	missense	84444	exon6			AGTATGCGGAGGT	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.584C>T	chr19.hg19:g.2193778C>T	ENSP00000381657:p.Ala195Val	54.0	0.0		26.0	16.0	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817061	0.90790	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	T;T	0.37235	1.21;1.21	4.34	4.34	0.51931	.	0.112447	0.64402	D	0.000012	T	0.68329	0.2989	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.78375	-0.2228	10	0.87932	D	0	-11.0759	15.988	0.80176	0.0:1.0:0.0:0.0	.	195	Q8TEK3-2	.	V	195;195;171	ENSP00000381657:A195V;ENSP00000404284:A171V	ENSP00000221482:A195V	A	+	2	0	DOT1L	2144778	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.528000	0.67129	2.249000	0.74217	0.561000	0.74099	GCG	.	.		0.607	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
LINGO3	645191	hgsc.bcm.edu	37	19	2290416	2290416	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:2290416C>T	ENST00000585527.1	-	1	1607	c.1360G>A	c.(1360-1362)Gcg>Acg	p.A454T	LINGO3_ENST00000404279.1_Missense_Mutation_p.A454T			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	454	Ig-like C2-type.					integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						GCCCGGCCCGCGCTGGTGGCC	0.791																																					p.A454T		Atlas-SNP	.											.	LINGO3	19	.	0			c.G1360A						.						1.0	1.0	1.0					19																	2290416		545	1142	1687	SO:0001583	missense	645191	exon2			GGCCCGCGCTGGT	AK091795	CCDS45905.1	19p13.3	2013-01-11	2007-02-01	2007-02-01		ENSG00000220008		"""Immunoglobulin superfamily / I-set domain containing"""	21206	protein-coding gene	gene with protein product		609792	"""leucine rich repeat neuronal 6B"""	LRRN6B		14686891	Standard	NM_001101391		Approved	LERN2	uc010dsx.1	P0C6S8		ENST00000585527.1:c.1360G>A	chr19.hg19:g.2290416C>T	ENSP00000467753:p.Ala454Thr	25.0	0.0		13.0	11.0	NM_001101391		Missense_Mutation	SNP	ENST00000585527.1	hg19	CCDS45905.1	.	.	.	.	.	.	.	.	.	.	c	0.466	-0.886868	0.02511	.	.	ENSG00000220008	ENST00000404279	T	0.77750	-1.12	4.12	-0.116	0.13555	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42854	0.1221	N	0.02142	-0.665	0.20196	N	0.999928	B	0.02656	0.0	B	0.04013	0.001	T	0.32079	-0.9920	9	0.10902	T	0.67	.	1.5461	0.02565	0.1488:0.4158:0.2211:0.2143	.	454	P0C6S8	LIGO3_HUMAN	T	454	ENSP00000384979:A454T	ENSP00000384979:A454T	A	-	1	0	LINGO3	2241416	0.014000	0.17966	0.605000	0.28930	0.075000	0.17131	-0.010000	0.12743	0.116000	0.18110	0.462000	0.41574	GCG	.	.		0.791	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391	
SEMA6B	10501	hgsc.bcm.edu	37	19	4548377	4548377	+	Missense_Mutation	SNP	G	G	A	rs145507498		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:4548377G>A	ENST00000586582.1	-	13	1662	c.1352C>T	c.(1351-1353)gCg>gTg	p.A451V	RN7SL121P_ENST00000584223.1_RNA|SEMA6B_ENST00000301293.3_Missense_Mutation_p.A451V|SEMA6B_ENST00000586965.1_Missense_Mutation_p.A451V	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	451	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		GACCGTCCCCGCCTCAGAACC	0.662																																					p.A451V		Atlas-SNP	.											.	SEMA6B	51	.	0			c.C1352T						.	G	VAL/ALA	2,4404		0,2,2201	55.0	55.0	55.0		1352	0.1	0.1	19	dbSNP_134	55	0,8600		0,0,4300	no	missense	SEMA6B	NM_032108.3	64	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	451/889	4548377	2,13004	2203	4300	6503	SO:0001583	missense	10501	exon13			GTCCCCGCCTCAG	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.1352C>T	chr19.hg19:g.4548377G>A	ENSP00000467290:p.Ala451Val	122.0	0.0		140.0	61.0	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	hg19	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	.	9.156	1.017611	0.19355	4.54E-4	0.0	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.10573	2.86	4.01	0.0592	0.14331	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.358123	0.30556	N	0.009370	T	0.05502	0.0145	N	0.11698	0.16	0.09310	N	1	B;B	0.15930	0.015;0.006	B;B	0.13407	0.009;0.009	T	0.32824	-0.9892	10	0.48119	T	0.1	.	8.6381	0.33962	0.284:0.0:0.716:0.0	.	451;451	B4DT36;Q9H3T3	.;SEM6B_HUMAN	V	451	ENSP00000301293:A451V	ENSP00000301292:A451V	A	-	2	0	SEMA6B	4499377	0.003000	0.15002	0.129000	0.21949	0.573000	0.36030	0.904000	0.28491	-0.093000	0.12396	0.485000	0.47835	GCG	.	G|1.000;A|0.000		0.662	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
ARRDC5	645432	hgsc.bcm.edu	37	19	4891359	4891359	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:4891359G>A	ENST00000381781.2	-	3	727	c.728C>T	c.(727-729)tCt>tTt	p.S243F	AC027319.1_ENST00000408608.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	243										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		GTCCAGCCGAGACCGCCGCTC	0.592																																					p.S243F		Atlas-SNP	.											.	ARRDC5	19	.	0			c.C728T						.						56.0	68.0	64.0					19																	4891359		2099	4205	6304	SO:0001583	missense	645432	exon3			AGCCGAGACCGCC		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.728C>T	chr19.hg19:g.4891359G>A	ENSP00000371200:p.Ser243Phe	56.0	0.0		48.0	17.0	NM_001080523		Missense_Mutation	SNP	ENST00000381781.2	hg19	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	G	7.436	0.639764	0.14386	.	.	ENSG00000205784	ENST00000381781	T	0.18338	2.22	4.92	-2.96	0.05547	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	2.609720	0.01383	N	0.013012	T	0.09949	0.0244	N	0.24115	0.695	0.09310	N	1	P	0.40266	0.71	B	0.38378	0.272	T	0.09640	-1.0665	10	0.33940	T	0.23	3.5095	0.6696	0.00856	0.2503:0.1522:0.3619:0.2355	.	243	A6NEK1	ARRD5_HUMAN	F	243	ENSP00000371200:S243F	ENSP00000371200:S243F	S	-	2	0	ARRDC5	4842359	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.152000	0.10159	-0.426000	0.07360	-0.961000	0.02630	TCT	.	.		0.592	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803	
ARRDC5	645432	hgsc.bcm.edu	37	19	4891371	4891371	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:4891371G>T	ENST00000381781.2	-	3	715	c.716C>A	c.(715-717)gCa>gAa	p.A239E	AC027319.1_ENST00000408608.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	239										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		CCGCCGCTCTGCACTGGGCGT	0.577																																					p.A239E		Atlas-SNP	.											.	ARRDC5	19	.	0			c.C716A						.						68.0	76.0	73.0					19																	4891371		2084	4215	6299	SO:0001583	missense	645432	exon3			CGCTCTGCACTGG		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.716C>A	chr19.hg19:g.4891371G>T	ENSP00000371200:p.Ala239Glu	55.0	0.0		51.0	17.0	NM_001080523		Missense_Mutation	SNP	ENST00000381781.2	hg19	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.576065	0.45902	.	.	ENSG00000205784	ENST00000381781	T	0.16324	2.35	4.92	4.92	0.64577	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	0.266274	0.19834	U	0.105015	T	0.25568	0.0622	L	0.29908	0.895	0.09310	N	0.999999	D	0.58620	0.983	P	0.60415	0.874	T	0.10428	-1.0630	10	0.22109	T	0.4	-32.0156	15.8766	0.79170	0.0:0.0:1.0:0.0	.	239	A6NEK1	ARRD5_HUMAN	E	239	ENSP00000371200:A239E	ENSP00000371200:A239E	A	-	2	0	ARRDC5	4842371	0.141000	0.22595	0.011000	0.14972	0.001000	0.01503	3.260000	0.51523	2.667000	0.90743	0.655000	0.94253	GCA	.	.		0.577	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803	
KDM4B	23030	hgsc.bcm.edu	37	19	5119732	5119732	+	Missense_Mutation	SNP	C	C	T	rs374489612	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5119732C>T	ENST00000159111.4	+	11	1402	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	KDM4B_ENST00000536461.1_Missense_Mutation_p.T429M	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	395					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GGGGAGGGTACGGCTGGGGCA	0.672													C|||	2	0.000399361	0.0015	0.0	5008	,	,		14792	0.0		0.0	False		,,,				2504	0.0				p.T395M		Atlas-SNP	.											.	KDM4B	120	.	0			c.C1184T						.	C	MET/THR	2,4274		0,2,2136	25.0	18.0	21.0		1184	-0.4	0.0	19		21	0,8426		0,0,4213	no	missense	KDM4B	NM_015015.2	81	0,2,6349	TT,TC,CC		0.0,0.0468,0.0157	benign	395/1097	5119732	2,12700	2138	4213	6351	SO:0001583	missense	23030	exon11			AGGGTACGGCTGG	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1184C>T	chr19.hg19:g.5119732C>T	ENSP00000159111:p.Thr395Met	194.0	1.0		181.0	155.0	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	C	5.454	0.268823	0.10349	4.68E-4	0.0	ENSG00000127663	ENST00000159111;ENST00000536461	T;T	0.16897	2.32;2.31	4.76	-0.385	0.12470	.	2.196000	0.02115	N	0.055111	T	0.10294	0.0252	N	0.11427	0.14	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.04013	0.001;0.0	T	0.30238	-0.9985	10	0.45353	T	0.12	-2.9184	6.6216	0.22806	0.0:0.3429:0.0:0.6571	.	429;395	F5GX28;O94953	.;KDM4B_HUMAN	M	395;429	ENSP00000159111:T395M;ENSP00000440495:T429M	ENSP00000159111:T395M	T	+	2	0	KDM4B	5070732	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.588000	0.23924	0.104000	0.17725	-0.258000	0.10820	ACG	.	.		0.672	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
SAFB2	9667	hgsc.bcm.edu	37	19	5604862	5604862	+	Missense_Mutation	SNP	G	G	A	rs142026681		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5604862G>A	ENST00000252542.4	-	10	1646	c.1382C>T	c.(1381-1383)gCg>gTg	p.A461V	SAFB2_ENST00000591310.1_5'UTR	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	461	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		GCACTTGGTCGCCTCGTCAGA	0.547													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17190	0.0		0.0	False		,,,				2504	0.0				p.A461V	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.C1382T						.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	87.0	70.0	76.0		1382	5.3	1.0	19	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	missense	SAFB2	NM_014649.2	64	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	461/954	5604862	2,13004	2203	4300	6503	SO:0001583	missense	9667	exon10			TTGGTCGCCTCGT	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.1382C>T	chr19.hg19:g.5604862G>A	ENSP00000252542:p.Ala461Val	83.0	0.0		62.0	18.0	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	hg19	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805080	0.70682	2.27E-4	1.16E-4	ENSG00000130254	ENST00000434962;ENST00000415313;ENST00000394625;ENST00000252542	D	0.83591	-1.74	5.34	5.34	0.76211	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.56097	D	0.000025	D	0.88377	0.6420	M	0.80422	2.495	0.80722	D	1	P	0.41947	0.766	P	0.49799	0.622	D	0.86308	0.1684	10	0.25751	T	0.34	-25.2929	19.0382	0.92987	0.0:0.0:1.0:0.0	.	461	Q14151	SAFB2_HUMAN	V	357;212;461;461	ENSP00000252542:A461V	ENSP00000252542:A461V	A	-	2	0	SAFB2	5555862	1.000000	0.71417	0.983000	0.44433	0.655000	0.38815	9.746000	0.98859	2.505000	0.84491	0.555000	0.69702	GCG	.	G|1.000;A|0.000		0.547	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649	
SAFB	6294	hgsc.bcm.edu	37	19	5661679	5661679	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5661679C>T	ENST00000292123.5	+	15	2120	c.2013C>T	c.(2011-2013)cgC>cgT	p.R671R	SAFB_ENST00000538656.1_Silent_p.R513R|SAFB_ENST00000433404.1_Silent_p.R501R|SAFB_ENST00000454510.1_Silent_p.R602R|SAFB_ENST00000592224.1_Silent_p.R670R|SAFB_ENST00000588852.1_Silent_p.R671R	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	671	Arg-rich.|Glu-rich.|Interaction with POLR2A.|Interaction with SAFB2.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GGCTGGAGCGCGAACGCATGC	0.701																																					p.R671R	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.C2013T						.						17.0	20.0	19.0					19																	5661679		2198	4292	6490	SO:0001819	synonymous_variant	6294	exon15			GGAGCGCGAACGC	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"""RNA binding motif (RRM) containing"""	10520	protein-coding gene	gene with protein product	"""Hsp27 ERE-TATA binding protein"""	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.2013C>T	chr19.hg19:g.5661679C>T		129.0	0.0		118.0	10.0	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Silent	SNP	ENST00000292123.5	hg19	CCDS12142.1																																																																																			.	.		0.701	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2		
TRIP10	9322	hgsc.bcm.edu	37	19	6743585	6743585	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:6743585C>T	ENST00000313244.9	+	6	524	c.489C>T	c.(487-489)aaC>aaT	p.N163N	TRIP10_ENST00000600428.1_Silent_p.N55N|TRIP10_ENST00000313285.8_Silent_p.N163N|TRIP10_ENST00000596758.1_Silent_p.N163N			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	163	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						AGGATATCAACGCCACCAAGG	0.622																																					p.N163N		Atlas-SNP	.											.	TRIP10	104	.	0			c.C489T						.						62.0	61.0	61.0					19																	6743585		2202	4300	6502	SO:0001819	synonymous_variant	9322	exon6			TATCAACGCCACC	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"""Cdc42-interacting protein"""	604504	"""salt tolerator"""	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.489C>T	chr19.hg19:g.6743585C>T		53.0	0.0		65.0	20.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Silent	SNP	ENST00000313244.9	hg19																																																																																				.	.		0.622	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2		
ZNF358	140467	hgsc.bcm.edu	37	19	7585482	7585482	+	Missense_Mutation	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:7585482C>A	ENST00000597229.1	+	2	1524	c.1354C>A	c.(1354-1356)Ctc>Atc	p.L452I	ZNF358_ENST00000394341.2_Missense_Mutation_p.L452I|CTD-2207O23.11_ENST00000602083.1_RNA|MCOLN1_ENST00000264079.6_5'Flank	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	452					embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						tggcttgggcctcagccctgg	0.687																																					p.L452I		Atlas-SNP	.											.	ZNF358	41	.	0			c.C1354A						.						21.0	23.0	22.0					19																	7585482		2058	4066	6124	SO:0001583	missense	140467	exon2			TTGGGCCTCAGCC	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"""Zinc fingers, C2H2-type"""	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.1354C>A	chr19.hg19:g.7585482C>A	ENSP00000472305:p.Leu452Ile	93.0	0.0		110.0	49.0	NM_018083	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	hg19	CCDS32890.2	.	.	.	.	.	.	.	.	.	.	C	12.36	1.914796	0.33815	.	.	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.08370	3.1	2.94	0.697	0.18081	.	.	.	.	.	T	0.03178	0.0093	N	0.08118	0	0.24609	N	0.99374	P	0.34522	0.455	B	0.27170	0.077	T	0.40757	-0.9546	9	0.36615	T	0.2	-16.2488	3.2665	0.06867	0.2585:0.5979:0.0:0.1436	.	452	Q9NW07	ZN358_HUMAN	I	452	ENSP00000377873:L452I	ENSP00000354703:L452I	L	+	1	0	ZNF358	7491482	0.001000	0.12720	0.143000	0.22291	0.306000	0.27790	0.032000	0.13732	0.249000	0.21456	0.462000	0.41574	CTC	.	.		0.687	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1		
XAB2	56949	hgsc.bcm.edu	37	19	7687717	7687717	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:7687717G>A	ENST00000358368.4	-	10	1339	c.1302C>T	c.(1300-1302)agC>agT	p.S434S	XAB2_ENST00000534844.1_Silent_p.S431S	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	434					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						GACACCACACGCTTGCCAGGT	0.657								Direct reversal of damage;Nucleotide excision repair (NER)																													p.S434S		Atlas-SNP	.											XAB2,NS,carcinoma,0,2	XAB2	69	.	0			c.C1302T						.						79.0	62.0	68.0					19																	7687717		2203	4300	6503	SO:0001819	synonymous_variant	56949	exon10			CCACACGCTTGCC	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.1302C>T	chr19.hg19:g.7687717G>A		101.0	0.0		103.0	9.0	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	hg19	CCDS32892.1																																																																																			.	.		0.657	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
CERS4	79603	hgsc.bcm.edu	37	19	8320763	8320763	+	Splice_Site	SNP	C	C	T	rs368700192		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:8320763C>T	ENST00000251363.5	+	6	768	c.468C>T	c.(466-468)caC>caT	p.H156H	CERS4_ENST00000559336.1_Splice_Site_p.H156H|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559450.1_Splice_Site_p.H156H|CERS4_ENST00000558331.1_Splice_Site_p.H105H	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	156	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										TCCTGTACCACGTGAGTATAC	0.587																																					p.H156H		Atlas-SNP	.											.	.	.	.	0			c.C468T						.	C		1,4405	2.1+/-5.4	0,1,2202	79.0	71.0	74.0		468	0.5	1.0	19		74	0,8600		0,0,4300	no	coding-synonymous-near-splice	CERS4	NM_024552.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		156/395	8320763	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	79603	exon6			GTACCACGTGAGT		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.468+1C>T	chr19.hg19:g.8320763C>T		47.0	0.0		52.0	19.0	NM_024552	D6W665	Silent	SNP	ENST00000251363.5	hg19	CCDS12197.1																																																																																			.	.		0.587	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	Silent
MUC16	94025	hgsc.bcm.edu	37	19	9071612	9071612	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:9071612A>G	ENST00000397910.4	-	3	16037	c.15834T>C	c.(15832-15834)tcT>tcC	p.S5278S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5280	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTGCGATGCAGACTCAGGAG	0.512																																					p.S5278S		Atlas-SNP	.											.	MUC16	4315	.	0			c.T15834C						.						177.0	172.0	174.0					19																	9071612		2069	4214	6283	SO:0001819	synonymous_variant	94025	exon3			CGATGCAGACTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15834T>C	chr19.hg19:g.9071612A>G		93.0	0.0		116.0	5.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF266	10781	hgsc.bcm.edu	37	19	9524021	9524021	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:9524021T>G	ENST00000592904.1	-	5	3656	c.1580A>C	c.(1579-1581)aAa>aCa	p.K527T	ZNF266_ENST00000592292.1_Missense_Mutation_p.K527T|ZNF266_ENST00000361151.1_Missense_Mutation_p.K527T|ZNF266_ENST00000588221.1_Missense_Mutation_p.K527T|ZNF266_ENST00000361451.2_Missense_Mutation_p.K527T|ZNF266_ENST00000590306.1_Missense_Mutation_p.K527T|ZNF266_ENST00000588933.1_Missense_Mutation_p.K527T			Q14584	ZN266_HUMAN	zinc finger protein 266	527					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)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						ACTGAAGGCTTTCCCGCACTC	0.443																																					p.K527T		Atlas-SNP	.											.	ZNF266	65	.	0			c.A1580C						.						92.0	81.0	85.0					19																	9524021		2203	4300	6503	SO:0001583	missense	10781	exon11			AAGGCTTTCCCGC	X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"""Zinc fingers, C2H2-type"""	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.1580A>C	chr19.hg19:g.9524021T>G	ENSP00000466714:p.Lys527Thr	127.0	0.0		124.0	43.0	NM_001271314	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	hg19	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.445700	0.84101	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.27890	1.64;1.64	2.4	2.4	0.29515	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.54447	0.1859	M	0.84326	2.69	0.26605	N	0.972956	D	0.89917	1.0	D	0.79784	0.993	T	0.38757	-0.9646	9	0.87932	D	0	.	8.6374	0.33957	0.0:0.0:0.0:1.0	.	527	Q14584	ZN266_HUMAN	T	527	ENSP00000354680:K527T;ENSP00000355047:K527T	ENSP00000355047:K527T	K	-	2	0	ZNF266	9385021	0.994000	0.37717	0.025000	0.17156	0.702000	0.40608	2.799000	0.47892	1.352000	0.45808	0.374000	0.22700	AAA	.	.		0.443	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1		
P2RY11	5032	hgsc.bcm.edu	37	19	10225062	10225062	+	Missense_Mutation	SNP	C	C	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:10225062C>G	ENST00000321826.4	+	2	957	c.773C>G	c.(772-774)gCc>gGc	p.A258G	PPAN-P2RY11_ENST00000428358.1_3'UTR|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A678G|PPAN_ENST00000556468.1_Missense_Mutation_p.A678G	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	258					activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			GCCCTCTACGCCAGCTCCTAT	0.677																																					p.A678G		Atlas-SNP	.											.	PPAN-P2RY11	81	.	0			c.C2033G						.						67.0	63.0	64.0					19																	10225062		2203	4299	6502	SO:0001583	missense	692312	exon13			TCTACGCCAGCTC	AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166	ENST00000321826.4:c.773C>G	chr19.hg19:g.10225062C>G	ENSP00000323872:p.Ala258Gly	59.0	0.0		57.0	29.0	NM_001040664	B2R8X9|O43190|Q9BYU4|Q9H170	Missense_Mutation	SNP	ENST00000321826.4	hg19	CCDS12226.1	.	.	.	.	.	.	.	.	.	.	c	18.75	3.690446	0.68271	.	.	ENSG00000243207;ENSG00000130810;ENSG00000244165	ENST00000393796;ENST00000556468;ENST00000321826	T;T;T	0.73258	-0.73;-0.73;-0.73	4.59	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	0.418212	0.21842	U	0.068318	T	0.79358	0.4432	M	0.80183	2.485	0.24933	N	0.991905	P	0.49783	0.928	P	0.54590	0.756	T	0.71354	-0.4618	10	0.48119	T	0.1	-2.6287	11.7579	0.51886	0.0:0.912:0.0:0.088	.	258	Q96G91	P2Y11_HUMAN	G	678;678;258	ENSP00000377385:A678G;ENSP00000450710:A678G;ENSP00000323872:A258G	ENSP00000323872:A258G	A	+	2	0	PPAN;P2RY11;PPAN-P2RY11	10086062	0.218000	0.23608	0.002000	0.10522	0.042000	0.13812	1.882000	0.39648	1.164000	0.42652	0.556000	0.70494	GCC	.	.		0.677	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
ICAM5	7087	hgsc.bcm.edu	37	19	10405166	10405166	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:10405166G>A	ENST00000221980.4	+	9	2143	c.2080G>A	c.(2080-2082)Ggt>Agt	p.G694S		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	694	Ig-like C2-type 8.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CGCCGCCCGGGGTCGCCCTTC	0.677																																					p.G694S		Atlas-SNP	.											.	ICAM5	53	.	0			c.G2080A						.						22.0	24.0	24.0					19																	10405166		2202	4298	6500	SO:0001583	missense	7087	exon9			GCCCGGGGTCGCC	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.2080G>A	chr19.hg19:g.10405166G>A	ENSP00000221980:p.Gly694Ser	142.0	0.0		130.0	51.0	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	hg19	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628501	0.67015	.	.	ENSG00000105376	ENST00000221980	T	0.14391	2.51	5.45	5.45	0.79879	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000065	T	0.47303	0.1438	M	0.92077	3.27	0.38983	D	0.958981	D	0.89917	1.0	D	0.97110	1.0	T	0.60732	-0.7205	10	0.72032	D	0.01	-18.9075	14.7756	0.69729	0.0:0.0:1.0:0.0	.	694	Q9UMF0	ICAM5_HUMAN	S	694	ENSP00000221980:G694S	ENSP00000221980:G694S	G	+	1	0	ICAM5	10266166	1.000000	0.71417	0.997000	0.53966	0.177000	0.22998	5.023000	0.64084	2.574000	0.86865	0.542000	0.68232	GGT	.	.		0.677	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
SLC44A2	57153	hgsc.bcm.edu	37	19	10748543	10748543	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:10748543C>T	ENST00000335757.5	+	18	2083	c.1707C>T	c.(1705-1707)taC>taT	p.Y569Y	SLC44A2_ENST00000586078.1_Silent_p.Y569Y|SLC44A2_ENST00000407327.4_Silent_p.Y567Y|SLC44A2_ENST00000588214.1_3'UTR			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	569					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	TTGCCATCTACGGCACCAATT	0.582																																					p.Y569Y		Atlas-SNP	.											.	SLC44A2	56	.	0			c.C1707T						.						159.0	145.0	150.0					19																	10748543		2203	4300	6503	SO:0001819	synonymous_variant	57153	exon18			CATCTACGGCACC	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"""Solute carriers"""	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.1707C>T	chr19.hg19:g.10748543C>T		118.0	0.0		99.0	34.0	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Silent	SNP	ENST00000335757.5	hg19	CCDS12245.1																																																																																			.	.		0.582	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1		
LDLR	3949	hgsc.bcm.edu	37	19	11217304	11217304	+	Missense_Mutation	SNP	G	G	A	rs139507589		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:11217304G>A	ENST00000558518.1	+	5	945	c.758G>A	c.(757-759)cGg>cAg	p.R253Q	LDLR_ENST00000535915.1_Missense_Mutation_p.R212Q|LDLR_ENST00000545707.1_Missense_Mutation_p.R126Q|LDLR_ENST00000455727.2_Intron|LDLR_ENST00000557933.1_Missense_Mutation_p.R253Q|LDLR_ENST00000558013.1_Missense_Mutation_p.R253Q	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	253	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.		R -> W (may contribute to familial hypercholesterolemia). {ECO:0000269|PubMed:10882754}.		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	CATGGCAGCCGGCAGTGTGAC	0.527																																					p.R253Q	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.G758A						.	G	GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	140.0	124.0	130.0		758,758,635,,395,377	4.0	1.0	19	dbSNP_134	130	0,8600		0,0,4300	no	missense,missense,missense,intron,missense,missense	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	43,43,43,,43,43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	253/861,253/859,212/820,,132/740,126/683	11217304	2,13004	2203	4300	6503	SO:0001583	missense	3949	exon5			GCAGCCGGCAGTG	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.758G>A	chr19.hg19:g.11217304G>A	ENSP00000454071:p.Arg253Gln	136.0	0.0		118.0	46.0	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	hg19	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455809	0.43634	4.54E-4	0.0	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915	D;D	0.94897	-3.55;-3.55	5.1	4.0	0.46444	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.231332	0.28748	N	0.014264	D	0.89891	0.6846	N	0.25957	0.775	0.42200	D	0.991769	B;B;B;B;B	0.33512	0.301;0.415;0.24;0.275;0.415	B;B;B;B;B	0.40565	0.215;0.191;0.191;0.333;0.114	D	0.85575	0.1236	10	0.33940	T	0.23	.	7.2448	0.26115	0.0998:0.0:0.7375:0.1627	.	126;132;212;265;253	B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;LDLR_HUMAN	Q	253;126;212	ENSP00000437639:R126Q;ENSP00000440520:R212Q	ENSP00000252444:R253Q	R	+	2	0	LDLR	11078304	0.900000	0.30661	0.996000	0.52242	0.619000	0.37552	1.193000	0.32162	1.010000	0.39314	0.462000	0.41574	CGG	.	G|1.000;A|0.000		0.527	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
ZNF700	90592	hgsc.bcm.edu	37	19	12059373	12059373	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:12059373C>T	ENST00000254321.5	+	4	677	c.534C>T	c.(532-534)cgC>cgT	p.R178R	ZNF763_ENST00000591944.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF700_ENST00000482090.1_Silent_p.R160R|ZNF763_ENST00000538752.1_Intron|ZNF763_ENST00000590798.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	178					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						TCAGGTATCGCCCATCCATTA	0.408																																					p.R181R		Atlas-SNP	.											.	ZNF700	81	.	0			c.C543T						.						97.0	97.0	97.0					19																	12059373		2203	4300	6503	SO:0001819	synonymous_variant	90592	exon4			GTATCGCCCATCC	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"""Zinc fingers, C2H2-type"", ""-"""	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.534C>T	chr19.hg19:g.12059373C>T		156.0	0.0		161.0	8.0	NM_001271848	B9EGU4	Silent	SNP	ENST00000254321.5	hg19	CCDS32915.1																																																																																			.	.		0.408	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566	
NANOS3	342977	hgsc.bcm.edu	37	19	13988407	13988407	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:13988407C>T	ENST00000397555.2	+	2	288	c.288C>T	c.(286-288)tgC>tgT	p.C96C	MIR181D_ENST00000384853.1_RNA|NANOS3_ENST00000591727.1_Intron|MIR181C_ENST00000384881.1_RNA|NANOS3_ENST00000339133.5_Silent_p.C115C	NM_001098622.2	NP_001092092.1	P60323	NANO3_HUMAN	nanos homolog 3 (Drosophila)	96					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	7			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			GTCCCCAGTGCGGCGCCACAC	0.662																																					p.C115C		Atlas-SNP	.											.	NANOS3	19	.	0			c.C345T						.						30.0	35.0	33.0					19																	13988407		2159	4263	6422	SO:0001819	synonymous_variant	342977	exon1			CCAGTGCGGCGCC	BM702754	CCDS42511.1	19p13.13	2003-12-01				ENSG00000187556			22048	protein-coding gene	gene with protein product		608229					Standard	NM_001098622		Approved	NANOS1L, NOS3	uc002mxj.4	P60323		ENST00000397555.2:c.288C>T	chr19.hg19:g.13988407C>T		69.0	0.0		56.0	24.0	NM_001098622	Q495E5	Silent	SNP	ENST00000397555.2	hg19																																																																																				.	.		0.662	NANOS3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_292819	
CC2D1A	54862	hgsc.bcm.edu	37	19	14024359	14024359	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:14024359C>T	ENST00000318003.7	+	6	897	c.656C>T	c.(655-657)gCg>gTg	p.A219V	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A219V	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	219	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|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 negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)	p.A219V(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			CCTAGAATCGCGTCAGCCCCA	0.667																																					p.A219V		Atlas-SNP	.											CC2D1A,NS,carcinoma,0,1	CC2D1A	67	.	1	Substitution - Missense(1)	endometrium(1)	c.C656T						.						29.0	37.0	35.0					19																	14024359		1965	4121	6086	SO:0001583	missense	54862	exon6			GAATCGCGTCAGC	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.656C>T	chr19.hg19:g.14024359C>T	ENSP00000313601:p.Ala219Val	180.0	1.0		171.0	64.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	C	9.837	1.189970	0.21954	.	.	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	T	0.21932	1.98	2.95	-5.0	0.03001	.	1.588220	0.04137	N	0.318934	T	0.10380	0.0254	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.001;0.005	B;B	0.06405	0.0;0.002	T	0.24835	-1.0149	10	0.33141	T	0.24	-1.3178	4.3426	0.11117	0.1638:0.2978:0.0:0.5384	.	219;219	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	V	219;57;194	ENSP00000313601:A219V	ENSP00000254346:A57V	A	+	2	0	CC2D1A	13885359	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.035000	0.01423	-0.956000	0.03631	-0.448000	0.05591	GCG	.	.		0.667	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
TPM4	7171	hgsc.bcm.edu	37	19	16192750	16192750	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:16192750C>T	ENST00000300933.4	+	2	420	c.160C>T	c.(160-162)Cga>Tga	p.R54*	TPM4_ENST00000344824.6_Nonsense_Mutation_p.R90*|TPM4_ENST00000538887.1_Nonsense_Mutation_p.R90*	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	54					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						CGCCCTCAACCGACGCATCCA	0.612			T	ALK	ALCL																																p.R90X		Atlas-SNP	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.C268T						.						46.0	47.0	47.0					19																	16192750		2203	4300	6503	SO:0001587	stop_gained	7171	exon3			CTCAACCGACGCA		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"""Tropomyosins"""	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.160C>T	chr19.hg19:g.16192750C>T	ENSP00000300933:p.Arg54*	55.0	0.0		48.0	23.0	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Nonsense_Mutation	SNP	ENST00000300933.4	hg19	CCDS12338.1	.	.	.	.	.	.	.	.	.	.	C	37	6.056672	0.97241	.	.	ENSG00000167460	ENST00000344824;ENST00000538887;ENST00000300933	.	.	.	4.62	3.57	0.40892	.	0.000000	0.52532	U	0.000080	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.1957	12.0321	0.53403	0.3305:0.6695:0.0:0.0	.	.	.	.	X	90;90;54	.	ENSP00000300933:R54X	R	+	1	2	TPM4	16053750	0.908000	0.30866	0.925000	0.36789	0.931000	0.56810	1.047000	0.30367	1.026000	0.39733	0.591000	0.81541	CGA	.	.		0.612	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290	
TMEM38A	79041	hgsc.bcm.edu	37	19	16797152	16797152	+	Missense_Mutation	SNP	G	G	A	rs78725797		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:16797152G>A	ENST00000187762.2	+	5	699	c.608G>A	c.(607-609)cGc>cAc	p.R203H		NM_024074.1	NP_076979.1	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A	203						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)	15						CAGCAGACCCGCTGGCTCCCA	0.562																																					p.R203H		Atlas-SNP	.											.	TMEM38A	32	.	0			c.G608A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	131.0	95.0	107.0		608	3.8	1.0	19	dbSNP_131	107	0,8600		0,0,4300	no	missense	TMEM38A	NM_024074.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	203/300	16797152	1,13005	2203	4300	6503	SO:0001583	missense	79041	exon5			AGACCCGCTGGCT	AK025981	CCDS12349.1	19p13.11	2013-05-23				ENSG00000072954			28462	protein-coding gene	gene with protein product		611235				17611541	Standard	NM_024074		Approved	MGC3169, TRIC-A	uc002nes.3	Q9H6F2		ENST00000187762.2:c.608G>A	chr19.hg19:g.16797152G>A	ENSP00000187762:p.Arg203His	48.0	0.0		44.0	13.0	NM_024074	A8K9P9	Missense_Mutation	SNP	ENST00000187762.2	hg19	CCDS12349.1	.	.	.	.	.	.	.	.	.	.	g	9.106	1.005306	0.19199	2.27E-4	0.0	ENSG00000072954	ENST00000187762	.	.	.	4.87	3.84	0.44239	.	0.110837	0.64402	D	0.000011	T	0.15349	0.0370	N	0.00869	-1.13	0.36185	D	0.849713	B	0.11235	0.004	B	0.08055	0.003	T	0.09907	-1.0653	9	0.33940	T	0.23	-42.5728	5.1808	0.15160	0.2785:0.0:0.7215:0.0	.	203	Q9H6F2	TM38A_HUMAN	H	203	.	ENSP00000187762:R203H	R	+	2	0	TMEM38A	16658152	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.170000	0.58229	2.257000	0.74773	0.655000	0.94253	CGC	.	.		0.562	TMEM38A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462841.1	NM_024074	
ANO8	57719	hgsc.bcm.edu	37	19	17434419	17434419	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:17434419T>C	ENST00000159087.4	-	18	3764	c.3606A>G	c.(3604-3606)ctA>ctG	p.L1202L		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	1202	Pro-rich.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						aggtgggcggtagcggtgggg	0.751																																					p.L1202L		Atlas-SNP	.											.	ANO8	67	.	0			c.A3606G						.						4.0	6.0	5.0					19																	17434419		1263	2728	3991	SO:0001819	synonymous_variant	57719	exon18			GGGCGGTAGCGGT	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.3606A>G	chr19.hg19:g.17434419T>C		48.0	0.0		44.0	4.0	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	hg19	CCDS32949.1																																																																																			.	.		0.751	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
ZNF208	7757	hgsc.bcm.edu	37	19	22155265	22155265	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:22155265T>C	ENST00000397126.4	-	4	2719	c.2571A>G	c.(2569-2571)ggA>ggG	p.G857G	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	857					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGGGTTTCTCTCCAGTATGAA	0.373																																					p.G857G		Atlas-SNP	.											.	ZNF208	817	.	0			c.A2571G						.						39.0	41.0	41.0					19																	22155265		2024	4204	6228	SO:0001819	synonymous_variant	7757	exon4			TTTCTCTCCAGTA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2571A>G	chr19.hg19:g.22155265T>C		52.0	0.0		42.0	15.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.373	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
URI1	8725	hgsc.bcm.edu	37	19	30503420	30503420	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:30503420C>A	ENST00000542441.2	+	10	1704	c.1407C>A	c.(1405-1407)ccC>ccA	p.P469P	URI1_ENST00000392271.1_Silent_p.P393P|URI1_ENST00000312051.6_Silent_p.P429P|URI1_ENST00000360605.4_Silent_p.P451P			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	469					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										AACTTTTGCCCTTATCAGTAA	0.368																																					p.P469P		Atlas-SNP	.											.	.	.	.	0			c.C1407A						.						67.0	72.0	70.0					19																	30503420		2203	4300	6503	SO:0001819	synonymous_variant	8725	exon10			TTTGCCCTTATCA	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	13236	protein-coding gene	gene with protein product	"""unconventional prefoldin RPB5 interactor"", ""RPB5-mediating protein"", ""protein phosphatase 1, regulatory subunit 19"""	603494	"""chromosome 19 open reading frame 2"""	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.1407C>A	chr19.hg19:g.30503420C>A		88.0	0.0		106.0	41.0	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	hg19	CCDS12420.1																																																																																			.	.		0.368	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447	
CHST8	64377	hgsc.bcm.edu	37	19	34263780	34263780	+	Missense_Mutation	SNP	C	C	T	rs557313187		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:34263780C>T	ENST00000262622.4	+	4	1845	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C	CHST8_ENST00000438847.3_Missense_Mutation_p.R363C|CHST8_ENST00000434302.1_Missense_Mutation_p.R363C	NM_022467.3	NP_071912.2	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	363					carbohydrate biosynthetic process (GO:0016051)|central nervous system development (GO:0007417)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(5)	27	Esophageal squamous(110;0.162)					GAGCCTCATCCGCGCGCCGCG	0.632													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18248	0.0		0.0	False		,,,				2504	0.0				p.R363C		Atlas-SNP	.											.	CHST8	70	.	0			c.C1087T						.						64.0	52.0	56.0					19																	34263780		2203	4300	6503	SO:0001583	missense	64377	exon5			CTCATCCGCGCGC	AB047801	CCDS12433.1	19q13.1	2008-02-05				ENSG00000124302		"""Sulfotransferases, membrane-bound"""	15993	protein-coding gene	gene with protein product		610190				10988300, 11001942	Standard	NM_001127895		Approved	GALNAC-4-ST1	uc002nut.4	Q9H2A9		ENST00000262622.4:c.1087C>T	chr19.hg19:g.34263780C>T	ENSP00000262622:p.Arg363Cys	102.0	0.0		91.0	41.0	NM_001127895	Q9H3N2	Missense_Mutation	SNP	ENST00000262622.4	hg19	CCDS12433.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662745	0.67700	.	.	ENSG00000124302	ENST00000434302;ENST00000438847;ENST00000262622	T;T;T	0.74002	-0.8;-0.8;-0.8	5.01	3.93	0.45458	.	0.812256	0.11161	N	0.593112	T	0.74076	0.3669	L	0.39898	1.24	0.37014	D	0.895879	D	0.61080	0.989	P	0.51453	0.67	T	0.77051	-0.2731	10	0.87932	D	0	-23.0001	11.4741	0.50286	0.0:0.5906:0.4093:0.0	.	363	Q9H2A9	CHST8_HUMAN	C	363	ENSP00000392604:R363C;ENSP00000393879:R363C;ENSP00000262622:R363C	ENSP00000262622:R363C	R	+	1	0	CHST8	38955620	0.973000	0.33851	0.560000	0.28344	0.527000	0.34593	6.047000	0.71038	2.331000	0.79229	0.297000	0.19635	CGC	.	.		0.632	CHST8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451453.1	NM_022467	
KIRREL2	84063	hgsc.bcm.edu	37	19	36357195	36357195	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:36357195A>G	ENST00000360202.5	+	15	2126	c.1928A>G	c.(1927-1929)aAc>aGc	p.N643S	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Intron|KIRREL2_ENST00000262625.7_Intron|APLP1_ENST00000221891.4_5'Flank|APLP1_ENST00000537454.2_5'Flank|KIRREL2_ENST00000592409.1_Missense_Mutation_p.N608S	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	643	Pro-rich.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TATGACTTCAACCCACACCTG	0.622																																					p.N643S		Atlas-SNP	.											.	KIRREL2	170	.	0			c.A1928G						.						72.0	75.0	74.0					19																	36357195		2203	4300	6503	SO:0001583	missense	84063	exon15			ACTTCAACCCACA	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1928A>G	chr19.hg19:g.36357195A>G	ENSP00000353331:p.Asn643Ser	67.0	0.0		82.0	33.0	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	hg19	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	A	0.210	-1.037379	0.02013	.	.	ENSG00000126259	ENST00000360202;ENST00000341658;ENST00000270294	T	0.63255	-0.03	5.1	0.204	0.15199	.	0.711674	0.12648	N	0.450717	T	0.33585	0.0868	N	0.08118	0	0.26540	N	0.974093	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.002	T	0.17137	-1.0379	9	.	.	.	-1.7079	4.7512	0.13061	0.3311:0.2578:0.4111:0.0	.	643;623;643	F1T0I2;Q6UWL6-4;Q6UWL6	.;.;KIRR2_HUMAN	S	643;623;154	ENSP00000353331:N643S	.	N	+	2	0	KIRREL2	41049035	0.189000	0.23263	0.208000	0.23602	0.843000	0.47879	0.401000	0.20948	0.026000	0.15269	0.459000	0.35465	AAC	.	.		0.622	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
ZNF461	92283	hgsc.bcm.edu	37	19	37130266	37130266	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:37130266T>G	ENST00000588268.1	-	6	1208	c.981A>C	c.(979-981)aaA>aaC	p.K327N	ZNF461_ENST00000360357.4_Missense_Mutation_p.K304N|ZNF461_ENST00000540605.2_5'UTR	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	327					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)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATTCATAGGGTTTTTCACCAG	0.413																																					p.K327N		Atlas-SNP	.											.	ZNF461	73	.	0			c.A981C						.						53.0	59.0	57.0					19																	37130266		2201	4300	6501	SO:0001583	missense	92283	exon6			ATAGGGTTTTTCA	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"""Zinc fingers, C2H2-type"", ""-"""	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.981A>C	chr19.hg19:g.37130266T>G	ENSP00000467931:p.Lys327Asn	117.0	0.0		104.0	38.0	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	hg19	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.139342	0.56936	.	.	ENSG00000197808	ENST00000396893;ENST00000396896;ENST00000360357;ENST00000540605	T	0.26067	1.76	3.6	3.6	0.41247	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47040	0.1424	M	0.75447	2.3	0.29751	N	0.836322	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.91635	0.993;0.999;0.988	T	0.42327	-0.9458	9	0.87932	D	0	.	7.151	0.25610	0.0:0.1116:0.0:0.8884	.	304;249;327	B4DRP8;Q59G30;Q8TAF7	.;.;ZN461_HUMAN	N	327;58;304;200	ENSP00000353515:K304N	ENSP00000353515:K304N	K	-	3	2	ZNF461	41822106	0.006000	0.16342	1.000000	0.80357	0.992000	0.81027	-0.567000	0.05916	1.632000	0.50472	0.477000	0.44152	AAA	.	.		0.413	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38573540	38573540	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:38573540C>T	ENST00000222345.6	+	3	1844	c.1335C>T	c.(1333-1335)tcC>tcT	p.S445S		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	445					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TGAGCTTCTCCCGGGCTTCCG	0.667																																					p.S445S		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C1335T						.						45.0	49.0	48.0					19																	38573540		2202	4300	6502	SO:0001819	synonymous_variant	23094	exon3			CTTCTCCCGGGCT	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.1335C>T	chr19.hg19:g.38573540C>T		96.0	0.0		85.0	39.0	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.667	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
MAP4K1	11184	hgsc.bcm.edu	37	19	39096218	39096218	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:39096218G>A	ENST00000591517.1	-	18	1381	c.1353C>T	c.(1351-1353)acC>acT	p.T451T	MAP4K1_ENST00000423454.2_Silent_p.T113T|MAP4K1_ENST00000586296.1_Intron|MAP4K1_ENST00000396857.2_Silent_p.T451T|MAP4K1_ENST00000589002.1_5'Flank|MAP4K1_ENST00000589130.1_Silent_p.T447T	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	451					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGAATGGGCGGTGAGGTGGG	0.672																																					p.T451T		Atlas-SNP	.											.	MAP4K1	165	.	0			c.C1353T						.						4.0	4.0	4.0					19																	39096218		1693	3833	5526	SO:0001819	synonymous_variant	11184	exon18			ATGGGCGGTGAGG	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6863	protein-coding gene	gene with protein product	"""hematopoietic progenitor kinase 1"""	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.1353C>T	chr19.hg19:g.39096218G>A		108.0	0.0		81.0	33.0	NM_007181		Silent	SNP	ENST00000591517.1	hg19	CCDS59385.1																																																																																			.	.		0.672	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600	
HNRNPL	3191	hgsc.bcm.edu	37	19	39329068	39329068	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:39329068G>A	ENST00000221419.5	-	10	1892	c.1526C>T	c.(1525-1527)cCg>cTg	p.P509L	AC104534.3_ENST00000594769.1_Missense_Mutation_p.R126C|HNRNPL_ENST00000600873.1_Missense_Mutation_p.P376L	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	509	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			CACCTCCAGCGGGGCGTTGAA	0.597																																					p.P509L		Atlas-SNP	.											.	HNRNPL	67	.	0			c.C1526T						.						67.0	58.0	61.0					19																	39329068		2203	4300	6503	SO:0001583	missense	3191	exon10			TCCAGCGGGGCGT	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1526C>T	chr19.hg19:g.39329068G>A	ENSP00000221419:p.Pro509Leu	78.0	0.0		109.0	39.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183061	0.78677	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750	.	.	.	5.87	5.87	0.94306	Nucleotide-binding, alpha-beta plait (1);	0.051568	0.85682	D	0.000000	D	0.83562	0.5281	M	0.82823	2.61	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.999	B;D;P	0.68765	0.364;0.96;0.662	D	0.84732	0.0746	9	0.87932	D	0	.	19.3531	0.94398	0.0:0.0:1.0:0.0	.	509;478;492	P14866;B2R959;Q6NTA2	HNRPL_HUMAN;.;.	L	509;376;376	.	ENSP00000221419:P509L	P	-	2	0	HNRNPL	44020908	1.000000	0.71417	0.993000	0.49108	0.963000	0.63663	5.429000	0.66495	2.941000	0.99782	0.655000	0.94253	CCG	.	.		0.597	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		
ADCK4	79934	hgsc.bcm.edu	37	19	41219998	41219998	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:41219998C>T	ENST00000324464.3	-	4	564	c.263G>A	c.(262-264)cGc>cAc	p.R88H	ADCK4_ENST00000450541.1_Missense_Mutation_p.R88H|ADCK4_ENST00000243583.6_Missense_Mutation_p.R88H	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	88						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			GCGGCTGATGCGGGAGGCAGG	0.562																																					p.R88H		Atlas-SNP	.											.	ADCK4	92	.	0			c.G263A						.						89.0	83.0	85.0					19																	41219998		2203	4300	6503	SO:0001583	missense	79934	exon4			CTGATGCGGGAGG	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.263G>A	chr19.hg19:g.41219998C>T	ENSP00000315118:p.Arg88His	145.0	0.0		142.0	28.0	NM_001142555	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	hg19	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	c	35	5.508631	0.96386	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.80393	-1.17;-1.37;-1.37	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.90920	0.7146	M	0.91354	3.2	0.58432	D	0.999999	D;D	0.69078	0.994;0.997	P;D	0.63381	0.717;0.914	D	0.92570	0.6065	10	0.66056	D	0.02	-2.9595	16.2208	0.82257	0.0:1.0:0.0:0.0	.	88;88	Q96D53;Q96D53-2	ADCK4_HUMAN;.	H	88	ENSP00000315118:R88H;ENSP00000412839:R88H;ENSP00000243583:R88H	ENSP00000243583:R88H	R	-	2	0	ADCK4	45911838	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.567000	0.73983	2.567000	0.86603	0.556000	0.70494	CGC	.	.		0.562	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
SNRPA	6626	hgsc.bcm.edu	37	19	41268862	41268862	+	Silent	SNP	G	G	A	rs374030639		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:41268862G>A	ENST00000243563.3	+	4	1033	c.483G>A	c.(481-483)ccG>ccA	p.P161P		NM_004596.4	NP_004587.1	P09012	SNRPA_HUMAN	small nuclear ribonucleoprotein polypeptide A	161	Pro-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snRNA binding (GO:0017069)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CGGGCCAGCCGCCCTACATGC	0.677																																					p.P161P		Atlas-SNP	.											.	SNRPA	20	.	0			c.G483A						.	G		0,4402		0,0,2201	28.0	27.0	28.0		483	-11.1	0.4	19		28	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	SNRPA	NM_004596.4		0,1,6499	AA,AG,GG		0.0116,0.0,0.0077		161/283	41268862	1,12999	2201	4299	6500	SO:0001819	synonymous_variant	6626	exon4			CCAGCCGCCCTAC	X06347	CCDS12565.1	19q13.1	2013-02-12				ENSG00000077312		"""RNA binding motif (RRM) containing"""	11151	protein-coding gene	gene with protein product		182285				1701111	Standard	NM_004596		Approved	U1A, U1-A, Mud1	uc002ooz.3	P09012		ENST00000243563.3:c.483G>A	chr19.hg19:g.41268862G>A		125.0	0.0		154.0	7.0	NM_004596		Silent	SNP	ENST00000243563.3	hg19	CCDS12565.1																																																																																			.	.		0.677	SNRPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463118.2	NM_004596	
EGLN2	112398	hgsc.bcm.edu	37	19	41307129	41307129	+	Missense_Mutation	SNP	C	C	T	rs140368149		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:41307129C>T	ENST00000593726.1	+	1	1680	c.652C>T	c.(652-654)Cgc>Tgc	p.R218C	EGLN2_ENST00000303961.4_Missense_Mutation_p.R218C|EGLN2_ENST00000594140.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR|CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000406058.2_Missense_Mutation_p.R218C			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	218					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	ACGGGGTGGGCGCCTGCGAGA	0.682																																					p.R218C		Atlas-SNP	.											.	EGLN2	31	.	0			c.C652T						.	C	CYS/ARG,CYS/ARG	0,4404		0,0,2202	50.0	54.0	52.0		652,652	4.1	1.0	19	dbSNP_134	52	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense	EGLN2	NM_053046.3,NM_080732.3	180,180	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	218/408,218/408	41307129	1,12999	2202	4298	6500	SO:0001583	missense	112398	exon2			GGTGGGCGCCTGC	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 1"""	606424	"""EGL nine (C.elegans) homolog 2"", ""egl nine homolog 2 (C. elegans)"""				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.652C>T	chr19.hg19:g.41307129C>T	ENSP00000469686:p.Arg218Cys	118.0	0.0		125.0	63.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.830995	0.71258	0.0	1.16E-4	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.26067	1.76;1.76	4.05	4.05	0.47172	Prolyl 4-hydroxylase, alpha subunit (1);	0.077318	0.49916	D	0.000135	T	0.17450	0.0419	L	0.29908	0.895	0.52099	D	0.999949	B	0.27559	0.181	B	0.24848	0.056	T	0.04976	-1.0914	10	0.38643	T	0.18	-10.4218	9.5003	0.39013	0.3315:0.6685:0.0:0.0	.	218	Q96KS0	EGLN2_HUMAN	C	218	ENSP00000307080:R218C;ENSP00000385253:R218C	ENSP00000307080:R218C	R	+	1	0	EGLN2	45998969	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.981000	0.40628	2.263000	0.75096	0.591000	0.81541	CGC	.	C|1.000;T|0.000		0.682	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1		
GSK3A	2931	hgsc.bcm.edu	37	19	42744195	42744195	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:42744195C>T	ENST00000222330.3	-	2	510	c.383G>A	c.(382-384)gGc>gAc	p.G128D	AC006486.1_ENST00000378108.1_5'Flank|GSK3A_ENST00000398249.4_Missense_Mutation_p.G46D|AC006486.9_ENST00000594664.1_Missense_Mutation_p.G41D	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	128	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|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 TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				CCCAAATGAGCCATTGCCAAT	0.572																																					p.G128D		Atlas-SNP	.											.	GSK3A	45	.	0			c.G383A						.						165.0	121.0	136.0					19																	42744195		2203	4300	6503	SO:0001583	missense	2931	exon2			AATGAGCCATTGC		CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.383G>A	chr19.hg19:g.42744195C>T	ENSP00000222330:p.Gly128Asp	129.0	0.0		111.0	12.0	NM_019884	O14959	Missense_Mutation	SNP	ENST00000222330.3	hg19	CCDS12599.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148837	0.94603	.	.	ENSG00000105723	ENST00000222330;ENST00000398249;ENST00000544315	D;D	0.91180	-2.8;-2.8	5.22	5.22	0.72569	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	0.85682	D	0.000000	D	0.96781	0.8949	H	0.94808	3.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97712	1.0191	10	0.87932	D	0	-6.3289	17.9284	0.88990	0.0:1.0:0.0:0.0	.	128;46	P49840;A8MT37	GSK3A_HUMAN;.	D	128;46;73	ENSP00000222330:G128D;ENSP00000381301:G46D	ENSP00000222330:G128D	G	-	2	0	GSK3A	47436035	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.273000	0.78527	2.622000	0.88805	0.555000	0.69702	GGC	.	.		0.572	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1		
CNFN	84518	hgsc.bcm.edu	37	19	42893103	42893103	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:42893103C>T	ENST00000222032.5	-	2	136	c.87G>A	c.(85-87)acG>acA	p.T29T	CNFN_ENST00000597255.1_Silent_p.T29T	NM_032488.3	NP_115877.2	Q9BYD5	CNFN_HUMAN	cornifelin	29					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				lung(1)|prostate(1)	2		Prostate(69;0.00899)				TGCAGCAGTCCGTGAGACCTG	0.617																																					p.T29T		Atlas-SNP	.											.	CNFN	5	.	0			c.G87A						.						128.0	96.0	106.0					19																	42893103		2203	4300	6503	SO:0001819	synonymous_variant	84518	exon2			GCAGTCCGTGAGA	AB049591	CCDS12606.1	19q13.31	2006-01-11				ENSG00000105427			30183	protein-coding gene	gene with protein product		611764					Standard	NM_032488		Approved	PLAC8L2	uc002otp.4	Q9BYD5		ENST00000222032.5:c.87G>A	chr19.hg19:g.42893103C>T		39.0	0.0		39.0	19.0	NM_032488	B2R569	Silent	SNP	ENST00000222032.5	hg19	CCDS12606.1																																																																																			.	.		0.617	CNFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463859.1	NM_032488	
ZNF227	7770	hgsc.bcm.edu	37	19	44739561	44739561	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:44739561C>T	ENST00000313040.7	+	6	1183	c.978C>T	c.(976-978)tgC>tgT	p.C326C	ZNF227_ENST00000589005.1_Silent_p.C275C|ZNF227_ENST00000391961.2_Silent_p.C275C	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	326					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)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				CTTATAGATGCGACAGTTGCG	0.393																																					p.C326C		Atlas-SNP	.											ZNF227,NS,carcinoma,0,1	ZNF227	62	.	0			c.C978T						.						66.0	68.0	67.0					19																	44739561		2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			TAGATGCGACAGT	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.978C>T	chr19.hg19:g.44739561C>T		77.0	0.0		57.0	27.0	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	hg19	CCDS12636.1																																																																																			.	.		0.393	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
ZNF235	9310	hgsc.bcm.edu	37	19	44791785	44791785	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:44791785A>G	ENST00000291182.4	-	5	1905	c.1803T>C	c.(1801-1803)tgT>tgC	p.C601C	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	601					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				GACATGCATCACACTTGAATG	0.473																																					p.C601C		Atlas-SNP	.											.	ZNF235	60	.	0			c.T1803C						.						162.0	148.0	152.0					19																	44791785		2203	4300	6503	SO:0001819	synonymous_variant	9310	exon5			TGCATCACACTTG	X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"""Zinc fingers, C2H2-type"", ""-"""	12866	protein-coding gene	gene with protein product		604749	"""zinc finger protein homologous to Zfp93 in mouse"""	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.1803T>C	chr19.hg19:g.44791785A>G		161.0	0.0		159.0	74.0	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Silent	SNP	ENST00000291182.4	hg19	CCDS33048.1																																																																																			.	.		0.473	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1		
PVR	5817	hgsc.bcm.edu	37	19	45162189	45162189	+	Intron	SNP	C	C	T	rs35385129	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:45162189C>T	ENST00000425690.3	+	6	1449				PVR_ENST00000406449.4_Missense_Mutation_p.R391C|PVR_ENST00000403059.4_Intron|PVR_ENST00000344956.4_Intron|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor						adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		CCagagctgccgtaattgagc	0.532																																					p.R391C		Atlas-SNP	.											.	PVR	23	.	0			c.C1171T						.						73.0	74.0	73.0					19																	45162189		2203	4300	6503	SO:0001627	intron_variant	5817	exon6			AGCTGCCGTAATT	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.1150+21C>T	chr19.hg19:g.45162189C>T		64.0	0.0		68.0	31.0	NM_001135770	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	hg19	CCDS12640.1	.	.	.	.	.	.	.	.	.	.	C	8.729	0.916225	0.17907	.	.	ENSG00000073008	ENST00000406449	D	0.88046	-2.33	2.11	0.956	0.19608	.	.	.	.	.	T	0.75664	0.3880	.	.	.	0.09310	N	1	D	0.54772	0.968	B	0.36959	0.237	T	0.65212	-0.6223	7	.	.	.	.	6.1885	0.20510	0.0:0.6791:0.3209:0.0	.	391	P15151-4	.	C	391	ENSP00000383907:R391C	.	R	+	1	0	PVR	49854029	0.001000	0.12720	0.000000	0.03702	0.205000	0.24178	0.662000	0.25038	0.397000	0.25310	0.555000	0.69702	CGT	.	C|0.834;A|0.166		0.532	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
APOE	348	hgsc.bcm.edu	37	19	45411140	45411140	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:45411140G>A	ENST00000252486.4	+	3	278	c.167G>A	c.(166-168)cGc>cAc	p.R56H		NM_000041.2	NP_000032.1	P02649	APOE_HUMAN	apolipoprotein E	56					aging (GO:0007568)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|artery morphogenesis (GO:0048844)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cGMP-mediated signaling (GO:0019934)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|cytoskeleton organization (GO:0007010)|fatty acid homeostasis (GO:0055089)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|intracellular transport (GO:0046907)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle remodeling (GO:0034374)|maintenance of location in cell (GO:0051651)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of blood coagulation (GO:0030195)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cholesterol biosynthetic process (GO:0045541)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of dendritic spine development (GO:0061000)|negative regulation of dendritic spine maintenance (GO:1902951)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lipid biosynthetic process (GO:0051055)|negative regulation of lipid transport across blood brain barrier (GO:1903001)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of phospholipid efflux (GO:1902999)|negative regulation of platelet activation (GO:0010544)|negative regulation of postsynaptic membrane organization (GO:1901627)|negative regulation of presynaptic membrane organization (GO:1901630)|nitric oxide mediated signal transduction (GO:0007263)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system axon regeneration (GO:0014012)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of axon extension (GO:0045773)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of dendritic spine maintenance (GO:1902952)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of lipid transport across blood brain barrier (GO:1903002)|positive regulation of low-density lipoprotein particle receptor catabolic process (GO:0032805)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipid efflux (GO:1902995)|positive regulation of postsynaptic membrane organization (GO:1901628)|positive regulation of presynaptic membrane organization (GO:1901631)|protein import (GO:0017038)|receptor-mediated endocytosis (GO:0006898)|regulation of axon extension (GO:0030516)|regulation of beta-amyloid clearance (GO:1900221)|regulation of Cdc42 protein signal transduction (GO:0032489)|regulation of neuron death (GO:1901214)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of tau-protein kinase activity (GO:1902947)|response to dietary excess (GO:0002021)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)|response to retinoic acid (GO:0032526)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|triglyceride metabolic process (GO:0006641)|vasodilation (GO:0042311)|very-low-density lipoprotein particle clearance (GO:0034447)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|high-density lipoprotein particle (GO:0034364)|intermediate-density lipoprotein particle (GO:0034363)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)|vesicle (GO:0031982)	antioxidant activity (GO:0016209)|beta-amyloid binding (GO:0001540)|cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle receptor binding (GO:0050750)|metal chelating activity (GO:0046911)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)|tau protein binding (GO:0048156)|very-low-density lipoprotein particle receptor binding (GO:0070326)			large_intestine(1)|lung(2)|prostate(1)	4	Lung NSC(12;0.0018)|all_lung(12;0.00481)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)	Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GATTACCTGCGCTGGGTGCAG	0.657																																					p.R56H		Atlas-SNP	.											.	APOE	11	.	0			c.G167A						.						43.0	42.0	42.0					19																	45411140		2203	4300	6503	SO:0001583	missense	348	exon3			ACCTGCGCTGGGT	K00396	CCDS12647.1	19q13.31	2013-01-24			ENSG00000130203	ENSG00000130203		"""Apolipoproteins"""	613	protein-coding gene	gene with protein product		107741	"""Alzheimer disease 2 (APOE*E4-associated, late onset)"""	AD2		10662539	Standard	NM_000041		Approved		uc002pab.3	P02649	OTTHUMG00000128901	ENST00000252486.4:c.167G>A	chr19.hg19:g.45411140G>A	ENSP00000252486:p.Arg56His	106.0	0.0		107.0	46.0	NM_000041	B2RC15|C0JYY5|Q9P2S4	Missense_Mutation	SNP	ENST00000252486.4	hg19	CCDS12647.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.557019	0.45590	.	.	ENSG00000130203	ENST00000252486;ENST00000446996;ENST00000434152;ENST00000425718	T;T;T	0.79653	-1.29;-1.29;-1.29	4.85	-0.0363	0.13888	Apolipoprotein/apolipophorin (1);	0.594848	0.15262	N	0.271759	T	0.75459	0.3852	M	0.81802	2.56	0.27077	N	0.963178	B	0.15930	0.015	B	0.08055	0.003	T	0.68142	-0.5487	10	0.59425	D	0.04	-13.5464	3.2725	0.06887	0.3015:0.0:0.5146:0.1839	.	56	P02649	APOE_HUMAN	H	56;56;101;56	ENSP00000252486:R56H;ENSP00000413135:R56H;ENSP00000410423:R56H	ENSP00000252486:R56H	R	+	2	0	APOE	50102980	0.984000	0.35163	1.000000	0.80357	0.897000	0.52465	0.635000	0.24629	0.564000	0.29238	0.561000	0.74099	CGC	.	.		0.657	APOE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250865.2	NM_000041	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48202008	48202008	+	Silent	SNP	C	C	T	rs371897707		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:48202008C>T	ENST00000396720.3	+	12	3560	c.3366C>T	c.(3364-3366)ggC>ggT	p.G1122G	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1122										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		TCTACCAGGGCGCCCTCCCCT	0.672											OREG0025594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G1122G		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.C3366T						.	C		1,3927		0,1,1963	29.0	31.0	30.0		3366	-8.5	0.2	19		30	0,8282		0,0,4141	no	coding-synonymous	GLTSCR1	NM_015711.3		0,1,6104	TT,TC,CC		0.0,0.0255,0.0082		1122/1561	48202008	1,12209	1964	4141	6105	SO:0001819	synonymous_variant	29998	exon12			CCAGGGCGCCCTC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.3366C>T	chr19.hg19:g.48202008C>T		67.0	0.0	952	47.0	22.0	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.		0.672	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
CA11	770	hgsc.bcm.edu	37	19	49148722	49148722	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:49148722G>A	ENST00000084798.4	-	2	759	c.80C>T	c.(79-81)cCa>cTa	p.P27L	SEC1P_ENST00000430145.2_RNA	NM_001217.3	NP_001208.2	O75493	CAH11_HUMAN	carbonic anhydrase XI	27						basolateral plasma membrane (GO:0016323)|extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	14		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000103)|all cancers(93;0.000119)|GBM - Glioblastoma multiforme(486;0.00634)|Epithelial(262;0.016)	Zonisamide(DB00909)	GTCAGGTGCTGGTCCGATGTG	0.652																																					p.P27L		Atlas-SNP	.											.	CA11	29	.	0			c.C80T						.						66.0	61.0	63.0					19																	49148722		2203	4300	6503	SO:0001583	missense	770	exon2			GGTGCTGGTCCGA	AF067662	CCDS12729.1	19q13.3	2012-07-02			ENSG00000063180	ENSG00000063180		"""Carbonic anhydrases"""	1370	protein-coding gene	gene with protein product	"""CA-RP XI"", ""carbonic anhydrase-related protein XI"", ""carbonic anhydrase-related protein 2"""	604644				9878252	Standard	XR_243956		Approved	CARP2, CARPX1	uc002pjz.1	O75493		ENST00000084798.4:c.80C>T	chr19.hg19:g.49148722G>A	ENSP00000084798:p.Pro27Leu	82.0	0.0		88.0	31.0	NM_001217	O60596|Q6FHI1|Q9UEC4	Missense_Mutation	SNP	ENST00000084798.4	hg19	CCDS12729.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163080	0.78226	.	.	ENSG00000063180	ENST00000084798	T	0.70631	-0.5	3.84	3.84	0.44239	.	0.100808	0.39834	N	0.001244	T	0.63861	0.2547	N	0.08118	0	0.44424	D	0.997344	D	0.64830	0.994	D	0.73708	0.981	T	0.57602	-0.7783	10	0.10636	T	0.68	.	11.5626	0.50785	0.0:0.0:1.0:0.0	.	27	O75493	CAH11_HUMAN	L	27	ENSP00000084798:P27L	ENSP00000084798:P27L	P	-	2	0	CA11	53840534	0.992000	0.36948	0.993000	0.49108	0.993000	0.82548	4.729000	0.62008	2.435000	0.82474	0.462000	0.41574	CCA	.	.		0.652	CA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466172.1	NM_001217	
FUT1	2523	hgsc.bcm.edu	37	19	49254381	49254381	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:49254381G>T	ENST00000310160.3	-	4	1132	c.158C>A	c.(157-159)gCc>gAc	p.A53D	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	53					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)		GCAGAAGATGGCCACTGGGGG	0.602																																					p.A53D		Atlas-SNP	.											.	FUT1	44	.	0			c.C158A						.						49.0	50.0	50.0					19																	49254381		2203	4300	6503	SO:0001583	missense	2523	exon4			AAGATGGCCACTG		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.158C>A	chr19.hg19:g.49254381G>T	ENSP00000312021:p.Ala53Asp	142.0	0.0		113.0	43.0	NM_000148	O14505|O14506|O14507	Missense_Mutation	SNP	ENST00000310160.3	hg19	CCDS12733.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.859363	0.51376	.	.	ENSG00000174951	ENST00000310160;ENST00000539428	D	0.97016	-4.21	4.53	3.46	0.39613	.	0.231427	0.30639	N	0.009190	D	0.96065	0.8718	M	0.63428	1.95	0.33636	D	0.606606	P	0.51653	0.947	P	0.54210	0.745	D	0.96781	0.9575	10	0.42905	T	0.14	-7.8449	10.4627	0.44590	0.0:0.1974:0.8026:0.0	.	53	P19526	FUT1_HUMAN	D	53	ENSP00000312021:A53D	ENSP00000312021:A53D	A	-	2	0	FUT1	53946193	0.807000	0.29009	0.999000	0.59377	0.204000	0.24138	0.964000	0.29306	1.223000	0.43536	0.655000	0.94253	GCC	.	.		0.602	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965147	49965147	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:49965147C>T	ENST00000293350.4	+	7	929	c.766C>T	c.(766-768)Cgt>Tgt	p.R256C	CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.R93C|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.R91C|ALDH16A1_ENST00000455361.2_Intron	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	256						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CTAGGAAGGGCGTGCCCTTCG	0.721																																					p.R256C		Atlas-SNP	.											ALDH16A1,colon,carcinoma,0,1	ALDH16A1	54	.	0			c.C766T						.						16.0	18.0	17.0					19																	49965147		2183	4280	6463	SO:0001583	missense	126133	exon7			GAAGGGCGTGCCC	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.766C>T	chr19.hg19:g.49965147C>T	ENSP00000293350:p.Arg256Cys	137.0	0.0		149.0	67.0	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	hg19	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377297	0.61735	.	.	ENSG00000161618	ENST00000293350;ENST00000540132;ENST00000433981	T;T;T	0.79033	-1.23;-1.23;-1.23	4.65	4.65	0.58169	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.759301	0.12974	N	0.423860	D	0.90521	0.7030	M	0.93150	3.385	0.50813	D	0.999893	D;D	0.89917	1.0;1.0	D;D	0.68621	0.953;0.959	D	0.91378	0.5125	10	0.87932	D	0	-8.4781	13.7969	0.63177	0.0:1.0:0.0:0.0	.	93;256	F5H4B6;Q8IZ83	.;A16A1_HUMAN	C	256;93;91	ENSP00000293350:R256C;ENSP00000445088:R93C;ENSP00000398675:R91C	ENSP00000293350:R256C	R	+	1	0	ALDH16A1	54656959	0.125000	0.22332	0.997000	0.53966	0.373000	0.29922	1.112000	0.31172	2.536000	0.85505	0.585000	0.79938	CGT	.	.		0.721	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
TBC1D17	79735	hgsc.bcm.edu	37	19	50391714	50391714	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50391714C>T	ENST00000221543.5	+	17	2079	c.1780C>T	c.(1780-1782)Ctg>Ttg	p.L594L	MIR4750_ENST00000584564.1_RNA|TBC1D17_ENST00000535102.2_Silent_p.L561L	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	594					autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		GATCCTGGGGCTGGCCCCGCC	0.736																																					p.L594L		Atlas-SNP	.											.	TBC1D17	39	.	0			c.C1780T						.						9.0	10.0	10.0					19																	50391714		2073	3992	6065	SO:0001819	synonymous_variant	79735	exon17			CTGGGGCTGGCCC	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1780C>T	chr19.hg19:g.50391714C>T		99.0	0.0		81.0	11.0	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	hg19	CCDS12785.1																																																																																			.	.		0.736	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
ZNF473	25888	hgsc.bcm.edu	37	19	50542425	50542425	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50542425T>C	ENST00000595661.1	+	4	512	c.17T>C	c.(16-18)gTg>gCg	p.V6A	ZNF473_ENST00000270617.3_Missense_Mutation_p.V6A|ZNF473_ENST00000601364.1_Missense_Mutation_p.V6A|ZNF473_ENST00000445728.3_5'UTR|ZNF473_ENST00000391821.2_Missense_Mutation_p.V6A			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	6	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		CAGGAATTTGTGACCCTCAAG	0.577																																					p.V6A		Atlas-SNP	.											.	ZNF473	86	.	0			c.T17C						.						163.0	143.0	150.0					19																	50542425		2203	4300	6503	SO:0001583	missense	25888	exon3			AATTTGTGACCCT	AB032967	CCDS33077.1	19q13.33	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.17T>C	chr19.hg19:g.50542425T>C	ENSP00000472808:p.Val6Ala	103.0	0.0		76.0	28.0	NM_015428	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	hg19	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.489092	0.44249	.	.	ENSG00000142528	ENST00000270617;ENST00000391821	T;T	0.05717	3.4;3.4	5.11	-7.21	0.01490	Krueppel-associated box (4);	1.795830	0.03316	N	0.191109	T	0.10637	0.0260	M	0.88842	2.985	0.09310	N	0.999996	B	0.09022	0.002	B	0.12156	0.007	T	0.41680	-0.9495	10	0.87932	D	0	0.645	2.6942	0.05129	0.1976:0.4028:0.1069:0.2927	.	6	Q8WTR7	ZN473_HUMAN	A	6	ENSP00000270617:V6A;ENSP00000375697:V6A	ENSP00000270617:V6A	V	+	2	0	ZNF473	55234237	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.824000	0.04438	-1.786000	0.01269	0.528000	0.53228	GTG	.	.		0.577	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390	
MYH14	79784	hgsc.bcm.edu	37	19	50794187	50794187	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50794187G>A	ENST00000596571.1	+	33	4886	c.4886G>A	c.(4885-4887)cGc>cAc	p.R1629H	MYH14_ENST00000440075.2_Missense_Mutation_p.R1670H|MYH14_ENST00000262269.8_Missense_Mutation_p.R1670H|MYH14_ENST00000425460.1_Missense_Mutation_p.R1637H|MYH14_ENST00000376970.2_Missense_Mutation_p.R1662H|MYH14_ENST00000601313.1_Missense_Mutation_p.R1670H|MYH14_ENST00000598205.1_Missense_Mutation_p.R1637H			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1629					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)		CGGAAGCAGCGCACTCTGGCC	0.657																																					p.R1670H		Atlas-SNP	.											MYH14_ENST00000262269,colon,carcinoma,0,1	MYH14	261	.	0			c.G5009A						.						19.0	25.0	23.0					19																	50794187		2066	4197	6263	SO:0001583	missense	79784	exon36			AGCAGCGCACTCT	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.4886G>A	chr19.hg19:g.50794187G>A	ENSP00000472819:p.Arg1629His	117.0	0.0		137.0	54.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.983989	0.74474	.	.	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47	4.42	4.42	0.53409	Myosin tail (1);	.	.	.	.	D	0.89132	0.6628	M	0.77406	2.37	0.49051	D	0.999747	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90495	0.4470	9	0.87932	D	0	.	14.8871	0.70579	0.0:0.0:1.0:0.0	.	1670;1629;1637	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	H	1670;1662;1637;1413;1670	ENSP00000406273:R1670H;ENSP00000366169:R1662H;ENSP00000407879:R1637H;ENSP00000262269:R1670H	ENSP00000262269:R1670H	R	+	2	0	MYH14	55485999	0.997000	0.39634	1.000000	0.80357	0.325000	0.28411	7.474000	0.81024	2.447000	0.82792	0.491000	0.48974	CGC	.	.		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
KLK10	5655	hgsc.bcm.edu	37	19	51520382	51520382	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:51520382C>T	ENST00000309958.3	-	3	471	c.253G>A	c.(253-255)Gcg>Acg	p.A85T	CTC-518B2.12_ENST00000596286.1_RNA|KLK10_ENST00000358789.3_Missense_Mutation_p.A85T|KLK10_ENST00000391805.1_Missense_Mutation_p.A85T	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	85	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		CCGCAGTGCGCGGCCGTCAGC	0.706											OREG0025646	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A85T		Atlas-SNP	.											.	KLK10	32	.	0			c.G253A						.						21.0	21.0	21.0					19																	51520382		2202	4296	6498	SO:0001583	missense	5655	exon3			AGTGCGCGGCCGT	AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"""Kallikreins"""	6358	protein-coding gene	gene with protein product		602673	"""kallikrein 10"""	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.253G>A	chr19.hg19:g.51520382C>T	ENSP00000311746:p.Ala85Thr	117.0	0.0	978	149.0	64.0	NM_145888	A6NC12|Q53YL3|Q99920|Q9GZW9	Missense_Mutation	SNP	ENST00000309958.3	hg19	CCDS12817.1	.	.	.	.	.	.	.	.	.	.	c	27.7	4.856623	0.91355	.	.	ENSG00000129451	ENST00000391805;ENST00000309958;ENST00000358789	D;D;D	0.96940	-4.18;-4.18;-4.18	4.43	4.43	0.53597	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.34460	N	0.003956	D	0.98604	0.9533	H	0.96208	3.785	0.35355	D	0.787717	D	0.89917	1.0	D	0.97110	1.0	D	0.99968	1.1923	10	0.87932	D	0	.	12.8949	0.58093	0.0:1.0:0.0:0.0	.	85	O43240	KLK10_HUMAN	T	85	ENSP00000375681:A85T;ENSP00000311746:A85T;ENSP00000351640:A85T	ENSP00000311746:A85T	A	-	1	0	KLK10	56212194	0.998000	0.40836	0.984000	0.44739	0.990000	0.78478	5.361000	0.66092	2.167000	0.68274	0.491000	0.48974	GCG	.	.		0.706	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776	
VSIG10L	147645	hgsc.bcm.edu	37	19	51840531	51840531	+	Nonsense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:51840531G>A	ENST00000335624.4	-	7	2265	c.2266C>T	c.(2266-2268)Cag>Tag	p.Q756*		NM_001163922.1	NP_001157394.1	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10 like	756						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)	4						GTCCCTGGCTGGCCCCCCAGG	0.647																																					p.Q756X		Atlas-SNP	.											.	VSIG10L	40	.	0			c.C2266T						.						53.0	64.0	61.0					19																	51840531		692	1591	2283	SO:0001587	stop_gained	147645	exon7			CTGGCTGGCCCCC		CCDS54300.1	19q13.41	2013-01-11				ENSG00000186806		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27111	protein-coding gene	gene with protein product						12477932	Standard	NM_001163922		Approved		uc002pwf.3	Q86VR7		ENST00000335624.4:c.2266C>T	chr19.hg19:g.51840531G>A	ENSP00000335623:p.Gln756*	128.0	0.0		129.0	52.0	NM_001163922		Nonsense_Mutation	SNP	ENST00000335624.4	hg19	CCDS54300.1	.	.	.	.	.	.	.	.	.	.	g	36	5.797998	0.96952	.	.	ENSG00000186806	ENST00000335624	.	.	.	4.76	4.76	0.60689	.	0.167813	0.28171	N	0.016333	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-2.1557	13.2634	0.60120	0.0:0.0:1.0:0.0	.	.	.	.	X	756	.	ENSP00000335623:Q756X	Q	-	1	0	VSIG10L	56532343	0.866000	0.29940	0.642000	0.29436	0.228000	0.25075	1.945000	0.40273	2.174000	0.68829	0.457000	0.33378	CAG	.	.		0.647	VSIG10L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464535.1	NM_001163922	
SIGLEC6	946	hgsc.bcm.edu	37	19	52034864	52034864	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:52034864T>C	ENST00000425629.3	-	1	193	c.39A>G	c.(37-39)ctA>ctG	p.L13L	SIGLEC6_ENST00000359982.4_Silent_p.L13L|SIGLEC6_ENST00000346477.3_Silent_p.L13L|SIGLEC6_ENST00000436458.1_Silent_p.L13L|SIGLEC6_ENST00000391797.3_Silent_p.L13L|SIGLEC6_ENST00000343300.4_Silent_p.L13L	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	13					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GCAGCAGCGGTAGCATCTCTG	0.687																																					p.L13L		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.A39G						.						17.0	21.0	20.0					19																	52034864		2160	4271	6431	SO:0001819	synonymous_variant	946	exon1			CAGCGGTAGCATC	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.39A>G	chr19.hg19:g.52034864T>C		213.0	0.0		188.0	62.0	NM_001177549	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Silent	SNP	ENST00000425629.3	hg19	CCDS12834.3																																																																																			.	.		0.687	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
ZNF841	284371	hgsc.bcm.edu	37	19	52569919	52569919	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:52569919A>G	ENST00000426391.2	-	5	1419	c.868T>C	c.(868-870)Tgt>Cgt	p.C290R	ZNF841_ENST00000359973.2_Missense_Mutation_p.C290R|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.C406R|ZNF841_ENST00000594295.1_Missense_Mutation_p.C406R|CTC-471J1.2_ENST00000569091.1_RNA			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	290					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(4)|kidney(3)|lung(3)	11						GTTTTGCCACATTCATTACAT	0.388																																					p.C406R		Atlas-SNP	.											.	ZNF841	183	.	0			c.T1216C						.						119.0	103.0	108.0					19																	52569919		692	1591	2283	SO:0001583	missense	284371	exon7			TGCCACATTCATT	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.868T>C	chr19.hg19:g.52569919A>G	ENSP00000415453:p.Cys290Arg	96.0	0.0		112.0	50.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	A	21.1	4.104998	0.77096	.	.	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	D;D;D	0.85955	-2.05;-2.05;-2.05	2.26	2.26	0.28386	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94248	0.8153	H	0.97852	4.09	0.52501	D	0.999954	D;D;D	0.89917	0.998;1.0;0.993	D;D;D	0.78314	0.991;0.991;0.985	D	0.93759	0.7065	9	0.87932	D	0	.	9.2133	0.37331	1.0:0.0:0.0:0.0	.	406;290;290	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	R	406;290;290	ENSP00000374185:C406R;ENSP00000415453:C290R;ENSP00000353060:C290R	ENSP00000353060:C290R	C	-	1	0	ZNF841	57261731	0.398000	0.25279	0.017000	0.16124	0.848000	0.48234	2.561000	0.45905	1.031000	0.39867	0.260000	0.18958	TGT	.	.		0.388	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ZNF578	147660	hgsc.bcm.edu	37	19	53014578	53014578	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:53014578A>G	ENST00000421239.2	+	6	1188	c.944A>G	c.(943-945)tAc>tGc	p.Y315C	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GAGAAACCTTACAAGTGTAAT	0.408																																					p.Y315C		Atlas-SNP	.											.	.	.	.	0			c.A944G						.						99.0	103.0	101.0					19																	53014578		2203	4300	6503	SO:0001583	missense	147660	exon6			AACCTTACAAGTG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.944A>G	chr19.hg19:g.53014578A>G	ENSP00000459216:p.Tyr315Cys	160.0	0.0		177.0	71.0	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	11.94	1.787735	0.31593	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.37	1.37	0.22104	.	.	.	.	.	T	0.58566	0.2131	M	0.82433	2.59	0.09310	N	1	D	0.76494	0.999	D	0.65323	0.934	T	0.45160	-0.9280	7	.	.	.	.	4.2923	0.10885	0.487:0.0:0.0:0.513	.	315	G3V4F6	.	C	315	.	.	Y	+	2	0	ZNF578	57706390	0.000000	0.05858	0.031000	0.17742	0.372000	0.29890	-0.421000	0.07053	0.640000	0.30582	0.246000	0.17985	TAC	.	.		0.408	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
LILRB3	11025	hgsc.bcm.edu	37	19	54721271	54721271	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:54721271C>T	ENST00000391750.1	-	13	1802	c.1666G>A	c.(1666-1668)Gcc>Acc	p.A556T	LILRB3_ENST00000245620.9_Missense_Mutation_p.A557T|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.A573T|LILRA6_ENST00000270464.5_Missense_Mutation_p.A557T|LILRB3_ENST00000346401.6_Missense_Mutation_p.A568T|LILRB3_ENST00000424807.1_Missense_Mutation_p.A556T|LILRA6_ENST00000419410.2_Missense_Mutation_p.A557T|LILRA6_ENST00000440558.2_Missense_Mutation_p.A556T|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	556					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGAGGAGAGGCCATTTCTCTC	0.577																																					p.A557T		Atlas-SNP	.											.	LILRB3	67	.	0			c.G1669A						.						128.0	129.0	129.0					19																	54721271		2202	4300	6502	SO:0001583	missense	11025	exon12			GAGAGGCCATTTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1666G>A	chr19.hg19:g.54721271C>T	ENSP00000375630:p.Ala556Thr	235.0	0.0		217.0	52.0	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	hg19	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103359	0.37145	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00500	6.97;6.97;6.96;6.98;7.02;6.97;6.97;6.99	2.45	-4.91	0.03085	.	.	.	.	.	T	0.00637	0.0021	L	0.44542	1.39	0.09310	N	1	D;B;B;P;B;B;P	0.89917	1.0;0.021;0.026;0.916;0.003;0.004;0.652	D;B;B;B;B;B;P	0.85130	0.997;0.03;0.017;0.434;0.01;0.008;0.646	T	0.41963	-0.9479	9	0.18276	T	0.48	.	0.6035	0.00748	0.1746:0.276:0.1725:0.3769	.	573;556;557;568;573;556;557	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	T	556;556;568;557;573;556;557;557	ENSP00000375630:A556T;ENSP00000412771:A556T;ENSP00000345184:A568T;ENSP00000245620:A557T;ENSP00000384274:A573T;ENSP00000390120:A556T;ENSP00000270464:A557T;ENSP00000411227:A557T	ENSP00000270464:A557T	A	-	1	0	LILRB3;LILRA6	59413083	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-1.210000	0.02999	-1.009000	0.03400	0.121000	0.15741	GCC	.	.		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
LENG8	114823	hgsc.bcm.edu	37	19	54967527	54967527	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:54967527G>A	ENST00000326764.5	+	10	1807	c.1328G>A	c.(1327-1329)aGc>aAc	p.S443N	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	406										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GACTCCGACAGCTCCTACTCA	0.672																																					p.S443N		Atlas-SNP	.											.	LENG8	73	.	0			c.G1328A						.						53.0	57.0	56.0					19																	54967527		2203	4300	6503	SO:0001583	missense	114823	exon10			CCGACAGCTCCTA	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1328G>A	chr19.hg19:g.54967527G>A	ENSP00000318374:p.Ser443Asn	62.0	0.0		60.0	26.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	hg19	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.670567	0.67814	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.36699	1.28;1.28;1.24	4.52	4.52	0.55395	.	0.109881	0.64402	D	0.000003	T	0.33381	0.0861	L	0.27053	0.805	0.42244	D	0.991949	B;P	0.46784	0.449;0.884	B;P	0.47864	0.185;0.559	T	0.03887	-1.0995	10	0.26408	T	0.33	-7.2268	15.6069	0.76679	0.0:0.0:1.0:0.0	.	443;406	Q96PV6-2;F8W9Q9	.;.	N	443;406;406;443	ENSP00000318374:S443N;ENSP00000365709:S406N;ENSP00000388053:S443N	ENSP00000301196:S406N	S	+	2	0	LENG8	59659339	1.000000	0.71417	0.985000	0.45067	0.986000	0.74619	5.566000	0.67372	2.466000	0.83321	0.555000	0.69702	AGC	.	.		0.672	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
EPS8L1	54869	hgsc.bcm.edu	37	19	55591068	55591068	+	Missense_Mutation	SNP	C	C	T	rs373089208		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55591068C>T	ENST00000201647.6	+	5	184	c.128C>T	c.(127-129)aCg>aTg	p.T43M	EPS8L1_ENST00000588359.1_5'Flank|EPS8L1_ENST00000540810.1_5'UTR|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000586329.1_Missense_Mutation_p.T25M|EPS8L1_ENST00000245618.5_5'Flank	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	43					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CACCTGGTGACGTTCTGCCTG	0.582																																					p.T43M	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.C128T						.	C	MET/THR	0,4406		0,0,2203	91.0	72.0	79.0		128	3.8	1.0	19		79	1,8599	1.2+/-3.3	0,1,4299	no	missense	EPS8L1	NM_133180.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	43/724	55591068	1,13005	2203	4300	6503	SO:0001583	missense	54869	exon5			TGGTGACGTTCTG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.128C>T	chr19.hg19:g.55591068C>T	ENSP00000201647:p.Thr43Met	110.0	0.0		94.0	30.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055187	0.75960	0.0	1.16E-4	ENSG00000131037	ENST00000310075;ENST00000201647	T	0.41400	1.0	3.85	3.85	0.44370	Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.073341	0.53938	D	0.000045	T	0.65923	0.2738	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.72821	-0.4177	10	0.87932	D	0	-22.5488	13.6399	0.62243	0.0:1.0:0.0:0.0	.	25;43	Q8TE68-3;Q8TE68	.;ES8L1_HUMAN	M	25;43	ENSP00000201647:T43M	ENSP00000201647:T43M	T	+	2	0	EPS8L1	60282880	1.000000	0.71417	0.992000	0.48379	0.816000	0.46133	6.675000	0.74493	1.860000	0.53959	0.313000	0.20887	ACG	.	.		0.582	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
PTPRH	5794	hgsc.bcm.edu	37	19	55693151	55693151	+	Missense_Mutation	SNP	C	C	T	rs201369294		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55693151C>T	ENST00000376350.3	-	20	3341	c.3319G>A	c.(3319-3321)Gcc>Acc	p.A1107T	SYT5_ENST00000590851.1_5'Flank|PTPRH_ENST00000263434.5_Missense_Mutation_p.A929T|SYT5_ENST00000354308.3_5'Flank|SYT5_ENST00000537500.1_5'Flank	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	1107					apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GCCTGGATGGCGGCCACGTTC	0.602																																					p.A1107T		Atlas-SNP	.											.	PTPRH	139	.	0			c.G3319A						.						128.0	125.0	126.0					19																	55693151		2203	4300	6503	SO:0001583	missense	5794	exon20			GGATGGCGGCCAC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.3319G>A	chr19.hg19:g.55693151C>T	ENSP00000365528:p.Ala1107Thr	116.0	0.0		95.0	40.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.037159	0.54896	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.06371	3.31;4.31	4.16	1.99	0.26369	.	0.000000	0.35466	N	0.003200	T	0.04815	0.0130	L	0.27053	0.805	0.09310	N	1	P;P	0.51933	0.949;0.949	B;P	0.44561	0.358;0.453	T	0.37174	-0.9717	10	0.38643	T	0.18	.	5.7617	0.18203	0.0:0.6497:0.1866:0.1637	.	929;1107	C9JCH2;Q9HD43	.;PTPRH_HUMAN	T	1107;929	ENSP00000365528:A1107T;ENSP00000263434:A929T	ENSP00000263434:A929T	A	-	1	0	PTPRH	60384963	0.002000	0.14202	0.021000	0.16686	0.030000	0.12068	0.700000	0.25601	1.046000	0.40249	0.650000	0.86243	GCC	.	C|0.999;T|0.001		0.602	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
RPL28	6158	hgsc.bcm.edu	37	19	55899324	55899324	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55899324G>A	ENST00000344063.2	+	4	861	c.232G>A	c.(232-234)Gtg>Atg	p.V78M	RPL28_ENST00000558815.1_Missense_Mutation_p.V78M|RPL28_ENST00000559463.1_Missense_Mutation_p.V78M|RPL28_ENST00000560583.1_Missense_Mutation_p.V78M|RPL28_ENST00000560055.1_Missense_Mutation_p.V78M|RPL28_ENST00000558131.1_Missense_Mutation_p.M71I|RPL28_ENST00000458349.2_Missense_Mutation_p.V78M			P46779	RL28_HUMAN	ribosomal protein L28	78					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CACCTCCTATGTGCGGACCAC	0.612																																					p.V78M		Atlas-SNP	.											.	RPL28	31	.	0			c.G232A						.						87.0	86.0	86.0					19																	55899324		2203	4300	6503	SO:0001583	missense	6158	exon4			TCCTATGTGCGGA	U14969	CCDS12924.1, CCDS46189.1, CCDS46190.1, CCDS46191.1, CCDS46192.1	19q13.4	2011-04-06				ENSG00000108107		"""L ribosomal proteins"""	10330	protein-coding gene	gene with protein product	"""60S ribosomal protein L28"""	603638				7772601, 9582194	Standard	NM_001136134		Approved	FLJ43307, L28	uc010yga.2	P46779		ENST00000344063.2:c.232G>A	chr19.hg19:g.55899324G>A	ENSP00000342787:p.Val78Met	89.0	0.0		80.0	33.0	NM_000991	B2R4A6|B4DEP9|C9JB50|E9PB24|G5E9L2|Q6IAY0|Q96FX1|Q9BWQ0	Missense_Mutation	SNP	ENST00000344063.2	hg19	CCDS12924.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.563526	0.45694	.	.	ENSG00000108107	ENST00000344063;ENST00000426763;ENST00000458349	T;T	0.45668	0.89;0.89	3.44	3.44	0.39384	.	0.673867	0.13775	N	0.363655	T	0.48095	0.1481	M	0.78285	2.405	0.26786	N	0.969502	P;P;B	0.42010	0.623;0.768;0.149	B;B;B	0.41988	0.268;0.372;0.122	T	0.47535	-0.9110	10	0.48119	T	0.1	.	13.1887	0.59697	0.0:0.0:1.0:0.0	.	78;78;78	B4DEP9;E9PB24;P46779	.;.;RL28_HUMAN	M	78	ENSP00000342787:V78M;ENSP00000401450:V78M	ENSP00000342787:V78M	V	+	1	0	RPL28	60591136	1.000000	0.71417	0.933000	0.37362	0.975000	0.68041	5.866000	0.69590	1.864000	0.54056	0.462000	0.41574	GTG	.	.		0.612	RPL28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416277.2	NM_000991	
ZNF628	89887	hgsc.bcm.edu	37	19	55992668	55992668	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55992668C>T	ENST00000598519.1	+	3	661	c.108C>T	c.(106-108)taC>taT	p.Y36Y	ZNF628_ENST00000391718.2_Silent_p.Y32Y			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	36					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)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		CGGCCCAGTACGAATGTGGGG	0.711																																					p.Y36Y		Atlas-SNP	.											.	ZNF628	75	.	0			c.C108T						.						22.0	23.0	23.0					19																	55992668		2199	4295	6494	SO:0001819	synonymous_variant	89887	exon3			CCAGTACGAATGT	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.108C>T	chr19.hg19:g.55992668C>T		129.0	0.0		148.0	56.0	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	hg19	CCDS33116.3																																																																																			.	.		0.711	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
U2AF2	11338	hgsc.bcm.edu	37	19	56185355	56185355	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:56185355C>T	ENST00000308924.4	+	12	1389	c.1349C>T	c.(1348-1350)aCg>aTg	p.T450M	CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|EPN1_ENST00000411543.2_5'Flank|U2AF2_ENST00000450554.2_Missense_Mutation_p.T446M|CTD-2537I9.12_ENST00000585940.1_RNA|U2AF2_ENST00000590551.1_Missense_Mutation_p.T282M|EPN1_ENST00000085079.7_5'Flank|EPN1_ENST00000270460.6_5'Flank			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	450	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T450M(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CAGGGCCTGACGGGCCGCAAG	0.577																																					p.T450M		Atlas-SNP	.											U2AF2,bile_duct,carcinoma,0,1	U2AF2	62	.	1	Substitution - Missense(1)	biliary_tract(1)	c.C1349T						.						89.0	84.0	86.0					19																	56185355		2203	4300	6503	SO:0001583	missense	11338	exon12			GCCTGACGGGCCG	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1349C>T	chr19.hg19:g.56185355C>T	ENSP00000307863:p.Thr450Met	117.0	0.0		99.0	37.0	NM_007279	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	hg19	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373101	0.82573	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.16324	2.35;2.35	4.42	4.42	0.53409	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	U	0.000000	T	0.40619	0.1124	M	0.71871	2.18	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.943	T	0.24190	-1.0167	10	0.42905	T	0.14	-22.4265	16.161	0.81712	0.0:1.0:0.0:0.0	.	450;446	P26368;P26368-2	U2AF2_HUMAN;.	M	450;446	ENSP00000307863:T450M;ENSP00000388475:T446M	ENSP00000307863:T450M	T	+	2	0	U2AF2	60877167	1.000000	0.71417	0.951000	0.38953	0.990000	0.78478	5.200000	0.65158	2.173000	0.68751	0.478000	0.44815	ACG	.	.		0.577	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279	
ZNF835	90485	hgsc.bcm.edu	37	19	57175770	57175770	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:57175770A>T	ENST00000537055.2	-	2	1028	c.797T>A	c.(796-798)aTc>aAc	p.I266N		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	266					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CTGGTGGCGGATGAGCGCTGA	0.677																																					p.I266N		Atlas-SNP	.											.	ZNF835	106	.	0			c.T797A						.						31.0	32.0	31.0					19																	57175770		2203	4300	6503	SO:0001583	missense	90485	exon2			TGGCGGATGAGCG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.797T>A	chr19.hg19:g.57175770A>T	ENSP00000444747:p.Ile266Asn	128.0	0.0		123.0	51.0	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.475900	0.44044	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.07114	3.22	2.12	-0.00638	0.14013	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08088	0.0202	N	0.04959	-0.14	0.09310	N	1	D	0.59357	0.985	P	0.61477	0.889	T	0.33266	-0.9875	9	0.45353	T	0.12	.	5.3168	0.15860	0.6931:0.0:0.3069:0.0	.	288	Q9Y2P0	ZN835_HUMAN	N	288;266	ENSP00000444747:I266N	ENSP00000341756:I288N	I	-	2	0	ZNF835	61867582	0.000000	0.05858	0.000000	0.03702	0.719000	0.41307	-2.552000	0.00927	-0.066000	0.12998	0.459000	0.35465	ATC	.	.		0.677	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
ZNF814	730051	hgsc.bcm.edu	37	19	58384994	58384994	+	Silent	SNP	G	G	A	rs562476717		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:58384994G>A	ENST00000435989.2	-	3	1998	c.1764C>T	c.(1762-1764)atC>atT	p.I588I	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	588					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TAAGGTGCCCGATTGAACTAA	0.453																																					p.I588I		Atlas-SNP	.											.	ZNF814	93	.	0			c.C1764T						.						93.0	75.0	81.0					19																	58384994		692	1591	2283	SO:0001819	synonymous_variant	730051	exon3			GTGCCCGATTGAA		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1764C>T	chr19.hg19:g.58384994G>A		122.0	0.0		102.0	47.0	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	hg19	CCDS46212.1																																																																																			.	.		0.453	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
ZNF544	27300	hgsc.bcm.edu	37	19	58773536	58773536	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:58773536T>C	ENST00000596652.1	+	6	1798	c.1564T>C	c.(1564-1566)Tgc>Cgc	p.C522R	ZNF544_ENST00000596825.1_3'UTR|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000269829.4_Missense_Mutation_p.C522R|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000415203.2_Missense_Mutation_p.C494R|ZNF544_ENST00000599953.1_Missense_Mutation_p.C380R|ZNF544_ENST00000600220.1_Missense_Mutation_p.C494R|ZNF544_ENST00000600044.1_Missense_Mutation_p.C494R			Q6NX49	ZN544_HUMAN	zinc finger protein 544	522					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(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		GCCCTATGAGTGCAACCTGTG	0.438																																					p.C522R		Atlas-SNP	.											.	ZNF544	57	.	0			c.T1564C						.						80.0	83.0	82.0					19																	58773536		2203	4300	6503	SO:0001583	missense	27300	exon7			TATGAGTGCAACC	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"""Zinc fingers, C2H2-type"", ""-"""	16759	protein-coding gene	gene with protein product	"""zinc finger protein AF020591"""						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.1564T>C	chr19.hg19:g.58773536T>C	ENSP00000469635:p.Cys522Arg	165.0	0.0		158.0	59.0	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	hg19	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.262069	0.39995	.	.	ENSG00000198131	ENST00000269829;ENST00000415203	D;D	0.85258	-1.96;-1.96	2.8	1.72	0.24424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94059	0.8096	H	0.97940	4.11	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	D	0.91846	0.5487	9	0.87932	D	0	.	7.4777	0.27387	0.1925:0.0:0.0:0.8075	.	494;494;522	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	R	522;494	ENSP00000269829:C522R;ENSP00000394341:C494R	ENSP00000269829:C522R	C	+	1	0	ZNF544	63465348	1.000000	0.71417	0.001000	0.08648	0.005000	0.04900	4.949000	0.63596	0.282000	0.22254	0.421000	0.28195	TGC	.	.		0.438	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480	
SLC27A5	10998	hgsc.bcm.edu	37	19	59011917	59011917	+	Missense_Mutation	SNP	G	G	A	rs558863851		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:59011917G>A	ENST00000263093.2	-	5	1448	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C	SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000601355.1_Missense_Mutation_p.R363C|SLC27A5_ENST00000599700.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	447					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GCCCCGCAGCGCCCCACATAG	0.602													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17577	0.0		0.0	False		,,,				2504	0.0				p.R447C		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C1339T						.						80.0	72.0	75.0					19																	59011917		2203	4300	6503	SO:0001583	missense	10998	exon5			CGCAGCGCCCCAC	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1339C>T	chr19.hg19:g.59011917G>A	ENSP00000263093:p.Arg447Cys	65.0	0.0		56.0	18.0	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	hg19	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408143	0.62399	.	.	ENSG00000083807	ENST00000263093	T	0.43294	0.95	5.33	4.28	0.50868	AMP-dependent synthetase/ligase (1);	0.377730	0.28393	N	0.015502	T	0.63954	0.2555	M	0.83118	2.625	0.30853	N	0.734336	D	0.76494	0.999	D	0.67725	0.953	T	0.70288	-0.4913	10	0.87932	D	0	-13.0742	11.6284	0.51160	0.0:0.0:0.822:0.178	.	447	Q9Y2P5	S27A5_HUMAN	C	447	ENSP00000263093:R447C	ENSP00000263093:R447C	R	-	1	0	SLC27A5	63703729	0.029000	0.19370	0.314000	0.25224	0.647000	0.38526	1.920000	0.40025	1.363000	0.46019	0.563000	0.77884	CGC	.	.		0.602	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
TRIM28	10155	hgsc.bcm.edu	37	19	59059077	59059077	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:59059077G>A	ENST00000253024.5	+	5	1125	c.836G>A	c.(835-837)aGc>aAc	p.S279N	TRIM28_ENST00000341753.6_Missense_Mutation_p.S197N	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	279	Interaction with MAGEC2.|Leucine zipper alpha helical coiled-coil region.|RBCC domain.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAGGTTCGCAGCTCGTAAGTG	0.602																																					p.S279N		Atlas-SNP	.											.	TRIM28	46	.	0			c.G836A						.						118.0	98.0	105.0					19																	59059077		2203	4300	6503	SO:0001583	missense	10155	exon5			TTCGCAGCTCGTA		CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	16384	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 157"""	601742	"""tripartite motif-containing 28"""			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.836G>A	chr19.hg19:g.59059077G>A	ENSP00000253024:p.Ser279Asn	165.0	0.0		125.0	39.0	NM_005762	O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	hg19	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	G	8.588	0.883850	0.17467	.	.	ENSG00000130726	ENST00000253024;ENST00000341753	T;T	0.67523	-0.04;-0.27	4.99	3.89	0.44902	B-box, C-terminal (1);	0.117868	0.56097	D	0.000035	T	0.45478	0.1344	N	0.11427	0.14	0.34896	D	0.746054	P;P	0.40731	0.728;0.608	B;B	0.43445	0.42;0.188	T	0.53415	-0.8442	10	0.02654	T	1	-34.7179	12.6235	0.56616	0.0:0.2675:0.7325:0.0	.	197;279	Q13263-2;Q13263	.;TIF1B_HUMAN	N	279;197	ENSP00000253024:S279N;ENSP00000342232:S197N	ENSP00000253024:S279N	S	+	2	0	TRIM28	63750889	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.331000	0.33793	2.499000	0.84300	0.555000	0.69702	AGC	.	.		0.602	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762	
NOP56	10528	hgsc.bcm.edu	37	20	2635511	2635511	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:2635511C>T	ENST00000329276.5	+	5	1003	c.487C>T	c.(487-489)Cgg>Tgg	p.R163W	SNORA51_ENST00000606420.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORD56_ENST00000413522.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORD57_ENST00000448188.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	163					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TAATGTGAACCGGGTGGACAA	0.507																																					p.R163W		Atlas-SNP	.											.	NOP56	73	.	0			c.C487T						.						173.0	168.0	170.0					20																	2635511		2203	4300	6503	SO:0001583	missense	10528	exon5			GTGAACCGGGTGG	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.487C>T	chr20.hg19:g.2635511C>T	ENSP00000370589:p.Arg163Trp	102.0	0.0		95.0	29.0	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	hg19	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.236678	0.39498	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	T;T	0.77750	-1.12;-1.12	5.89	3.79	0.43588	.	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89514	0.3773	10	0.87932	D	0	-15.3937	8.3385	0.32230	0.2177:0.6984:0.0:0.0839	.	163	O00567	NOP56_HUMAN	W	163	ENSP00000370589:R163W;ENSP00000388497:R163W	ENSP00000370589:R163W	R	+	1	2	NOP56	2583511	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	1.509000	0.35780	1.494000	0.48533	-0.266000	0.10368	CGG	.	.		0.507	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
UBOX5	22888	hgsc.bcm.edu	37	20	3102753	3102753	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3102753T>C	ENST00000217173.2	-	3	1003	c.532A>G	c.(532-534)Acc>Gcc	p.T178A	UBOX5_ENST00000348031.2_Missense_Mutation_p.T178A|UBOX5-AS1_ENST00000446537.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						GTCACATGGGTGATACAGATC	0.577																																					p.T178A		Atlas-SNP	.											.	UBOX5	47	.	0			c.A532G						.						68.0	61.0	63.0					20																	3102753		2203	4300	6503	SO:0001583	missense	22888	exon3			CATGGGTGATACA	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"""RING-type (C3HC4) zinc fingers"", ""U-box domain containing"""	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.532A>G	chr20.hg19:g.3102753T>C	ENSP00000217173:p.Thr178Ala	110.0	0.0		99.0	42.0	NM_014948		Missense_Mutation	SNP	ENST00000217173.2	hg19	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	T	8.988	0.977004	0.18812	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.48836	0.8;0.8	5.19	5.19	0.71726	.	0.124327	0.53938	U	0.000048	T	0.36193	0.0958	L	0.35288	1.05	0.39081	D	0.960917	B;B;B	0.32350	0.366;0.361;0.366	B;B;B	0.23574	0.047;0.042;0.047	T	0.31392	-0.9945	10	0.41790	T	0.15	-17.3227	15.0487	0.71846	0.0:0.0:0.0:1.0	.	178;178;178	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	A	178	ENSP00000217173:T178A;ENSP00000311726:T178A	ENSP00000217173:T178A	T	-	1	0	UBOX5	3050753	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	4.739000	0.62080	1.950000	0.56595	0.379000	0.24179	ACC	.	.		0.577	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948	
ATRN	8455	hgsc.bcm.edu	37	20	3556555	3556555	+	Missense_Mutation	SNP	A	A	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3556555A>C	ENST00000262919.5	+	13	2242	c.2174A>C	c.(2173-2175)gAc>gCc	p.D725A	ATRN_ENST00000446916.2_Missense_Mutation_p.D725A	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	725	PSI 1.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						TGGTGCAATGACCATTGTGTC	0.453																																					p.D725A		Atlas-SNP	.											.	ATRN	118	.	0			c.A2174C						.						95.0	84.0	88.0					20																	3556555		2203	4300	6503	SO:0001583	missense	8455	exon13			GCAATGACCATTG	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.2174A>C	chr20.hg19:g.3556555A>C	ENSP00000262919:p.Asp725Ala	66.0	0.0		67.0	26.0	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	hg19	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959695	0.74016	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.18502	3.39;2.21	5.79	5.79	0.91817	.	0.204186	0.50627	D	0.000103	T	0.23249	0.0562	M	0.65498	2.005	0.43868	D	0.996477	B;P	0.42296	0.372;0.775	B;B	0.39771	0.309;0.225	T	0.01697	-1.1293	10	0.44086	T	0.13	-25.0048	15.797	0.78420	1.0:0.0:0.0:0.0	.	725;725	O75882;O75882-2	ATRN_HUMAN;.	A	725;725;651	ENSP00000262919:D725A;ENSP00000416587:D725A	ENSP00000262919:D725A	D	+	2	0	ATRN	3504555	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.976000	0.63785	2.204000	0.70986	0.460000	0.39030	GAC	.	.		0.453	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
ATRN	8455	hgsc.bcm.edu	37	20	3575207	3575207	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3575207A>G	ENST00000262919.5	+	20	3472	c.3404A>G	c.(3403-3405)gAc>gGc	p.D1135G	ATRN_ENST00000446916.2_Missense_Mutation_p.D1135G	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	1135	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						GTCAAGGGGGACGAGTGCCAG	0.597																																					p.D1135G		Atlas-SNP	.											.	ATRN	118	.	0			c.A3404G						.						85.0	70.0	75.0					20																	3575207		2203	4300	6503	SO:0001583	missense	8455	exon20			AGGGGGACGAGTG	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.3404A>G	chr20.hg19:g.3575207A>G	ENSP00000262919:p.Asp1135Gly	146.0	0.0		145.0	41.0	NM_139321	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	hg19	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	A	31	5.085824	0.94100	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.55588	0.51;0.51	5.85	5.85	0.93711	EGF-like, laminin (1);	0.229658	0.50627	D	0.000114	T	0.70448	0.3225	M	0.88775	2.98	0.80722	D	1	P;P	0.49090	0.919;0.801	P;B	0.51453	0.67;0.393	T	0.77056	-0.2729	10	0.66056	D	0.02	-13.6339	15.8975	0.79346	1.0:0.0:0.0:0.0	.	1135;1135	O75882;O75882-2	ATRN_HUMAN;.	G	1135;1135;1061	ENSP00000262919:D1135G;ENSP00000416587:D1135G	ENSP00000262919:D1135G	D	+	2	0	ATRN	3523207	1.000000	0.71417	0.974000	0.42286	0.999000	0.98932	9.197000	0.94985	2.237000	0.73441	0.528000	0.53228	GAC	.	.		0.597	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
BMP2	650	hgsc.bcm.edu	37	20	6759209	6759209	+	Missense_Mutation	SNP	G	G	A	rs140884062		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:6759209G>A	ENST00000378827.4	+	3	1883	c.664G>A	c.(664-666)Gcc>Acc	p.A222T		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	222					activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						ACAGGGACACGCCAACCATGG	0.517																																					p.A222T		Atlas-SNP	.											BMP2,caecum,carcinoma,0,1	BMP2	45	.	0			c.G664A						.	G	THR/ALA	0,4406		0,0,2203	54.0	48.0	50.0		664	-1.5	0.0	20	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	missense	BMP2	NM_001200.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	222/397	6759209	1,13005	2203	4300	6503	SO:0001583	missense	650	exon3			GGACACGCCAACC		CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.664G>A	chr20.hg19:g.6759209G>A	ENSP00000368104:p.Ala222Thr	133.0	1.0		116.0	5.0	NM_001200		Missense_Mutation	SNP	ENST00000378827.4	hg19	CCDS13099.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.727275	0.30593	0.0	1.16E-4	ENSG00000125845	ENST00000378827	T	0.62498	0.02	5.76	-1.45	0.08828	Transforming growth factor-beta, N-terminal (1);	0.842625	0.11159	N	0.593292	T	0.41903	0.1179	L	0.27053	0.805	0.20563	N	0.999887	B	0.06786	0.001	B	0.04013	0.001	T	0.21552	-1.0242	10	0.23891	T	0.37	.	6.7317	0.23387	0.4242:0.2291:0.3467:0.0	.	222	P12643	BMP2_HUMAN	T	222	ENSP00000368104:A222T	ENSP00000368104:A222T	A	+	1	0	BMP2	6707209	0.011000	0.17503	0.040000	0.18447	0.956000	0.61745	0.262000	0.18460	-0.086000	0.12550	-0.312000	0.09012	GCC	.	G|1.000;A|0.000		0.517	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3		
JAG1	182	hgsc.bcm.edu	37	20	10620156	10620156	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:10620156T>C	ENST00000254958.5	-	26	4162	c.3647A>G	c.(3646-3648)tAc>tGc	p.Y1216C	JAG1_ENST00000423891.2_Missense_Mutation_p.Y1057C	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1216					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CTATACGATGTACTCCATTCG	0.532									Alagille Syndrome																												p.Y1216C		Atlas-SNP	.											.	JAG1	213	.	0			c.A3647G						.						186.0	165.0	172.0					20																	10620156		2203	4300	6503	SO:0001583	missense	182	exon26	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	ACGATGTACTCCA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.3647A>G	chr20.hg19:g.10620156T>C	ENSP00000254958:p.Tyr1216Cys	128.0	0.0		120.0	46.0	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	hg19	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123379	0.56613	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.87491	-2.24;-2.26	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.89815	0.6824	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.91190	0.4983	10	0.87932	D	0	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	1216	P78504	JAG1_HUMAN	C	1216;1057	ENSP00000254958:Y1216C;ENSP00000389519:Y1057C	ENSP00000254958:Y1216C	Y	-	2	0	JAG1	10568156	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.630000	0.83225	2.326000	0.78906	0.533000	0.62120	TAC	.	.		0.532	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
FLRT3	23767	hgsc.bcm.edu	37	20	14307168	14307168	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:14307168C>T	ENST00000378053.3	-	2	1241	c.985G>A	c.(985-987)Gtg>Atg	p.V329M	FLRT3_ENST00000341420.4_Missense_Mutation_p.V329M|FLRT3_ENST00000462077.1_5'Flank|MACROD2_ENST00000217246.4_Intron|MACROD2_ENST00000310348.4_Intron	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	329	LRRCT.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		AGCCCACGCACGTTGACCTTC	0.463																																					p.V329M		Atlas-SNP	.											.	FLRT3	67	.	0			c.G985A						.						126.0	112.0	117.0					20																	14307168		2203	4300	6503	SO:0001583	missense	23767	exon2			CACGCACGTTGAC	AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"""Fibronectin type III domain containing"""	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.985G>A	chr20.hg19:g.14307168C>T	ENSP00000367292:p.Val329Met	221.0	0.0		210.0	77.0	NM_013281	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	hg19	CCDS13121.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698854	0.68501	.	.	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.61510	0.1;0.1	6.06	6.06	0.98353	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77075	0.4077	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.76364	-0.2986	10	0.62326	D	0.03	-9.9021	20.6397	0.99537	0.0:1.0:0.0:0.0	.	329	Q9NZU0	FLRT3_HUMAN	M	329	ENSP00000367292:V329M;ENSP00000339912:V329M	ENSP00000339912:V329M	V	-	1	0	FLRT3	14255168	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.818000	0.86416	2.880000	0.98712	0.650000	0.86243	GTG	.	.		0.463	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281	
DZANK1	55184	hgsc.bcm.edu	37	20	18365673	18365673	+	Missense_Mutation	SNP	C	C	T	rs143185709		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:18365673C>T	ENST00000358866.6	-	19	2102	c.2080G>A	c.(2080-2082)Gcc>Acc	p.A694T	DZANK1_ENST00000329494.5_Missense_Mutation_p.A672T|DZANK1_ENST00000357236.4_Missense_Mutation_p.A580T|DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000262547.5_Missense_Mutation_p.A694T			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	694							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						AGTAAAGTGGCGGTGCTCTCT	0.493																																					p.A694T		Atlas-SNP	.											DZANK1,caecum,carcinoma,0,4	DZANK1	65	.	0			c.G2080A						.						23.0	26.0	25.0					20																	18365673		1868	4077	5945	SO:0001583	missense	55184	exon20			AAGTGGCGGTGCT	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"""Ankyrin repeat domain containing"""	15858	protein-coding gene	gene with protein product	"""ankyrin repeat domain 64"""		"""chromosome 20 open reading frame 12"""	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.2080G>A	chr20.hg19:g.18365673C>T	ENSP00000351734:p.Ala694Thr	100.0	0.0		88.0	29.0	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	hg19	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.293171	0.23564	.	.	ENSG00000089091	ENST00000377630;ENST00000262547;ENST00000329494;ENST00000414623;ENST00000377637;ENST00000357236	T;T;T;T	0.70631	0.64;0.64;-0.5;0.64	5.17	1.09	0.20402	.	0.652897	0.14669	N	0.305449	T	0.50137	0.1598	L	0.35341	1.055	0.09310	N	1	B;B;B;B	0.33238	0.152;0.403;0.039;0.089	B;B;B;B	0.19148	0.011;0.024;0.011;0.007	T	0.21999	-1.0229	10	0.16420	T	0.52	-0.2673	9.2467	0.37529	0.0:0.6975:0.0:0.3025	.	713;580;694;479	B7Z631;Q9NVP4-4;Q9NVP4;A6NKD0	.;.;DZAN1_HUMAN;.	T	527;694;672;526;479;580	ENSP00000366857:A527T;ENSP00000262547:A694T;ENSP00000328866:A672T;ENSP00000349774:A580T	ENSP00000262547:A694T	A	-	1	0	C20orf12	18313673	0.027000	0.19231	0.001000	0.08648	0.902000	0.53008	0.112000	0.15479	-0.024000	0.13941	-0.150000	0.13652	GCC	.	.		0.493	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407	
C20orf78	100128496	hgsc.bcm.edu	37	20	18805926	18805926	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:18805926T>C	ENST00000278779.4	-	2	201	c.100A>G	c.(100-102)Aag>Gag	p.K34E		NM_001242671.1	NP_001229600.1	Q9BR46	CT078_HUMAN	chromosome 20 open reading frame 78	34										central_nervous_system(1)	1						AATGGGCTCTTGTGGGACCCC	0.478																																					p.K34E		Atlas-SNP	.											.	C20orf78	2	.	0			c.A100G						.																																			SO:0001583	missense	100128496	exon2			GGCTCTTGTGGGA	AL035563	CCDS56181.1	20p11.23	2011-10-07			ENSG00000149443	ENSG00000149443			16210	protein-coding gene	gene with protein product						11780052	Standard	NM_001242671		Approved	dJ1068E13.1	uc002wrj.2	Q9BR46	OTTHUMG00000031982	ENST00000278779.4:c.100A>G	chr20.hg19:g.18805926T>C	ENSP00000278779:p.Lys34Glu	94.0	0.0		79.0	26.0	NM_001242671		Missense_Mutation	SNP	ENST00000278779.4	hg19	CCDS56181.1	.	.	.	.	.	.	.	.	.	.	T	7.412	0.635021	0.14322	.	.	ENSG00000149443	ENST00000278779	.	.	.	2.57	1.45	0.22620	.	.	.	.	.	T	0.18800	0.0451	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.20638	-1.0269	6	0.87932	D	0	.	4.3447	0.11127	0.0:0.1645:0.0:0.8355	.	.	.	.	E	34	.	ENSP00000278779:K34E	K	-	1	0	C20orf78	18753926	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.144000	0.10280	0.412000	0.25729	0.496000	0.49642	AAG	.	.		0.478	C20orf78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078191.2	NM_178462	
PAX1	5075	hgsc.bcm.edu	37	20	21687178	21687178	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:21687178G>A	ENST00000398485.2	+	2	443	c.389G>A	c.(388-390)gGc>gAc	p.G130D	PAX1_ENST00000460221.1_Intron|PAX1_ENST00000444366.2_Missense_Mutation_p.G106D	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	130	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				bone morphogenesis (GO:0060349)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|parathyroid gland development (GO:0060017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sclerotome development (GO:0061056)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(21)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	38						GCGCAGCTGGGCATCCGACCC	0.662																																					p.G130D		Atlas-SNP	.											.	PAX1	152	.	0			c.G389A						.						38.0	40.0	39.0					20																	21687178		2203	4298	6501	SO:0001583	missense	5075	exon2			AGCTGGGCATCCG		CCDS13146.2, CCDS74709.1	20p11.22	2007-07-12	2007-07-12		ENSG00000125813	ENSG00000125813		"""Paired boxes"""	8615	protein-coding gene	gene with protein product		167411	"""paired box gene 1"""			1358810	Standard	NM_006192		Approved		uc002wsj.3	P15863	OTTHUMG00000032034	ENST00000398485.2:c.389G>A	chr20.hg19:g.21687178G>A	ENSP00000381499:p.Gly130Asp	72.0	0.0		86.0	27.0	NM_006192	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Missense_Mutation	SNP	ENST00000398485.2	hg19	CCDS13146.2	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579920	0.65992	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.99795	-6.78;-6.78	5.14	5.14	0.70334	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	H	0.94847	3.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.96619	0.9458	10	0.87932	D	0	.	18.2175	0.89890	0.0:0.0:1.0:0.0	.	106;36;130	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	D	130;106	ENSP00000381499:G130D;ENSP00000410355:G106D	ENSP00000381499:G130D	G	+	2	0	PAX1	21635178	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	9.654000	0.98509	2.382000	0.81193	0.655000	0.94253	GGC	.	.		0.662	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3		
NANP	140838	hgsc.bcm.edu	37	20	25604493	25604493	+	Splice_Site	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:25604493A>T	ENST00000304788.3	-	1	317		c.e1+1		RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA|RP4-694B14.5_ENST00000420803.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA	NM_152667.2	NP_689880.1	Q8TBE9	NANP_HUMAN	N-acetylneuraminic acid phosphatase						carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate biosynthetic process (GO:0046380)		N-acylneuraminate-9-phosphatase activity (GO:0050124)			endometrium(2)|lung(2)|prostate(1)	5						TGGGGACGTTACCTCCAACAT	0.697																																					.		Atlas-SNP	.											.	NANP	10	.	0			c.90+2T>A						.						32.0	33.0	33.0					20																	25604493		2200	4299	6499	SO:0001630	splice_region_variant	140838	exon2			GACGTTACCTCCA	AL031673	CCDS13173.1	20p11.1	2006-10-24	2006-01-24	2006-01-24	ENSG00000170191	ENSG00000170191			16140	protein-coding gene	gene with protein product		610763	"""chromosome 20 open reading frame 147"", ""haloacid dehalogenase-like hydrolase domain containing 4"""	C20orf147, HDHD4		16237198	Standard	NM_152667		Approved	dJ694B14.3, MGC26833	uc002wuy.3	Q8TBE9	OTTHUMG00000032132	ENST00000304788.3:c.90+1T>A	chr20.hg19:g.25604493A>T		155.0	0.0		143.0	47.0	NM_152667	B3KP12|Q5JYN8|Q8TE97|Q9Y3N0	Splice_Site	SNP	ENST00000304788.3	hg19	CCDS13173.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.001319	0.74818	.	.	ENSG00000170191	ENST00000304788	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6532	0.56774	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NANP	25552493	1.000000	0.71417	0.994000	0.49952	0.668000	0.39293	6.461000	0.73522	1.866000	0.54105	0.459000	0.35465	.	.	.		0.697	NANP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078457.2	NM_152667	Intron
BPIFB4	149954	hgsc.bcm.edu	37	20	31671633	31671633	+	Silent	SNP	C	C	T	rs578066819		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:31671633C>T	ENST00000375483.3	+	3	630	c.630C>T	c.(628-630)ggC>ggT	p.G210G		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	210	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										GTGTCCTGGGCGTGCTCGGCG	0.642													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17430	0.0		0.0	False		,,,				2504	0.0				p.G210G		Atlas-SNP	.											.	.	.	.	0			c.C630T						.						36.0	42.0	40.0					20																	31671633		2198	4293	6491	SO:0001819	synonymous_variant	149954	exon3			CCTGGGCGTGCTC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.630C>T	chr20.hg19:g.31671633C>T		88.0	0.0		87.0	28.0	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	hg19	CCDS13213.2																																																																																			.	.		0.642	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33588879	33588879	+	IGR	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:33588879G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Missense_Mutation_p.R1840H			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein						calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			CAGACGGTGCGCGAGCTCCAG	0.642																																					p.R1840H		Atlas-SNP	.											.	MYH7B	145	.	0			c.G5519A						.						35.0	46.0	42.0					20																	33588879		2201	4300	6501	SO:0001628	intergenic_variant	57644	exon41			CGGTGCGCGAGCT	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319		chr20.hg19:g.33588879G>A		201.0	0.0		243.0	100.0	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107039	0.77096	.	.	ENSG00000078814	ENST00000262873	T	0.80824	-1.42	4.55	4.55	0.56014	Myosin tail (1);	0.000000	0.34628	N	0.003817	T	0.74566	0.3733	L	0.37750	1.13	0.35897	D	0.830083	D	0.59767	0.986	P	0.49597	0.616	T	0.79899	-0.1608	10	0.66056	D	0.02	.	5.3998	0.16288	0.2473:0.0:0.7527:0.0	.	1798	A7E2Y1	MYH7B_HUMAN	H	1840	ENSP00000262873:R1840H	ENSP00000262873:R1840H	R	+	2	0	MYH7B	33052540	1.000000	0.71417	0.948000	0.38648	0.818000	0.46254	7.439000	0.80444	2.368000	0.80403	0.462000	0.41574	CGC	.	.		0.642	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
EDEM2	55741	hgsc.bcm.edu	37	20	33719574	33719574	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:33719574T>C	ENST00000374492.3	-	7	820	c.715A>G	c.(715-717)Att>Gtt	p.I239V	EDEM2_ENST00000374491.3_Missense_Mutation_p.I202V|EDEM2_ENST00000541621.1_Missense_Mutation_p.I18V|EDEM2_ENST00000542871.1_5'UTR|EDEM2_ENST00000540582.1_Missense_Mutation_p.I198V	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	239					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGCACATCAATGTGGTTGCCG	0.587																																					p.I239V	Esophageal Squamous(51;906 1021 24535 36410 39145)	Atlas-SNP	.											.	EDEM2	46	.	0			c.A715G						.						95.0	94.0	94.0					20																	33719574		2203	4300	6503	SO:0001583	missense	55741	exon7			CATCAATGTGGTT	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.715A>G	chr20.hg19:g.33719574T>C	ENSP00000363616:p.Ile239Val	111.0	0.0		102.0	32.0	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	hg19	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.477501	0.44044	.	.	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000541621;ENST00000540582	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	5.6	5.6	0.85130	.	0.043964	0.85682	D	0.000000	T	0.61949	0.2388	L	0.41415	1.275	0.58432	D	0.999994	B;B;B;B	0.27286	0.048;0.174;0.142;0.172	B;B;B;B	0.33392	0.086;0.163;0.125;0.143	T	0.60224	-0.7305	10	0.37606	T	0.19	-14.0668	8.2659	0.31813	0.0:0.1478:0.0:0.8522	.	198;18;202;239	F5GZ44;G3V1Q0;Q9BV94-2;Q9BV94	.;.;.;EDEM2_HUMAN	V	202;239;18;198	ENSP00000363615:I202V;ENSP00000363616:I239V;ENSP00000443528:I18V;ENSP00000441548:I198V	ENSP00000363615:I202V	I	-	1	0	EDEM2	33183235	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.131000	0.64751	2.122000	0.65172	0.528000	0.53228	ATT	.	.		0.587	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217	
CEP250	11190	hgsc.bcm.edu	37	20	34090970	34090970	+	Silent	SNP	C	C	T	rs562343473		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:34090970C>T	ENST00000397527.1	+	30	5493	c.4773C>T	c.(4771-4773)acC>acT	p.T1591T	CEP250_ENST00000342580.4_Silent_p.T1535T	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1591	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)			TGGCTTTGACCCACCTTACGC	0.562													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19629	0.0		0.0	False		,,,				2504	0.0				p.T1591T		Atlas-SNP	.											.	CEP250	141	.	0			c.C4773T						.						38.0	35.0	36.0					20																	34090970		2203	4300	6503	SO:0001819	synonymous_variant	11190	exon30			TTTGACCCACCTT	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.4773C>T	chr20.hg19:g.34090970C>T		124.0	0.0		128.0	51.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	hg19	CCDS13255.1																																																																																			.	.		0.562	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
RALGAPB	57148	hgsc.bcm.edu	37	20	37182643	37182643	+	Missense_Mutation	SNP	C	C	T	rs138852733		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:37182643C>T	ENST00000262879.6	+	22	3580	c.3296C>T	c.(3295-3297)cCg>cTg	p.P1099L	RALGAPB_ENST00000397040.1_Missense_Mutation_p.P1099L|RALGAPB_ENST00000397042.3_Missense_Mutation_p.P1095L|RALGAPB_ENST00000397038.1_Missense_Mutation_p.P877L			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1099					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TGCAAGCCCCCGCCTCCTGCC	0.453																																					p.P1099L		Atlas-SNP	.											.	RALGAPB	134	.	0			c.C3296T						.						92.0	93.0	93.0					20																	37182643		2203	4300	6503	SO:0001583	missense	57148	exon22			AGCCCCCGCCTCC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.3296C>T	chr20.hg19:g.37182643C>T	ENSP00000262879:p.Pro1099Leu	176.0	0.0		208.0	47.0	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	C	34	5.307384	0.95629	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000397038;ENST00000397040;ENST00000438490	D;D;D;D;D	0.92965	-3.14;-3.14;-3.14;-3.14;-3.14	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.94000	0.8078	L	0.33339	1.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.93539	0.6876	10	0.46703	T	0.11	.	20.0851	0.97797	0.0:1.0:0.0:0.0	.	1095;1099	A2A2E9;Q86X10	.;RLGPB_HUMAN	L	1099;1095;877;1099;927	ENSP00000262879:P1099L;ENSP00000380235:P1095L;ENSP00000380231:P877L;ENSP00000380233:P1099L;ENSP00000416646:P927L	ENSP00000262879:P1099L	P	+	2	0	RALGAPB	36616057	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.664000	0.61540	2.758000	0.94735	0.650000	0.86243	CCG	.	C|1.000;A|0.000		0.453	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
PPP1R16B	26051	hgsc.bcm.edu	37	20	37536807	37536807	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:37536807A>T	ENST00000299824.1	+	10	1354	c.1165A>T	c.(1165-1167)Acc>Tcc	p.T389S	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.T347S	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	389					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				CATCAGGGAGACCAGGACAGA	0.597																																					p.T389S		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.A1165T						.						100.0	91.0	94.0					20																	37536807		2203	4300	6503	SO:0001583	missense	26051	exon10			AGGGAGACCAGGA	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1165A>T	chr20.hg19:g.37536807A>T	ENSP00000299824:p.Thr389Ser	373.0	0.0		338.0	126.0	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	hg19	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.995|7.995	0.754180|0.754180	0.15778|0.15778	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000438192|ENST00000299824;ENST00000373331	.|T;T	.|0.71222	.|-0.31;-0.55	5.79|5.79	3.54|3.54	0.40534|0.40534	.|.	.|0.355587	.|0.33670	.|N	.|0.004672	T|T	0.42314|0.42314	0.1197|0.1197	N|N	0.08118|0.08118	0|0	0.28938|0.28938	N|N	0.891184|0.891184	.|P;B	.|0.37688	.|0.605;0.07	.|B;B	.|0.34093	.|0.175;0.044	T|T	0.38972|0.38972	-0.9636|-0.9636	5|10	.|0.10377	.|T	.|0.69	.|.	8.375|8.375	0.32438|0.32438	0.7984:0.1336:0.068:0.0|0.7984:0.1336:0.068:0.0	.|.	.|347;389	.|E9PFS8;Q96T49	.|.;PP16B_HUMAN	S|S	289|389;347	.|ENSP00000299824:T389S;ENSP00000362428:T347S	.|ENSP00000299824:T389S	R|T	+|+	3|1	2|0	PPP1R16B|PPP1R16B	36970221|36970221	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.734000|2.734000	0.47368|0.47368	1.021000|1.021000	0.39600|0.39600	0.524000|0.524000	0.50904|0.50904	AGA|ACC	.	.		0.597	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
SPINT3	10816	hgsc.bcm.edu	37	20	44141453	44141453	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:44141453G>A	ENST00000217428.6	-	2	123	c.108C>T	c.(106-108)tgC>tgT	p.C36C		NM_006652.1	NP_006643.1	P49223	SPIT3_HUMAN	serine peptidase inhibitor, Kunitz type, 3	36	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)	1						TAGGAAAAGCGCATACATTTG	0.463																																					p.C36C		Atlas-SNP	.											.	SPINT3	12	.	0			c.C108T						.						93.0	79.0	83.0					20																	44141453		692	1591	2283	SO:0001819	synonymous_variant	10816	exon2			AAAAGCGCATACA	X77166	CCDS46608.1	20q12-q13.2	2012-08-20	2005-08-17		ENSG00000101446	ENSG00000101446			11248	protein-coding gene	gene with protein product		613941	"""serine protease inhibitor, Kunitz type, 3"""			21988899	Standard	NM_006652		Approved	HKIB9	uc010ghg.1	P49223	OTTHUMG00000032585	ENST00000217428.6:c.108C>T	chr20.hg19:g.44141453G>A		84.0	0.0		58.0	19.0	NM_006652	A6NCQ6|Q6UDR8|Q96KK2	Silent	SNP	ENST00000217428.6	hg19	CCDS46608.1																																																																																			.	.		0.463	SPINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079464.5	NM_006652	
SNX21	90203	hgsc.bcm.edu	37	20	44469566	44469566	+	Missense_Mutation	SNP	C	C	T	rs563427177		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:44469566C>T	ENST00000491381.1	+	4	804	c.736C>T	c.(736-738)Cgg>Tgg	p.R246W	SNX21_ENST00000462307.1_3'UTR|SNX21_ENST00000344780.4_3'UTR|SNX21_ENST00000372542.1_Missense_Mutation_p.R237W|SNX21_ENST00000342644.5_Intron			Q969T3	SNX21_HUMAN	sorting nexin family member 21	246	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				GGAGCTGCGGCGGGCACAGAG	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		13806	0.001		0.0	False		,,,				2504	0.0				p.R246W		Atlas-SNP	.											.	SNX21	23	.	0			c.C736T						.						20.0	23.0	22.0					20																	44469566		2197	4267	6464	SO:0001583	missense	90203	exon4			CTGCGGCGGGCAC	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.736C>T	chr20.hg19:g.44469566C>T	ENSP00000418593:p.Arg246Trp	84.0	0.0		73.0	39.0	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	hg19	CCDS13377.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.874668	0.51695	.	.	ENSG00000124104	ENST00000491381;ENST00000372542	T;T	0.66638	-0.22;-0.22	4.32	3.36	0.38483	Phox homologous domain (2);Tetratricopeptide-like helical (1);	0.276731	0.36134	N	0.002777	T	0.50205	0.1602	L	0.39898	1.24	0.23524	N	0.997492	P;P	0.51537	0.946;0.946	B;B	0.37422	0.249;0.249	T	0.51576	-0.8688	10	0.72032	D	0.01	-9.0455	7.0255	0.24938	0.3236:0.4945:0.1818:0.0	.	237;246	Q5JZH3;Q969T3	.;SNX21_HUMAN	W	246;237	ENSP00000418593:R246W;ENSP00000361620:R237W	ENSP00000361620:R237W	R	+	1	2	SNX21	43902973	0.961000	0.32948	0.982000	0.44146	0.837000	0.47467	2.223000	0.42936	1.012000	0.39366	0.462000	0.41574	CGG	.	.		0.662	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421	
ZNF335	63925	hgsc.bcm.edu	37	20	44596429	44596429	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:44596429C>T	ENST00000322927.2	-	5	858	c.758G>A	c.(757-759)cGg>cAg	p.R253Q	ZNF335_ENST00000426788.1_Missense_Mutation_p.R98Q|ZNF335_ENST00000494955.1_5'UTR	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	253					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GGTGCTGCTCCGGTACTGGCA	0.637																																					p.R253Q		Atlas-SNP	.											ZNF335,colon,carcinoma,0,1	ZNF335	115	.	0			c.G758A						.						67.0	63.0	65.0					20																	44596429		2203	4300	6503	SO:0001583	missense	63925	exon5			CTGCTCCGGTACT	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.758G>A	chr20.hg19:g.44596429C>T	ENSP00000325326:p.Arg253Gln	56.0	0.0		57.0	28.0	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.856930	0.91433	.	.	ENSG00000198026	ENST00000322927;ENST00000426788	T;T	0.28666	1.6;1.6	4.78	4.78	0.61160	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.079918	0.52532	D	0.000063	T	0.22859	0.0552	N	0.19112	0.55	0.36281	D	0.855805	D;D	0.59357	0.981;0.985	P;P	0.48873	0.458;0.593	T	0.08722	-1.0708	10	0.37606	T	0.19	-27.6024	6.5587	0.22474	0.0:0.8062:0.0:0.1938	.	98;253	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	Q	253;98	ENSP00000325326:R253Q;ENSP00000397098:R98Q	ENSP00000325326:R253Q	R	-	2	0	ZNF335	44029836	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.475000	0.66787	2.469000	0.83416	0.561000	0.74099	CGG	.	.		0.637	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
CD40	958	hgsc.bcm.edu	37	20	44750964	44750964	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:44750964A>G	ENST00000372285.3	+	3	295	c.223A>G	c.(223-225)Aca>Gca	p.T75A	CD40_ENST00000489304.1_3'UTR|CD40_ENST00000372276.3_Missense_Mutation_p.T75A	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	75					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				GAACAGAGAGACACACTGCCA	0.532									Immune Deficiency with Hyper-IgM																												p.T75A		Atlas-SNP	.											.	CD40	33	.	0			c.A223G						.						93.0	81.0	85.0					20																	44750964		2203	4300	6503	SO:0001583	missense	958	exon3	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	AGAGAGACACACT	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11919	protein-coding gene	gene with protein product		109535	"""tumor necrosis factor receptor superfamily, member 5"""	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.223A>G	chr20.hg19:g.44750964A>G	ENSP00000361359:p.Thr75Ala	119.0	0.0		102.0	39.0	NM_152854	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Missense_Mutation	SNP	ENST00000372285.3	hg19	CCDS13393.1	.	.	.	.	.	.	.	.	.	.	a	4.782	0.145441	0.09134	.	.	ENSG00000101017	ENST00000372285;ENST00000372276	T;T	0.70399	-0.48;-0.48	4.55	0.636	0.17729	TNFR/CD27/30/40/95 cysteine-rich region (2);	1.368000	0.04645	N	0.405978	T	0.56775	0.2008	L	0.28400	0.85	0.09310	N	1	B;B;B;B	0.29378	0.005;0.243;0.017;0.029	B;B;B;B	0.27608	0.012;0.081;0.006;0.015	T	0.31888	-0.9927	10	0.09590	T	0.72	0.1609	9.9895	0.41863	0.4695:0.5305:0.0:0.0	.	58;75;75;75	Q09LL4;P25942-2;P25942;Q6P2H9	.;.;TNR5_HUMAN;.	A	75	ENSP00000361359:T75A;ENSP00000361350:T75A	ENSP00000361350:T75A	T	+	1	0	CD40	44184371	0.003000	0.15002	0.018000	0.16275	0.018000	0.09664	0.742000	0.26216	-0.011000	0.14247	0.378000	0.23410	ACA	.	.		0.532	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250	
SULF2	55959	hgsc.bcm.edu	37	20	46307534	46307534	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:46307534A>G	ENST00000359930.4	-	8	1930	c.1079T>C	c.(1078-1080)gTc>gCc	p.V360A	CTD-2653D5.1_ENST00000526566.2_RNA|SULF2_ENST00000361612.4_Missense_Mutation_p.V360A|SULF2_ENST00000484875.1_Missense_Mutation_p.V360A|SULF2_ENST00000467815.1_Missense_Mutation_p.V360A	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	360					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						AATGTTGAGGACGATGTGGGG	0.627																																					p.V360A		Atlas-SNP	.											.	SULF2	131	.	0			c.T1079C						.						92.0	84.0	87.0					20																	46307534		2203	4300	6503	SO:0001583	missense	55959	exon8			TTGAGGACGATGT	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1079T>C	chr20.hg19:g.46307534A>G	ENSP00000353007:p.Val360Ala	34.0	0.0		56.0	29.0	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	hg19	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	a	22.5	4.301289	0.81136	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815	D;D;D;D	0.97114	-4.25;-4.25;-4.25;-4.25	5.26	5.26	0.73747	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.96947	0.9003	M	0.64997	1.995	0.58432	D	0.999999	D;P	0.56521	0.976;0.915	P;P	0.51516	0.672;0.604	D	0.97168	0.9842	10	0.62326	D	0.03	-28.6635	15.1843	0.72986	1.0:0.0:0.0:0.0	.	360;360	Q8IWU5-2;Q8IWU5	.;SULF2_HUMAN	A	360	ENSP00000353007:V360A;ENSP00000418290:V360A;ENSP00000354662:V360A;ENSP00000418442:V360A	ENSP00000353007:V360A	V	-	2	0	SULF2	45740941	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.573000	0.82421	1.994000	0.58287	0.375000	0.23000	GTC	.	.		0.627	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
PTGIS	5740	hgsc.bcm.edu	37	20	48156217	48156217	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:48156217C>T	ENST00000244043.4	-	5	592	c.563G>A	c.(562-564)cGc>cAc	p.R188H	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	188					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	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 (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	TTCATGGGTGCGTGGCAGCGC	0.647																																					p.R188H		Atlas-SNP	.											PTGIS,NS,carcinoma,0,1	PTGIS	60	.	0			c.G563A						.						50.0	48.0	48.0					20																	48156217		2203	4300	6503	SO:0001583	missense	5740	exon5			TGGGTGCGTGGCA		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.563G>A	chr20.hg19:g.48156217C>T	ENSP00000244043:p.Arg188His	41.0	0.0		49.0	20.0	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Missense_Mutation	SNP	ENST00000244043.4	hg19	CCDS13419.1	.	.	.	.	.	.	.	.	.	.	C	8.624	0.892030	0.17613	.	.	ENSG00000124212	ENST00000244043	T	0.68624	-0.34	5.15	-0.819	0.10829	.	0.930319	0.08935	N	0.872410	T	0.47563	0.1452	N	0.25890	0.77	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.29088	-1.0023	10	0.35671	T	0.21	-26.1822	4.6513	0.12596	0.0:0.3708:0.2821:0.3471	.	188	Q16647	PTGIS_HUMAN	H	188	ENSP00000244043:R188H	ENSP00000244043:R188H	R	-	2	0	PTGIS	47589624	0.807000	0.29009	0.929000	0.37066	0.814000	0.46013	1.043000	0.30316	-0.075000	0.12798	0.561000	0.74099	CGC	.	.		0.647	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
KCNG1	3755	hgsc.bcm.edu	37	20	49626762	49626762	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:49626762C>T	ENST00000371571.4	-	2	399	c.114G>A	c.(112-114)gcG>gcA	p.A38A	KCNG1_ENST00000506387.1_5'Flank|KCNG1_ENST00000396017.3_Silent_p.A38A|RP5-955M13.4_ENST00000424566.1_RNA	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	38					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GGCGGTAGAACGCGCCCTTGA	0.697																																					p.A38A		Atlas-SNP	.											.	KCNG1	86	.	0			c.G114A						.						19.0	22.0	21.0					20																	49626762		2192	4269	6461	SO:0001819	synonymous_variant	3755	exon2			GTAGAACGCGCCC	AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.114G>A	chr20.hg19:g.49626762C>T		40.0	0.0		30.0	9.0	NM_002237	A8K3S4|O43528|Q5JXL5|Q9BRC1	Silent	SNP	ENST00000371571.4	hg19	CCDS13436.1																																																																																			.	.		0.697	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237	
SALL4	57167	hgsc.bcm.edu	37	20	50408386	50408386	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:50408386C>T	ENST00000217086.4	-	2	747	c.636G>A	c.(634-636)ccG>ccA	p.P212P	SALL4_ENST00000395997.3_Silent_p.P212P|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	212					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CGAGGACCCACGGGATGCTGT	0.627																																					p.P212P		Atlas-SNP	.											.	SALL4	168	.	0			c.G636A						.						68.0	69.0	69.0					20																	50408386		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			GACCCACGGGATG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.636G>A	chr20.hg19:g.50408386C>T		42.0	0.0		51.0	29.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.627	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
ZNF217	7764	hgsc.bcm.edu	37	20	52192757	52192757	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:52192757G>A	ENST00000371471.2	-	4	2971	c.2546C>T	c.(2545-2547)cCt>cTt	p.P849L	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.P849L			O75362	ZN217_HUMAN	zinc finger protein 217	849					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			ATCCGGTGCAGGGGAAACACT	0.517																																					p.P849L		Atlas-SNP	.											.	ZNF217	227	.	0			c.C2546T						.						95.0	98.0	97.0					20																	52192757		2203	4300	6503	SO:0001583	missense	7764	exon3			GGTGCAGGGGAAA	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2546C>T	chr20.hg19:g.52192757G>A	ENSP00000360526:p.Pro849Leu	87.0	0.0		65.0	33.0	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.376112	0.24857	.	.	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.10477	2.87;2.87	5.1	2.08	0.27032	.	0.651039	0.14769	N	0.299494	T	0.08846	0.0219	L	0.43152	1.355	0.09310	N	1	P	0.38922	0.651	B	0.33392	0.163	T	0.18209	-1.0344	10	0.66056	D	0.02	-11.4983	7.9334	0.29916	0.1478:0.1327:0.7196:0.0	.	849	O75362	ZN217_HUMAN	L	849;849;9	ENSP00000360526:P849L;ENSP00000304308:P849L	ENSP00000304308:P849L	P	-	2	0	ZNF217	51626164	0.175000	0.23083	0.001000	0.08648	0.003000	0.03518	1.649000	0.37281	0.181000	0.19994	-0.172000	0.13284	CCT	.	.		0.517	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
ZNF217	7764	hgsc.bcm.edu	37	20	52198883	52198883	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:52198883G>A	ENST00000371471.2	-	2	908	c.483C>T	c.(481-483)tgC>tgT	p.C161C	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Silent_p.C161C			O75362	ZN217_HUMAN	zinc finger protein 217	161					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			ATCTTCTTCCGCACATGTTAC	0.448																																					p.C161C		Atlas-SNP	.											ZNF217_ENST00000371471,colon,carcinoma,0,2	ZNF217	227	.	0			c.C483T						.						155.0	154.0	154.0					20																	52198883		2203	4300	6503	SO:0001819	synonymous_variant	7764	exon1			TCTTCCGCACATG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.483C>T	chr20.hg19:g.52198883G>A		94.0	0.0		79.0	34.0	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	hg19	CCDS13443.1																																																																																			.	.		0.448	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
CSTF1	1477	hgsc.bcm.edu	37	20	54978541	54978541	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:54978541C>T	ENST00000217109.4	+	6	1406	c.1054C>T	c.(1054-1056)Cgc>Tgc	p.R352C	CSTF1_ENST00000493039.1_3'UTR	NM_001033521.1|NM_001324.2	NP_001028693.1|NP_001315.1	Q05048	CSTF1_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa	352					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R352C(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	15			Colorectal(105;0.202)			TTTAAGTGGACGCCAGGTGCA	0.527																																					p.R352C		Atlas-SNP	.											CSTF1,NS,carcinoma,0,1	CSTF1	29	.	1	Substitution - Missense(1)	prostate(1)	c.C1054T						.						90.0	81.0	84.0					20																	54978541		2203	4300	6503	SO:0001583	missense	1477	exon6			AGTGGACGCCAGG		CCDS13452.1	20q13.31	2013-01-10	2002-08-29		ENSG00000101138	ENSG00000101138		"""WD repeat domain containing"""	2483	protein-coding gene	gene with protein product		600369	"""cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kD"""			1358884, 11257228	Standard	NM_001033521		Approved		uc002xxl.1	Q05048	OTTHUMG00000032791	ENST00000217109.4:c.1054C>T	chr20.hg19:g.54978541C>T	ENSP00000217109:p.Arg352Cys	103.0	0.0		102.0	42.0	NM_001033522	Q5QPD8	Missense_Mutation	SNP	ENST00000217109.4	hg19	CCDS13452.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.830246	0.50845	.	.	ENSG00000101138	ENST00000217109;ENST00000425890	T	0.59364	0.27	5.45	4.49	0.54785	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.39172	0.1068	N	0.22421	0.69	0.80722	D	1	P	0.50710	0.938	B	0.34346	0.18	T	0.46386	-0.9195	10	0.72032	D	0.01	-20.0546	13.5181	0.61551	0.284:0.716:0.0:0.0	.	352	Q05048	CSTF1_HUMAN	C	352;339	ENSP00000217109:R352C	ENSP00000217109:R352C	R	+	1	0	CSTF1	54411948	0.997000	0.39634	0.988000	0.46212	0.815000	0.46073	3.566000	0.53805	1.397000	0.46682	0.650000	0.86243	CGC	.	.		0.527	CSTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079794.2	NM_001033521	
STX16	8675	hgsc.bcm.edu	37	20	57242608	57242608	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:57242608T>C	ENST00000371141.4	+	3	931	c.207T>C	c.(205-207)ggT>ggC	p.G69G	STX16_ENST00000361770.5_Silent_p.G52G|STX16_ENST00000496003.1_3'UTR|STX16-NPEPL1_ENST00000530122.1_Silent_p.G69G|STX16_ENST00000361830.3_Silent_p.G69G|STX16_ENST00000358029.4_Silent_p.G65G|STX16_ENST00000359617.4_Silent_p.G16G|STX16_ENST00000355957.5_Silent_p.G52G|STX16_ENST00000371132.4_Silent_p.G48G	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	69					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			CAGCGATTGGTGTGACAAAAC	0.413																																					p.G69G		Atlas-SNP	.											.	STX16	36	.	0			c.T207C						.						147.0	137.0	140.0					20																	57242608		2203	4300	6503	SO:0001819	synonymous_variant	8675	exon3			GATTGGTGTGACA	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.207T>C	chr20.hg19:g.57242608T>C		121.0	0.0		146.0	70.0	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	hg19	CCDS13468.1																																																																																			.	.		0.413	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
LAMA5	3911	hgsc.bcm.edu	37	20	60887270	60887270	+	Missense_Mutation	SNP	T	T	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:60887270T>G	ENST00000252999.3	-	69	9529	c.9463A>C	c.(9463-9465)Agc>Cgc	p.S3155R	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3155	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TCCTGGGCGCTGTGGAAGCCG	0.682																																					p.S3155R		Atlas-SNP	.											.	LAMA5	268	.	0			c.A9463C						.						32.0	35.0	34.0					20																	60887270		2194	4291	6485	SO:0001583	missense	3911	exon69			GGGCGCTGTGGAA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.9463A>C	chr20.hg19:g.60887270T>G	ENSP00000252999:p.Ser3155Arg	231.0	0.0		175.0	72.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	15.31	2.795012	0.50208	.	.	ENSG00000130702	ENST00000252999	T	0.78003	-1.14	4.06	1.58	0.23477	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.210351	0.48286	D	0.000185	T	0.74261	0.3693	L	0.54323	1.7	0.80722	D	1	P	0.48998	0.918	P	0.49387	0.609	T	0.72786	-0.4188	10	0.87932	D	0	.	5.5549	0.17111	0.1524:0.0935:0.0:0.754	.	3155	O15230	LAMA5_HUMAN	R	3155	ENSP00000252999:S3155R	ENSP00000252999:S3155R	S	-	1	0	LAMA5	60320665	0.003000	0.15002	0.997000	0.53966	0.071000	0.16799	0.746000	0.26275	0.735000	0.32537	0.454000	0.30748	AGC	.	.		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
DIDO1	11083	hgsc.bcm.edu	37	20	61527589	61527589	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:61527589T>A	ENST00000266070.4	-	8	2535	c.2210A>T	c.(2209-2211)aAt>aTt	p.N737I	DIDO1_ENST00000395335.2_Missense_Mutation_p.N737I|DIDO1_ENST00000395340.1_Missense_Mutation_p.N737I|DIDO1_ENST00000395343.1_Missense_Mutation_p.N737I	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	737	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ACACACCTGATTTTTAGGGTC	0.423																																					p.N737I	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A2210T						.						184.0	167.0	173.0					20																	61527589		2203	4300	6503	SO:0001583	missense	11083	exon8			ACCTGATTTTTAG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.2210A>T	chr20.hg19:g.61527589T>A	ENSP00000266070:p.Asn737Ile	117.0	0.0		128.0	47.0	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.000211	0.93227	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.7	5.7	0.88788	Transcription elongation factor S-IIM (1);Transcription elongation factor S-II, central domain (4);	0.000000	0.46145	D	0.000315	D	0.86435	0.5932	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90029	0.4133	10	0.87932	D	0	-38.3716	15.9774	0.80079	0.0:0.0:0.0:1.0	.	737;737	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	I	737	ENSP00000266070:N737I;ENSP00000378752:N737I;ENSP00000378749:N737I;ENSP00000378744:N737I	ENSP00000266070:N737I	N	-	2	0	DIDO1	60998034	1.000000	0.71417	0.910000	0.35882	0.955000	0.61496	7.927000	0.87577	2.179000	0.69175	0.533000	0.62120	AAT	.	.		0.423	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
SLC17A9	63910	hgsc.bcm.edu	37	20	61588143	61588143	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:61588143C>T	ENST00000370351.4	+	2	217	c.86C>T	c.(85-87)aCg>aTg	p.T29M	SLC17A9_ENST00000488738.1_3'UTR|SLC17A9_ENST00000370349.3_Missense_Mutation_p.T23M	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	29					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						TGGACGGGGACGCTGCTGCTG	0.652																																					p.T29M		Atlas-SNP	.											.	SLC17A9	54	.	0			c.C86T						.						23.0	27.0	26.0					20																	61588143		2097	4216	6313	SO:0001583	missense	63910	exon2			CGGGGACGCTGCT	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.86C>T	chr20.hg19:g.61588143C>T	ENSP00000359376:p.Thr29Met	65.0	0.0		54.0	21.0	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	hg19	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	C	1.930	-0.446286	0.04604	.	.	ENSG00000101194	ENST00000370351;ENST00000370349;ENST00000411611	T;T;T	0.58797	0.31;0.31;0.31	4.91	0.72	0.18214	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.674794	0.15589	N	0.254520	T	0.39545	0.1082	L	0.32530	0.975	0.09310	N	1	B;B;B	0.20459	0.045;0.016;0.027	B;B;B	0.23018	0.012;0.019;0.043	T	0.25152	-1.0140	10	0.09843	T	0.71	.	8.7004	0.34323	0.0:0.517:0.0:0.483	.	49;29;23	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	M	29;23;49	ENSP00000359376:T29M;ENSP00000359374:T23M;ENSP00000388215:T49M	ENSP00000359374:T23M	T	+	2	0	SLC17A9	61058588	0.926000	0.31397	0.000000	0.03702	0.009000	0.06853	1.599000	0.36751	0.269000	0.21961	-0.140000	0.14226	ACG	.	.		0.652	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
YTHDF1	54915	hgsc.bcm.edu	37	20	61834090	61834090	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:61834090T>C	ENST00000370339.3	-	4	1543	c.1202A>G	c.(1201-1203)gAc>gGc	p.D401G	YTHDF1_ENST00000370333.4_Missense_Mutation_p.D351G|YTHDF1_ENST00000370334.4_Intron	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	401	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.						N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						GCGGTGGATGTCGTCCTCAGA	0.542																																					p.D401G		Atlas-SNP	.											.	YTHDF1	66	.	0			c.A1202G						.						99.0	87.0	91.0					20																	61834090		2203	4300	6503	SO:0001583	missense	54915	exon4			TGGATGTCGTCCT	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"""YTH domain family 1"""	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.1202A>G	chr20.hg19:g.61834090T>C	ENSP00000359364:p.Asp401Gly	91.0	0.0		106.0	39.0	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	hg19	CCDS13511.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.221784	0.58560	.	.	ENSG00000149658	ENST00000370339;ENST00000370333	T;T	0.34859	1.34;1.34	4.72	4.72	0.59763	YTH domain (2);	0.000000	0.85682	D	0.000000	T	0.71409	0.3336	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81901	-0.0720	10	0.87932	D	0	-42.5169	14.5032	0.67737	0.0:0.0:0.0:1.0	.	401	Q9BYJ9	YTHD1_HUMAN	G	401;351	ENSP00000359364:D401G;ENSP00000359358:D351G	ENSP00000359358:D351G	D	-	2	0	YTHDF1	61304535	1.000000	0.71417	0.216000	0.23742	0.492000	0.33523	7.875000	0.87205	1.896000	0.54893	0.482000	0.46254	GAC	.	.		0.542	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798	
HELZ2	85441	hgsc.bcm.edu	37	20	62198473	62198473	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:62198473C>T	ENST00000467148.1	-	6	2307	c.2238G>A	c.(2236-2238)acG>acA	p.T746T	HELZ2_ENST00000427522.2_Silent_p.T177T	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	746	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CAATGGCGTCCGTGCAGCGGT	0.662																																					p.T746T		Atlas-SNP	.											.	.	.	.	0			c.G2238A						.						63.0	61.0	62.0					20																	62198473		2202	4299	6501	SO:0001819	synonymous_variant	85441	exon7			GGCGTCCGTGCAG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.2238G>A	chr20.hg19:g.62198473C>T		79.0	0.0		51.0	4.0	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	.		0.662	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
URB1	9875	hgsc.bcm.edu	37	21	33687279	33687279	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:33687279C>T	ENST00000382751.3	-	39	6881	c.6766G>A	c.(6766-6768)Gcc>Acc	p.A2256T		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	2256						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						ACCACGATGGCCTCCTCTTCA	0.642																																					p.A2256T		Atlas-SNP	.											.	URB1	176	.	0			c.G6766A						.						36.0	39.0	38.0					21																	33687279		692	1591	2283	SO:0001583	missense	9875	exon39			CGATGGCCTCCTC	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.6766G>A	chr21.hg19:g.33687279C>T	ENSP00000372199:p.Ala2256Thr	175.0	0.0		155.0	63.0	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	hg19	CCDS46645.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457031	0.43634	.	.	ENSG00000142207	ENST00000382751	T	0.32753	1.44	5.97	2.92	0.33932	.	0.350128	0.32401	N	0.006147	T	0.26304	0.0642	L	0.43923	1.385	0.19775	N	0.999953	B	0.21071	0.051	B	0.20577	0.03	T	0.15925	-1.0420	10	0.33141	T	0.24	-18.5357	13.3884	0.60809	0.0:0.534:0.466:0.0	.	2256	O60287	NPA1P_HUMAN	T	2256	ENSP00000372199:A2256T	ENSP00000372199:A2256T	A	-	1	0	URB1	32609150	0.033000	0.19621	0.191000	0.23289	0.184000	0.23303	0.250000	0.18235	0.802000	0.34089	0.591000	0.81541	GCC	.	.		0.642	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
TCP10L	140290	hgsc.bcm.edu	37	21	33951121	33951121	+	Silent	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:33951121T>A	ENST00000300258.3	-	4	494	c.381A>T	c.(379-381)ggA>ggT	p.G127G	LINC00846_ENST00000334165.4_lincRNA|TCP10L_ENST00000472557.1_Silent_p.G41G	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	127					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						GTGAAATTTTTCCAAAAGCAG	0.368																																					p.G127G		Atlas-SNP	.											.	TCP10L	24	.	0			c.A381T						.						118.0	111.0	113.0					21																	33951121		2203	4300	6503	SO:0001819	synonymous_variant	140290	exon4			AATTTTTCCAAAA	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"""t-complex 10 (a murine tcp homolog)-like"", ""t-complex 10 (mouse)-like"""			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.381A>T	chr21.hg19:g.33951121T>A		242.0	0.0		223.0	80.0	NM_144659	Q53EW0|Q96LN5	Silent	SNP	ENST00000300258.3	hg19	CCDS13616.1																																																																																			.	.		0.368	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659	
DOPEY2	9980	hgsc.bcm.edu	37	21	37600040	37600040	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:37600040G>A	ENST00000399151.3	+	13	1615	c.1530G>A	c.(1528-1530)gtG>gtA	p.V510V		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	510					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCTGCCTGGTGCAGCCTCTTG	0.502																																					p.V510V		Atlas-SNP	.											.	DOPEY2	184	.	0			c.G1530A						.						75.0	65.0	69.0					21																	37600040		2203	4300	6503	SO:0001819	synonymous_variant	9980	exon13			CCTGGTGCAGCCT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.1530G>A	chr21.hg19:g.37600040G>A		81.0	0.0		49.0	19.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	hg19	CCDS13643.1																																																																																			.	.		0.502	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
DOPEY2	9980	hgsc.bcm.edu	37	21	37603120	37603120	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:37603120A>G	ENST00000399151.3	+	14	2123	c.2038A>G	c.(2038-2040)Aac>Gac	p.N680D		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	680					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CAGCAGGAAGAACTCTTGGGA	0.547																																					p.N680D		Atlas-SNP	.											.	DOPEY2	184	.	0			c.A2038G						.						83.0	75.0	78.0					21																	37603120		2203	4300	6503	SO:0001583	missense	9980	exon14			AGGAAGAACTCTT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.2038A>G	chr21.hg19:g.37603120A>G	ENSP00000382104:p.Asn680Asp	131.0	0.0		138.0	66.0	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.596630	0.28445	.	.	ENSG00000142197	ENST00000399151	T	0.11385	2.78	5.43	1.68	0.24146	.	0.648666	0.16682	N	0.203888	T	0.07279	0.0184	L	0.36672	1.1	0.20764	N	0.99985	B;B	0.23249	0.082;0.049	B;B	0.20767	0.031;0.014	T	0.40608	-0.9554	10	0.19590	T	0.45	.	5.4609	0.16615	0.6557:0.1353:0.209:0.0	.	680;680	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	D	680	ENSP00000382104:N680D	ENSP00000382104:N680D	N	+	1	0	DOPEY2	36524990	0.000000	0.05858	0.799000	0.32177	0.547000	0.35210	0.316000	0.19469	0.106000	0.17784	0.402000	0.26972	AAC	.	.		0.547	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
COL18A1	80781	hgsc.bcm.edu	37	21	46910776	46910776	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:46910776G>A	ENST00000359759.4	+	20	3324	c.3303G>A	c.(3301-3303)cgG>cgA	p.R1101R	COL18A1_ENST00000355480.5_Silent_p.R866R|COL18A1_ENST00000400337.2_Silent_p.R686R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1101	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GAGGCAGCCGGGGAGAAAAGG	0.647																																					p.R866R		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2598A						.						13.0	15.0	14.0					21																	46910776		1448	3162	4610	SO:0001819	synonymous_variant	80781	exon20			CAGCCGGGGAGAA		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3303G>A	chr21.hg19:g.46910776G>A		142.0	0.0		169.0	83.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	hg19																																																																																				.	.		0.647	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
COL6A1	1291	hgsc.bcm.edu	37	21	47422161	47422161	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47422161G>A	ENST00000361866.3	+	32	2210	c.2096G>A	c.(2095-2097)gGc>gAc	p.G699D	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	699	C-terminal globular domain.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		TGGATGGCGGGCGGCACCTTC	0.697																																					p.G699D		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2096A						.						11.0	11.0	11.0					21																	47422161		2162	4263	6425	SO:0001583	missense	1291	exon32			TGGCGGGCGGCAC	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2096G>A	chr21.hg19:g.47422161G>A	ENSP00000355180:p.Gly699Asp	90.0	0.0		97.0	21.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	hg19	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.022783	0.54683	.	.	ENSG00000142156	ENST00000361866	D	0.86366	-2.11	4.63	4.63	0.57726	von Willebrand factor, type A (3);	0.069270	0.64402	D	0.000018	D	0.94463	0.8218	M	0.91038	3.17	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	D	0.94825	0.7990	10	0.42905	T	0.14	-22.672	17.4727	0.87650	0.0:0.0:1.0:0.0	.	699	P12109	CO6A1_HUMAN	D	699	ENSP00000355180:G699D	ENSP00000355180:G699D	G	+	2	0	COL6A1	46246589	1.000000	0.71417	0.197000	0.23402	0.183000	0.23260	6.641000	0.74324	2.134000	0.65973	0.462000	0.41574	GGC	.	.		0.697	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
COL6A2	1292	hgsc.bcm.edu	37	21	47551948	47551948	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47551948A>G	ENST00000300527.4	+	28	2646	c.2542A>G	c.(2542-2544)Aac>Gac	p.N848D		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	848	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GGGTGAGCAGAACTTCCACAA	0.701																																					p.N848D		Atlas-SNP	.											.	COL6A2	351	.	0			c.A2542G						.						18.0	19.0	18.0					21																	47551948		2192	4292	6484	SO:0001583	missense	1292	exon28			GAGCAGAACTTCC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2542A>G	chr21.hg19:g.47551948A>G	ENSP00000300527:p.Asn848Asp	107.0	0.0		112.0	54.0	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.924200	0.52653	.	.	ENSG00000142173	ENST00000300527	T	0.78924	-1.22	4.18	4.18	0.49190	von Willebrand factor, type A (3);	0.051650	0.64402	D	0.000001	T	0.80281	0.4594	M	0.75447	2.3	0.80722	D	1	P	0.43701	0.815	P	0.45998	0.5	T	0.81647	-0.0838	10	0.48119	T	0.1	-35.6117	13.2466	0.60026	1.0:0.0:0.0:0.0	.	848	P12110	CO6A2_HUMAN	D	848	ENSP00000300527:N848D	ENSP00000300527:N848D	N	+	1	0	COL6A2	46376376	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	6.023000	0.70848	1.541000	0.49316	0.260000	0.18958	AAC	.	.		0.701	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
PCNT	5116	hgsc.bcm.edu	37	21	47848330	47848330	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47848330C>T	ENST00000359568.5	+	35	7623	c.7516C>T	c.(7516-7518)Ctg>Ttg	p.L2506L	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2506					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GGAAAAGTCCCTGGAGCATCT	0.657																																					p.L2506L		Atlas-SNP	.											.	PCNT	283	.	0			c.C7516T						.						42.0	32.0	36.0					21																	47848330		2202	4298	6500	SO:0001819	synonymous_variant	5116	exon35			AAGTCCCTGGAGC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7516C>T	chr21.hg19:g.47848330C>T		127.0	0.0		114.0	48.0	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	hg19	CCDS33592.1																																																																																			.	.		0.657	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
PCNT	5116	hgsc.bcm.edu	37	21	47848382	47848382	+	Missense_Mutation	SNP	C	C	A	rs368569999		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47848382C>A	ENST00000359568.5	+	35	7675	c.7568C>A	c.(7567-7569)gCg>gAg	p.A2523E	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2523					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GAGATCCAGGCGCTGCGTGCC	0.662																																					p.A2523E		Atlas-SNP	.											.	PCNT	283	.	0			c.C7568A						.						34.0	27.0	30.0					21																	47848382		2201	4299	6500	SO:0001583	missense	5116	exon35			TCCAGGCGCTGCG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7568C>A	chr21.hg19:g.47848382C>A	ENSP00000352572:p.Ala2523Glu	107.0	0.0		91.0	43.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.291281	0.59976	.	.	ENSG00000160299	ENST00000359568	T	0.01548	4.78	4.39	4.39	0.52855	.	0.000000	0.32190	N	0.006460	T	0.04182	0.0116	L	0.49350	1.555	0.31121	N	0.708795	D;D	0.61697	0.99;0.974	P;P	0.61397	0.888;0.875	T	0.02553	-1.1142	10	0.02654	T	1	.	10.9292	0.47207	0.2909:0.7091:0.0:0.0	.	2405;2523	O95613-2;O95613	.;PCNT_HUMAN	E	2523	ENSP00000352572:A2523E	ENSP00000352572:A2523E	A	+	2	0	PCNT	46672810	0.986000	0.35501	0.995000	0.50966	0.648000	0.38561	2.616000	0.46376	2.375000	0.81037	0.563000	0.77884	GCG	.	.		0.662	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
IL17RA	23765	hgsc.bcm.edu	37	22	17588634	17588634	+	Missense_Mutation	SNP	T	T	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:17588634T>A	ENST00000319363.6	+	12	1196	c.1063T>A	c.(1063-1065)Tac>Aac	p.Y355N		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	355					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		AAGTGAAAAATACAGTGATGA	0.468																																					p.Y355N		Atlas-SNP	.											.	IL17RA	62	.	0			c.T1063A						.						125.0	123.0	123.0					22																	17588634		2203	4300	6503	SO:0001583	missense	23765	exon12			GAAAAATACAGTG	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1063T>A	chr22.hg19:g.17588634T>A	ENSP00000320936:p.Tyr355Asn	110.0	0.0		86.0	32.0	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	hg19	CCDS13739.1	.	.	.	.	.	.	.	.	.	.	T	4.881	0.163755	0.09287	.	.	ENSG00000177663	ENST00000319363	T	0.05513	3.43	3.83	-4.53	0.03462	.	2.187910	0.01505	N	0.017658	T	0.06962	0.0177	L	0.44542	1.39	0.09310	N	1	B	0.18610	0.029	B	0.16722	0.016	T	0.35748	-0.9776	10	0.29301	T	0.29	0.8733	8.9589	0.35834	0.0:0.6318:0.1535:0.2147	.	355	Q96F46	I17RA_HUMAN	N	355	ENSP00000320936:Y355N	ENSP00000320936:Y355N	Y	+	1	0	IL17RA	15968634	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.687000	0.05156	-1.083000	0.03097	-1.563000	0.00883	TAC	.	.		0.468	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339	
SLC25A1	6576	hgsc.bcm.edu	37	22	19165655	19165655	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:19165655G>A	ENST00000215882.5	-	2	349	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W	SLC25A1_ENST00000451283.1_5'UTR|SLC25A1_ENST00000461267.1_5'UTR|CLTCL1_ENST00000442042.2_5'Flank	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	65					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|citrate transport (GO:0015746)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	citrate transmembrane transporter activity (GO:0015137)			cervix(1)|lung(1)	2	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)		CCGATGCCCCGGTACCGCGGC	0.756																																					p.R72W		Atlas-SNP	.											.	SLC25A1	14	.	0			c.C214T						.						5.0	7.0	6.0					22																	19165655		2037	4032	6069	SO:0001583	missense	6576	exon1			TGCCCCGGTACCG	U25147	CCDS13758.1, CCDS74817.1	22q11	2013-05-22			ENSG00000100075	ENSG00000100075		"""Solute carriers"""	10979	protein-coding gene	gene with protein product		190315	"""solute carrier family 20 (mitochondrial citrate transporter), member 3"""	SLC20A3		8666394, 9254007	Standard	NM_001256534		Approved	CTP	uc002zoz.4	P53007	OTTHUMG00000150123	ENST00000215882.5:c.193C>T	chr22.hg19:g.19165655G>A	ENSP00000215882:p.Arg65Trp	132.0	0.0		117.0	8.0	NM_001256534	A8K8E8|Q9BSK6	Missense_Mutation	SNP	ENST00000215882.5	hg19	CCDS13758.1	.	.	.	.	.	.	.	.	.	.	G	32	5.116777	0.94385	.	.	ENSG00000100075	ENST00000215882	T	0.79940	-1.32	4.77	2.46	0.29980	Mitochondrial carrier domain (2);	0.113003	0.56097	D	0.000031	D	0.89424	0.6711	M	0.92691	3.335	0.80722	D	1	D	0.71674	0.998	P	0.58970	0.849	D	0.91248	0.5027	10	0.87932	D	0	-2.5554	12.2745	0.54726	0.0:0.0:0.5691:0.4309	.	65	P53007	TXTP_HUMAN	W	65	ENSP00000215882:R65W	ENSP00000215882:R65W	R	-	1	2	SLC25A1	17545655	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.510000	0.53393	0.947000	0.37659	0.549000	0.68633	CGG	.	.		0.756	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984	
C22orf29	79680	hgsc.bcm.edu	37	22	19839777	19839777	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:19839777C>T	ENST00000405640.1	-	2	676	c.8G>A	c.(7-9)cGt>cAt	p.R3H	C22orf29_ENST00000484072.1_Intron|GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.R3H|C22orf29_ENST00000407472.1_Missense_Mutation_p.R3H|GNB1L_ENST00000403325.1_Intron|GNB1L_ENST00000460402.1_Intron			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	3					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)					GCACCGGCCACGAGGCATGCT	0.632																																					p.R3H		Atlas-SNP	.											.	C22orf29	23	.	0			c.G8A						.						46.0	48.0	48.0					22																	19839777		2191	4268	6459	SO:0001583	missense	79680	exon3			CGGCCACGAGGCA	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.8G>A	chr22.hg19:g.19839777C>T	ENSP00000384924:p.Arg3His	155.0	0.0		144.0	52.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849042	0.32699	.	.	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640;ENST00000416337	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	3.69	-3.65	0.04502	.	.	.	.	.	T	0.14313	0.0346	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.26916	-1.0089	9	0.62326	D	0.03	0.0166	8.8206	0.35023	0.0:0.3949:0.0:0.6051	.	3	Q7L3V2	CV029_HUMAN	H	3	ENSP00000386111:R3H;ENSP00000330596:R3H;ENSP00000384924:R3H;ENSP00000392994:R3H	ENSP00000330596:R3H	R	-	2	0	C22orf29	18219777	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.581000	0.02119	-0.624000	0.05611	-0.768000	0.03414	CGT	.	.		0.632	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627	
RTN4R	65078	hgsc.bcm.edu	37	22	20229291	20229291	+	Silent	SNP	G	G	A	rs374126911		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:20229291G>A	ENST00000043402.7	-	2	1803	c.1365C>T	c.(1363-1365)tgC>tgT	p.C455C	RTN4R_ENST00000469601.1_5'Flank	NM_023004.5	NP_075380.1	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor	455					axonogenesis (GO:0007409)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			lung(1)|ovary(1)|prostate(1)	3	Colorectal(54;0.0993)					GGGTGAGGCTGCAGGTGAGGC	0.692																																					p.C455C		Atlas-SNP	.											.	RTN4R	14	.	0			c.C1365T						.	G		0,4196		0,0,2098	10.0	7.0	8.0		1365	0.8	0.9	22		8	1,8319		0,1,4159	no	coding-synonymous	RTN4R	NM_023004.5		0,1,6257	AA,AG,GG		0.012,0.0,0.0080		455/474	20229291	1,12515	2098	4160	6258	SO:0001819	synonymous_variant	65078	exon2			GAGGCTGCAGGTG	AF283463	CCDS13777.1	22q11	2008-05-02			ENSG00000040608	ENSG00000040608			18601	protein-coding gene	gene with protein product		605566				11201742	Standard	NM_023004		Approved	NOGOR	uc002zrv.3	Q9BZR6	OTTHUMG00000150572	ENST00000043402.7:c.1365C>T	chr22.hg19:g.20229291G>A		136.0	0.0		139.0	57.0	NM_023004	D3DX28	Silent	SNP	ENST00000043402.7	hg19	CCDS13777.1	.	.	.	.	.	.	.	.	.	.	G	2.979	-0.210662	0.06140	0.0	1.2E-4	ENSG00000040608	ENST00000416372;ENST00000425986	.	.	.	3.02	0.841	0.18918	.	.	.	.	.	T	0.51363	0.1670	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37454	-0.9705	4	.	.	.	.	5.1608	0.15060	0.2921:0.0:0.7079:0.0	.	.	.	.	V	475;541	.	.	A	-	2	0	RTN4R	18609291	0.004000	0.15560	0.933000	0.37362	0.453000	0.32348	0.597000	0.24059	0.146000	0.19002	0.305000	0.20034	GCA	.	.		0.692	RTN4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318950.2		
RIMBP3	85376	hgsc.bcm.edu	37	22	20458139	20458139	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:20458139G>A	ENST00000426804.1	-	1	3647	c.3163C>T	c.(3163-3165)Cgg>Tgg	p.R1055W	SCARNA18_ENST00000516215.1_RNA|SCARNA17_ENST00000516762.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1055	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			ACCTCCACCCGCGCCCGGTAG	0.637																																					p.R1055W		Atlas-SNP	.											.	RIMBP3	42	.	0			c.C3163T						.						71.0	92.0	85.0					22																	20458139		2131	4250	6381	SO:0001583	missense	85376	exon1			CCACCCGCGCCCG	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3163C>T	chr22.hg19:g.20458139G>A	ENSP00000391564:p.Arg1055Trp	1061.0	0.0		1049.0	170.0	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	hg19	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	G	4.244	0.044204	0.08196	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.59638	0.25	3.56	-3.28	0.05033	Fibronectin, type III (2);	0.376219	0.25657	N	0.029179	T	0.43612	0.1255	M	0.68952	2.095	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.38714	-0.9648	10	0.87932	D	0	-1.125	1.0843	0.01649	0.4062:0.1452:0.2911:0.1575	.	961	Q9UFD9	RIM3A_HUMAN	W	961;1055	ENSP00000391564:R1055W	ENSP00000347318:R961W	R	-	1	2	RIMBP3	18838139	0.005000	0.15991	0.001000	0.08648	0.030000	0.12068	1.052000	0.30429	-0.673000	0.05259	-0.552000	0.04208	CGG	.	.		0.637	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
GNAZ	2781	hgsc.bcm.edu	37	22	23438309	23438309	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:23438309C>T	ENST00000248996.4	+	2	1093	c.427C>T	c.(427-429)Cgc>Tgc	p.R143C	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	143					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		CTGCTTCAGCCGCTCCAGCGA	0.657																																					p.R143C		Atlas-SNP	.											.	GNAZ	45	.	0			c.C427T						.						61.0	52.0	55.0					22																	23438309		2203	4300	6503	SO:0001583	missense	2781	exon2			TTCAGCCGCTCCA		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.427C>T	chr22.hg19:g.23438309C>T	ENSP00000248996:p.Arg143Cys	74.0	0.0		42.0	8.0	NM_002073	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	hg19	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.850237	0.91277	.	.	ENSG00000128266	ENST00000248996;ENST00000456059	D	0.90504	-2.68	4.85	4.85	0.62838	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.93229	0.7843	H	0.94886	3.595	0.80722	D	1	D	0.65815	0.995	B	0.41299	0.353	D	0.95381	0.8473	10	0.87932	D	0	.	17.3371	0.87285	0.0:1.0:0.0:0.0	.	143	P19086	GNAZ_HUMAN	C	143;91	ENSP00000248996:R143C	ENSP00000248996:R143C	R	+	1	0	GNAZ	21768309	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.613000	0.61176	2.428000	0.82296	0.655000	0.94253	CGC	.	.		0.657	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073	
SLC2A11	66035	hgsc.bcm.edu	37	22	24219966	24219966	+	Missense_Mutation	SNP	G	G	A	rs144951215		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:24219966G>A	ENST00000345044.6	+	6	863	c.595G>A	c.(595-597)Ggg>Agg	p.G199R	SLC2A11_ENST00000316185.8_Missense_Mutation_p.G202R|SLC2A11_ENST00000398356.2_Missense_Mutation_p.G206R|AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000467660.1_3'UTR|RN7SL268P_ENST00000491172.2_RNA			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	199					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						CCTGGTGCCCGGGGCGCTCCA	0.677																																					p.G206R		Atlas-SNP	.											.	SLC2A11	32	.	0			c.G616A						.	G	ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	20.0	18.0	18.0		595,604,616	1.4	0.0	22	dbSNP_134	18	1,8599		0,1,4299	no	missense,missense,missense	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	125,125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	199/497,202/500,206/504	24219966	1,13005	2203	4300	6503	SO:0001583	missense	66035	exon7			GTGCCCGGGGCGC	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.595G>A	chr22.hg19:g.24219966G>A	ENSP00000342542:p.Gly199Arg	126.0	0.0		106.0	38.0	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	hg19	CCDS46673.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018991	0.35606	0.0	1.16E-4	ENSG00000133460	ENST00000345044;ENST00000398356;ENST00000398359;ENST00000407566;ENST00000316185	T;T;T	0.73897	-0.79;-0.79;-0.79	3.52	1.39	0.22231	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.256061	0.37530	N	0.002046	T	0.81550	0.4846	M	0.76328	2.33	0.09310	N	1	D;D;D;D;D	0.76494	0.999;0.999;0.997;0.999;0.999	P;D;D;D;D	0.71656	0.905;0.956;0.947;0.974;0.974	T	0.69591	-0.5104	10	0.87932	D	0	.	7.0897	0.25277	0.2391:0.0:0.7609:0.0	.	206;202;199;206;206	E7ENI4;Q9BYW1-3;Q9BYW1;E9PH55;Q6P4C1	.;.;GTR11_HUMAN;.;.	R	199;206;206;206;202	ENSP00000342542:G199R;ENSP00000381399:G206R;ENSP00000326748:G202R	ENSP00000326748:G202R	G	+	1	0	SLC2A11	22549966	0.888000	0.30383	0.039000	0.18376	0.126000	0.20510	4.498000	0.60373	0.785000	0.33685	0.603000	0.83216	GGG	.	G|1.000;A|0.000		0.677	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
GGT5	2687	hgsc.bcm.edu	37	22	24628858	24628858	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:24628858C>T	ENST00000327365.4	-	4	945	c.529G>A	c.(529-531)Gcc>Acc	p.A177T	GGT5_ENST00000263112.7_Missense_Mutation_p.A145T|GGT5_ENST00000398292.3_Missense_Mutation_p.A177T|GGT5_ENST00000418439.2_Missense_Mutation_p.G101D	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	177					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						AGGACAGGGGCCACCACATGC	0.701																																					p.A177T		Atlas-SNP	.											.	GGT5	61	.	0			c.G529A						.						34.0	37.0	36.0					22																	24628858		2193	4293	6486	SO:0001583	missense	2687	exon4			CAGGGGCCACCAC	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.529G>A	chr22.hg19:g.24628858C>T	ENSP00000330080:p.Ala177Thr	256.0	0.0		220.0	72.0	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	hg19	CCDS13825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.53|12.53	1.964787|1.964787	0.34659|0.34659	.|.	.|.	ENSG00000099998|ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292|ENST00000418439	T;T;T|T	0.20598|0.21031	2.06;2.06;2.06|2.03	3.64|3.64	0.217|0.217	0.15264|0.15264	.|.	0.280853|.	0.35151|.	N|.	0.003404|.	T|T	0.05686|0.05686	0.0149|0.0149	N|N	0.02876|0.02876	-0.465|-0.465	0.09310|0.09310	N|N	1|1	B;B;B;B|B	0.15141|0.29909	0.01;0.012;0.0;0.012|0.261	B;B;B;B|B	0.28305|0.20955	0.053;0.088;0.007;0.088|0.032	T|T	0.36187|0.36187	-0.9758|-0.9758	10|9	0.20519|0.08837	T|T	0.43|0.75	-38.1671|-38.1671	3.7817|3.7817	0.08683|0.08683	0.3159:0.1896:0.4946:0.0|0.3159:0.1896:0.4946:0.0	.|.	145;177;177;177|101	P36269-2;Q53XM9;Q6GMP0;P36269|E7EUG3	.;.;.;GGT5_HUMAN|.	T|D	177;145;92;177|101	ENSP00000330080:A177T;ENSP00000263112:A145T;ENSP00000381340:A177T|ENSP00000392146:G101D	ENSP00000263112:A145T|ENSP00000392146:G101D	A|G	-|-	1|2	0|0	GGT5|GGT5	22958858|22958858	0.990000|0.990000	0.36364|0.36364	0.237000|0.237000	0.24090|0.24090	0.036000|0.036000	0.12997|0.12997	2.004000|2.004000	0.40854|0.40854	0.173000|0.173000	0.19788|0.19788	-1.426000|-1.426000	0.01102|0.01102	GCC|GGC	.	.		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
ADRBK2	157	hgsc.bcm.edu	37	22	26100174	26100174	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:26100174C>T	ENST00000324198.6	+	15	1518	c.1326C>T	c.(1324-1326)ggC>ggT	p.G442G		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	442	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	GTCACGGAGGCGGGTAGGCCA	0.463																																					p.G442G		Atlas-SNP	.											.	ADRBK2	78	.	0			c.C1326T						.						66.0	65.0	65.0					22																	26100174		2203	4300	6503	SO:0001819	synonymous_variant	157	exon15			CGGAGGCGGGTAG	X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"""Pleckstrin homology (PH) domain containing"""	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.1326C>T	chr22.hg19:g.26100174C>T		166.0	0.0		134.0	58.0	NM_005160	Q9UGW9	Silent	SNP	ENST00000324198.6	hg19	CCDS13832.1																																																																																			.	.		0.463	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160	
MYO18B	84700	hgsc.bcm.edu	37	22	26306993	26306993	+	Silent	SNP	C	C	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:26306993C>A	ENST00000407587.2	+	33	5512	c.5343C>A	c.(5341-5343)ggC>ggA	p.G1781G	MYO18B_ENST00000536101.1_Silent_p.G1780G|MYO18B_ENST00000335473.7_Silent_p.G1780G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1780	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ATTTGGAAGGCTTGATCGGAA	0.498																																					p.G1780G		Atlas-SNP	.											.	MYO18B	322	.	0			c.C5340A						.						70.0	71.0	71.0					22																	26306993		1972	4153	6125	SO:0001819	synonymous_variant	84700	exon33			GGAAGGCTTGATC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5343C>A	chr22.hg19:g.26306993C>A		104.0	0.0		100.0	29.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.		0.498	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
RASL10A	10633	hgsc.bcm.edu	37	22	29706652	29706652	+	IGR	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:29706652C>T	ENST00000216101.6	-	0	1490				GAS2L1_ENST00000360113.2_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000341313.6_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000407647.2_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000406549.3_Nonsense_Mutation_p.R256*|RASL10A_ENST00000608559.1_5'Flank|GAS2L1_ENST00000407854.1_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000471961.1_Nonsense_Mutation_p.R256*|GAS2L1_ENST00000403764.1_Nonsense_Mutation_p.R256*	NM_006477.4	NP_006468.1	Q92737	RSLAA_HUMAN	RAS-like, family 10, member A						small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)	1						CGTGATGGTGCGAGTGGGTGG	0.711																																					p.R256X		Atlas-SNP	.											.	GAS2L1	54	.	0			c.C766T						.						54.0	54.0	54.0					22																	29706652		2202	4295	6497	SO:0001628	intergenic_variant	10634	exon4			ATGGTGCGAGTGG	Y07847	CCDS13854.1	22q12.2	2014-05-09			ENSG00000100276	ENSG00000100276			16954	protein-coding gene	gene with protein product		602220				8975699, 15731001	Standard	NM_006477		Approved	RRP22	uc031rxl.1	Q92737	OTTHUMG00000151106		chr22.hg19:g.29706652C>T		63.0	0.0		47.0	24.0	NM_152237	Q49AU5|Q6PI03	Nonsense_Mutation	SNP	ENST00000216101.6	hg19	CCDS13854.1	.	.	.	.	.	.	.	.	.	.	c	36	5.853070	0.97030	.	.	ENSG00000185340	ENST00000407647;ENST00000333679;ENST00000406549;ENST00000360113;ENST00000341313;ENST00000403764;ENST00000471961;ENST00000407854	.	.	.	4.17	1.78	0.24846	.	0.180905	0.35179	N	0.003395	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.949	10.6805	0.45811	0.1541:0.7123:0.1336:0.0	.	.	.	.	X	256	.	ENSP00000332834:R256X	R	+	1	2	GAS2L1	28036652	1.000000	0.71417	0.958000	0.39756	0.946000	0.59487	4.363000	0.59473	0.902000	0.36520	0.306000	0.20318	CGA	.	.		0.711	RASL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321342.1		
SEC14L6	730005	hgsc.bcm.edu	37	22	30928661	30928661	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:30928661C>T	ENST00000402034.2	-	5	273	c.274G>A	c.(274-276)Gac>Aac	p.D92N		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	92	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						CCCTCACCGTCGTGGCCGCAT	0.612																																					p.D92N		Atlas-SNP	.											.	SEC14L6	6	.	0			c.G274A						.																																			SO:0001583	missense	730005	exon5			CACCGTCGTGGCC		CCDS54518.1	22q12.2	2011-05-06			ENSG00000214491	ENSG00000214491			40047	protein-coding gene	gene with protein product							Standard	NM_001193336		Approved		uc021wnu.1	B5MCN3	OTTHUMG00000151267	ENST00000402034.2:c.274G>A	chr22.hg19:g.30928661C>T	ENSP00000385695:p.Asp92Asn	112.0	0.0		111.0	42.0	NM_001193336		Missense_Mutation	SNP	ENST00000402034.2	hg19	CCDS54518.1	.	.	.	.	.	.	.	.	.	.	.	17.76	3.467630	0.63625	.	.	ENSG00000214491	ENST00000402034	D	0.88741	-2.42	3.37	-0.184	0.13280	.	.	.	.	.	D	0.92417	0.7593	M	0.87971	2.92	0.80722	D	1	.	.	.	.	.	.	D	0.90603	0.4546	7	0.87932	D	0	-0.1395	8.7245	0.34460	0.0:0.7266:0.0:0.2734	.	.	.	.	N	92	ENSP00000385695:D92N	ENSP00000385695:D92N	D	-	1	0	SEC14L6	29258661	0.999000	0.42202	0.000000	0.03702	0.001000	0.01503	4.250000	0.58772	-0.069000	0.12931	-0.450000	0.05554	GAC	.	.		0.612	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
SLC35E4	339665	hgsc.bcm.edu	37	22	31042723	31042723	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:31042723G>A	ENST00000343605.4	+	2	1557	c.758G>A	c.(757-759)cGc>cAc	p.R253H	SLC35E4_ENST00000406566.1_Intron|SLC35E4_ENST00000300385.8_Intron	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	253	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						GGCGACTCTCGCCTCTGGGCC	0.667																																					p.R253H		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G758A						.						49.0	36.0	40.0					22																	31042723		2203	4300	6503	SO:0001583	missense	339665	exon2			ACTCTCGCCTCTG		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"""Solute carriers"""	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.758G>A	chr22.hg19:g.31042723G>A	ENSP00000339626:p.Arg253His	61.0	0.0		59.0	29.0	NM_001001479	Q567P0	Missense_Mutation	SNP	ENST00000343605.4	hg19	CCDS13882.1	.	.	.	.	.	.	.	.	.	.	G	9.981	1.228147	0.22542	.	.	ENSG00000100036	ENST00000343605	T	0.65549	-0.16	5.02	-1.51	0.08664	Domain of unknown function DUF250 (1);	0.304838	0.34291	N	0.004098	T	0.45498	0.1345	L	0.41961	1.31	0.41875	D	0.990296	B	0.11235	0.004	B	0.10450	0.005	T	0.27434	-1.0074	10	0.12430	T	0.62	-16.2139	10.0811	0.42391	0.4756:0.0:0.5244:0.0	.	253	Q6ICL7	S35E4_HUMAN	H	253	ENSP00000339626:R253H	ENSP00000339626:R253H	R	+	2	0	SLC35E4	29372723	0.018000	0.18449	0.901000	0.35422	0.751000	0.42716	0.282000	0.18829	-0.010000	0.14271	-0.258000	0.10820	CGC	.	.		0.667	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973	
DUSP18	150290	hgsc.bcm.edu	37	22	31059555	31059555	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:31059555C>T	ENST00000334679.3	-	2	941	c.436G>A	c.(436-438)Ggc>Agc	p.G146S	DUSP18_ENST00000461301.1_Intron|DUSP18_ENST00000404885.1_Missense_Mutation_p.G146S|DUSP18_ENST00000403268.1_Missense_Mutation_p.R109Q|DUSP18_ENST00000407308.1_Missense_Mutation_p.G146S	NM_152511.3	NP_689724.3	Q8NEJ0	DUS18_HUMAN	dual specificity phosphatase 18	146	Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(1)|lung(1)|prostate(1)|skin(1)	4						TCCCAAAAGCCGCTGTTGGGT	0.557																																					p.G146S		Atlas-SNP	.											DUSP18,NS,carcinoma,0,1	DUSP18	10	.	0			c.G436A						.						109.0	96.0	101.0					22																	31059555		2203	4300	6503	SO:0001583	missense	150290	exon2			AAAAGCCGCTGTT	AF461689	CCDS13883.1	22q12.1	2011-06-09				ENSG00000167065		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18484	protein-coding gene	gene with protein product		611446				12408986	Standard	NM_152511		Approved	DUSP20	uc003aiw.1	Q8NEJ0		ENST00000334679.3:c.436G>A	chr22.hg19:g.31059555C>T	ENSP00000333917:p.Gly146Ser	102.0	1.0		108.0	41.0	NM_152511	B3KPA4	Missense_Mutation	SNP	ENST00000334679.3	hg19	CCDS13883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.422402|5.422402	0.96111|0.96111	.|.	.|.	ENSG00000167065|ENSG00000167065	ENST00000404885;ENST00000407308;ENST00000334679;ENST00000342474|ENST00000403268	D;D;D;D|.	0.85484|.	-1.99;-1.99;-1.99;-1.99|.	5.27|5.27	5.27|5.27	0.74061|0.74061	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.81197|0.81197	0.4772|0.4772	M|M	0.85197|0.85197	2.74|2.74	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.65773|.	0.938|.	T|T	0.79196|0.79196	-0.1903|-0.1903	10|6	0.40728|0.24483	T|T	0.16|0.36	.|.	18.5145|18.5145	0.90931|0.90931	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	146|.	Q8NEJ0|.	DUS18_HUMAN|.	S|Q	146|109	ENSP00000385463:G146S;ENSP00000386063:G146S;ENSP00000333917:G146S;ENSP00000340795:G146S|.	ENSP00000333917:G146S|ENSP00000384946:R109Q	G|R	-|-	1|2	0|0	DUSP18|DUSP18	29389555|29389555	1.000000|1.000000	0.71417|0.71417	0.944000|0.944000	0.38274|0.38274	0.897000|0.897000	0.52465|0.52465	4.890000|4.890000	0.63178|0.63178	2.471000|2.471000	0.83476|0.83476	0.655000|0.655000	0.94253|0.94253	GGC|CGG	.	.		0.557	DUSP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321400.1		
SMTN	6525	hgsc.bcm.edu	37	22	31484696	31484696	+	Silent	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:31484696T>C	ENST00000347557.2	+	5	524	c.306T>C	c.(304-306)gcT>gcC	p.A102A	SMTN_ENST00000333137.7_Silent_p.A102A|SMTN_ENST00000475548.1_3'UTR|SMTN_ENST00000358743.1_Silent_p.A102A	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	102					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						TGCGAAGCGCTGGTGAGTATG	0.657																																					p.A158A		Atlas-SNP	.											.	SMTN	219	.	0			c.T474C						.						63.0	54.0	57.0					22																	31484696		2201	4300	6501	SO:0001819	synonymous_variant	6525	exon4			AAGCGCTGGTGAG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.306T>C	chr22.hg19:g.31484696T>C		172.0	0.0		154.0	13.0	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Silent	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	T	4.327	0.060099	0.08339	.	.	ENSG00000183963	ENST00000438223	.	.	.	4.79	-9.57	0.00562	.	.	.	.	.	T	0.71013	0.3290	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.79713	-0.1688	4	.	.	.	-13.5919	20.9408	0.99941	0.0:0.8283:0.0782:0.0935	.	.	.	.	R	157	.	.	W	+	1	0	SMTN	29814696	0.001000	0.12720	0.000000	0.03702	0.395000	0.30598	-1.951000	0.01529	-3.031000	0.00266	-0.904000	0.02843	TGG	.	.		0.657	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
RFPL2	10739	hgsc.bcm.edu	37	22	32586994	32586994	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:32586994C>T	ENST00000400237.1	-	5	1837	c.902G>A	c.(901-903)cGc>cAc	p.R301H	RFPL2_ENST00000489846.1_5'UTR|RFPL2_ENST00000400236.3_Missense_Mutation_p.R211H|RFPL2_ENST00000248980.4_Missense_Mutation_p.R240H|RFPL2_ENST00000248983.4_Missense_Mutation_p.R211H			O75678	RFPL2_HUMAN	ret finger protein-like 2	301	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						CTGTAACTTGCGGTCTACGAA	0.512																																					p.R301H		Atlas-SNP	.											.	RFPL2	81	.	0			c.G902A						.						41.0	61.0	54.0					22																	32586994		2202	4294	6496	SO:0001583	missense	10739	exon5			AACTTGCGGTCTA	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"""RING-type (C3HC4) zinc fingers"""	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.902G>A	chr22.hg19:g.32586994C>T	ENSP00000383096:p.Arg301His	234.0	0.0		218.0	108.0	NM_001098527		Missense_Mutation	SNP	ENST00000400237.1	hg19	CCDS43009.2	.	.	.	.	.	.	.	.	.	.	C	5.006	0.186849	0.09547	.	.	ENSG00000128253	ENST00000248980;ENST00000248983;ENST00000400236;ENST00000400237	T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35	0.351	-0.702	0.11265	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.50701	0.1631	L	0.33710	1.025	0.09310	N	1	B;B	0.15473	0.013;0.0	B;B	0.18561	0.022;0.005	T	0.37056	-0.9722	9	0.54805	T	0.06	.	5.6019	0.17359	0.0:0.6559:0.344:0.0	.	301;240	O75678;O75678-3	RFPL2_HUMAN;.	H	240;211;211;301	ENSP00000248980:R240H;ENSP00000248983:R211H;ENSP00000383095:R211H;ENSP00000383096:R301H	ENSP00000248980:R240H	R	-	2	0	RFPL2	30916994	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-3.805000	0.00362	-0.711000	0.04995	-0.714000	0.03626	CGC	.	.		0.512	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605	
GGA1	26088	hgsc.bcm.edu	37	22	38016853	38016853	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:38016853A>G	ENST00000343632.4	+	6	847	c.461A>G	c.(460-462)gAc>gGc	p.D154G	GGA1_ENST00000406772.1_Missense_Mutation_p.D81G|GGA1_ENST00000381756.5_Missense_Mutation_p.D171G|GGA1_ENST00000325180.8_Missense_Mutation_p.D154G|GGA1_ENST00000337437.4_Missense_Mutation_p.D121G	NM_001172687.1|NM_013365.4	NP_001166158.1|NP_037497.1	Q9UJY5	GGA1_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 1	154	Interaction with ARF3.				intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	10	Melanoma(58;0.0574)					CTTCCAGATGACACTACCTTT	0.522																																					p.D154G		Atlas-SNP	.											.	GGA1	39	.	0			c.A461G						.						159.0	129.0	139.0					22																	38016853		2203	4300	6503	SO:0001583	missense	26088	exon6			CAGATGACACTAC	AF190862	CCDS13951.1, CCDS33643.1, CCDS54526.1	22q13.31	2010-02-12	2010-02-12		ENSG00000100083	ENSG00000100083			17842	protein-coding gene	gene with protein product		606004				10747088, 10747089, 16407204	Standard	NM_013365		Approved		uc003atc.3	Q9UJY5	OTTHUMG00000030985	ENST00000343632.4:c.461A>G	chr22.hg19:g.38016853A>G	ENSP00000341344:p.Asp154Gly	118.0	0.0		110.0	37.0	NM_001001560	A8K3D3|B0QYR7|Q5TG07|Q86YA9|Q8NCS6|Q9BW94|Q9UG00|Q9UGW0|Q9UGW1	Missense_Mutation	SNP	ENST00000343632.4	hg19	CCDS13951.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891503	0.52014	.	.	ENSG00000100083	ENST00000343632;ENST00000381756;ENST00000429218;ENST00000325180;ENST00000337437;ENST00000449944;ENST00000406772;ENST00000413251;ENST00000423024	T;T;T;T;T;T	0.38887	2.17;1.89;2.24;1.11;1.28;1.15	5.56	4.52	0.55395	.	0.092463	0.64402	D	0.000001	T	0.38081	0.1027	L	0.54323	1.7	0.80722	D	1	B;B;B	0.29835	0.258;0.034;0.013	B;B;B	0.31245	0.126;0.015;0.022	T	0.25398	-1.0133	10	0.37606	T	0.19	-21.3779	10.8912	0.46996	0.9266:0.0:0.0734:0.0	.	171;154;154	Q6IC75;Q86YA9;Q9UJY5	.;.;GGA1_HUMAN	G	154;171;81;154;121;146;81;81;81	ENSP00000341344:D154G;ENSP00000371175:D171G;ENSP00000321288:D154G;ENSP00000338647:D121G;ENSP00000390416:D146G;ENSP00000385287:D81G	ENSP00000321288:D154G	D	+	2	0	GGA1	36346799	1.000000	0.71417	0.617000	0.29091	0.955000	0.61496	5.285000	0.65633	2.102000	0.63906	0.460000	0.39030	GAC	.	.		0.522	GGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075873.3	NM_013365	
MICALL1	85377	hgsc.bcm.edu	37	22	38315101	38315101	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:38315101G>A	ENST00000215957.6	+	5	611	c.485G>A	c.(484-486)aGc>aAc	p.S162N		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	162	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					ACCCCCAGCAGCACGTGCGCA	0.672																																					p.S162N		Atlas-SNP	.											.	MICALL1	53	.	0			c.G485A						.						13.0	11.0	12.0					22																	38315101		2152	4176	6328	SO:0001583	missense	85377	exon5			CCAGCAGCACGTG	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.485G>A	chr22.hg19:g.38315101G>A	ENSP00000215957:p.Ser162Asn	96.0	0.0		101.0	47.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	hg19	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111079	0.77210	.	.	ENSG00000100139	ENST00000445494;ENST00000215957	T;T	0.74209	-0.82;0.37	4.99	4.99	0.66335	Zinc finger, LIM-type (2);	0.000000	0.64402	D	0.000003	D	0.87924	0.6300	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	D	0.89597	0.3832	10	0.62326	D	0.03	.	18.4596	0.90734	0.0:0.0:1.0:0.0	.	162	Q8N3F8	MILK1_HUMAN	N	78;162	ENSP00000404543:S78N;ENSP00000215957:S162N	ENSP00000215957:S162N	S	+	2	0	MICALL1	36645047	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	7.544000	0.82117	2.570000	0.86706	0.563000	0.77884	AGC	.	.		0.672	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
PICK1	9463	hgsc.bcm.edu	37	22	38470413	38470413	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:38470413C>T	ENST00000404072.3	+	12	1281	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C	PICK1_ENST00000356976.3_Missense_Mutation_p.R312C|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	312	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					CTCCCAGATGCGCAAGGATGT	0.652																																					p.R312C		Atlas-SNP	.											.	PICK1	30	.	0			c.C934T						.						35.0	37.0	36.0					22																	38470413		2203	4300	6503	SO:0001583	missense	9463	exon12			CAGATGCGCAAGG	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"""protein kinase C, alpha binding protein"", ""protein interacting with PRKCA"""	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.934C>T	chr22.hg19:g.38470413C>T	ENSP00000385205:p.Arg312Cys	200.0	0.0		191.0	42.0	NM_012407	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	hg19	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.124859	0.77436	.	.	ENSG00000100151	ENST00000404072;ENST00000356976	D;D	0.81821	-1.54;-1.54	4.57	3.48	0.39840	Arfaptin-like (3);	0.047265	0.85682	D	0.000000	D	0.89273	0.6668	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90458	0.4444	10	0.87932	D	0	-16.8451	11.8046	0.52147	0.3177:0.6823:0.0:0.0	.	312	Q9NRD5	PICK1_HUMAN	C	312	ENSP00000385205:R312C;ENSP00000349465:R312C	ENSP00000349465:R312C	R	+	1	0	PICK1	36800359	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.645000	0.54389	2.251000	0.74343	0.563000	0.77884	CGC	.	.		0.652	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407	
CBX6	23466	hgsc.bcm.edu	37	22	39262901	39262901	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39262901G>A	ENST00000407418.3	-	5	675	c.552C>T	c.(550-552)ggC>ggT	p.G184G	CBX6_ENST00000216083.6_Silent_p.G166G			O95503	CBX6_HUMAN	chromobox homolog 6	184					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(58;0.04)					cgccgccAGCGCCCTTGTCGA	0.677																																					p.G184G		Atlas-SNP	.											.	CBX6	26	.	0			c.C552T						.						10.0	11.0	11.0					22																	39262901		2189	4252	6441	SO:0001819	synonymous_variant	23466	exon5			GCCAGCGCCCTTG		CCDS13980.1	22q13.1	2013-04-23			ENSG00000183741	ENSG00000183741			1556	protein-coding gene	gene with protein product							Standard	NM_014292		Approved		uc003awl.3	O95503	OTTHUMG00000150456	ENST00000407418.3:c.552C>T	chr22.hg19:g.39262901G>A		86.0	0.0		73.0	17.0	NM_014292	A8KAH0|Q96EM5	Silent	SNP	ENST00000407418.3	hg19	CCDS13980.1																																																																																			.	.		0.677	CBX6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318190.1	NM_014292	
MIEF1	54471	hgsc.bcm.edu	37	22	39908399	39908399	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39908399T>C	ENST00000325301.2	+	5	909	c.485T>C	c.(484-486)gTg>gCg	p.V162A	MIEF1_ENST00000402881.1_Missense_Mutation_p.V162A|MIEF1_ENST00000404569.1_Missense_Mutation_p.V162A	NM_019008.4	NP_061881.2	Q9NQG6	MID51_HUMAN	mitochondrial elongation factor 1	162	Dimerization.|Important for interaction with DNM1L.				mitochondrial fission (GO:0000266)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|GDP binding (GO:0019003)|identical protein binding (GO:0042802)										CAAGCTGCTGTGGACATATGT	0.597																																					p.V162A		Atlas-SNP	.											.	SMCR7L	33	.	0			c.T485C						.						51.0	49.0	50.0					22																	39908399		2203	4300	6503	SO:0001583	missense	54471	exon5			CTGCTGTGGACAT	AL365515	CCDS13995.1	22q13.1	2013-09-23	2013-09-23	2013-09-23	ENSG00000100335	ENSG00000100335			25979	protein-coding gene	gene with protein product		615497	"""Smith-Magenis syndrome chromosome region, candidate 7-like"""	SMCR7L		21508961, 21701560	Standard	NM_019008		Approved	FLJ20232, MiD51	uc003axx.3	Q9NQG6	OTTHUMG00000151105	ENST00000325301.2:c.485T>C	chr22.hg19:g.39908399T>C	ENSP00000327124:p.Val162Ala	58.0	0.0		64.0	23.0	NM_019008	Q7L890|Q9BUI3	Missense_Mutation	SNP	ENST00000325301.2	hg19	CCDS13995.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.929634	0.34096	.	.	ENSG00000100335	ENST00000402881;ENST00000325301;ENST00000404569	T;T;T	0.11712	2.75;2.77;2.77	5.67	5.67	0.87782	.	0.064498	0.64402	D	0.000007	T	0.10252	0.0251	L	0.36672	1.1	0.54753	D	0.999985	B;P	0.44006	0.231;0.824	B;B	0.41202	0.055;0.35	T	0.17471	-1.0368	10	0.09084	T	0.74	-20.4286	15.9007	0.79373	0.0:0.0:0.0:1.0	.	162;162	Q9NQG6;B0QY95	MID51_HUMAN;.	A	162	ENSP00000385110:V162A;ENSP00000327124:V162A;ENSP00000385191:V162A	ENSP00000327124:V162A	V	+	2	0	SMCR7L	38238345	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.009000	0.88606	2.158000	0.67659	0.477000	0.44152	GTG	.	.		0.597	MIEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321325.1	NM_019008	
EFCAB6	64800	hgsc.bcm.edu	37	22	44067890	44067890	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:44067890C>T	ENST00000262726.7	-	15	1856	c.1603G>A	c.(1603-1605)Gtc>Atc	p.V535I	EFCAB6_ENST00000396231.2_Missense_Mutation_p.V383I	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	535	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				GGACAGAAGACGTGCATGATT	0.353																																					p.V535I		Atlas-SNP	.											.	EFCAB6	177	.	0			c.G1603A						.						104.0	101.0	102.0					22																	44067890		2203	4300	6503	SO:0001583	missense	64800	exon15			AGAAGACGTGCAT	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1603G>A	chr22.hg19:g.44067890C>T	ENSP00000262726:p.Val535Ile	174.0	0.0		156.0	58.0	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	hg19	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	0.076	-1.193115	0.01607	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.30714	1.52;1.52	5.04	0.534	0.17127	EF-hand-like domain (1);	1.335570	0.04589	N	0.396360	T	0.20007	0.0481	N	0.17082	0.46	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.25082	-1.0142	10	0.36615	T	0.2	-2.2762	7.3377	0.26619	0.0:0.4606:0.0:0.5394	.	535	Q5THR3	EFCB6_HUMAN	I	383;535	ENSP00000379533:V383I;ENSP00000262726:V535I	ENSP00000262726:V535I	V	-	1	0	EFCAB6	42399223	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.238000	0.08977	-0.110000	0.12022	-0.367000	0.07326	GTC	.	.		0.353	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
CELSR1	9620	hgsc.bcm.edu	37	22	46829297	46829297	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:46829297T>C	ENST00000262738.3	-	5	4603	c.4604A>G	c.(4603-4605)tAc>tGc	p.Y1535C		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1535	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TACCTTGTTGTAGTACTGCAC	0.647																																					p.Y1535C		Atlas-SNP	.											.	CELSR1	242	.	0			c.A4604G						.						65.0	56.0	59.0					22																	46829297		2203	4300	6503	SO:0001583	missense	9620	exon5			TTGTTGTAGTACT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.4604A>G	chr22.hg19:g.46829297T>C	ENSP00000262738:p.Tyr1535Cys	51.0	0.0		42.0	11.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.231476	0.79688	.	.	ENSG00000075275	ENST00000262738	T	0.78246	-1.16	4.62	4.62	0.57501	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.64402	U	0.000007	D	0.88145	0.6358	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89696	0.3901	10	0.62326	D	0.03	.	13.9979	0.64414	0.0:0.0:0.0:1.0	.	1535	Q9NYQ6	CELR1_HUMAN	C	1535	ENSP00000262738:Y1535C	ENSP00000262738:Y1535C	Y	-	2	0	CELSR1	45207961	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.335000	0.79234	1.857000	0.53885	0.533000	0.62120	TAC	.	.		0.647	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
PLCXD1	55344	hgsc.bcm.edu	37	X	209880	209880	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:209880G>A	ENST00000381657.2	+	6	1242	c.728G>A	c.(727-729)cGc>cAc	p.R243H	PLCXD1_ENST00000399012.1_Missense_Mutation_p.R243H|PLCXD1_ENST00000381663.3_Missense_Mutation_p.R243H	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	243					lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	11		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)				AGCTGCGGCCGCCCAGGTACC	0.647																																					p.R243H		Atlas-SNP	.											.	PLCXD1	18	.	0			c.G728A						.						81.0	72.0	75.0					X																	209880		2203	4296	6499	SO:0001583	missense	55344	exon6			GCGGCCGCCCAGG	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"""Pseudoautosomal regions / PAR1"""	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.728G>A	chrX.hg19:g.209880G>A	ENSP00000371073:p.Arg243His	208.0	0.0		181.0	38.0	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	hg19	CCDS14103.1	.	.	.	.	.	.	.	.	.	.	.	11.30	1.596973	0.28445	.	.	ENSG00000182378	ENST00000399012;ENST00000381657;ENST00000381663	T;T;T	0.31247	1.5;1.5;1.5	1.45	1.45	0.22620	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.124124	0.52532	N	0.000062	T	0.16854	0.0405	.	.	.	0.09310	N	1	P	0.51147	0.942	B	0.36134	0.218	T	0.16958	-1.0385	9	0.35671	T	0.21	-29.046	8.4059	0.32614	0.0:0.0:1.0:0.0	.	243	Q9NUJ7	PLCX1_HUMAN	H	243	ENSP00000381976:R243H;ENSP00000371073:R243H;ENSP00000371079:R243H	ENSP00000371073:R243H	R	+	2	0	PLCXD1	149880	0.998000	0.40836	0.572000	0.28498	0.390000	0.30446	5.640000	0.67875	0.768000	0.33290	0.394000	0.25966	CGC	.	.		0.647	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390	
CSF2RA	1438	hgsc.bcm.edu	37	X	1424529	1424529	+	Intron	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:1424529G>A	ENST00000381524.3	+	12	1311				CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000432318.2_Intron|CSF2RA_ENST00000361536.3_Intron|CSF2RA_ENST00000501036.2_Intron|CSF2RA_ENST00000417535.2_Intron|CSF2RA_ENST00000355805.2_Intron|CSF2RA_ENST00000381500.1_Intron|CSF2RA_ENST00000355432.3_Intron|CSF2RA_ENST00000381509.3_Silent_p.P378P|CSF2RA_ENST00000381529.3_Intron|CSF2RA_ENST00000498153.1_Intron			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)						response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		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)			Sargramostim(DB00020)	AGATGGGACCGCAGCGTCACC	0.637																																					p.P378P	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.G1134A						.						121.0	127.0	125.0					X																	1424529		692	1591	2283	SO:0001627	intron_variant	1438	exon13			GGGACCGCAGCGT	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.1125+109G>A	chrX.hg19:g.1424529G>A		600.0	0.0		576.0	250.0	NM_001161531	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Silent	SNP	ENST00000381524.3	hg19	CCDS35191.1																																																																																			.	.		0.637	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
SHROOM2	357	hgsc.bcm.edu	37	X	9866241	9866241	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:9866241C>T	ENST00000380913.3	+	5	2892	c.2802C>T	c.(2800-2802)gtC>gtT	p.V934V	SHROOM2_ENST00000493668.1_3'UTR	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	934					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				AAGCTTCTGTCGAACTGCGAA	0.577																																					p.V934V		Atlas-SNP	.											.	SHROOM2	139	.	0			c.C2802T						.						12.0	11.0	11.0					X																	9866241		2172	4266	6438	SO:0001819	synonymous_variant	357	exon5			TTCTGTCGAACTG	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.2802C>T	chrX.hg19:g.9866241C>T		268.0	0.0		244.0	137.0	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	hg19	CCDS14135.1																																																																																			.	.		0.577	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765564	27765564	+	Silent	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:27765564A>G	ENST00000451261.2	+	5	951	c.552A>G	c.(550-552)cgA>cgG	p.R184R		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	184										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						CCCTGCCCCGACCTCGCTGGC	0.602																																					p.R184R		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A552G						.						47.0	43.0	44.0					X																	27765564		692	1591	2283	SO:0001819	synonymous_variant	347442	exon1			GCCCCGACCTCGC		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.552A>G	chrX.hg19:g.27765564A>G		136.0	1.0		109.0	87.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.602	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
DMD	1756	hgsc.bcm.edu	37	X	31496268	31496268	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:31496268G>A	ENST00000357033.4	-	59	9098	c.8892C>T	c.(8890-8892)ggC>ggT	p.G2964G	DMD_ENST00000445312.1_5'Flank|DMD_ENST00000378677.2_Silent_p.G2960G|DMD_ENST00000343523.2_Silent_p.G504G|DMD_ENST00000474231.1_Silent_p.G504G|DMD_ENST00000541735.1_Silent_p.G504G|DMD_ENST00000378707.3_Silent_p.G504G|DMD_ENST00000359836.1_Silent_p.G504G	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2964					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TGAGGAGATCGCCCACGGGCT	0.532																																					p.G2964G		Atlas-SNP	.											.	DMD	2127	.	0			c.C8892T						.						57.0	47.0	50.0					X																	31496268		2202	4300	6502	SO:0001819	synonymous_variant	1756	exon59			GAGATCGCCCACG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.8892C>T	chrX.hg19:g.31496268G>A		56.0	0.0		48.0	35.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	0.194	-1.050338	0.01981	.	.	ENSG00000198947	ENST00000465285	.	.	.	5.4	-10.8	0.00216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6471	0.17596	0.1701:0.1452:0.4746:0.21	.	.	.	.	X	693	.	.	R	-	1	2	DMD	31406189	0.000000	0.05858	0.017000	0.16124	0.324000	0.28378	-2.946000	0.00680	-4.954000	0.00026	-1.515000	0.00940	CGA	.	.		0.532	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49127168	49127168	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:49127168G>A	ENST00000055335.6	+	1	852	c.836G>A	c.(835-837)cGc>cAc	p.R279H	LL0XNC01-7P3.1_ENST00000602455.1_lincRNA|PPP1R3F_ENST00000495799.1_Intron|PPP1R3F_ENST00000438316.1_5'UTR|PPP1R3F_ENST00000466508.1_5'UTR	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	279	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)	p.R279H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					AACCACGGCCGCAACTACACA	0.682													G|||	1	0.000264901	0.0	0.0	3775	,	,		11622	0.0		0.0	False		,,,				2504	0.001				p.R279H		Atlas-SNP	.											.	PPP1R3F	56	.	1	Substitution - Missense(1)	endometrium(1)	c.G836A						.						31.0	20.0	24.0					X																	49127168		2200	4295	6495	SO:0001583	missense	89801	exon1			ACGGCCGCAACTA		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.836G>A	chrX.hg19:g.49127168G>A	ENSP00000055335:p.Arg279His	78.0	0.0		83.0	66.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	hg19	CCDS35254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.99|15.99	2.995935|2.995935	0.54147|0.54147	.|.	.|.	ENSG00000049769|ENSG00000049769	ENST00000471261|ENST00000055335	.|T	.|0.64803	.|-0.12	4.06|4.06	3.09|3.09	0.35607|0.35607	.|Putative phosphatase regulatory subunit (2);	.|.	.|.	.|.	.|.	T|T	0.51432|0.51432	0.1674|0.1674	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	.|D	.|0.58620	.|0.983	.|P	.|0.49597	.|0.616	T|T	0.53995|0.53995	-0.8359|-0.8359	5|9	.|0.66056	.|D	.|0.02	-2.3334|-2.3334	4.9887|4.9887	0.14203|0.14203	0.177:0.0:0.823:0.0|0.177:0.0:0.823:0.0	.|.	.|279	.|Q6ZSY5	.|PPR3F_HUMAN	T|H	29|279	.|ENSP00000055335:R279H	.|ENSP00000055335:R279H	A|R	+|+	1|2	0|0	PPP1R3F|PPP1R3F	49014112|49014112	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	0.942000|0.942000	0.29017|0.29017	1.843000|1.843000	0.53566|0.53566	0.513000|0.513000	0.50165|0.50165	GCA|CGC	.	.		0.682	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
WNK3	65267	hgsc.bcm.edu	37	X	54321142	54321142	+	Missense_Mutation	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:54321142A>T	ENST00000375159.2	-	7	1536	c.1537T>A	c.(1537-1539)Tct>Act	p.S513T	WNK3_ENST00000354646.2_Missense_Mutation_p.S513T|WNK3_ENST00000375169.3_Missense_Mutation_p.S513T			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	513					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						TTCCCCATAGACTTGCACTGA	0.478																																					p.S513T		Atlas-SNP	.											.	WNK3	218	.	0			c.T1537A						.						94.0	84.0	87.0					X																	54321142		2203	4300	6503	SO:0001583	missense	65267	exon8			CCATAGACTTGCA	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.1537T>A	chrX.hg19:g.54321142A>T	ENSP00000364301:p.Ser513Thr	42.0	0.0		49.0	46.0	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	4.087	0.014155	0.07959	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.70986	-0.5;-0.53;-0.53	4.74	3.47	0.39725	.	0.854177	0.09985	N	0.730552	T	0.54367	0.1854	L	0.27053	0.805	0.09310	N	1	B;B	0.31730	0.337;0.147	B;B	0.31614	0.133;0.063	T	0.43798	-0.9369	10	0.33141	T	0.24	-1.7498	5.4726	0.16678	0.6545:0.1741:0.0:0.1715	.	513;513	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	T	513	ENSP00000364312:S513T;ENSP00000346667:S513T;ENSP00000364301:S513T	ENSP00000346667:S513T	S	-	1	0	WNK3	54337867	0.000000	0.05858	0.477000	0.27303	0.282000	0.26991	-0.257000	0.08745	1.662000	0.50781	0.481000	0.45027	TCT	.	.		0.478	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
KIAA2022	340533	hgsc.bcm.edu	37	X	73963111	73963111	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:73963111G>A	ENST00000055682.6	-	3	1892	c.1281C>T	c.(1279-1281)ggC>ggT	p.G427G		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	427					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TAGCAAGATGGCCCTGCTTTG	0.428																																					p.G427G		Atlas-SNP	.											.	KIAA2022	262	.	0			c.C1281T						.						180.0	147.0	158.0					X																	73963111		2203	4300	6503	SO:0001819	synonymous_variant	340533	exon3			AAGATGGCCCTGC		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"""XLMR-related protein, neurite extension"""	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.1281C>T	chrX.hg19:g.73963111G>A		44.0	0.0		47.0	39.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Silent	SNP	ENST00000055682.6	hg19	CCDS35337.1																																																																																			.	.		0.428	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537	
ATRX	546	hgsc.bcm.edu	37	X	76920179	76920179	+	Missense_Mutation	SNP	T	T	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:76920179T>C	ENST00000373344.5	-	11	4112	c.3898A>G	c.(3898-3900)Aaa>Gaa	p.K1300E	ATRX_ENST00000395603.3_Missense_Mutation_p.K1262E|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1300	Interaction with DAXX.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GTTCTTTTTTTCCCTTCTTCT	0.373			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.K1300E		Atlas-SNP	.		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX	833	.	1	Unknown(1)	bone(1)	c.A3898G						.						184.0	165.0	171.0					X																	76920179		2203	4296	6499	SO:0001583	missense	546	exon11			TTTTTTTCCCTTC	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.3898A>G	chrX.hg19:g.76920179T>C	ENSP00000362441:p.Lys1300Glu	58.0	0.0		34.0	25.0	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	hg19	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	T	10.27	1.303879	0.23736	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.92299	-3.01;-3.01	4.89	3.7	0.42460	.	0.081603	0.47852	U	0.000203	D	0.94169	0.8129	M	0.62723	1.935	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.80764	0.994;0.991;0.98	D	0.92170	0.5743	10	0.39692	T	0.17	-11.9863	10.3878	0.44152	0.149:0.0:0.0:0.851	.	1232;1262;1300	P46100-6;P46100-4;P46100	.;.;ATRX_HUMAN	E	1300;1262;1227	ENSP00000362441:K1300E;ENSP00000378967:K1262E	ENSP00000362441:K1300E	K	-	1	0	ATRX	76806835	1.000000	0.71417	0.679000	0.29978	0.174000	0.22865	3.566000	0.53805	0.611000	0.30052	-0.391000	0.06502	AAA	.	.		0.373	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
BRWD3	254065	hgsc.bcm.edu	37	X	79965042	79965042	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:79965042C>T	ENST00000373275.4	-	21	2576	c.2360G>A	c.(2359-2361)cGc>cAc	p.R787H	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	787					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						CTGTGTCCTGCGTAAAGAACG	0.388																																					p.R787H		Atlas-SNP	.											.	BRWD3	251	.	0			c.G2360A						.						151.0	105.0	121.0					X																	79965042		2203	4300	6503	SO:0001583	missense	254065	exon21			GTCCTGCGTAAAG		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.2360G>A	chrX.hg19:g.79965042C>T	ENSP00000362372:p.Arg787His	72.0	0.0		87.0	64.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	hg19	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.619414	0.66787	.	.	ENSG00000165288	ENST00000373275	T	0.30182	1.54	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.38321	0.1036	M	0.79258	2.445	0.47407	D	0.999411	B	0.24721	0.11	B	0.18561	0.022	T	0.20907	-1.0261	9	.	.	.	-8.7575	18.3472	0.90326	0.0:1.0:0.0:0.0	.	787	Q6RI45	BRWD3_HUMAN	H	787	ENSP00000362372:R787H	.	R	-	2	0	BRWD3	79851698	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.628000	0.67791	2.273000	0.75805	0.600000	0.82982	CGC	.	.		0.388	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	
KLHL4	56062	hgsc.bcm.edu	37	X	86877225	86877225	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:86877225G>T	ENST00000373119.4	+	5	1084	c.939G>T	c.(937-939)gaG>gaT	p.E313D	KLHL4_ENST00000373114.4_Missense_Mutation_p.E313D	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	313						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						ACTTCATTGAGGTAATAAAAA	0.323																																					p.E313D		Atlas-SNP	.											.	KLHL4	263	.	0			c.G939T						.						61.0	54.0	56.0					X																	86877225		2203	4300	6503	SO:0001583	missense	56062	exon5			CATTGAGGTAATA	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.939G>T	chrX.hg19:g.86877225G>T	ENSP00000362211:p.Glu313Asp	273.0	0.0		247.0	172.0	NM_019117	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	hg19	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.747727	0.30955	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.70749	-0.51;-0.51	5.48	1.5	0.22942	BTB/Kelch-associated (2);	0.112471	0.64402	N	0.000016	T	0.55625	0.1932	L	0.38649	1.16	0.47276	D	0.999373	B;B	0.20887	0.025;0.049	B;B	0.28916	0.074;0.096	T	0.37197	-0.9716	10	0.39692	T	0.17	.	3.7946	0.08734	0.2392:0.0:0.3173:0.4435	.	313;313	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	D	313	ENSP00000362211:E313D;ENSP00000362206:E313D	ENSP00000362206:E313D	E	+	3	2	KLHL4	86763881	1.000000	0.71417	0.925000	0.36789	0.901000	0.52897	2.111000	0.41883	-0.137000	0.11455	-0.322000	0.08575	GAG	.	.		0.323	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
PCDH11X	27328	hgsc.bcm.edu	37	X	91873881	91873881	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:91873881G>A	ENST00000373094.1	+	7	4831	c.3986G>A	c.(3985-3987)cGc>cAc	p.R1329H	PCDH11X_ENST00000373088.1_Missense_Mutation_p.R1292H|PCDH11X_ENST00000298274.8_Missense_Mutation_p.R1292H|PCDH11X_ENST00000361655.2_Missense_Mutation_p.R1311H|PCDH11X_ENST00000406881.1_Missense_Mutation_p.R1321H|PCDH11X_ENST00000373097.1_Missense_Mutation_p.R1319H|PCDH11X_ENST00000504220.2_3'UTR	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1329					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						TTCACTCCACGCCAACAGGCC	0.403																																					p.R1329H	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.G3986A						.						135.0	128.0	130.0					X																	91873881		2203	4300	6503	SO:0001583	missense	27328	exon7			CTCCACGCCAACA	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3986G>A	chrX.hg19:g.91873881G>A	ENSP00000362186:p.Arg1329His	225.0	0.0		199.0	24.0	NM_032968	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	G	6.890	0.533717	0.13188	.	.	ENSG00000102290	ENST00000373094;ENST00000373097;ENST00000373088;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T	0.54279	0.61;0.62;0.63;0.58;0.61;0.63	4.57	3.69	0.42338	.	.	.	.	.	T	0.29158	0.0725	N	0.08118	0	0.09310	N	1	P;P;P;P;P	0.49358	0.923;0.923;0.923;0.923;0.875	B;B;B;B;B	0.34722	0.188;0.188;0.188;0.188;0.092	T	0.03651	-1.1016	9	0.49607	T	0.09	.	12.3924	0.55366	0.0:0.3405:0.6595:0.0	.	1292;1311;1321;1319;1329	Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7	.;.;.;.;PC11X_HUMAN	H	1329;1319;1292;1311;1321;1329;1292	ENSP00000362186:R1329H;ENSP00000362189:R1319H;ENSP00000362180:R1292H;ENSP00000355105:R1311H;ENSP00000384758:R1321H;ENSP00000298274:R1292H	ENSP00000298274:R1292H	R	+	2	0	PCDH11X	91760537	0.004000	0.15560	0.005000	0.12908	0.074000	0.17049	1.310000	0.33551	0.704000	0.31869	0.459000	0.35465	CGC	.	.		0.403	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
GUCY2F	2986	hgsc.bcm.edu	37	X	108691376	108691376	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:108691376G>A	ENST00000218006.2	-	6	1782	c.1491C>T	c.(1489-1491)atC>atT	p.I497I		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	497					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						TGATCAACTGGATTTTATTTA	0.408																																					p.I497I		Atlas-SNP	.											.	GUCY2F	178	.	0			c.C1491T						.						120.0	104.0	110.0					X																	108691376		2203	4300	6503	SO:0001819	synonymous_variant	2986	exon6			CAACTGGATTTTA	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.1491C>T	chrX.hg19:g.108691376G>A		76.0	0.0		73.0	63.0	NM_001522	Q9UJF1	Silent	SNP	ENST00000218006.2	hg19	CCDS14545.1																																																																																			.	.		0.408	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
NXT2	55916	hgsc.bcm.edu	37	X	108779154	108779154	+	5'Flank	SNP	G	G	T	rs142540133	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:108779154G>T	ENST00000372106.1	+	0	0				NXT2_ENST00000372107.1_5'Flank|NXT2_ENST00000218004.1_Nonsense_Mutation_p.G15*|NXT2_ENST00000372103.1_5'Flank	NM_001242617.1	NP_001229546.1	Q9NPJ8	NXT2_HUMAN	nuclear transport factor 2-like export factor 2						mRNA transport (GO:0051028)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	6						AGACAGAGAAGGATACCAAAG	0.393																																					p.G15X		Atlas-SNP	.											.	NXT2	16	.	0			c.G43T						.						67.0	58.0	61.0					X																	108779154		2203	4300	6503	SO:0001631	upstream_gene_variant	55916	exon1			AGAGAAGGATACC	AF246127	CCDS14546.1, CCDS56605.1, CCDS56606.1	Xq22.3	2008-02-05			ENSG00000101888	ENSG00000101888			18151	protein-coding gene	gene with protein product		300320				11073998	Standard	NM_018698		Approved	P15-2	uc004eoe.2	Q9NPJ8	OTTHUMG00000022185		chrX.hg19:g.108779154G>T	Exception_encountered	373.0	0.0		394.0	31.0	NM_018698	D3DUY1|Q0VAN8|Q5JYV5|Q5JYV6|Q5JYV7|Q9H8U0|Q9NQ64|Q9NRL7|Q9Y3M4|Q9Y3M5	Nonsense_Mutation	SNP	ENST00000372106.1	hg19	CCDS56605.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.000689	0.54254	.	.	ENSG00000101888	ENST00000218004	.	.	.	4.18	-5.42	0.02640	.	1.115670	0.06935	N	0.811772	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.0526	0.03574	0.2432:0.4283:0.1873:0.1412	.	.	.	.	X	15	.	ENSP00000218004:G15X	G	+	1	0	NXT2	108665810	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.162000	0.10012	-1.176000	0.02747	-0.384000	0.06662	GGA	.	G|1.000;C|0.000		0.393	NXT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057886.1	NM_018698	
AMOT	154796	hgsc.bcm.edu	37	X	112033910	112033910	+	Missense_Mutation	SNP	G	G	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:112033910G>T	ENST00000524145.1	-	8	2101	c.2027C>A	c.(2026-2028)gCt>gAt	p.A676D	AMOT_ENST00000304758.1_Missense_Mutation_p.A267D|AMOT_ENST00000371959.3_Missense_Mutation_p.A676D|AMOT_ENST00000371958.1_Missense_Mutation_p.A444D|AMOT_ENST00000371962.1_Missense_Mutation_p.A444D			Q4VCS5	AMOT_HUMAN	angiomotin	676					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						TGTCATATCAGCTTCCAGAGC	0.498																																					p.A676D		Atlas-SNP	.											.	AMOT	204	.	0			c.C2027A						.						202.0	182.0	189.0					X																	112033910		2203	4300	6503	SO:0001583	missense	154796	exon7			ATATCAGCTTCCA	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.2027C>A	chrX.hg19:g.112033910G>T	ENSP00000429013:p.Ala676Asp	108.0	0.0		98.0	73.0	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	hg19	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	G	32	5.110473	0.94292	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000371958	T;T;T;T;T	0.29142	2.01;1.84;2.09;1.84;1.58	6.08	6.08	0.98989	Angiomotin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.57666	0.2069	M	0.79123	2.44	0.80722	D	1	D	0.56968	0.978	D	0.65443	0.935	T	0.56768	-0.7924	10	0.48119	T	0.1	-13.2289	18.3623	0.90379	0.0:0.0:1.0:0.0	.	676	Q4VCS5	AMOT_HUMAN	D	267;676;444;676;444	ENSP00000305557:A267D;ENSP00000361027:A676D;ENSP00000361030:A444D;ENSP00000429013:A676D;ENSP00000361026:A444D	ENSP00000305557:A267D	A	-	2	0	AMOT	111920566	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.562000	0.86427	0.600000	0.82982	GCT	.	.		0.498	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
BCORL1	63035	hgsc.bcm.edu	37	X	129185838	129185838	+	Missense_Mutation	SNP	A	A	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:129185838A>G	ENST00000218147.7	+	12	4897	c.4700A>G	c.(4699-4701)gAa>gGa	p.E1567G	BCORL1_ENST00000303743.5_Missense_Mutation_p.E1641G|BCORL1_ENST00000359304.2_Missense_Mutation_p.E1437G|BCORL1_ENST00000540052.1_Missense_Mutation_p.E1567G			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1567					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						CTTACAGAGGAAAAAGACGGG	0.473																																					p.E1567G		Atlas-SNP	.											.	BCORL1	213	.	0			c.A4700G						.						202.0	188.0	192.0					X																	129185838		2203	4300	6503	SO:0001583	missense	63035	exon11			CAGAGGAAAAAGA	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4700A>G	chrX.hg19:g.129185838A>G	ENSP00000218147:p.Glu1567Gly	91.0	0.0		102.0	91.0	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	hg19	CCDS14616.1	.	.	.	.	.	.	.	.	.	.	A	1.979	-0.434698	0.04669	.	.	ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822	T;T;T;T;T	0.41065	1.01;1.44;1.01;1.01;1.5	5.53	1.67	0.24075	.	0.478772	0.15564	N	0.255788	T	0.09862	0.0242	N	0.00436	-1.5	0.21386	N	0.99971	B;B	0.06786	0.001;0.0	B;B	0.04013	0.0;0.001	T	0.29971	-0.9994	10	0.14656	T	0.56	0.3218	3.558	0.07871	0.3209:0.2323:0.4468:0.0	.	1641;1567	Q5H9F3-3;Q5H9F3	.;BCORL_HUMAN	G	1567;1641;1437;1567;1241	ENSP00000218147:E1567G;ENSP00000307541:E1641G;ENSP00000352253:E1437G;ENSP00000437775:E1567G;ENSP00000399483:E1241G	ENSP00000218147:E1567G	E	+	2	0	BCORL1	129013519	1.000000	0.71417	0.399000	0.26333	0.831000	0.47069	2.055000	0.41345	0.210000	0.20664	0.417000	0.27973	GAA	.	.		0.473	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946	
PNMA5	114824	hgsc.bcm.edu	37	X	152158844	152158844	+	Silent	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:152158844G>A	ENST00000439251.1	-	2	1737	c.1299C>T	c.(1297-1299)aaC>aaT	p.N433N	PNMA5_ENST00000361887.5_Silent_p.N433N|PNMA5_ENST00000535214.1_Silent_p.N433N|PNMA5_ENST00000452693.1_Silent_p.N433N	NM_001103150.1	NP_001096620.1	Q96PV4	PNMA5_HUMAN	paraneoplastic Ma antigen family member 5	433					positive regulation of apoptotic process (GO:0043065)					breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					CCCCTGCCTCGTTTCCCAACT	0.612																																					p.N433N		Atlas-SNP	.											.	PNMA5	63	.	0			c.C1299T						.						102.0	81.0	88.0					X																	152158844		2203	4300	6503	SO:0001819	synonymous_variant	114824	exon2			TGCCTCGTTTCCC	AB067521	CCDS14718.1	Xq28	2012-02-09	2012-02-09		ENSG00000198883	ENSG00000198883		"""Paraneoplastic Ma antigens"""	18743	protein-coding gene	gene with protein product	"""paraneoplastic antigen family 5"""	300916	"""paraneoplastic antigen like 5"""			16214224	Standard	NM_052926		Approved	KIAA1934	uc004fgy.4	Q96PV4	OTTHUMG00000024184	ENST00000439251.1:c.1299C>T	chrX.hg19:g.152158844G>A		61.0	0.0		70.0	51.0	NM_001103150	B4DI72|B7Z9Y9|Q495L5|Q8NET3	Silent	SNP	ENST00000439251.1	hg19	CCDS14718.1																																																																																			.	.		0.612	PNMA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060925.1	NM_052926	
L1CAM	3897	hgsc.bcm.edu	37	X	153138119	153138119	+	Missense_Mutation	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:153138119G>A	ENST00000370060.1	-	4	314	c.125C>T	c.(124-126)cCa>cTa	p.P42L	L1CAM_ENST00000538883.1_Missense_Mutation_p.P44L|L1CAM_ENST00000361699.4_Missense_Mutation_p.P42L|L1CAM_ENST00000370055.1_Missense_Mutation_p.P37L|L1CAM_ENST00000361981.3_Missense_Mutation_p.P37L|L1CAM_ENST00000543994.1_Missense_Mutation_p.P44L|L1CAM_ENST00000370057.3_Missense_Mutation_p.P42L	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	42	Ig-like C2-type 1.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCGCCGTGGAGACTGTTC	0.602																																					p.P42L		Atlas-SNP	.											.	L1CAM	189	.	0			c.C125T						.						112.0	82.0	92.0					X																	153138119		2203	4300	6503	SO:0001583	missense	3897	exon3			CGCCGTGGAGACT	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	6470	protein-coding gene	gene with protein product		308840	"""antigen identified by monoclonal antibody R1"""	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.125C>T	chrX.hg19:g.153138119G>A	ENSP00000359077:p.Pro42Leu	115.0	0.0		101.0	73.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629893	0.87660	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699;ENST00000439496;ENST00000407935;ENST00000420165;ENST00000458029	T;T;T;T;T;T;T;T;T;T;D	0.96491	-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-1.34;-4.03	4.69	4.69	0.59074	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000011	D	0.96759	0.8942	M	0.78456	2.415	0.80722	D	1	P;P;P	0.52577	0.944;0.858;0.954	P;P;P	0.53266	0.696;0.661;0.722	D	0.96651	0.9481	10	0.62326	D	0.03	.	11.2495	0.49017	0.0:0.0:0.8168:0.1832	.	37;42;42	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	L	42;44;42;44;37;37;42;42;37;37;42	ENSP00000359077:P42L;ENSP00000438430:P44L;ENSP00000359074:P42L;ENSP00000439645:P44L;ENSP00000354712:P37L;ENSP00000359072:P37L;ENSP00000355380:P42L;ENSP00000402407:P42L;ENSP00000384902:P37L;ENSP00000392524:P37L;ENSP00000396079:P42L	ENSP00000355380:P42L	P	-	2	0	L1CAM	152791313	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	3.707000	0.54838	2.176000	0.68965	0.529000	0.55759	CCA	.	.		0.602	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	
MECP2	4204	hgsc.bcm.edu	37	X	153296806	153296806	+	Missense_Mutation	SNP	G	G	A	rs28934906		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:153296806G>A	ENST00000303391.6	-	4	722	c.473C>T	c.(472-474)aCg>aTg	p.T158M	MECP2_ENST00000460227.1_5'Flank|MECP2_ENST00000407218.1_Intron|MECP2_ENST00000453960.2_Missense_Mutation_p.T170M	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	158	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.		T -> A (in RTT). {ECO:0000269|PubMed:11269512, ECO:0000269|PubMed:15057977}.|T -> M (in RTT; dbSNP:rs28934906). {ECO:0000269|PubMed:10508514, ECO:0000269|PubMed:10577905, ECO:0000269|PubMed:10745042, ECO:0000269|PubMed:10767337, ECO:0000269|PubMed:10814719, ECO:0000269|PubMed:10944854, ECO:0000269|PubMed:10991688, ECO:0000269|PubMed:10991689, ECO:0000269|PubMed:11055898, ECO:0000269|PubMed:11241840, ECO:0000269|PubMed:11269512, ECO:0000269|PubMed:11376998, ECO:0000269|PubMed:11402105, ECO:0000269|PubMed:11738883, ECO:0000269|PubMed:12567420, ECO:0000269|PubMed:12966523, ECO:0000269|PubMed:15057977}.		adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCAGTTACCGTGAAGTCAAA	0.562																																					p.T170M		Atlas-SNP	.											.	MECP2	41	.	0			c.C509T	GRCh37	CM992178	MECP2	M	rs28934906	.						71.0	68.0	69.0					X																	153296806		2203	4300	6503	SO:0001583	missense	4204	exon3			GTTACCGTGAAGT	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"""mental retardation, X-linked 16"", ""mental retardation, X-linked 79"", ""Rett syndrome"", ""methyl CpG binding protein 2 (Rett syndrome)"""	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.473C>T	chrX.hg19:g.153296806G>A	ENSP00000301948:p.Thr158Met	98.0	0.0		79.0	68.0	NM_001110792	O15233|Q6QHH9|Q7Z384	Missense_Mutation	SNP	ENST00000303391.6	hg19	CCDS14741.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860099	0.71834	.	.	ENSG00000169057	ENST00000303391;ENST00000545451;ENST00000453960;ENST00000369964	D;D	0.99436	-5.9;-5.9	5.48	5.48	0.80851	Methyl-CpG DNA binding (4);DNA-binding, integrase-type (1);	0.000000	0.85682	D	0.000000	D	0.99290	0.9752	L	0.50333	1.59	0.80722	A	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99758	1.1020	9	0.87932	D	0	-12.1252	17.0301	0.86458	0.0:0.0:1.0:0.0	rs28934906	170;158	P51608-2;P51608	.;MECP2_HUMAN	M	158;158;170;158	ENSP00000301948:T158M;ENSP00000395535:T170M	ENSP00000301948:T158M	T	-	2	0	MECP2	152950000	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.283000	0.95860	2.285000	0.76669	0.600000	0.82982	ACG	.	G|1.000;|0.000		0.562	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992	
FLNA	2316	hgsc.bcm.edu	37	X	153599342	153599342	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:153599342C>T	ENST00000369850.3	-	2	508	c.272G>A	c.(271-273)cGc>cAc	p.R91H	FLNA_ENST00000344736.4_Missense_Mutation_p.R91H|FLNA_ENST00000422373.1_Missense_Mutation_p.R91H|FLNA_ENST00000360319.4_Missense_Mutation_p.R91H	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	91	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GTTGTGCTTGCGGTGCATCTT	0.607																																					p.R91H		Atlas-SNP	.											.	FLNA	373	.	0			c.G272A						.						55.0	52.0	53.0					X																	153599342		2201	4298	6499	SO:0001583	missense	2316	exon2			TGCTTGCGGTGCA	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.272G>A	chrX.hg19:g.153599342C>T	ENSP00000358866:p.Arg91His	87.0	0.0		86.0	4.0	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	hg19	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856260	0.71834	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56	5.13	5.13	0.70059	Calponin homology domain (5);	0.071778	0.52532	D	0.000062	D	0.96024	0.8705	L	0.57536	1.79	0.80722	D	1	B;D	0.69078	0.063;0.997	B;P	0.60473	0.016;0.875	D	0.96469	0.9347	10	0.66056	D	0.02	.	17.3547	0.87332	0.0:1.0:0.0:0.0	.	91;91	P21333-2;P21333	.;FLNA_HUMAN	H	91;64;91;91;91	ENSP00000353467:R91H;ENSP00000416926:R91H;ENSP00000358866:R91H;ENSP00000358863:R91H	ENSP00000358863:R91H	R	-	2	0	FLNA	153252536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.630000	0.83225	2.131000	0.65755	0.525000	0.51046	CGC	.	.		0.607	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
SPRY3	10251	hgsc.bcm.edu	37	X	155004148	155004148	+	Silent	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:155004148C>T	ENST00000302805.2	+	2	1046	c.615C>T	c.(613-615)aaC>aaT	p.N205N		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	205	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATGAAGACAACTGTGCTGATG	0.562																																					p.N205N		Atlas-SNP	.											.	SPRY3	52	.	0			c.C615T						.	C		0,4406		0,0,2203	265.0	235.0	245.0		615	2.9	1.0	X		245	1,8591		0,1,4295	no	coding-synonymous	SPRY3	NM_005840.1		0,1,6498	TT,TC,CC		0.0116,0.0,0.0077		205/289	155004148	1,12997	2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			AGACAACTGTGCT	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"""Pseudoautosomal regions / PAR2"""	11271	protein-coding gene	gene with protein product	"""antagonist of FGF signaling"""	300531	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.615C>T	chrX.hg19:g.155004148C>T		154.0	0.0		154.0	57.0	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	hg19	CCDS14769.4	.	.	.	.	.	.	.	.	.	.	C	4.447	0.082729	0.08533	0.0	1.16E-4	ENSG00000168939	ENST00000369437	.	.	.	2.94	2.94	0.34122	.	.	.	.	.	T	0.46483	0.1395	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.40213	-0.9575	5	0.87932	D	0	-14.1758	10.9825	0.47504	0.0:1.0:0.0:0.0	.	.	.	.	I	106	.	ENSP00000358445:T106I	T	+	2	0	SPRY3	154657342	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	1.648000	0.37271	1.494000	0.48533	0.279000	0.19357	ACT	.	.		0.562	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840	
PCDH11Y	83259	hgsc.bcm.edu	37	Y	5369160	5369160	+	Silent	SNP	A	A	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrY:5369160A>T	ENST00000215473.6	+	3	3192	c.3192A>T	c.(3190-3192)ggA>ggT	p.G1064G				Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked	1064					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						GTGATGGTGGACTGGGAGACC	0.532																																					p.G1064G		Atlas-SNP	.											.	PCDH11Y	163	.	0			c.A3192T						.																																			SO:0001819	synonymous_variant	83259	exon3			TGGTGGACTGGGA	AF332217	CCDS14776.1, CCDS14777.1, CCDS76066.1	Yp11.2	2010-01-26	2002-05-22	2002-05-24	ENSG00000099715	ENSG00000099715		"""Cadherins / Protocadherins : Non-clustered"""	15813	protein-coding gene	gene with protein product		400022	"""protocadherin 22"""	PCDH22		10644456, 11003707	Standard	NM_032971		Approved	PCDHY	uc004fqo.3	Q9BZA8	OTTHUMG00000035105	ENST00000215473.6:c.3192A>T	chrY.hg19:g.5369160A>T		413.0	2.0		411.0	288.0	NM_032973	Q70LR6|Q70LR8|Q70LS0|Q70LS1|Q70LS2|Q70LS3|Q70LS4|Q70LS5|Q8WY34|Q9BZA9|Q9H4E1	Silent	SNP	ENST00000215473.6	hg19																																																																																				.	.		0.532	PCDH11Y-201	KNOWN	basic	protein_coding	protein_coding		NM_032973	
DDX3Y	8653	hgsc.bcm.edu	37	Y	15026814	15026814	+	Missense_Mutation	SNP	C	C	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrY:15026814C>T	ENST00000336079.3	+	9	884	c.778C>T	c.(778-780)Cgc>Tgc	p.R260C	DDX3Y_ENST00000463199.1_3'UTR|DDX3Y_ENST00000360160.4_Missense_Mutation_p.R260C	NM_001122665.1|NM_004660.3	NP_001116137.1|NP_004651.2	O15523	DDX3Y_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked	260	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			kidney(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	5						AAGGTATGGGCGCCGCAAACA	0.308																																					p.R260C		Atlas-SNP	.											.	DDX3Y	13	.	0			c.C778T						.						31.0	31.0	31.0					Y																	15026814		580	1901	2481	SO:0001583	missense	8653	exon9			TATGGGCGCCGCA	AF000984	CCDS14782.1	Yq11	2013-07-16	2013-07-16	2003-06-20	ENSG00000067048	ENSG00000067048		"""DEAD-boxes"""	2699	protein-coding gene	gene with protein product		400010	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked"""	DBY		9381176	Standard	NM_004660		Approved		uc004fsv.2	O15523	OTTHUMG00000036324	ENST00000336079.3:c.778C>T	chrY.hg19:g.15026814C>T	ENSP00000336725:p.Arg260Cys	179.0	0.0		148.0	121.0	NM_004660	B4DK29|B4DXX7|Q8IYV7	Missense_Mutation	SNP	ENST00000336079.3	hg19	CCDS14782.1																																																																																			.	.		0.308	DDX3Y-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088407.1	NM_004660	
NLGN4Y	22829	hgsc.bcm.edu	37	Y	16942179	16942179	+	3'UTR	SNP	G	G	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrY:16942179G>A	ENST00000476359.1	+	0	1926							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						CGACCTGCACGCGCAGTACGG	0.617																																					p.A461T		Atlas-SNP	.											.	NLGN4Y	44	.	0			c.G1381A						.																																			SO:0001624	3_prime_UTR_variant	22829	exon5			CTGCACGCGCAGT		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"""neuroligin 4, Y linked"""			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*1923G>A	chrY.hg19:g.16942179G>A		247.0	0.0		197.0	163.0	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Missense_Mutation	SNP	ENST00000476359.1	hg19																																																																																				.	.		0.617	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893	
DIRAS1	148252	hgsc.bcm.edu	37	19	2717762	2717762	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:2717762delC	ENST00000323469.4	-	2	226	c.43delG	c.(43-45)gcgfs	p.A15fs	DIRAS1_ENST00000585334.1_Frame_Shift_Del_p.A15fs	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	15					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|lung(2)|ovary(2)|prostate(1)	6				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)		ACGCCGCCCGCCCCGAACACC	0.682																																					p.A15fs		Atlas-Indel,Pindel	.											DIRAS1,NS,carcinoma,0,1	DIRAS1	26	.	0			c.44delC						.						48.0	46.0	46.0					19																	2717762		2203	4298	6501	SO:0001589	frameshift_variant	148252	exon2			.	BC030660	CCDS12092.1	19p13.3	2014-05-09				ENSG00000176490			19127	protein-coding gene	gene with protein product		607862				12107278	Standard	NM_145173		Approved	Di-Ras1, GBTS1, RIG	uc002lwf.3	O95057		ENST00000323469.4:c.43delG	chr19.hg19:g.2717762delC	ENSP00000325836:p.Ala15fs	46.0	0.0		23.0	17.0	NM_145173		Frame_Shift_Del	DEL	ENST00000323469.4	hg19	CCDS12092.1																																																																																			.	.		0.682	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1		
KAT6B	23522	hgsc.bcm.edu	37	10	76784946	76784949	+	Frame_Shift_Del	DEL	ACAA	ACAA	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	ACAA	ACAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:76784946_76784949delACAA	ENST00000287239.4	+	17	4092_4095	c.3603_3606delACAA	c.(3601-3606)agacaafs	p.RQ1201fs	KAT6B_ENST00000372725.1_Frame_Shift_Del_p.RQ909fs|KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372711.1_Frame_Shift_Del_p.RQ1018fs|RP11-77G23.2_ENST00000413431.1_RNA|KAT6B_ENST00000372724.1_Frame_Shift_Del_p.RQ909fs|RP11-77G23.5_ENST00000436608.1_RNA|KAT6B_ENST00000372714.1_Frame_Shift_Del_p.RQ909fs	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1201					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)										GGAAGAAAAGACAAACAGAGGAAG	0.451																																					p.1201_1202del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.3602_3605del						.																																			SO:0001589	frameshift_variant	23522	exon17			.	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.3603_3606delACAA	chr10.hg19:g.76784946_76784949delACAA	ENSP00000287239:p.Arg1201fs	272.0	0.0		211.0	73.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Frame_Shift_Del	DEL	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.451	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
KCNK17	89822	hgsc.bcm.edu	37	6	39272281	39272281	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:39272281delC	ENST00000373231.4	-	3	735	c.503delG	c.(502-504)ggcfs	p.G168fs	KCNK17_ENST00000453413.2_Frame_Shift_Del_p.G168fs	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	168					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						CTGCCAGGTGCCCCCCAGCCT	0.607																																					p.G168fs		Atlas-Indel,Pindel	.											.	KCNK17	61	.	0			c.504delC						.						53.0	58.0	56.0					6																	39272281		2203	4300	6503	SO:0001589	frameshift_variant	89822	exon3			.	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.503delG	chr6.hg19:g.39272281delC	ENSP00000362328:p.Gly168fs	148.0	0.0		233.0	47.0	NM_001135111	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Frame_Shift_Del	DEL	ENST00000373231.4	hg19	CCDS4842.1																																																																																			.	.		0.607	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460	
SLC26A7	115111	hgsc.bcm.edu	37	8	92352747	92352747	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:92352747delA	ENST00000276609.3	+	8	1233	c.994delA	c.(994-996)aaafs	p.K333fs	SLC26A7_ENST00000523719.1_Frame_Shift_Del_p.K333fs|SLC26A7_ENST00000309536.2_Frame_Shift_Del_p.K333fs	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7									p.K333fs*20(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			AGGATCTGCCAAAAAATTCAA	0.502																																					p.A331fs		Atlas-Indel,Pindel	.											.	SLC26A7	207	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.993delC						.						97.0	90.0	92.0					8																	92352747		2203	4300	6503	SO:0001589	frameshift_variant	115111	exon8			.	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"""Solute carriers"""	14467	protein-coding gene	gene with protein product		608479	"""solute carrier family 26, member 7"""			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.994delA	chr8.hg19:g.92352747delA	ENSP00000276609:p.Lys333fs	77.0	0.0		80.0	33.0	NM_052832		Frame_Shift_Del	DEL	ENST00000276609.3	hg19	CCDS6254.1																																																																																			.	.		0.502	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1		
SCAP	22937	hgsc.bcm.edu	37	3	47455478	47455481	+	Frame_Shift_Del	DEL	CTGT	CTGT	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CTGT	CTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47455478_47455481delCTGT	ENST00000265565.5	-	23	4115_4118	c.3703_3706delACAG	c.(3703-3708)acagtcfs	p.TV1235fs	SCAP_ENST00000441517.2_Frame_Shift_Del_p.TV979fs|SCAP_ENST00000545718.1_Frame_Shift_Del_p.TV842fs	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	1235	Interaction with SREBF2. {ECO:0000250}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CCCAGGTAGACTGTCTGTAACAGG	0.583																																					p.1235_1236del	Pancreas(149;978 1908 29304 37806 46700)	Atlas-Indel,Pindel	.											.	SCAP	88	.	0			c.3704_3707del						.																																			SO:0001589	frameshift_variant	22937	exon23			.	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.3703_3706delACAG	chr3.hg19:g.47455482_47455485delCTGT	ENSP00000265565:p.Thr1235fs	77.0	0.0		90.0	36.0	NM_012235	Q8N2E0|Q8WUA1	Frame_Shift_Del	DEL	ENST00000265565.5	hg19	CCDS2755.2																																																																																			.	.		0.583	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	
NAIP	4671	hgsc.bcm.edu	37	5	70280772	70280772	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:70280772delA	ENST00000517649.1	-	12	2394	c.2104delT	c.(2104-2106)tcafs	p.S702fs	NAIP_ENST00000503719.2_Frame_Shift_Del_p.S540fs|NAIP_ENST00000523981.1_Frame_Shift_Del_p.S540fs|NAIP_ENST00000194097.4_Frame_Shift_Del_p.S702fs|NAIP_ENST00000508426.2_Frame_Shift_Del_p.S702fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	702	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		AAGCAACATGAAAAAAACCCT	0.438																																					p.S702fs		Atlas-INDEL	.											.	NAIP	38	.	0			c.2105delC						.																																			SO:0001589	frameshift_variant	4671	exon12			.	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"""Baculoviral IAP repeat containing"", ""Nucleotide-binding domain and leucine rich repeat containing"""	7634	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1"", ""NLR family, BIR domain containing 1"""	600355	"""baculoviral IAP repeat-containing 1"""	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.2104delT	chr5.hg19:g.70280772delA	ENSP00000428657:p.Ser702fs	248.0	0.0		214.0	22.0	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.		0.438	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536	
KMT2B	9757	hgsc.bcm.edu	37	19	36223002	36223002	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:36223002delG	ENST00000222270.7	+	27	5631	c.5631delG	c.(5629-5631)ttgfs	p.L1877fs	KMT2B_ENST00000420124.1_Frame_Shift_Del_p.L1877fs|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1877					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G1881fs*16(1)									GGAGGCCCTTGGGGGGTGTCT	0.672																																					p.L1877fs		Atlas-Indel,Pindel	.											.	MLL4	229	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.5630delT						.						11.0	12.0	12.0					19																	36223002		1860	4086	5946	SO:0001589	frameshift_variant	8085	exon27			.	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5631delG	chr19.hg19:g.36223002delG	ENSP00000222270:p.Leu1877fs	90.0	0.0		66.0	27.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Del	DEL	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.672	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
PADI1	29943	hgsc.bcm.edu	37	1	17555492	17555492	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:17555492delC	ENST00000375471.4	+	8	967	c.875delC	c.(874-876)gccfs	p.A292fs		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	292					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	TTCCGCATGGCCCCCTGGATC	0.637																																					p.A292fs	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-Indel,Pindel	.											.	PADI1	77	.	0			c.874delG						.						44.0	33.0	37.0					1																	17555492		2202	4300	6502	SO:0001589	frameshift_variant	29943	exon8			.	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.875delC	chr1.hg19:g.17555492delC	ENSP00000364620:p.Ala292fs	56.0	0.0		52.0	23.0	NM_013358	A1L4K6|Q70SX6	Frame_Shift_Del	DEL	ENST00000375471.4	hg19	CCDS178.1																																																																																			.	.		0.637	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
AGBL2	79841	hgsc.bcm.edu	37	11	47701557	47701557	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47701557delG	ENST00000525123.1	-	13	2269	c.1984delC	c.(1984-1986)cttfs	p.L663fs	AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000528244.1_Frame_Shift_Del_p.L625fs|AGBL2_ENST00000357610.3_Frame_Shift_Del_p.L663fs|AGBL2_ENST00000298861.4_Frame_Shift_Del_p.L663fs	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	663						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						AAGTCCAGAAGGGTGTCACAG	0.428																																					p.L662fs		Atlas-Indel,Pindel	.											.	AGBL2	73	.	0			c.1985delT						.						111.0	106.0	107.0					11																	47701557		2201	4298	6499	SO:0001589	frameshift_variant	79841	exon13			.		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"""cytoplasmic carboxypeptidase 2"""					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1984delC	chr11.hg19:g.47701557delG	ENSP00000435582:p.Leu663fs	140.0	0.0		109.0	45.0	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Frame_Shift_Del	DEL	ENST00000525123.1	hg19	CCDS7944.1																																																																																			.	.		0.428	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
RIMBP3C	150221	hgsc.bcm.edu	37	22	21902792	21902792	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:21902792delC	ENST00000433039.1	-	1	2958	c.2474delG	c.(2473-2475)ggcfs	p.G825fs	RIMBP3C_ENST00000331505.5_Frame_Shift_Del_p.G731fs|UBE2L3_ENST00000458578.2_5'Flank|RN7SKP221_ENST00000410420.1_RNA	NM_001128633.1	NP_001122105.1	A6NJZ7	RIM3C_HUMAN	RIMS binding protein 3C	825										large_intestine(1)	1						AGCCGCCGAGCCCCCCATTTC	0.622																																					p.G825fs		Atlas-INDEL	.											.	RIMBP3C	6	.	0			c.2475delC						.																																			SO:0001589	frameshift_variant	150221	exon1			.		CCDS46669.1	22q11.21	2008-10-21			ENSG00000183246	ENSG00000183246			33892	protein-coding gene	gene with protein product		612701				17855024	Standard	NM_001128633		Approved		uc002zuq.4	A6NJZ7	OTTHUMG00000150825	ENST00000433039.1:c.2474delG	chr22.hg19:g.21902792delC	ENSP00000390630:p.Gly825fs	174.0	0.0		169.0	17.0	NM_001128633		Frame_Shift_Del	DEL	ENST00000433039.1	hg19	CCDS46669.1																																																																																			.	.		0.622	RIMBP3C-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		XM_036942	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24470144	24470144	+	Splice_Site	DEL	T	T	-	rs375757538		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:24470144delT	ENST00000335125.6	+	4	605		c.e4+2		DHRS4L2_ENST00000382755.4_Splice_Site|DHRS4L2_ENST00000545240.1_Intron|DHRS4L2_ENST00000397071.1_Intron|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000537912.1_Intron|DHRS4L2_ENST00000534993.1_Intron|DHRS4L2_ENST00000558753.1_Intron	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		GAAACGAGGGTACAGAGAGTG	0.552																																					.		Atlas-Indel,Pindel	.											.	DHRS4L2	29	.	0			c.176+1T>-						.						90.0	95.0	94.0					14																	24470144		2196	4299	6495	SO:0001630	splice_region_variant	317749	exon4			.		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.479+2T>-	chr14.hg19:g.24470144delT		555.0	0.0		577.0	209.0	NM_001193636	Q3YLD4	Splice_Site	DEL	ENST00000335125.6	hg19	CCDS9606.2																																																																																			.	.		0.552	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		Intron
EPHA3	2042	hgsc.bcm.edu	37	3	89499362	89499363	+	Frame_Shift_Ins	INS	-	-	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:89499362_89499363insC	ENST00000336596.2	+	15	2757_2758	c.2532_2533insC	c.(2533-2535)cccfs	p.P845fs	EPHA3_ENST00000494014.1_Frame_Shift_Ins_p.P845fs	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	845	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		ATCGACTGCCACCCCCCATGGA	0.465										TSP Lung(6;0.00050)																											p.P844fs		Atlas-Indel,Pindel	.											.	EPHA3	501	.	0			c.2532_2533insC						.																																			SO:0001589	frameshift_variant	2042	exon15			.	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2538dupC	chr3.hg19:g.89499368_89499368dupC	ENSP00000337451:p.Pro845fs	226.0	0.0		272.0	112.0	NM_005233	Q9H2V3|Q9H2V4	Frame_Shift_Ins	INS	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.465	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62882287	62882288	+	Intron	DEL	AA	AA	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:62882287_62882288delAA	ENST00000584306.1	-	7	3356				LRRC37A3_ENST00000400877.3_Intron|LRRC37A3_ENST00000339474.5_Intron|LRRC37A3_ENST00000319651.5_Intron	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3							integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TAAGATTTCTAAAAAAAAAAGA	0.307																																					.		Atlas-INDEL	.											.	LRRC37A3	75	.	0			.						.																																			SO:0001627	intron_variant	374819	.			.	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.2826-3TT>-	chr17.hg19:g.62882295_62882296delAA		264.0	0.0		234.0	22.0	.	Q49A01|Q49A80|Q8NB33	Splice_Site	DEL	ENST00000584306.1	hg19	CCDS32708.1																																																																																			.	.		0.307	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
OR5D18	219438	hgsc.bcm.edu	37	11	55587264	55587264	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55587264delC	ENST00000333976.4	+	1	179	c.159delC	c.(157-159)aacfs	p.N53fs		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TCAAAATCAACCCCAAACTGC	0.448																																					p.N53fs		Atlas-Indel,Pindel	.											.	OR5D18	121	.	0			c.158delA						.						238.0	218.0	224.0					11																	55587264		2200	4296	6496	SO:0001589	frameshift_variant	219438	exon1			.	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.159delC	chr11.hg19:g.55587264delC	ENSP00000335025:p.Asn53fs	112.0	0.0		143.0	32.0	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Frame_Shift_Del	DEL	ENST00000333976.4	hg19	CCDS31510.1																																																																																			.	.		0.448	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
LRRC72	100506049	hgsc.bcm.edu	37	7	16577286	16577286	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:16577286delA	ENST00000401542.2	+	3	256	c.199delA	c.(199-201)aaafs	p.K68fs		NM_001195280.1	NP_001182209.1	A6NJI9	LRC72_HUMAN	leucine rich repeat containing 72	68																	TTCTAGGTTTAAAAAATTAAA	0.284																																					p.F66fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.198delT						.																																			SO:0001589	frameshift_variant	100506049	exon3			.		CCDS56464.1	7p21.1	2011-10-07			ENSG00000205858	ENSG00000205858			42972	protein-coding gene	gene with protein product							Standard	NM_001195280		Approved		uc022aaf.1	A6NJI9	OTTHUMG00000152446	ENST00000401542.2:c.199delA	chr7.hg19:g.16577286delA	ENSP00000384971:p.Lys68fs	616.0	0.0		927.0	273.0	NM_001195280		Frame_Shift_Del	DEL	ENST00000401542.2	hg19	CCDS56464.1																																																																																			.	.		0.284	LRRC72-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326249.2		
FOXK2	3607	hgsc.bcm.edu	37	17	80521292	80521293	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:80521292_80521293delAG	ENST00000335255.5	+	2	656_657	c.482_483delAG	c.(481-483)aagfs	p.K161fs		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	161					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			TCCAGCGAGAAGAGAGAGAAGC	0.535																																					p.161_161del		Atlas-Indel,Pindel	.											.	FOXK2	46	.	0			c.481_482del						.																																			SO:0001589	frameshift_variant	3607	exon2			.	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.482_483delAG	chr17.hg19:g.80521298_80521299delAG	ENSP00000335677:p.Lys161fs	140.0	0.0		73.0	45.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Frame_Shift_Del	DEL	ENST00000335255.5	hg19	CCDS11813.1																																																																																			.	.		0.535	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
COL1A2	1278	hgsc.bcm.edu	37	7	94052290	94052290	+	Frame_Shift_Del	DEL	C	C	-	rs145355907		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:94052290delC	ENST00000297268.6	+	40	2896	c.2425delC	c.(2425-2427)cccfs	p.P810fs		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	810			Missing (in OI2). {ECO:0000269|PubMed:1339453}.|Missing (in OI2). {ECO:0000269|PubMed:18996919}.		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)	CCCTCCTGGTCCCCCTGGTCC	0.532										HNSCC(75;0.22)																											p.G808fs		Atlas-INDEL	.											.	COL1A2	240	.	0			c.2424delT						.						161.0	159.0	159.0					7																	94052290		2203	4300	6503	SO:0001589	frameshift_variant	1278	exon40			.	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.2425delC	chr7.hg19:g.94052290delC	ENSP00000297268:p.Pro810fs	169.0	0.0		178.0	11.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Frame_Shift_Del	DEL	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.532	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
SORCS3	22986	hgsc.bcm.edu	37	10	106401491	106401491	+	Frame_Shift_Del	DEL	C	C	-	rs373150688		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:106401491delC	ENST00000369701.3	+	1	633	c.406delC	c.(406-408)cccfs	p.P137fs		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	137					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CCGGGCGCAGCCCCCAATCAC	0.716																																					p.Q135fs	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-Indel,Pindel	.											.	SORCS3	282	.	0			c.405delG						.						3.0	3.0	3.0					10																	106401491		1634	3275	4909	SO:0001589	frameshift_variant	22986	exon1			.	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.406delC	chr10.hg19:g.106401491delC	ENSP00000358715:p.Pro137fs	68.0	0.0		72.0	30.0	NM_014978	Q5VXF9|Q9NQJ2	Frame_Shift_Del	DEL	ENST00000369701.3	hg19	CCDS7558.1																																																																																			.	.		0.716	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
MARCH4	57574	hgsc.bcm.edu	37	2	217124185	217124186	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:217124185_217124186insG	ENST00000273067.4	-	4	2848_2849	c.1082_1083insC	c.(1081-1083)cctfs	p.P361fs	AC012513.6_ENST00000417481.1_RNA	NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	361						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		CAGCCTGGGCAGGGCCCTGCTC	0.639																																					p.P361fs		Atlas-Indel,Pindel	.											.	MARCH4	50	.	0			c.1083_1084insC						.																																			SO:0001589	frameshift_variant	57574	exon4			.	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	29269	protein-coding gene	gene with protein product		608208	"""membrane-associated ring finger (C3HC4) 4"""			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.1083dupC	chr2.hg19:g.217124188_217124188dupG	ENSP00000273067:p.Pro361fs	113.0	0.0		89.0	31.0	NM_020814	Q4KMN7|Q86WR8	Frame_Shift_Ins	INS	ENST00000273067.4	hg19	CCDS33376.1																																																																																			.	.		0.639	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814	
DYRK1A	1859	hgsc.bcm.edu	37	21	38852951	38852951	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:38852951delA	ENST00000398960.2	+	4	414	c.339delA	c.(337-339)gcafs	p.A113fs	DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000338785.3_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000398956.2_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000321219.8_Frame_Shift_Del_p.A113fs|DYRK1A_ENST00000339659.4_Frame_Shift_Del_p.A104fs|DYRK1A_ENST00000451934.1_Frame_Shift_Del_p.A113fs	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	113					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TTTACTATGCAAAAAAGAAGC	0.363																																					p.A113fs	Melanoma(114;464 1602 31203 43785 45765)	Atlas-Indel,Pindel	.											.	DYRK1A	85	.	0			c.338delC						.						98.0	97.0	98.0					21																	38852951		2203	4300	6503	SO:0001589	frameshift_variant	1859	exon4			.	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.339delA	chr21.hg19:g.38852951delA	ENSP00000381932:p.Ala113fs	216.0	0.0		225.0	70.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Frame_Shift_Del	DEL	ENST00000398960.2	hg19	CCDS42925.1																																																																																			.	.		0.363	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
GPC2	221914	hgsc.bcm.edu	37	7	99769524	99769525	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:99769524_99769525insG	ENST00000292377.2	-	7	1214_1215	c.1047_1048insC	c.(1045-1050)cccgacfs	p.D350fs	GPC2_ENST00000471050.1_5'UTR	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	350					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGCACCGGGTCGGGGGGGCCGC	0.723																																					p.D350fs		Atlas-Indel,Pindel	.											.	GPC2	49	.	0			c.1048_1049insC						.			14,3444		1,12,1716						0.2	0.0			4	22,6962		2,18,3472	no	frameshift	GPC2	NM_152742.1		3,30,5188	A1A1,A1R,RR		0.315,0.4049,0.3448				36,10406				SO:0001589	frameshift_variant	221914	exon7			.	BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"""Proteoglycans / Cell Surface : Glypicans"""	4450	protein-coding gene	gene with protein product	"""glypican proteoglycan 2, cerebroglycan proteoglycan"""		"""glypican 2 (cerebroglycan)"""			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.1048dupC	chr7.hg19:g.99769531_99769531dupG	ENSP00000292377:p.Asp350fs	71.0	0.0		59.0	19.0	NM_152742	A4D2A7	Frame_Shift_Ins	INS	ENST00000292377.2	hg19	CCDS5689.1																																																																																			.	.		0.723	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742	
BHLHE41	79365	hgsc.bcm.edu	37	12	26275589	26275590	+	In_Frame_Ins	INS	-	-	GCT			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:26275589_26275590insGCT	ENST00000242728.4	-	5	1205_1206	c.858_859insAGC	c.(856-861)ggcggc>ggcAGCggc	p.286_287GG>GSG	RP11-283G6.3_ENST00000545819.1_RNA|RP11-283G6.3_ENST00000535914.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	286					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						ccgctgccgccgccgcGGGAAT	0.787																																					p.G287delinsSG		Atlas-INDEL	.											.	BHLHE41	20	.	0			c.859_860insAGC						.																																			SO:0001652	inframe_insertion	79365	exon5			.	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"""Basic helix-loop-helix proteins"""	16617	protein-coding gene	gene with protein product	"""differentially expressed in chondrocytes 2"", ""Enhancer-of-split and hairy-related protein 1"""	606200	"""basic helix-loop-helix domain containing, class B, 3"""	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.858_859insAGC	chr12.hg19:g.26275589_26275590insGCT	ENSP00000242728:p.Gly286_Gly287insSer	46.0	0.0		26.0	10.0	NM_030762	A2I2N8	In_Frame_Ins	INS	ENST00000242728.4	hg19	CCDS8706.1																																																																																			.	.		0.787	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762	
RPN2	6185	hgsc.bcm.edu	37	20	35860726	35860726	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:35860726delC	ENST00000237530.6	+	14	1920	c.1609delC	c.(1609-1611)cccfs	p.P538fs	RPN2_ENST00000470352.1_Intron|RPN2_ENST00000373622.5_Frame_Shift_Del_p.P506fs	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	538					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				TGAGAAGAGGCCCCCCACCGT	0.577																																					p.R536fs		Atlas-Indel,Pindel	.											.	RPN2	45	.	0			c.1608delG						.						213.0	186.0	195.0					20																	35860726		2203	4300	6503	SO:0001589	frameshift_variant	6185	exon14			.	Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"""oligosaccharyltransferase complex subunit (non-catalytic)"""	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1609delC	chr20.hg19:g.35860726delC	ENSP00000237530:p.Pro538fs	72.0	0.0		81.0	33.0	NM_002951	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Frame_Shift_Del	DEL	ENST00000237530.6	hg19	CCDS13291.1																																																																																			.	.		0.577	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951	
SSH2	85464	hgsc.bcm.edu	37	17	27959374	27959375	+	Frame_Shift_Ins	INS	-	-	G	rs376316249		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:27959374_27959375insG	ENST00000269033.3	-	15	2907_2908	c.2756_2757insC	c.(2755-2757)ccafs	p.P919fs	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Frame_Shift_Ins_p.P946fs	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	919					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ATGAATGTTCTGGGGGGGCTTC	0.48																																					p.P919fs		Atlas-Indel,Pindel	.											.	SSH2	107	.	0			c.2757_2758insC						.																																			SO:0001589	frameshift_variant	85464	exon15			.	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2757dupC	chr17.hg19:g.27959381_27959381dupG	ENSP00000269033:p.Pro919fs	63.0	0.0		70.0	22.0	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Frame_Shift_Ins	INS	ENST00000269033.3	hg19	CCDS11253.1																																																																																			.	.		0.480	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	
PIGZ	80235	hgsc.bcm.edu	37	3	196674301	196674301	+	Frame_Shift_Del	DEL	C	C	-	rs200103570		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:196674301delC	ENST00000412723.1	-	3	1613	c.1467delG	c.(1465-1467)gggfs	p.G489fs		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	489					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		AGTCCTCAGTCCCCCCCATGT	0.627																																					p.T490fs		Atlas-Indel,Pindel	.											.	PIGZ	34	.	0			c.1468delA						.						65.0	64.0	64.0					3																	196674301		2203	4300	6503	SO:0001589	frameshift_variant	80235	exon3			.	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.1467delG	chr3.hg19:g.196674301delC	ENSP00000413405:p.Gly489fs	64.0	0.0		56.0	17.0	NM_025163	Q9H9G6	Frame_Shift_Del	DEL	ENST00000412723.1	hg19	CCDS3324.1																																																																																			.	.		0.627	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
ATF4	468	hgsc.bcm.edu	37	22	39918267	39918267	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39918267delG	ENST00000337304.2	+	2	1598	c.716delG	c.(715-717)aggfs	p.R239fs	ATF4_ENST00000396680.1_Frame_Shift_Del_p.R239fs|ATF4_ENST00000404241.2_Frame_Shift_Del_p.R239fs	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	239					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	CCCTCTACCAGGGGCTCTCCA	0.537																																					p.R239fs		Atlas-Indel,Pindel	.											.	ATF4	27	.	0			c.715delA						.						19.0	20.0	19.0					22																	39918267		2203	4299	6502	SO:0001589	frameshift_variant	468	exon3			.	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.716delG	chr22.hg19:g.39918267delG	ENSP00000336790:p.Arg239fs	411.0	0.0		348.0	136.0	NM_182810	Q9UH31	Frame_Shift_Del	DEL	ENST00000337304.2	hg19	CCDS13996.1																																																																																			.	.		0.537	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
ANKRD11	29123	hgsc.bcm.edu	37	16	89348566	89348568	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:89348566_89348568delTCT	ENST00000301030.4	-	9	4842_4844	c.4382_4384delAGA	c.(4381-4386)aagaga>aga	p.K1461del	ANKRD11_ENST00000378330.2_In_Frame_Del_p.K1461del	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1461	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		tgtttctctctcttcttcttctc	0.483																																					p.1461_1462del		Atlas-Indel,Pindel	.											.	ANKRD11	195	.	0			c.4383_4385del						.			0,4264		0,0,2132						5.1	0.0			86	3,8251		1,1,4125	no	coding	ANKRD11	NM_013275.4		1,1,6257	A1A1,A1R,RR		0.0363,0.0,0.024				3,12515				SO:0001651	inframe_deletion	29123	exon10			.	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4382_4384delAGA	chr16.hg19:g.89348575_89348577delTCT	ENSP00000301030:p.Lys1461del	70.0	0.0		63.0	29.0	NM_001256182	Q6NTG1|Q6QMF8	In_Frame_Del	DEL	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.		0.483	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
UBA2	10054	hgsc.bcm.edu	37	19	34949675	34949675	+	Splice_Site	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:34949675delT	ENST00000246548.4	+	13	1317	c.1247delT	c.(1246-1248)att>at	p.I416fs	UBA2_ENST00000592791.1_5'UTR|UBA2_ENST00000439527.2_Splice_Site_p.I320fs	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	416					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CCTCCAAAGATTTTTTTGAAT	0.388																																					p.I416fs		Atlas-Indel,Pindel	.											.	UBA2	53	.	0			c.1246delA						.						88.0	91.0	90.0					19																	34949675		2203	4300	6503	SO:0001630	splice_region_variant	10054	exon13			.	BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"""Ubiquitin-like modifier activating enzymes"""	30661	protein-coding gene	gene with protein product	"""UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"""	613295	"""SUMO1 activating enzyme subunit 2"""	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.1246-1T>-	chr19.hg19:g.34949675delT		170.0	0.0		142.0	12.0	NM_005499	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Frame_Shift_Del	DEL	ENST00000246548.4	hg19	CCDS12439.1																																																																																			.	.		0.388	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499	Frame_Shift_Del
CNGB1	1258	hgsc.bcm.edu	37	16	57918254	57918254	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:57918254delG	ENST00000251102.8	-	33	3630	c.3570delC	c.(3568-3570)cccfs	p.P1190fs	CNGB1_ENST00000564448.1_Frame_Shift_Del_p.P1184fs	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	1190					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						CCGGGGGCTCGGGGGGCGTCC	0.741																																					p.E1191fs	Colon(156;1293 1853 16336 28962 38659)	Atlas-Indel,Pindel	.											.	CNGB1	105	.	0			c.3571delG						.						10.0	12.0	12.0					16																	57918254		1713	3794	5507	SO:0001589	frameshift_variant	1258	exon33			.	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.3570delC	chr16.hg19:g.57918254delG	ENSP00000251102:p.Pro1190fs	73.0	0.0		75.0	27.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Frame_Shift_Del	DEL	ENST00000251102.8	hg19	CCDS42169.1																																																																																			.	.		0.741	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21740616	21740616	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:21740616delG	ENST00000434111.1	+	1	2954	c.2469delG	c.(2467-2469)atgfs	p.M823fs	RN7SKP63_ENST00000363187.1_RNA	NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	823																	CCCTGGAAATGGGGGGCTCGG	0.617																																					p.M823fs		Atlas-INDEL	.											.	RIMBP3C	6	.	0			c.2468delT						.																																			SO:0001589	frameshift_variant	150221	exon1			.		CCDS46668.1	22q11.21	2008-10-23			ENSG00000196934	ENSG00000274600			33891	protein-coding gene	gene with protein product		612700				17855024	Standard	NM_001128635		Approved			A6NNM3	OTTHUMG00000150819	ENST00000434111.1:c.2469delG	chr22.hg19:g.21740616delG	ENSP00000407925:p.Met823fs	200.0	0.0		159.0	19.0	NM_001128633		Frame_Shift_Del	DEL	ENST00000434111.1	hg19	CCDS46668.1																																																																																			.	.		0.617	RIMBP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320196.2	XM_036936	
CSN1S1	1446	hgsc.bcm.edu	37	4	70810695	70810695	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:70810695delA	ENST00000246891.4	+	15	579	c.530delA	c.(529-531)gaafs	p.E177fs	CSN1S1_ENST00000505782.1_Frame_Shift_Del_p.E161fs|CSN1S1_ENST00000444405.3_Frame_Shift_Del_p.E168fs|CSN1S1_ENST00000507772.1_Frame_Shift_Del_p.E169fs|CSN1S1_ENST00000507763.1_Frame_Shift_Del_p.E168fs	NM_001890.1	NP_001881.1	P47710	CASA1_HUMAN	casein alpha s1	177						extracellular region (GO:0005576)|extracellular space (GO:0005615)	transporter activity (GO:0005215)			lung(5)|prostate(1)|upper_aerodigestive_tract(1)	7						GAAAATTATGAAAAAAATAAC	0.393																																					p.E177fs		Atlas-Indel,Pindel	.											.	CSN1S1	20	.	0			c.529delG						.						165.0	155.0	158.0					4																	70810695		1858	4101	5959	SO:0001589	frameshift_variant	1446	exon15			.	X78416	CCDS47067.1, CCDS54769.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000126545	ENSG00000126545			2445	protein-coding gene	gene with protein product		115450	"""casein, alpha"""	CASA, CSN1		9050925, 7619062	Standard	NM_001890		Approved		uc003hep.1	P47710	OTTHUMG00000160843	ENST00000246891.4:c.530delA	chr4.hg19:g.70810695delA	ENSP00000246891:p.Glu177fs	141.0	0.0		154.0	68.0	NM_001890	A1A510|A1A511|E9PB60|Q4PNR5	Frame_Shift_Del	DEL	ENST00000246891.4	hg19	CCDS47067.1																																																																																			.	.		0.393	CSN1S1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362629.1		
PML	5371	hgsc.bcm.edu	37	15	74337203	74337203	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:74337203delC	ENST00000268058.3	+	9	2599	c.2503delC	c.(2503-2505)cccfs	p.P836fs	PML_ENST00000565898.1_Frame_Shift_Del_p.P788fs	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	836					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|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)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CACCACGTTGCCCCCTGCCCA	0.637			T	"""RARA, PAX5"""	"""APL, ALL"""																																p.L834fs		Atlas-Indel,Pindel	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.2502delG						.						45.0	47.0	46.0					15																	74337203		2196	4294	6490	SO:0001589	frameshift_variant	5371	exon9			.	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.2503delC	chr15.hg19:g.74337203delC	ENSP00000268058:p.Pro836fs	75.0	0.0		82.0	28.0	NM_033238	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Frame_Shift_Del	DEL	ENST00000268058.3	hg19	CCDS10255.1																																																																																			.	.		0.637	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
RSF1	51773	hgsc.bcm.edu	37	11	77411876	77411876	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:77411876delT	ENST00000308488.6	-	6	2700	c.2398delA	c.(2398-2400)agafs	p.R800fs	RSF1_ENST00000360355.2_Frame_Shift_Del_p.R769fs|RSF1_ENST00000480887.1_Frame_Shift_Del_p.R548fs			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	800					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CCTTCCCCTCTTTTTTTATCA	0.368																																					p.R800fs		Atlas-Indel,Pindel	.											.	RSF1	105	.	0			c.2399delG						.						145.0	145.0	145.0					11																	77411876		2200	4292	6492	SO:0001589	frameshift_variant	51773	exon6			.	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.2398delA	chr11.hg19:g.77411876delT	ENSP00000311513:p.Arg800fs	40.0	0.0		36.0	14.0	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Frame_Shift_Del	DEL	ENST00000308488.6	hg19	CCDS8253.1																																																																																			.	.		0.368	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
DNAH10	196385	hgsc.bcm.edu	37	12	124403305	124403305	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:124403305delG	ENST00000409039.3	+	64	10986	c.10961delG	c.(10960-10962)aggfs	p.R3654fs		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3654					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCAGCCAGGAGGGGGGCCATC	0.567																																					p.R3654fs		Atlas-Indel,Pindel	.											.	DNAH10	888	.	0			c.10960delA						.						37.0	41.0	40.0					12																	124403305		1932	4133	6065	SO:0001589	frameshift_variant	196385	exon64			.	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.10961delG	chr12.hg19:g.124403305delG	ENSP00000386770:p.Arg3654fs	76.0	0.0		97.0	23.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Frame_Shift_Del	DEL	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.		0.567	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
NPY4R	5540	hgsc.bcm.edu	37	10	47087814	47087814	+	Frame_Shift_Del	DEL	C	C	-	rs555663093	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:47087814delC	ENST00000395716.1	+	2	1116	c.1031delC	c.(1030-1032)gccfs	p.A344fs	NPY4R_ENST00000374312.1_Frame_Shift_Del_p.A344fs			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	344					blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										CAGCAGAGCGCCCCCCTGGAG	0.562													CCCCCC|CCCCCC|CCCCC|deletion	14	0.00279553	0.0091	0.0029	5008	,	,		42658	0.0		0.0	False		,,,				2504	0.0				p.A344fs		Atlas-Indel,Pindel	.											.	PPYR1	54	.	0			c.1030delG						.			74,4188		23,28,2080	126.0	128.0	127.0			-9.9	0.0	10		127	104,8148		50,4,4072	no	frameshift	PPYR1	NM_005972.4		73,32,6152	A1A1,A1R,RR		1.2603,1.7363,1.4224			47087814	178,12336	2203	4300	6503	SO:0001589	frameshift_variant	5540	exon3			.		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.1031delC	chr10.hg19:g.47087814delC	ENSP00000379066:p.Ala344fs	215.0	0.0		224.0	25.0	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Frame_Shift_Del	DEL	ENST00000395716.1	hg19	CCDS31193.1																																																																																			.	.		0.562	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
NOVA2	4858	hgsc.bcm.edu	37	19	46476610	46476610	+	5'UTR	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:46476610delG	ENST00000263257.5	-	0	194				NOVA2_ENST00000599462.1_5'Flank	NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2						regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		CGGGCTCCATGGGGGGGGCCT	0.761																																					p.M1fs		Atlas-INDEL	.											.	NOVA2	38	.	0			c.1delA						.						2.0	3.0	3.0					19																	46476610		1128	2587	3715	SO:0001623	5_prime_UTR_variant	4858	exon1			.	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"""neuro-oncological ventral antigen 3"""	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.-1C>-	chr19.hg19:g.46476610delG		36.0	0.0		27.0	11.0	NM_002516	O43267|Q9UEA1	Frame_Shift_Del	DEL	ENST00000263257.5	hg19	CCDS12679.1																																																																																			.	.		0.761	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516	
LY6G6D	58530	hgsc.bcm.edu	37	6	31683313	31683313	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:31683313delC	ENST00000375825.3	+	2	90	c.90delC	c.(88-90)agcfs	p.S30fs	XXbac-BPG32J3.20_ENST00000461287.1_5'Flank|MEGT1_ENST00000503322.1_Frame_Shift_Del_p.S279fs|LY6G6F_ENST00000556581.1_Frame_Shift_Del_p.S279fs|LY6G6E_ENST00000383418.4_5'Flank|LY6G6E_ENST00000409239.1_5'Flank	NM_021246.2	NP_067069.2	O95868	LY66D_HUMAN	lymphocyte antigen 6 complex, locus G6D	30	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|plasma membrane (GO:0005886)				central_nervous_system(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						GTGGTGGAAGCCCCAGCAGTT	0.622																																					p.S30fs		Atlas-INDEL	.											.	LY6G6D	11	.	0			c.89delG						.						78.0	73.0	75.0					6																	31683313		1511	2709	4220	SO:0001589	frameshift_variant	58530	exon2			.		CCDS34404.1	6p21.3	2008-08-29	2002-07-29	2002-08-01	ENSG00000244355	ENSG00000244355			13935	protein-coding gene	gene with protein product		606038	"""chromosome 6 open reading frame 23"""	C6orf23		12079290	Standard	NM_021246		Approved	MEGT1, Ly6-D, G6D, LY6-D, NG25		O95868	OTTHUMG00000137370	ENST00000375825.3:c.90delC	chr6.hg19:g.31683313delC	ENSP00000364985:p.Ser30fs	110.0	0.0		136.0	11.0	NM_021246	A2BEY8|B0UXC1|B0V019|B0V1Y6|Q4VX50	Frame_Shift_Del	DEL	ENST00000375825.3	hg19	CCDS34404.1																																																																																			.	.		0.622	LY6G6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144875.2		
ARAP1	116985	hgsc.bcm.edu	37	11	72437830	72437830	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:72437830delG	ENST00000393609.3	-	3	546	c.344delC	c.(343-345)ccafs	p.P116fs	ARAP1_ENST00000359373.5_Frame_Shift_Del_p.P116fs|ARAP1_ENST00000455638.2_Frame_Shift_Del_p.P116fs	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	116					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						CGGGATGGGTGGGGCAGCGGG	0.697																																					p.P115fs	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-Indel,Pindel	.											.	ARAP1	168	.	0			c.345delA						.						8.0	10.0	9.0					11																	72437830		1787	3854	5641	SO:0001589	frameshift_variant	116985	exon3			.	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.344delC	chr11.hg19:g.72437830delG	ENSP00000377233:p.Pro116fs	166.0	0.0		174.0	59.0	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Del	DEL	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.		0.697	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
RIC3	79608	hgsc.bcm.edu	37	11	8159886	8159887	+	Frame_Shift_Ins	INS	-	-	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:8159886_8159887insT	ENST00000309737.6	-	3	358_359	c.359_360insA	c.(358-360)aagfs	p.K120fs	RIC3_ENST00000539720.1_Frame_Shift_Ins_p.K71fs|RIC3_ENST00000335425.7_Intron|RIC3_ENST00000343202.4_Frame_Shift_Ins_p.K120fs|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000425599.2_Frame_Shift_Ins_p.K120fs			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	120					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.K120N(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TTGTTTTCCCCTTTGAGAGCTG	0.441																																					p.K120fs		Atlas-Indel,Pindel	.											.	RIC3	42	.	1	Substitution - Missense(1)	lung(1)	c.360_361insA						.																																			SO:0001589	frameshift_variant	79608	exon3			.		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"""resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"""			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.360dupA	chr11.hg19:g.8159889_8159889dupT	ENSP00000308820:p.Lys120fs	62.0	0.0		60.0	26.0	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Frame_Shift_Ins	INS	ENST00000309737.6	hg19	CCDS55742.1																																																																																			.	.		0.441	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
RBBP6	5930	hgsc.bcm.edu	37	16	24580479	24580479	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:24580479delA	ENST00000319715.4	+	17	2900	c.2468delA	c.(2467-2469)gaafs	p.E823fs	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Frame_Shift_Del_p.E789fs	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	823					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		GACCCATTTGAAAAAGAACGC	0.378																																					p.E823fs		Atlas-Indel,Pindel	.											.	RBBP6	158	.	0			c.2467delG						.						51.0	54.0	53.0					16																	24580479		2195	4300	6495	SO:0001589	frameshift_variant	5930	exon17			.		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.2468delA	chr16.hg19:g.24580479delA	ENSP00000317872:p.Glu823fs	336.0	0.0		317.0	119.0	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Frame_Shift_Del	DEL	ENST00000319715.4	hg19	CCDS10621.1																																																																																			.	.		0.378	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
CEACAM5	1048	hgsc.bcm.edu	37	19	42224866	42224866	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:42224866delC	ENST00000221992.6	+	8	1910	c.1796delC	c.(1795-1797)tccfs	p.S599fs	CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000398599.4_Frame_Shift_Del_p.S598fs|CEACAM5_ENST00000405816.1_Frame_Shift_Del_p.S599fs	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	599	Ig-like 7.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CCCATCATTTCCCCCCCAGAC	0.547																																					p.S599fs		Atlas-Indel,Pindel	.											.	CEACAM5	84	.	0			c.1795delT						.						136.0	141.0	139.0					19																	42224866		2203	4300	6503	SO:0001589	frameshift_variant	1048	exon8			.	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1796delC	chr19.hg19:g.42224866delC	ENSP00000221992:p.Ser599fs	156.0	0.0		176.0	64.0	NM_004363	H9KVA7	Frame_Shift_Del	DEL	ENST00000221992.6	hg19	CCDS12584.1																																																																																			.	.		0.547	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
ZNF500	26048	hgsc.bcm.edu	37	16	4802884	4802885	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:4802884_4802885insG	ENST00000219478.6	-	6	1234_1235	c.935_936insC	c.(934-936)ccafs	p.P312fs	ZNF500_ENST00000545009.1_Frame_Shift_Ins_p.P312fs|RP11-127I20.7_ENST00000588099.1_RNA|ZNF500_ENST00000591026.1_5'UTR			O60304	ZN500_HUMAN	zinc finger protein 500	312					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)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						GTCTTCCTGGTGGGGGGCCGCC	0.663																																					p.P312fs		Atlas-Indel,Pindel	.											.	ZNF500	45	.	0			c.936_937insC						.																																			SO:0001589	frameshift_variant	26048	exon6			.	AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.936dupC	chr16.hg19:g.4802890_4802890dupG	ENSP00000219478:p.Pro312fs	52.0	0.0		73.0	24.0	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Frame_Shift_Ins	INS	ENST00000219478.6	hg19	CCDS32383.1																																																																																			.	.		0.663	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507	
USP38	84640	hgsc.bcm.edu	37	4	144135967	144135968	+	Frame_Shift_Ins	INS	-	-	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:144135967_144135968insA	ENST00000307017.4	+	9	3344_3345	c.2838_2839insA	c.(2839-2841)aaafs	p.K947fs	USP38_ENST00000510377.1_Frame_Shift_Ins_p.K947fs	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	947	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)					TGCTTTTGTATAAAAAACAGCA	0.371																																					p.Y946fs		Atlas-Indel,Pindel	.											.	USP38	92	.	0			c.2838_2839insA						.																																			SO:0001589	frameshift_variant	84640	exon9			.	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.2844dupA	chr4.hg19:g.144135973_144135973dupA	ENSP00000303434:p.Lys947fs	313.0	0.0		280.0	107.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Frame_Shift_Ins	INS	ENST00000307017.4	hg19	CCDS3758.1																																																																																			.	.		0.371	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
PCDHGC3	5098	hgsc.bcm.edu	37	5	140857742	140857742	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:140857742delA	ENST00000308177.3	+	1	2163	c.2059delA	c.(2059-2061)aaafs	p.K688fs	PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB7_ENST00000398594.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	688					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGGAGCAGAAAAAAAATCT	0.502											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q686fs		Atlas-Indel,Pindel	.											.	PCDHGC3	173	.	0			c.2058delG						.						111.0	140.0	130.0					5																	140857742		2203	4300	6503	SO:0001589	frameshift_variant	5098	exon1			.	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.2059delA	chr5.hg19:g.140857742delA	ENSP00000312070:p.Lys688fs	78.0	0.0	1659	82.0	28.0	NM_032402	O60622|Q08192|Q9Y5C4	Frame_Shift_Del	DEL	ENST00000308177.3	hg19	CCDS4261.1																																																																																			.	.		0.502	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
LAMA5	3911	hgsc.bcm.edu	37	20	60885264	60885264	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:60885264delG	ENST00000252999.3	-	77	10770	c.10704delC	c.(10702-10704)cccfs	p.P3568fs	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3568	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			ACTGCAAGTAGGGGGGCGTCC	0.647																																					p.Y3569fs		Atlas-Indel,Pindel	.											.	LAMA5	268	.	0			c.10705delT						.						35.0	41.0	39.0					20																	60885264		2200	4294	6494	SO:0001589	frameshift_variant	3911	exon77			.	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.10704delC	chr20.hg19:g.60885264delG	ENSP00000252999:p.Pro3568fs	74.0	0.0		78.0	18.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Frame_Shift_Del	DEL	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.		0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
PHF10	55274	hgsc.bcm.edu	37	6	170123958	170123959	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:170123958_170123959insG	ENST00000339209.4	-	1	192_193	c.69_70insC	c.(67-72)cccggafs	p.G24fs	RP1-266L20.4_ENST00000430250.1_RNA|RP1-266L20.2_ENST00000413088.1_RNA|PHF10_ENST00000366780.4_Frame_Shift_Ins_p.G24fs	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	24					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		GACTGCGCTCCGGGGGTGGCTG	0.832																																					p.G24fs		Atlas-Indel,Pindel	.											.	PHF10	76	.	0			c.70_71insC						.																																			SO:0001589	frameshift_variant	55274	exon1			.	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"""Zinc fingers, PHD-type"""	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.70dupC	chr6.hg19:g.170123963_170123963dupG	ENSP00000341805:p.Gly24fs	21.0	0.0		29.0	19.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Frame_Shift_Ins	INS	ENST00000339209.4	hg19	CCDS5308.2																																																																																			.	.		0.832	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288	
FBXL7	23194	hgsc.bcm.edu	37	5	15928504	15928504	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:15928504delC	ENST00000504595.1	+	3	1114	c.633delC	c.(631-633)tgcfs	p.C211fs	FBXL7_ENST00000329673.7_Frame_Shift_Del_p.C199fs|FBXL7_ENST00000510662.1_Frame_Shift_Del_p.C164fs	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	211					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						CCCAGTGCTGCCCCGAACTGA	0.587																																					p.C211fs		Atlas-Indel,Pindel	.											FBXL7,right_upper_lobe,carcinoma,0,1	FBXL7	138	.	0			c.632delG						.						67.0	68.0	67.0					5																	15928504		2074	4199	6273	SO:0001589	frameshift_variant	23194	exon3			.	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"""F-boxes / Leucine-rich repeats"""	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.633delC	chr5.hg19:g.15928504delC	ENSP00000423630:p.Cys211fs	124.0	0.0		126.0	20.0	NM_012304	B9EGF1|D6RDY7|O94926	Frame_Shift_Del	DEL	ENST00000504595.1	hg19	CCDS54833.1																																																																																			.	.		0.587	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304	
LYST	1130	hgsc.bcm.edu	37	1	235860518	235860519	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:235860518_235860519insG	ENST00000389794.3	-	46	10602_10603	c.10428_10429insC	c.(10426-10431)cccagtfs	p.S3477fs	LYST_ENST00000473037.1_5'UTR|LYST_ENST00000389793.2_Frame_Shift_Ins_p.S3477fs			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3477					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ACTGGAGCACTGGGGGAACCCA	0.475																																					p.S3477fs		Atlas-Indel,Pindel	.											.	LYST	370	.	0			c.10429_10430insC						.																																			SO:0001589	frameshift_variant	1130	exon46			.	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.10429dupC	chr1.hg19:g.235860523_235860523dupG	ENSP00000374444:p.Ser3477fs	469.0	0.0		483.0	147.0	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Ins	INS	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.		0.475	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
DMTF1	9988	hgsc.bcm.edu	37	7	86817443	86817444	+	Frame_Shift_Ins	INS	-	-	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:86817443_86817444insA	ENST00000394703.5	+	15	1800_1801	c.1237_1238insA	c.(1237-1239)caafs	p.Q413fs	DMTF1_ENST00000432937.2_Frame_Shift_Ins_p.Q325fs|DMTF1_ENST00000331242.7_Frame_Shift_Ins_p.Q413fs|DMTF1_ENST00000413276.2_Intron|DMTF1_ENST00000414194.2_Frame_Shift_Ins_p.Q147fs	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	413	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					ACATGAGAACCAAAAAAACAAC	0.411																																					p.Q413fs		Atlas-Indel,Pindel	.											.	DMTF1	48	.	0			c.1237_1238insA						.																																			SO:0001589	frameshift_variant	9988	exon13			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.1244dupA	chr7.hg19:g.86817450_86817450dupA	ENSP00000378193:p.Gln413fs	158.0	0.0		168.0	60.0	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Ins	INS	ENST00000394703.5	hg19	CCDS5601.1																																																																																			.	.		0.411	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	
SPATA31A2	642265	hgsc.bcm.edu	37	9	39890593	39890593	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:39890593delA	ENST00000456183.2	+	4	3609	c.3580delA	c.(3580-3582)aaafs	p.K1194fs		NM_001040065.1	NP_001035154.1	Q5RGS2	S31A2_HUMAN	SPATA31 subfamily A, member 2	1194					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAAAACAGTGAAAAACAGATC	0.448																																					p.V1193fs		Atlas-INDEL	.											.	.	.	.	0			c.3579delG						.						1.0	1.0	1.0					9																	39890593		1	3	4	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.3580delA	chr9.hg19:g.39890593delA	ENSP00000406957:p.Lys1194fs	119.0	0.0		139.0	34.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000456183.2	hg19	CCDS43809.1																																																																																			.	.		0.448	SPATA31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037739.1	NM_001040065	
TRIM15	89870	hgsc.bcm.edu	37	6	30139690	30139692	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:30139690_30139692delAGA	ENST00000376694.4	+	7	1431_1433	c.962_964delAGA	c.(961-966)cagaag>cag	p.K323del	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	323	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						TACACCCGGCAGAAGAAGAGCCT	0.67																																					p.321_321del		Atlas-Indel,Pindel	.											.	TRIM15	34	.	0			c.961_963del						.																																			SO:0001651	inframe_deletion	89870	exon7			.	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16284	protein-coding gene	gene with protein product			"""zinc finger protein 178"", ""tripartite motif-containing 15"""	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.962_964delAGA	chr6.hg19:g.30139696_30139698delAGA	ENSP00000365884:p.Lys323del	275.0	0.0		375.0	108.0	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	In_Frame_Del	DEL	ENST00000376694.4	hg19	CCDS4677.1																																																																																			.	.		0.670	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
RAB42	115273	hgsc.bcm.edu	37	1	28920546	28920547	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:28920546_28920547insG	ENST00000373826.3	+	2	541_542	c.235_236insG	c.(235-237)tggfs	p.W79fs	TAF12_ENST00000471683.1_Intron|RAB42_ENST00000465518.1_3'UTR	NM_152304.1	NP_689517.1	Q8N4Z0	RAB42_HUMAN	RAB42, member RAS oncogene family	79					small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00618)|all_lung(284;0.00909)|Breast(348;0.0249)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0577)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00298)|KIRC - Kidney renal clear cell carcinoma(1967;0.00948)|BRCA - Breast invasive adenocarcinoma(304;0.0213)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAGAGGGCTGGGGGGGTGTC	0.584																																					p.W192fs		Atlas-Indel,Pindel	.											.,1	RAB42	10	.	0			c.574_575insG						.																																			SO:0001589	frameshift_variant	115273	exon2			.	BC033175	CCDS325.1	1p35.3	2014-02-12	2006-04-28		ENSG00000188060	ENSG00000188060		"""RAB, member RAS oncogene"""	28702	protein-coding gene	gene with protein product			"""RAB42, member RAS homolog family"""				Standard	NM_152304		Approved	MGC45806	uc001bqv.3	Q8N4Z0	OTTHUMG00000003656	ENST00000373826.3:c.242dupG	chr1.hg19:g.28920553_28920553dupG	ENSP00000362932:p.Trp79fs	137.0	0.0		92.0	31.0	NM_001193532	B2R5G2	Frame_Shift_Ins	INS	ENST00000373826.3	hg19	CCDS325.1																																																																																			.	.		0.584	RAB42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010371.1	NM_152304	
EVC2	132884	hgsc.bcm.edu	37	4	5696122	5696122	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:5696122delA	ENST00000344408.5	-	3	443	c.390delT	c.(388-390)tttfs	p.F130fs	EVC2_ENST00000344938.1_Frame_Shift_Del_p.F130fs|EVC2_ENST00000310917.2_Frame_Shift_Del_p.F50fs	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	130					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AGGAGGGTATAAAAGCAAATA	0.413																																					p.I131fs		Atlas-Indel,Pindel	.											.	EVC2	202	.	0			c.391delA						.						140.0	147.0	144.0					4																	5696122		2203	4300	6503	SO:0001589	frameshift_variant	132884	exon3			.	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.390delT	chr4.hg19:g.5696122delA	ENSP00000342144:p.Phe130fs	371.0	0.0		398.0	161.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Frame_Shift_Del	DEL	ENST00000344408.5	hg19	CCDS3382.2																																																																																			.	.		0.413	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
LZTS3	9762	hgsc.bcm.edu	37	20	3145661	3145663	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:3145661_3145663delCTT	ENST00000329152.3	-	3	2856_2858	c.1459_1461delAAG	c.(1459-1461)aagdel	p.K487del	LZTS3_ENST00000360342.3_In_Frame_Del_p.K441del|LZTS3_ENST00000337576.5_In_Frame_Del_p.K441del			O60299	LZTS3_HUMAN		487						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											GCTGCTCCTCCTTCTCCCGCAGC	0.685																																					p.487_488del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1460_1462del						.																																			SO:0001651	inframe_deletion	0	exon3			.																												ENST00000329152.3:c.1459_1461delAAG	chr20.hg19:g.3145661_3145663delCTT	ENSP00000332123:p.Lys487del	74.0	0.0		56.0	18.0	NM_014731	A2A2Q7|D3DVX6|Q8IXX8	In_Frame_Del	DEL	ENST00000329152.3	hg19	CCDS13049.1																																																																																			.	.		0.685	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2		
ATXN1	6310	hgsc.bcm.edu	37	6	16327684	16327684	+	Frame_Shift_Del	DEL	G	G	-	rs202200269	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:16327684delG	ENST00000244769.4	-	8	1794	c.858delC	c.(856-858)cccfs	p.P286fs	ATXN1_ENST00000436367.1_Frame_Shift_Del_p.P286fs	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	286					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CGACCTGGGAGGGGGGCCCCA	0.682																																					p.S287fs		Atlas-Indel,Pindel	.											.	ATXN1	117	.	0			c.859delT						.						31.0	34.0	33.0					6																	16327684		2203	4300	6503	SO:0001589	frameshift_variant	6310	exon8			.	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.858delC	chr6.hg19:g.16327684delG	ENSP00000244769:p.Pro286fs	174.0	0.0		206.0	58.0	NM_000332	Q17S02|Q9UJG2|Q9Y4J1	Frame_Shift_Del	DEL	ENST00000244769.4	hg19	CCDS34342.1																																																																																			.	.		0.682	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
NAP1L5	266812	hgsc.bcm.edu	37	4	89618583	89618583	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:89618583delT	ENST00000323061.5	-	1	803	c.323delA	c.(322-324)aagfs	p.K108fs	HERC3_ENST00000402738.1_Intron|HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	108					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)		GTCATTATACTTTTTTTCCAG	0.493																																					p.K108fs		Atlas-Indel,Pindel	.											.	NAP1L5	23	.	0			c.324delG						.						73.0	77.0	76.0					4																	89618583		2203	4300	6503	SO:0001589	frameshift_variant	266812	exon1			.	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.323delA	chr4.hg19:g.89618583delT	ENSP00000320488:p.Lys108fs	72.0	0.0		83.0	31.0	NM_153757		Frame_Shift_Del	DEL	ENST00000323061.5	hg19	CCDS3632.1																																																																																			.	.		0.493	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757	
COL1A1	1277	hgsc.bcm.edu	37	17	48276626	48276626	+	Frame_Shift_Del	DEL	G	G	-	rs72667016		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:48276626delG	ENST00000225964.5	-	5	550	c.432delC	c.(430-432)cccfs	p.P144fs		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	144					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	cggggggtccggggggtccgg	0.682			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta																														p.G145fs		Atlas-Indel,Pindel	.		Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	.	COL1A1	158	.	0			c.433delG	GRCh37	CD063493	COL1A1	D	rs72667016	.			10,2100		3,4,1048	1.0	2.0	2.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene		5.2	0.3	17	dbSNP_130	2	13,4777		4,5,2386	no	frameshift	COL1A1	NM_000088.3		7,9,3434	A1A1,A1R,RR		0.2714,0.4739,0.3333			48276626	23,6877	1258	2831	4089	SO:0001589	frameshift_variant	1277	exon5			.	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.432delC	chr17.hg19:g.48276626delG	ENSP00000225964:p.Pro144fs	287.0	0.0		260.0	54.0	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Frame_Shift_Del	DEL	ENST00000225964.5	hg19	CCDS11561.1																																																																																			.	.		0.682	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
CADM2	253559	hgsc.bcm.edu	37	3	85961535	85961536	+	Frame_Shift_Ins	INS	-	-	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:85961535_85961536insA	ENST00000407528.2	+	5	577_578	c.515_516insA	c.(514-519)ttaaaafs	p.LK172fs	CADM2_ENST00000383699.3_Frame_Shift_Ins_p.LK181fs|CADM2_ENST00000405615.2_Frame_Shift_Ins_p.LK174fs	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	172	Ig-like C2-type 1.				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)		GTAAAATATTTAAAAGAAGAGG	0.386																																					p.L181fs		Atlas-Indel,Pindel	.											.	CADM2	195	.	0			c.542_543insA						.																																			SO:0001589	frameshift_variant	253559	exon6			.	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.519dupA	chr3.hg19:g.85961539_85961539dupA	ENSP00000384575:p.Leu172fs	389.0	0.0		397.0	145.0	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Frame_Shift_Ins	INS	ENST00000407528.2	hg19	CCDS54614.1																																																																																			.	.		0.386	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
ZC3H14	79882	hgsc.bcm.edu	37	14	89039079	89039079	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr14:89039079delA	ENST00000251038.5	+	6	814	c.589delA	c.(589-591)aaafs	p.K198fs	ZC3H14_ENST00000557607.1_Frame_Shift_Del_p.K43fs|ZC3H14_ENST00000302216.8_Frame_Shift_Del_p.K198fs|ZC3H14_ENST00000336693.4_Frame_Shift_Del_p.K164fs|ZC3H14_ENST00000393514.5_Frame_Shift_Del_p.K198fs|ZC3H14_ENST00000359301.3_Frame_Shift_Del_p.K164fs|ZC3H14_ENST00000556945.1_Frame_Shift_Del_p.K198fs|ZC3H14_ENST00000555755.1_Frame_Shift_Del_p.K198fs	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	198						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						CTTATCTCAGAAAAAACCTAC	0.413																																					p.Q196fs		Atlas-Indel,Pindel	.											.	ZC3H14	71	.	0			c.588delG						.						172.0	177.0	176.0					14																	89039079		2203	4300	6503	SO:0001589	frameshift_variant	79882	exon6			.	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"""Zinc fingers, CCCH-type domain containing"""	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.589delA	chr14.hg19:g.89039079delA	ENSP00000251038:p.Lys198fs	176.0	0.0		156.0	58.0	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Frame_Shift_Del	DEL	ENST00000251038.5	hg19	CCDS32133.1																																																																																			.	.		0.413	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824	
POLD1	5424	hgsc.bcm.edu	37	19	50905061	50905061	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:50905061delC	ENST00000440232.2	+	4	396	c.343delC	c.(343-345)cccfs	p.P117fs	POLD1_ENST00000599857.1_Frame_Shift_Del_p.P117fs|POLD1_ENST00000595904.1_Frame_Shift_Del_p.P117fs	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	117					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|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)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GCCTGGGGGGCCCCCACCATC	0.662								DNA polymerases (catalytic subunits)																													p.G114fs		Atlas-Indel,Pindel	.											.	POLD1	174	.	0			c.342delG						.						31.0	36.0	35.0					19																	50905061		2200	4293	6493	SO:0001589	frameshift_variant	5424	exon4			.		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.343delC	chr19.hg19:g.50905061delC	ENSP00000406046:p.Pro117fs	90.0	0.0		77.0	28.0	NM_002691	Q8NER3|Q96H98	Frame_Shift_Del	DEL	ENST00000440232.2	hg19	CCDS12795.1																																																																																			.	.		0.662	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
VWA5B2	90113	hgsc.bcm.edu	37	3	183952090	183952090	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:183952090delC	ENST00000426955.2	+	5	825	c.725delC	c.(724-726)gccfs	p.A242fs	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Frame_Shift_Del_p.A23fs	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	253										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						CGGGCAGATGCCCCCCCTCAT	0.617																																					p.A242fs		Atlas-Indel,Pindel	.											.	VWA5B2	47	.	0			c.724delG						.						37.0	38.0	38.0					3																	183952090		692	1591	2283	SO:0001589	frameshift_variant	90113	exon5			.		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.725delC	chr3.hg19:g.183952090delC	ENSP00000398688:p.Ala242fs	100.0	0.0		109.0	50.0	NM_138345	B9EGN7	Frame_Shift_Del	DEL	ENST00000426955.2	hg19	CCDS54686.1																																																																																			.	.		0.617	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
NUP214	8021	hgsc.bcm.edu	37	9	134073007	134073008	+	Frame_Shift_Ins	INS	-	-	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:134073007_134073008insC	ENST00000359428.5	+	29	4270_4271	c.4126_4127insC	c.(4126-4128)gccfs	p.A1376fs	NUP214_ENST00000451030.1_Frame_Shift_Ins_p.A1377fs|NUP214_ENST00000411637.2_Frame_Shift_Ins_p.A1366fs|NUP214_ENST00000483497.2_Frame_Shift_Ins_p.A202fs|NUP214_ENST00000465486.2_3'UTR			P35658	NU214_HUMAN	nucleoporin 214kDa	1376	11 X 5 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TAATTTTACTGCCCCCCCGGTG	0.545			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.A1376fs	Pancreas(4;24 48 25510 30394 32571)	Atlas-Indel,Pindel	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.,3	NUP214	166	.	0			c.4126_4127insC						.																																			SO:0001589	frameshift_variant	8021	exon29			.	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4133dupC	chr9.hg19:g.134073014_134073014dupC	ENSP00000352400:p.Ala1376fs	173.0	0.0		157.0	52.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Frame_Shift_Ins	INS	ENST00000359428.5	hg19	CCDS6940.1																																																																																			.	.		0.545	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
DCHS2	54798	hgsc.bcm.edu	37	4	155158059	155158059	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:155158059delT	ENST00000357232.4	-	25	6379	c.6380delA	c.(6379-6381)aacfs	p.N2127fs		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2127	Cadherin 19. {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)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AACATATGTGTTTTCACGGGT	0.378																																					p.N2127fs		Atlas-Indel,Pindel	.											.	DCHS2	594	.	0			c.6381delC						.						133.0	129.0	131.0					4																	155158059		2203	4300	6503	SO:0001589	frameshift_variant	54798	exon25			.	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6380delA	chr4.hg19:g.155158059delT	ENSP00000349768:p.Asn2127fs	93.0	0.0		75.0	25.0	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.		0.378	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
SYT2	127833	hgsc.bcm.edu	37	1	202568405	202568407	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:202568405_202568407delTCT	ENST00000367267.1	-	8	1184_1186	c.992_994delAGA	c.(991-996)aagacc>acc	p.K331del	SYT2_ENST00000367268.4_In_Frame_Del_p.K331del	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	331	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GGGTTCAGGGTCTTCTTCTTCAC	0.542																																					p.331_332del		Atlas-Indel,Pindel	.											.	SYT2	51	.	0			c.993_995del						.																																			SO:0001651	inframe_deletion	127833	exon8			.	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"""Synaptotagmins"""	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.992_994delAGA	chr1.hg19:g.202568411_202568413delTCT	ENSP00000356236:p.Lys331del	114.0	0.0		122.0	43.0	NM_001136504	Q496K5|Q8NBE5	In_Frame_Del	DEL	ENST00000367267.1	hg19	CCDS1427.1																																																																																			.	.		0.542	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
SIRPB1	10326	hgsc.bcm.edu	37	20	1600524	1600524	+	Frame_Shift_Del	DEL	T	T	-	rs1535882	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:1600524delT	ENST00000381605.4	-	1	131	c.67delA	c.(67-69)agafs	p.R23fs	SIRPB1_ENST00000381603.3_Frame_Shift_Del_p.R23fs|SIRPB1_ENST00000279477.7_Frame_Shift_Del_p.R23fs|RP4-576H24.4_ENST00000564763.1_Frame_Shift_Del_p.R23fs|SIRPB1_ENST00000568365.1_Frame_Shift_Del_p.R23fs|SIRPB1_ENST00000381596.1_5'UTR	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	23			R -> G (in dbSNP:rs1535882).		cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTGTGAGTCTCCCCAGCAGT	0.562																																					p.R23fs		Atlas-Indel,Pindel	.											.	SIRPB1	83	.	0			c.68delG						.						97.0	87.0	90.0					20																	1600524		2203	4300	6503	SO:0001589	frameshift_variant	10326	exon1			.	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.67delA	chr20.hg19:g.1600524delT	ENSP00000371018:p.Arg23fs	99.0	0.0		96.0	39.0	NM_001083910	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Frame_Shift_Del	DEL	ENST00000381605.4	hg19	CCDS13019.1																																																																																			.	.		0.562	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52133551	52133551	+	Splice_Site	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:52133551delC	ENST00000534261.2	-	2	437		c.e2+1		SIGLEC5_ENST00000429354.3_Intron|SIGLEC5_ENST00000599649.1_Intron|SIGLEC5_ENST00000570106.2_Splice_Site|SIGLEC5_ENST00000222107.4_Intron			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5						cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		AGCTCACTCACCCCCCCACAG	0.677																																					.		Atlas-INDEL	.											.	SIGLEC5	67	.	0			c.37+2G>-						.						1.0	1.0	1.0					19																	52133551		662	1813	2475	SO:0001630	splice_region_variant	8778	exon2			.	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.37+1G>-	chr19.hg19:g.52133551delC		159.0	0.0		142.0	28.0	NM_003830		Splice_Site	DEL	ENST00000534261.2	hg19	CCDS33088.1																																																																																			.	.		0.677	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	Intron
RBM27	54439	hgsc.bcm.edu	37	5	145609290	145609290	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:145609290delA	ENST00000265271.5	+	5	572	c.406delA	c.(406-408)aaafs	p.K137fs	RBM27_ENST00000506502.1_Frame_Shift_Del_p.K137fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	137	Arg-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GACACGTGAGAAAAAAAGAGA	0.393																																					p.E135fs		Atlas-Indel,Pindel	.											.	RBM27	119	.	0			c.405delG						.						145.0	144.0	144.0					5																	145609290		1568	3582	5150	SO:0001589	frameshift_variant	54439	exon5			.	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.406delA	chr5.hg19:g.145609290delA	ENSP00000265271:p.Lys137fs	130.0	0.0		114.0	49.0	NM_018989	Q8IYW9	Frame_Shift_Del	DEL	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.		0.393	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
C1orf127	148345	hgsc.bcm.edu	37	1	11007833	11007833	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:11007833delC	ENST00000377008.4	-	11	2304	c.1858delG	c.(1858-1860)gccfs	p.A620fs	C1orf127_ENST00000377004.4_Frame_Shift_Del_p.A787fs			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	620										NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGGAGTGAGGCCCCCCGGCCA	0.627																																					p.A787fs		Atlas-Indel,Pindel	.											.	C1orf127	134	.	0			c.2360delC						.						24.0	24.0	24.0					1																	11007833		2203	4300	6503	SO:0001589	frameshift_variant	148345	exon12			.	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1858delG	chr1.hg19:g.11007833delC	ENSP00000366207:p.Ala620fs	87.0	0.0		97.0	37.0	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Frame_Shift_Del	DEL	ENST00000377008.4	hg19																																																																																				.	.		0.627	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
APOB	338	hgsc.bcm.edu	37	2	21225513	21225514	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:21225513_21225514delTA	ENST00000233242.1	-	29	12907_12908	c.12780_12781delTA	c.(12778-12783)cataaafs	p.HK4260fs	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4260					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTATTAGTTTATGTTTCCTTA	0.361																																					p.4261_4261del		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.12781_12782del						.																																			SO:0001589	frameshift_variant	338	exon29			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.12780_12781delTA	chr2.hg19:g.21225513_21225514delTA	ENSP00000233242:p.His4260fs	138.0	0.0		123.0	48.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.361	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
IPO7	10527	hgsc.bcm.edu	37	11	9435806	9435806	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:9435806delA	ENST00000379719.3	+	5	626	c.484delA	c.(484-486)aaafs	p.K163fs		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	163					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TCAAAGGTATAAAAAACCAGA	0.328																																					p.Y161X		Atlas-Indel,Pindel	.											.	IPO7	72	.	0			c.483delT						.						63.0	61.0	62.0					11																	9435806		2201	4296	6497	SO:0001589	frameshift_variant	10527	exon5			.	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.484delA	chr11.hg19:g.9435806delA	ENSP00000369042:p.Lys163fs	83.0	0.0		97.0	23.0	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Frame_Shift_Del	DEL	ENST00000379719.3	hg19	CCDS31425.1																																																																																			.	.		0.328	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	
LILRB5	10990	hgsc.bcm.edu	37	19	54754663	54754664	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:54754663_54754664insG	ENST00000316219.5	-	13	1866_1867	c.1759_1760insC	c.(1759-1761)ctgfs	p.L587fs	LILRB5_ENST00000449561.2_Frame_Shift_Ins_p.L588fs|LILRB5_ENST00000345866.6_Frame_Shift_Ins_p.L488fs|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_3'UTR	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	587					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTGGATGGCCAGGGGGGCGTAG	0.604																																					p.L588fs		Atlas-Indel,Pindel	.											.	LILRB5	176	.	0			c.1763_1764insC						.																																			SO:0001589	frameshift_variant	10990	exon13			.	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1760dupC	chr19.hg19:g.54754669_54754669dupG	ENSP00000320390:p.Leu587fs	94.0	0.0		120.0	44.0	NM_001081442	Q8N760	Frame_Shift_Ins	INS	ENST00000316219.5	hg19	CCDS12885.1																																																																																			.	.		0.604	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
ICT1	3396	hgsc.bcm.edu	37	17	73008822	73008822	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:73008822delC	ENST00000301585.5	+	1	54	c.41delC	c.(40-42)gccfs	p.A14fs		NM_001545.1	NP_001536.1	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1	14					mitochondrial translational termination (GO:0070126)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)|translation release factor activity, codon nonspecific (GO:0016150)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)|urinary_tract(1)	6	all_lung(278;0.226)					CTGAGCCGAGCCGGAGTCTGG	0.687											OREG0024724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A14fs		Atlas-Indel,Pindel	.											.	ICT1	17	.	0			c.40delG						.						12.0	11.0	11.0					17																	73008822		2168	4256	6424	SO:0001589	frameshift_variant	3396	exon1			.	X81788	CCDS11711.1	17q25	2014-02-12				ENSG00000167862			5359	protein-coding gene	gene with protein product		603000				8575443, 20186120	Standard	NM_001545		Approved	DS-1	uc002jmm.3	Q14197		ENST00000301585.5:c.41delC	chr17.hg19:g.73008822delC	ENSP00000301585:p.Ala14fs	88.0	0.0	1142	82.0	33.0	NM_001545	B2RAD1|Q53HM7|Q53Y11	Frame_Shift_Del	DEL	ENST00000301585.5	hg19	CCDS11711.1																																																																																			.	.		0.687	ICT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445314.1	NM_001545	
FAM98C	147965	hgsc.bcm.edu	37	19	38893823	38893823	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:38893823delG	ENST00000252530.5	+	1	49	c.30delG	c.(28-30)gagfs	p.E10fs	FAM98C_ENST00000588262.1_Frame_Shift_Del_p.E10fs|FAM98C_ENST00000343358.7_Frame_Shift_Del_p.E10fs	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	10										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)			AAGCGTGGGAGGGGGCCGCGG	0.726																																					p.E10fs		Atlas-Indel,Pindel	.											.	FAM98C	39	.	0			c.29delA						.						15.0	23.0	20.0					19																	38893823		2016	4153	6169	SO:0001589	frameshift_variant	147965	exon1			.		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.30delG	chr19.hg19:g.38893823delG	ENSP00000252530:p.Glu10fs	123.0	0.0		105.0	52.0	NM_174905	A6NMW3|Q66K45	Frame_Shift_Del	DEL	ENST00000252530.5	hg19	CCDS42562.1																																																																																			.	.		0.726	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905	
DGCR8	54487	hgsc.bcm.edu	37	22	20074009	20074009	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:20074009delG	ENST00000351989.3	+	2	952	c.523delG	c.(523-525)gggfs	p.G176fs	DGCR8_ENST00000383024.2_Frame_Shift_Del_p.G176fs|MIR3618_ENST00000580330.1_RNA|MIR1306_ENST00000408439.1_RNA|DGCR8_ENST00000407755.1_Frame_Shift_Del_p.G176fs	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	176	Necessary for interaction with NCL.|Necessary for nuclear localization and retention.				gene expression (GO:0010467)|primary miRNA processing (GO:0031053)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					GGTAGGCATAGGGGGTGAGAG	0.552																																					p.I174fs		Atlas-Indel,Pindel	.											.	DGCR8	53	.	0			c.522delA						.						139.0	131.0	134.0					22																	20074009		2203	4300	6503	SO:0001589	frameshift_variant	54487	exon2			.	AF165527, AB050770	CCDS13773.1, CCDS54501.1	22q11.2	2013-05-02	2013-05-02		ENSG00000128191	ENSG00000128191			2847	protein-coding gene	gene with protein product		609030	"""chromosome 22 open reading frame 12"", ""DiGeorge syndrome critical region gene 8"""	C22orf12		21454614	Standard	NM_001190326		Approved	DGCRK6, Gy1, pasha	uc002zri.3	Q8WYQ5	OTTHUMG00000150503	ENST00000351989.3:c.523delG	chr22.hg19:g.20074009delG	ENSP00000263209:p.Gly176fs	70.0	0.0		67.0	20.0	NM_001190326	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Frame_Shift_Del	DEL	ENST00000351989.3	hg19	CCDS13773.1																																																																																			.	.		0.552	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1		
COL6A1	1291	hgsc.bcm.edu	37	21	47414118	47414119	+	Frame_Shift_Ins	INS	-	-	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:47414118_47414119insC	ENST00000361866.3	+	20	1487_1488	c.1373_1374insC	c.(1372-1377)ggccccfs	p.GP458fs		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	458	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GGAAGAGAAGGCCCCGTTGGTG	0.639																																					p.G458fs		Atlas-Indel,Pindel	.											.	COL6A1	101	.	0			c.1373_1374insC						.																																			SO:0001589	frameshift_variant	1291	exon20			.	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1377dupC	chr21.hg19:g.47414122_47414122dupC	ENSP00000355180:p.Gly458fs	263.0	0.0		255.0	87.0	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Frame_Shift_Ins	INS	ENST00000361866.3	hg19	CCDS13727.1																																																																																			.	.		0.639	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
IL17C	27189	hgsc.bcm.edu	37	16	88705522	88705522	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:88705522delC	ENST00000244241.4	+	2	189	c.140delC	c.(139-141)gccfs	p.A47fs		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C	47					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|neutrophil differentiation (GO:0030223)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)	p.H50fs*68(1)		large_intestine(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0477)		CTCGGCCAGGCCCCCCCACAC	0.687																																					p.A47fs		Atlas-Indel,Pindel	.											.,1	IL17C	6	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.139delG						.						39.0	47.0	45.0					16																	88705522		1993	4143	6136	SO:0001589	frameshift_variant	27189	exon2			.	AF152099	CCDS42217.1	16q24	2011-07-14			ENSG00000124391	ENSG00000124391		"""Interleukins and interleukin receptors"""	5983	protein-coding gene	gene with protein product		604628				10639155	Standard	NM_013278		Approved	IL-17C, CX2, IL-21, MGC126884, MGC138401	uc002fla.3	Q9P0M4		ENST00000244241.4:c.140delC	chr16.hg19:g.88705522delC	ENSP00000244241:p.Ala47fs	96.0	0.0		107.0	45.0	NM_013278	Q3MIG8|Q9HC75	Frame_Shift_Del	DEL	ENST00000244241.4	hg19	CCDS42217.1																																																																																			.	.		0.687	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	NM_013278	
LRP1	4035	hgsc.bcm.edu	37	12	57556223	57556223	+	Frame_Shift_Del	DEL	C	C	-	rs34108076		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:57556223delC	ENST00000243077.3	+	14	2792	c.2326delC	c.(2326-2328)cccfs	p.P777fs		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	777					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)	AGGAGGCGCACCCCCCACTGT	0.607																																					p.A775fs		Atlas-Indel,Pindel	.											.	LRP1	428	.	0			c.2325delA						.						150.0	122.0	132.0					12																	57556223		2203	4300	6503	SO:0001589	frameshift_variant	4035	exon14			.	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.2326delC	chr12.hg19:g.57556223delC	ENSP00000243077:p.Pro777fs	72.0	0.0		68.0	28.0	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Frame_Shift_Del	DEL	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
MPZ	4359	hgsc.bcm.edu	37	1	161276499	161276499	+	Splice_Site	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:161276499delT	ENST00000533357.1	-	3	513	c.447delA	c.(445-447)aaa>aa	p.K149fs	MPZ_ENST00000336559.4_Splice_Site_p.K149fs|MPZ_ENST00000360451.6_Splice_Site_p.K159fs|MPZ_ENST00000491222.2_5'UTR|MPZ_ENST00000526189.1_Intron	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	149					cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			TTCTCACACCTTTTTCAAAGA	0.522																																					p.V150fs		Atlas-INDEL	.											.	MPZ	29	.	0			c.448delG						.						150.0	128.0	136.0					1																	161276499		2203	4300	6503	SO:0001630	splice_region_variant	4359	exon3			.	BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"""Immunoglobulin superfamily / V-set domain containing"""	7225	protein-coding gene	gene with protein product		159440	"""Charcot-Marie-Tooth neuropathy 1B"""	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.448+1A>-	chr1.hg19:g.161276499delT		173.0	0.0		145.0	11.0	NM_000530	Q16072|Q5VTH4|Q92677|Q9BR67	Frame_Shift_Del	DEL	ENST00000533357.1	hg19	CCDS1229.2																																																																																			.	.		0.522	MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530	Frame_Shift_Del
TP53	7157	hgsc.bcm.edu	37	17	7578275	7578277	+	In_Frame_Del	DEL	GAG	GAG	-	rs587778718		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:7578275_7578277delGAG	ENST00000269305.4	-	6	761_763	c.572_574delCTC	c.(571-576)cctcag>cag	p.P191del	TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_In_Frame_Del_p.P191del|TP53_ENST00000359597.4_In_Frame_Del_p.P191del|TP53_ENST00000445888.2_In_Frame_Del_p.P191del|TP53_ENST00000420246.2_In_Frame_Del_p.P191del|TP53_ENST00000413465.2_In_Frame_Del_p.P191del	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	191	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q192*(83)|p.0?(8)|p.P191del(7)|p.Q99*(6)|p.?(6)|p.Q60*(6)|p.P191delP(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.P191L(2)|p.P191R(2)|p.G187fs*16(2)|p.P59delP(2)|p.P98delP(2)|p.P191fs*56(1)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191H(1)|p.P191P(1)|p.P191_Q192delPQ(1)|p.D186_P191delDGLAPP(1)|p.Q192K(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.Q192fs*56(1)|p.Q192del(1)|p.Q192fs*16(1)|p.L188_P191del(1)|p.Q192fs*30(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATAAGATGCTGAGGAGGGGCCAG	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.191_192del	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,carcinoma,-1,2	TP53	33396	.	156	Substitution - Nonsense(95)|Deletion - In frame(23)|Deletion - Frameshift(8)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Substitution - Missense(6)|Insertion - Frameshift(2)|Complex - frameshift(1)|Substitution - coding silent(1)	breast(27)|ovary(21)|urinary_tract(15)|lung(13)|upper_aerodigestive_tract(12)|large_intestine(9)|skin(9)|oesophagus(8)|biliary_tract(7)|haematopoietic_and_lymphoid_tissue(6)|kidney(6)|stomach(5)|liver(5)|bone(4)|central_nervous_system(3)|pancreas(2)|cervix(1)|endometrium(1)|eye(1)|prostate(1)	c.573_575del	GRCh37	CD972478	TP53	D		.																																			SO:0001651	inframe_deletion	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.572_574delCTC	chr17.hg19:g.7578278_7578280delGAG	ENSP00000269305:p.Pro191del	215.0	0.0		85.0	63.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	In_Frame_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
FOXE1	2304	hgsc.bcm.edu	37	9	100617015	100617015	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:100617015delC	ENST00000375123.3	+	1	1480	c.819delC	c.(817-819)aacfs	p.N273fs		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	273	Ala-rich.				anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				GGCCGGCCAACCCCTCCGCCT	0.791																																					p.N273fs		Atlas-Indel,Pindel	.											.	FOXE1	19	.	0			c.818delA						.						1.0	1.0	1.0					9																	100617015		636	1543	2179	SO:0001589	frameshift_variant	2304	exon1			.	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"""Forkhead boxes"""	3806	protein-coding gene	gene with protein product		602617	"""forkhead box E2"""	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.819delC	chr9.hg19:g.100617015delC	ENSP00000364265:p.Asn273fs	234.0	0.0		162.0	29.0	NM_004473	O75765|Q5T109|Q99526	Frame_Shift_Del	DEL	ENST00000375123.3	hg19	CCDS35078.1																																																																																			.	.		0.791	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1		
TCF7L2	6934	hgsc.bcm.edu	37	10	114900984	114900984	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:114900984delC	ENST00000355995.4	+	6	1101	c.594delC	c.(592-594)cacfs	p.H198fs	TCF7L2_ENST00000369395.1_Frame_Shift_Del_p.H223fs|TCF7L2_ENST00000352065.5_Frame_Shift_Del_p.H175fs|TCF7L2_ENST00000543371.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000538897.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000542695.1_5'UTR|TCF7L2_ENST00000355717.4_Frame_Shift_Del_p.H222fs|TCF7L2_ENST00000545257.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000369397.4_Frame_Shift_Del_p.H175fs|TCF7L2_ENST00000369389.1_5'Flank|TCF7L2_ENST00000349937.2_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000536810.1_Frame_Shift_Del_p.H198fs|TCF7L2_ENST00000534894.1_Frame_Shift_Del_p.H198fs			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	198	Pro-rich.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|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 type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		ACCATGTCCACCCCCTCACGC	0.572			T	VTI1A	colorectal																																p.H222fs		Atlas-Indel,Pindel	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.665delA						.						184.0	154.0	164.0					10																	114900984		2203	4300	6503	SO:0001589	frameshift_variant	6934	exon6			.	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.594delC	chr10.hg19:g.114900984delC	ENSP00000348274:p.His198fs	148.0	0.0		127.0	42.0	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Frame_Shift_Del	DEL	ENST00000355995.4	hg19																																																																																				.	.		0.572	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756	
NXN	64359	hgsc.bcm.edu	37	17	726873	726874	+	Splice_Site	INS	-	-	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:726873_726874insA	ENST00000336868.3	-	3	701_702	c.610_611insT	c.(610-612)tgg>tTgg	p.W204fs	NXN_ENST00000538650.1_5'Flank|NXN_ENST00000537628.2_5'UTR|NXN_ENST00000577098.1_5'Flank|NXN_ENST00000575801.1_Splice_Site_p.W96fs	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	204	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		AACACTCACCCAATGTGCGGAG	0.584																																					p.W204fs		Atlas-Indel,Pindel	.											.	NXN	32	.	0			c.611_612insT						.																																			SO:0001630	splice_region_variant	64359	exon3			.		CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.612+1->T	chr17.hg19:g.726875_726875dupA		125.0	0.0		74.0	52.0	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Frame_Shift_Ins	INS	ENST00000336868.3	hg19	CCDS10998.1																																																																																			.	.		0.584	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1		Frame_Shift_Ins
AVPR1A	552	hgsc.bcm.edu	37	12	63541343	63541343	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:63541343delA	ENST00000299178.2	-	2	1158	c.1053delT	c.(1051-1053)tttfs	p.F351fs		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	351					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	GATGGCCACTAAAAAACATGT	0.398																																					p.S352fs		Atlas-Indel,Pindel	.											.	AVPR1A	85	.	0			c.1054delA						.						152.0	145.0	148.0					12																	63541343		2203	4300	6503	SO:0001589	frameshift_variant	552	exon2			.	L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.1053delT	chr12.hg19:g.63541343delA	ENSP00000299178:p.Phe351fs	155.0	0.0		173.0	63.0	NM_000706		Frame_Shift_Del	DEL	ENST00000299178.2	hg19	CCDS8965.1																																																																																			.	.		0.398	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1		
PTPN23	25930	hgsc.bcm.edu	37	3	47451532	47451532	+	Frame_Shift_Del	DEL	C	C	-	rs77776224	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47451532delC	ENST00000265562.4	+	20	2321	c.2244delC	c.(2242-2244)ctcfs	p.L748fs	PTPN23_ENST00000431726.1_Frame_Shift_Del_p.L622fs	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	748	Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGCGCAGCCTCCCCCCTGACA	0.701																																					p.L748fs		Atlas-Indel,Pindel	.											.	PTPN23	85	.	0			c.2243delT						.						35.0	34.0	35.0					3																	47451532		2203	4296	6499	SO:0001589	frameshift_variant	25930	exon20			.	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.2244delC	chr3.hg19:g.47451532delC	ENSP00000265562:p.Leu748fs	260.0	0.0		245.0	23.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Frame_Shift_Del	DEL	ENST00000265562.4	hg19	CCDS2754.1																																																																																			.	.		0.701	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
RLTPR	146206	hgsc.bcm.edu	37	16	67688265	67688265	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:67688265delG	ENST00000334583.6	+	31	3580	c.3252delG	c.(3250-3252)gagfs	p.E1084fs	RLTPR_ENST00000545661.1_Frame_Shift_Del_p.E1048fs	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1084					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)		CGGCCACTGAGGGGGGCGCCA	0.652																																					p.E1084fs		Atlas-Indel,Pindel	.											.	RLTPR	124	.	0			c.3251delA						.						14.0	17.0	16.0					16																	67688265		1931	4087	6018	SO:0001589	frameshift_variant	146206	exon31			.	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.3252delG	chr16.hg19:g.67688265delG	ENSP00000334958:p.Glu1084fs	137.0	0.0		128.0	65.0	NM_001013838	B8X2Z3	Frame_Shift_Del	DEL	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.		0.652	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
DNAJC2	27000	hgsc.bcm.edu	37	7	102953447	102953447	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:102953447delT	ENST00000379263.3	-	16	1988	c.1738delA	c.(1738-1740)atafs	p.I580fs	DNAJC2_ENST00000249270.7_Frame_Shift_Del_p.I527fs|PMPCB_ENST00000249269.4_3'UTR|PMPCB_ENST00000420236.2_Intron	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	580	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GCTTCTGCTATTTTTTCCCAT	0.398																																					p.I580fs		Atlas-Indel,Pindel	.											.	DNAJC2	46	.	0			c.1739delT						.						267.0	247.0	253.0					7																	102953447		1852	4090	5942	SO:0001589	frameshift_variant	27000	exon16			.	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"""Heat shock proteins / DNAJ (HSP40)"""	13192	protein-coding gene	gene with protein product		605502	"""zuotin related factor 1"""	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1738delA	chr7.hg19:g.102953447delT	ENSP00000368565:p.Ile580fs	131.0	0.0		133.0	24.0	NM_014377	A4VCI0|Q9BVX1	Frame_Shift_Del	DEL	ENST00000379263.3	hg19	CCDS43628.1																																																																																			.	.		0.398	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1		
TRIM66	9866	hgsc.bcm.edu	37	11	8642705	8642705	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:8642705delG	ENST00000299550.6	-	15	3085	c.2891delC	c.(2890-2892)ccafs	p.P964fs	TRIM66_ENST00000402157.2_Frame_Shift_Del_p.P993fs	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	964						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TATTGGGGCTGGGGGGCCCTT	0.572																																					p.P964fs		Atlas-Indel,Pindel	.											.	TRIM66	45	.	0			c.2892delA						.						48.0	51.0	50.0					11																	8642705		692	1591	2283	SO:0001589	frameshift_variant	9866	exon15			.	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.2891delC	chr11.hg19:g.8642705delG	ENSP00000299550:p.Pro964fs	134.0	0.0		129.0	51.0	NM_014818	Q9BQQ4	Frame_Shift_Del	DEL	ENST00000299550.6	hg19																																																																																				.	.		0.572	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
ARHGAP24	83478	hgsc.bcm.edu	37	4	86916149	86916149	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:86916149delA	ENST00000395184.1	+	9	1808	c.1342delA	c.(1342-1344)aaafs	p.K448fs	ARHGAP24_ENST00000395183.2_Frame_Shift_Del_p.K353fs|ARHGAP24_ENST00000264343.4_Frame_Shift_Del_p.K355fs	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	448					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AGGTCTTGAGAAAACCCAAAC	0.498																																					p.E447fs		Atlas-Indel,Pindel	.											.	ARHGAP24	116	.	0			c.1341delG						.						59.0	66.0	64.0					4																	86916149		2203	4300	6503	SO:0001589	frameshift_variant	83478	exon9			.	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1342delA	chr4.hg19:g.86916149delA	ENSP00000378611:p.Lys448fs	158.0	0.0		162.0	59.0	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Frame_Shift_Del	DEL	ENST00000395184.1	hg19	CCDS34025.1																																																																																			.	.		0.498	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
SOX8	30812	hgsc.bcm.edu	37	16	1034924	1034924	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:1034924delC	ENST00000293894.3	+	3	994	c.879delC	c.(877-879)ggcfs	p.G293fs		NM_014587.3	NP_055402.2	P57073	SOX8_HUMAN	SRY (sex determining region Y)-box 8	293					adipose tissue development (GO:0060612)|astrocyte fate commitment (GO:0060018)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|enteric nervous system development (GO:0048484)|fat cell differentiation (GO:0045444)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of gliogenesis (GO:0014015)|positive regulation of kidney development (GO:0090184)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone levels (GO:0010817)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|ureter morphogenesis (GO:0072197)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|lung(5)|prostate(2)|skin(1)	10		Hepatocellular(780;0.00308)				CCCTGGGCGGCCCCGCCCCAC	0.701																																					p.G293fs		Atlas-Indel,Pindel	.											.	SOX8	29	.	0			c.878delG						.						15.0	16.0	15.0					16																	1034924		2184	4279	6463	SO:0001589	frameshift_variant	30812	exon3			.	AF164104	CCDS10428.1	16p13.3	2008-05-23			ENSG00000005513	ENSG00000005513		"""SRY (sex determining region Y)-boxes"""	11203	protein-coding gene	gene with protein product		605923				10662550, 10684944	Standard	NM_014587		Approved		uc002ckn.3	P57073	OTTHUMG00000122101	ENST00000293894.3:c.879delC	chr16.hg19:g.1034924delC	ENSP00000293894:p.Gly293fs	232.0	0.0		209.0	19.0	NM_014587	Q9NZW2	Frame_Shift_Del	DEL	ENST00000293894.3	hg19	CCDS10428.1																																																																																			.	.		0.701	SOX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242867.1		
GLI1	2735	hgsc.bcm.edu	37	12	57865761	57865761	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:57865761delC	ENST00000228682.2	+	12	3329	c.3238delC	c.(3238-3240)cccfs	p.P1081fs	GLI1_ENST00000546141.1_Frame_Shift_Del_p.P1040fs|GLI1_ENST00000543426.1_Frame_Shift_Del_p.P953fs	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	1081					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)			TCCCTCTGGGCCCCCCAACAT	0.557																																					p.G1079fs	Pancreas(157;841 1936 10503 41495 50368)	Atlas-Indel,Pindel	.											.	GLI1	141	.	0			c.3237delG						.						84.0	85.0	84.0					12																	57865761		2203	4300	6503	SO:0001589	frameshift_variant	2735	exon12			.		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.3238delC	chr12.hg19:g.57865761delC	ENSP00000228682:p.Pro1081fs	149.0	0.0		129.0	56.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Frame_Shift_Del	DEL	ENST00000228682.2	hg19	CCDS8940.1																																																																																			.	.		0.557	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
COBL	23242	hgsc.bcm.edu	37	7	51095511	51095511	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:51095511delT	ENST00000265136.7	-	10	3447	c.3282delA	c.(3280-3282)aaafs	p.K1094fs	COBL_ENST00000395542.2_Frame_Shift_Del_p.K1176fs	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1094					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					CAGGTTTGAATTTTTTCTTCG	0.488																																					p.F1095fs	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-Indel,Pindel	.											.	COBL	167	.	0			c.3283delT						.						173.0	158.0	163.0					7																	51095511		2203	4300	6503	SO:0001589	frameshift_variant	23242	exon10			.	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3282delA	chr7.hg19:g.51095511delT	ENSP00000265136:p.Lys1094fs	197.0	0.0		155.0	50.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Frame_Shift_Del	DEL	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.488	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
GUSB	2990	hgsc.bcm.edu	37	7	65426023	65426023	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:65426023delT	ENST00000304895.4	-	12	1947	c.1817delA	c.(1816-1818)aagfs	p.K606fs	GUSB_ENST00000345660.6_Frame_Shift_Del_p.K555fs|GUSB_ENST00000421103.1_Frame_Shift_Del_p.K460fs	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	606			K -> N (in MPS7). {ECO:0000269|PubMed:8644704}.		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)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						GAAGATCCCCTTTTTATTCCC	0.453																																					p.K606fs		Atlas-Indel,Pindel	.											.	GUSB	52	.	0			c.1818delG						.						191.0	186.0	188.0					7																	65426023		2203	4300	6503	SO:0001589	frameshift_variant	2990	exon12			.	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.1817delA	chr7.hg19:g.65426023delT	ENSP00000302728:p.Lys606fs	72.0	0.0		80.0	31.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Frame_Shift_Del	DEL	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.453	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
C19orf38	255809	hgsc.bcm.edu	37	19	10961063	10961063	+	Frame_Shift_Del	DEL	G	G	-	rs534745530		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:10961063delG	ENST00000397820.4	+	2	267	c.160delG	c.(160-162)gggfs	p.G55fs	C19orf38_ENST00000592854.1_Frame_Shift_Del_p.G55fs	NM_001136482.1	NP_001129954.1	A8MVS5	HIDE1_HUMAN	chromosome 19 open reading frame 38	55						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)	2						ACTGTATCGAGGGGGGCAGGT	0.667																																					p.R53fs		Atlas-Indel,Pindel	.											.	C19orf38	14	.	0			c.159delA						.						23.0	25.0	25.0					19																	10961063		692	1591	2283	SO:0001589	frameshift_variant	255809	exon2			.		CCDS45970.1	19p13.2	2011-08-02	2008-04-14		ENSG00000214212	ENSG00000214212			34073	protein-coding gene	gene with protein product	"""Highly expressed in immature dendritic cell transcript 1"""						Standard	NM_001136482		Approved	HIDE1	uc010dxm.1	A8MVS5		ENST00000397820.4:c.160delG	chr19.hg19:g.10961063delG	ENSP00000380920:p.Gly55fs	93.0	0.0		97.0	46.0	NM_001136482	B2RXI3	Frame_Shift_Del	DEL	ENST00000397820.4	hg19	CCDS45970.1																																																																																			.	.		0.667	C19orf38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452622.1	NM_001136482	
ZNF490	57474	hgsc.bcm.edu	37	19	12692077	12692077	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:12692077delT	ENST00000311437.6	-	5	934	c.812delA	c.(811-813)aatfs	p.N271fs	CTD-2192J16.20_ENST00000593682.1_5'Flank|ZNF490_ENST00000465656.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	271					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(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						TCCAGTGTGATTTTTTTCATG	0.413																																					p.N271fs		Atlas-Indel,Pindel	.											.	ZNF490	42	.	0			c.813delT						.						87.0	86.0	87.0					19																	12692077		2203	4300	6503	SO:0001589	frameshift_variant	57474	exon5			.	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.812delA	chr19.hg19:g.12692077delT	ENSP00000311521:p.Asn271fs	82.0	0.0		83.0	29.0	NM_020714		Frame_Shift_Del	DEL	ENST00000311437.6	hg19	CCDS12272.1																																																																																			.	.		0.413	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
IBTK	25998	hgsc.bcm.edu	37	6	82891683	82891683	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:82891683delT	ENST00000306270.7	-	26	4187	c.3638delA	c.(3637-3639)aagfs	p.K1213fs	IBTK_ENST00000503631.1_Frame_Shift_Del_p.K1012fs|IBTK_ENST00000510291.1_Frame_Shift_Del_p.K1198fs	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1213					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		AGTAACAGACTTTTTTTCTTC	0.343																																					p.K1213fs		Atlas-Indel,Pindel	.											.	IBTK	128	.	0			c.3639delG						.						51.0	53.0	52.0					6																	82891683		2203	4300	6503	SO:0001589	frameshift_variant	25998	exon26			.	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3638delA	chr6.hg19:g.82891683delT	ENSP00000305721:p.Lys1213fs	111.0	0.0		65.0	44.0	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Frame_Shift_Del	DEL	ENST00000306270.7	hg19	CCDS34490.1																																																																																			.	.		0.343	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	
GPR101	83550	hgsc.bcm.edu	37	X	136112908	136112909	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chrX:136112908_136112909delCT	ENST00000298110.1	-	1	924_925	c.925_926delAG	c.(925-927)agcfs	p.S310fs		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	310						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					CACCGTGCTGCTCTCTCTGACC	0.599																																					p.309_309del		Atlas-Indel,Pindel	.											.	GPR101	96	.	0			c.926_927del						.																																			SO:0001589	frameshift_variant	83550	exon1			.	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"""GPCR / Class A : Orphans"""	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.925_926delAG	chrX.hg19:g.136112914_136112915delCT	ENSP00000298110:p.Ser310fs	51.0	0.0		47.0	40.0	NM_054021	Q5JSM8|Q8NG93	Frame_Shift_Del	DEL	ENST00000298110.1	hg19	CCDS14662.1																																																																																			.	.		0.599	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1		
NEB	4703	hgsc.bcm.edu	37	2	152467281	152467281	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:152467281delT	ENST00000172853.10	-	75	11323	c.11176delA	c.(11176-11178)agcfs	p.S3726fs	NEB_ENST00000427231.2_Frame_Shift_Del_p.S3969fs|NEB_ENST00000397345.3_Frame_Shift_Del_p.S3969fs|NEB_ENST00000604864.1_Frame_Shift_Del_p.S3969fs|NEB_ENST00000409198.1_Frame_Shift_Del_p.S3726fs|NEB_ENST00000603639.1_Frame_Shift_Del_p.S3969fs			P20929	NEBU_HUMAN	nebulin	3726					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTTACTTGGCTGATATTGGCA	0.413																																					p.S3969fs		Atlas-Indel,Pindel	.											.	NEB	1697	.	0			c.11906delG						.						73.0	67.0	69.0					2																	152467281		1905	4127	6032	SO:0001589	frameshift_variant	4703	exon79			.	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.11176delA	chr2.hg19:g.152467281delT	ENSP00000172853:p.Ser3726fs	124.0	0.0		70.0	32.0	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Frame_Shift_Del	DEL	ENST00000172853.10	hg19																																																																																				.	.		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
C1QTNF4	114900	hgsc.bcm.edu	37	11	47612245	47612245	+	Frame_Shift_Del	DEL	G	G	-	rs371580513		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:47612245delG	ENST00000302514.3	-	2	634	c.118delC	c.(118-120)ctgfs	p.L40fs		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	40	C1q 1. {ECO:0000255|PROSITE- ProRule:PRU00368}.					extracellular space (GO:0005615)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						GTGCCCTCCAGGGGGGTGGTG	0.726																																					p.L40fs		Atlas-Indel,Pindel	.											C1QTNF4,NS,carcinoma,0,1	C1QTNF4	19	.	0			c.119delT						.			10,4238		4,2,2118	17.0	17.0	17.0			4.3	0.9	11		17	27,8189		12,3,4093	no	frameshift	C1QTNF4	NM_031909.2		16,5,6211	A1A1,A1R,RR		0.3286,0.2354,0.2969			47612245	37,12427	2194	4289	6483	SO:0001589	frameshift_variant	114900	exon2			.	AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247			14346	protein-coding gene	gene with protein product	"""complement-c1q tumor necrosis factor-related protein 4"""	614911				16094384	Standard	NM_031909		Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.118delC	chr11.hg19:g.47612245delG	ENSP00000302274:p.Leu40fs	128.0	0.0		156.0	52.0	NM_031909	Q8IV25	Frame_Shift_Del	DEL	ENST00000302514.3	hg19	CCDS7942.1																																																																																			.	.		0.726	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391772.1	NM_031909	
CLDN9	9080	hgsc.bcm.edu	37	16	3063895	3063895	+	Frame_Shift_Del	DEL	G	G	-	rs374732646		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:3063895delG	ENST00000445369.2	+	1	1439	c.532delG	c.(532-534)gggfs	p.G179fs		NM_020982.3	NP_066192.1	O95484	CLD9_HUMAN	claudin 9	179					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(1)|lung(5)|prostate(2)	10						TATGCTGGGCGGGGGGCTCCT	0.721																																					p.G177fs		Atlas-Indel,Pindel	.											.	CLDN9	33	.	0			c.531delC						.						16.0	21.0	19.0					16																	3063895		2174	4262	6436	SO:0001589	frameshift_variant	9080	exon1			.	AJ130941	CCDS10487.1	16p13.3	2008-08-01			ENSG00000213937	ENSG00000213937		"""Claudins"""	2051	protein-coding gene	gene with protein product		615799				9441748, 18234789	Standard	NM_020982		Approved		uc010uwo.1	O95484	OTTHUMG00000129000	ENST00000445369.2:c.532delG	chr16.hg19:g.3063895delG	ENSP00000398017:p.Gly179fs	72.0	0.0		77.0	36.0	NM_020982		Frame_Shift_Del	DEL	ENST00000445369.2	hg19	CCDS10487.1																																																																																			.	.		0.721	CLDN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250989.1	NM_020982	
RBM8A	9939	hgsc.bcm.edu	37	1	145509916	145509916	+	3'UTR	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:145509916delT	ENST00000330165.8	+	0	1299				RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000596355.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000447686.2_RNA|RP11-315I20.1_ENST00000600340.1_RNA|GNRHR2_ENST00000312753.5_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA	NM_005105.3	NP_005096.1	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GATGTCACAGTTTTTTGTACT	0.408																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	114814	.			.	AF127761	CCDS72872.1	1q21.1	2013-02-12			ENSG00000131795			"""RNA binding motif (RRM) containing"""	9905	protein-coding gene	gene with protein product		605313		RBM8		11004516, 11013075	Standard	NM_005105		Approved	ZNRP, BOV-1A, BOV-1B, BOV-1C, RBM8B, Y14	uc001ent.2	Q9Y5S9	OTTHUMG00000013736	ENST00000330165.8:c.*705T>-	chr1.hg19:g.145509916delT		105.0	0.0		142.0	29.0	.	B3KQI9|Q6FHD1|Q6IQ40|Q9GZX8|Q9NZI4	RNA	DEL	ENST00000330165.8	hg19	CCDS916.1																																																																																			.	.		0.408	RBM8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038503.2	NM_005105	
ST20	400410	hgsc.bcm.edu	37	15	80216041	80216042	+	5'UTR	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr15:80216041_80216042insG	ENST00000485386.1	-	0	2_3				C15orf37_ENST00000560255.1_3'UTR|ST20-MTHFS_ENST00000479961.1_5'UTR|ST20-MTHFS_ENST00000494999.1_5'UTR|C15ORF37_ENST00000542003.1_Frame_Shift_Ins_p.R175fs			Q9HBF5	ST20_HUMAN	suppressor of tumorigenicity 20						extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						GTCCGGGATTCGGGGAGGCAGC	0.688																																					.		Atlas-Indel,Pindel	.											.	C15orf37	6	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	283687	.			.	AF249277	CCDS42067.1	15q25.1	2007-07-16				ENSG00000180953			33520	protein-coding gene	gene with protein product							Standard	NM_001100879		Approved	HCCS-1		Q9HBF5		ENST00000485386.1:c.-260->C	chr15.hg19:g.80216045_80216045dupG		100.0	0.0		77.0	24.0	.		RNA	INS	ENST00000485386.1	hg19	CCDS42067.1																																																																																			.	.		0.688	ST20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416729.1		
PLCXD3	345557	hgsc.bcm.edu	37	5	41382215	41382215	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:41382215delA	ENST00000377801.3	-	2	599	c.525delT	c.(523-525)tttfs	p.F175fs	PLCXD3_ENST00000328457.3_Frame_Shift_Del_p.F175fs			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	175	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						CTTCCTGGGCAAAAATCGCTG	0.443																																					p.A176fs		Atlas-Indel,Pindel	.											.	PLCXD3	86	.	0			c.526delG						.						96.0	96.0	96.0					5																	41382215		2202	4300	6502	SO:0001589	frameshift_variant	345557	exon2			.		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.525delT	chr5.hg19:g.41382215delA	ENSP00000367032:p.Phe175fs	170.0	0.0		149.0	56.0	NM_001005473	A6NL04	Frame_Shift_Del	DEL	ENST00000377801.3	hg19	CCDS34150.1																																																																																			.	.		0.443	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875	
FAM178B	51252	hgsc.bcm.edu	37	2	97587274	97587275	+	Frame_Shift_Ins	INS	-	-	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:97587274_97587275insT	ENST00000417561.3	-	15	1847_1848	c.1848_1849insA	c.(1846-1851)aaagttfs	p.V617fs	FAM178B_ENST00000327896.3_Frame_Shift_Ins_p.V437fs|FAM178B_ENST00000490605.2_Frame_Shift_Ins_p.V469fs			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	617										large_intestine(1)|ovary(1)	2						TGGAGGTCAACTTTGGGCAGCA	0.619																																					p.V469fs		Atlas-Indel,Pindel	.											.	FAM178B	35	.	0			c.1405_1406insA						.																																			SO:0001589	frameshift_variant	51252	exon11			.	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.1849dupA	chr2.hg19:g.97587277_97587277dupT	ENSP00000413245:p.Val617fs	270.0	0.0		281.0	107.0	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Frame_Shift_Ins	INS	ENST00000417561.3	hg19																																																																																				.	.		0.619	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
CNBD2	140894	hgsc.bcm.edu	37	20	34618504	34618504	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:34618504delC	ENST00000373973.3	+	12	1838	c.1665delC	c.(1663-1665)ctcfs	p.L555fs	CNBD2_ENST00000538900.1_3'UTR|CNBD2_ENST00000349339.1_Frame_Shift_Del_p.L551fs			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	555																	AGAAATACCTCCCCCCATTGA	0.458																																					p.L551fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1652delT						.						222.0	216.0	218.0					20																	34618504		2203	4300	6503	SO:0001589	frameshift_variant	140894	exon12			.	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 152"", ""cyclic nucleotide (cNMP) binding domain containing 1"""	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.1665delC	chr20.hg19:g.34618504delC	ENSP00000363084:p.Leu555fs	294.0	0.0		219.0	69.0	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Frame_Shift_Del	DEL	ENST00000373973.3	hg19																																																																																				.	.		0.458	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834	
TBCC	6903	hgsc.bcm.edu	37	6	42713333	42713333	+	Frame_Shift_Del	DEL	G	G	-	rs201664636	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:42713333delG	ENST00000372876.1	-	1	501	c.479delC	c.(478-480)ccgfs	p.P160fs	TBCC_ENST00000244625.2_Frame_Shift_Del_p.P160fs	NM_003192.2	NP_003183	Q15814	TBCC_HUMAN	tubulin folding cofactor C	160					'de novo' posttranslational protein folding (GO:0051084)|cell morphogenesis (GO:0000902)|cellular protein metabolic process (GO:0044267)|GTP catabolic process (GO:0006184)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)	chaperone binding (GO:0051087)|GTPase activity (GO:0003924)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(3)	14	Colorectal(47;0.196)		all cancers(41;0.00122)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.125)			TTCAACTGCCGGGGGGATGCC	0.632																																					p.P160fs		Atlas-Indel,Pindel	.											.	TBCC	31	.	0			c.480delG						.																																			SO:0001589	frameshift_variant	6903	exon1			.	U61234	CCDS4872.1	6p21.1	2008-02-05	2006-11-21		ENSG00000124659	ENSG00000124659			11580	protein-coding gene	gene with protein product		602971	"""tubulin-specific chaperone c"""			8706133, 11847227	Standard	NM_003192		Approved	CFC	uc003osl.3	Q15814	OTTHUMG00000014704	ENST00000372876.1:c.479delC	chr6.hg19:g.42713333delG	ENSP00000361967:p.Pro160fs	173.0	0.0		488.0	85.0	NM_003192	Q53Y43|Q5T787	Frame_Shift_Del	DEL	ENST00000372876.1	hg19	CCDS4872.1																																																																																			.	.		0.632	TBCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040559.1	NM_003192	
MAML3	55534	hgsc.bcm.edu	37	4	140811112	140811123	+	In_Frame_Del	DEL	TGCTGCTGCTGT	TGCTGCTGCTGT	-	rs62344938|rs62344939		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TGCTGCTGCTGT	TGCTGCTGCTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:140811112_140811123delTGCTGCTGCTGT	ENST00000509479.2	-	2	2323_2334	c.1467_1478delACAGCAGCAGCA	c.(1465-1479)caacagcagcagcag>cag	p.489_493QQQQQ>Q	MAML3_ENST00000327122.5_In_Frame_Del_p.333_337QQQQQ>Q|MAML3_ENST00000398940.1_In_Frame_Del_p.28_32QQQQQ>Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					ctgctgctgctgctgctgctgttgctgttgct	0.547																																					p.490_493del		Atlas-INDEL	.											.	MAML3	192	.	0			c.1468_1479del						.			852,3360		97,658,1351						1.5	1.0		dbSNP_130	17	2205,5999		132,1941,2029	no	coding	MAML3	NM_018717.4		229,2599,3380	A1A1,A1R,RR		26.8771,20.2279,24.6215				3057,9359				SO:0001651	inframe_deletion	55534	exon2			.	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1467_1478delACAGCAGCAGCA	chr4.hg19:g.140811112_140811123delTGCTGCTGCTGT	ENSP00000421180:p.Gln505_Gln508del	70.0	0.0		80.0	12.0	NM_018717		In_Frame_Del	DEL	ENST00000509479.2	hg19	CCDS54805.1																																																																																			.	.		0.547	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
SCAP	22937	hgsc.bcm.edu	37	3	47461047	47461048	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:47461047_47461048insG	ENST00000265565.5	-	13	2122_2123	c.1710_1711insC	c.(1708-1713)cccagcfs	p.S571fs	SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000441517.2_Frame_Shift_Ins_p.S316fs|SCAP_ENST00000545718.1_Frame_Shift_Ins_p.S179fs	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	571					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		TCCGGGTGGCTGGGGGGCAGCA	0.658																																					p.S571fs	Pancreas(149;978 1908 29304 37806 46700)	Atlas-Indel,Pindel	.											.	SCAP	88	.	0			c.1711_1712insC						.																																			SO:0001589	frameshift_variant	22937	exon13			.	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.1711dupC	chr3.hg19:g.47461053_47461053dupG	ENSP00000265565:p.Ser571fs	168.0	0.0		155.0	58.0	NM_012235	Q8N2E0|Q8WUA1	Frame_Shift_Ins	INS	ENST00000265565.5	hg19	CCDS2755.2																																																																																			.	.		0.658	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	
PTPRD	5789	hgsc.bcm.edu	37	9	8521421	8521421	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:8521421delC	ENST00000381196.4	-	17	1360	c.817delG	c.(817-819)gcafs	p.A273fs	PTPRD_ENST00000397611.3_Frame_Shift_Del_p.A270fs|PTPRD_ENST00000537002.1_Frame_Shift_Del_p.A270fs|PTPRD_ENST00000360074.4_Frame_Shift_Del_p.A260fs|PTPRD_ENST00000397606.3_Frame_Shift_Del_p.A263fs|PTPRD_ENST00000358503.5_Frame_Shift_Del_p.A260fs|PTPRD_ENST00000355233.5_Frame_Shift_Del_p.A273fs|PTPRD_ENST00000486161.1_Frame_Shift_Del_p.A273fs|PTPRD_ENST00000397617.3_Frame_Shift_Del_p.A263fs|PTPRD_ENST00000540109.1_Frame_Shift_Del_p.A273fs|PTPRD_ENST00000356435.5_Frame_Shift_Del_p.A273fs	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	273	Ig-like C2-type 3.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		AGATCTTCTGCCCCCAACATC	0.453										TSP Lung(15;0.13)																											p.A273fs		Atlas-Indel,Pindel	.											.	PTPRD	1348	.	0			c.818delC						.						178.0	158.0	165.0					9																	8521421		2203	4300	6503	SO:0001589	frameshift_variant	5789	exon9			.	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.817delG	chr9.hg19:g.8521421delC	ENSP00000370593:p.Ala273fs	96.0	0.0		85.0	35.0	NM_130391	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Frame_Shift_Del	DEL	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.		0.453	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
COL4A1	1282	hgsc.bcm.edu	37	13	110864792	110864792	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:110864792delG	ENST00000375820.4	-	6	480	c.359delC	c.(358-360)ccafs	p.P120fs	COL4A1_ENST00000543140.1_Frame_Shift_Del_p.P120fs	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	120					axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)	p.P120Q(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TGGAATACCTGGGGGGCCTGG	0.453																																					p.P120fs		Atlas-Indel,Pindel	.											.	COL4A1	372	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.360delA						.						133.0	156.0	148.0					13																	110864792		2203	4300	6503	SO:0001589	frameshift_variant	1282	exon6			.	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.359delC	chr13.hg19:g.110864792delG	ENSP00000364979:p.Pro120fs	107.0	0.0		103.0	46.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Frame_Shift_Del	DEL	ENST00000375820.4	hg19	CCDS9511.1																																																																																			.	.		0.453	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
OR5D13	390142	hgsc.bcm.edu	37	11	55541296	55541296	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:55541296delT	ENST00000361760.1	+	1	383	c.383delT	c.(382-384)gttfs	p.V128fs		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				TTTGTGGCAGTTTGTAAACCC	0.443																																					p.V128fs		Atlas-Indel,Pindel	.											.	OR5D13	96	.	0			c.382delG						.						240.0	234.0	236.0					11																	55541296		2200	4296	6496	SO:0001589	frameshift_variant	390142	exon1			.	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"""GPCR / Class A : Olfactory receptors"""	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.383delT	chr11.hg19:g.55541296delT	ENSP00000354800:p.Val128fs	134.0	0.0		156.0	62.0	NM_001001967	Q6IF68|Q6IFC9	Frame_Shift_Del	DEL	ENST00000361760.1	hg19	CCDS31507.1																																																																																			.	.		0.443	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967	
TRIP6	7205	hgsc.bcm.edu	37	7	100465745	100465746	+	Frame_Shift_Ins	INS	-	-	G	rs201628297	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100465745_100465746insG	ENST00000200457.4	+	3	613_614	c.253_254insG	c.(253-255)aggfs	p.R85fs		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	85					focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCTGCAGACAGGGGGGGCCTT	0.639																																					p.R85fs		Atlas-Indel,Pindel	.											.	TRIP6	45	.	0			c.253_254insG						.																																			SO:0001589	frameshift_variant	7205	exon3			.	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.260dupG	chr7.hg19:g.100465752_100465752dupG	ENSP00000200457:p.Arg85fs	206.0	0.0		202.0	82.0	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Frame_Shift_Ins	INS	ENST00000200457.4	hg19	CCDS5708.1																																																																																			.	.		0.639	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
MAK	4117	hgsc.bcm.edu	37	6	10764807	10764808	+	Frame_Shift_Ins	INS	-	-	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:10764807_10764808insC	ENST00000313243.2	-	14	2131_2132	c.1749_1750insG	c.(1747-1752)gggcagfs	p.Q584fs	SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000354489.2_Frame_Shift_Ins_p.Q584fs|RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000538030.1_3'UTR|MAK_ENST00000474039.1_Frame_Shift_Ins_p.Q584fs			P20794	MAK_HUMAN	male germ cell-associated kinase	584					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CCTGAAAACTGCCCCCGACCAG	0.411																																					p.Q609fs		Atlas-Indel,Pindel	.											.	MAK	47	.	0			c.1825_1826insG						.																																			SO:0001589	frameshift_variant	4117	exon15			.		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1750dupG	chr6.hg19:g.10764812_10764812dupC	ENSP00000313021:p.Gln584fs	98.0	0.0		118.0	28.0	NM_001242957	F1T0K6|G1FL29|Q547D0|Q9NUH7	Frame_Shift_Ins	INS	ENST00000313243.2	hg19	CCDS4516.1																																																																																			.	.		0.411	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	
MIA3	375056	hgsc.bcm.edu	37	1	222824056	222824056	+	Intron	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:222824056delA	ENST00000344922.5	+	10	3823				MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Intron|MIA3_ENST00000344441.6_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3						chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		AATATAAGGTAAAAACTTCTT	0.264																																					.		Atlas-Indel,Pindel	.											.	MIA3	167	.	0			c.3798+2A>-						.						62.0	69.0	67.0					1																	222824056		1794	4040	5834	SO:0001627	intron_variant	375056	exon10			.		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3798+3A>-	chr1.hg19:g.222824056delA		471.0	0.0		409.0	159.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Splice_Site	DEL	ENST00000344922.5	hg19	CCDS41470.1																																																																																			.	.		0.264	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
OARD1	221443	hgsc.bcm.edu	37	6	41039018	41039018	+	Intron	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:41039018delA	ENST00000479950.1	-	3	353				OARD1_ENST00000464633.1_Intron|OARD1_ENST00000480585.1_Intron|OARD1_ENST00000373154.2_Intron|OARD1_ENST00000486443.1_Intron|NFYA_ENST00000341376.6_5'Flank|OARD1_ENST00000244558.9_Intron|OARD1_ENST00000482515.1_Intron|OARD1_ENST00000424266.2_Intron|OARD1_ENST00000471367.1_Intron|NFYA_ENST00000353205.5_5'Flank|OARD1_ENST00000467234.1_5'Flank|OARD1_ENST00000468811.1_Intron|OARD1_ENST00000469104.1_Intron|OARD1_ENST00000463088.1_Intron			Q9Y530	OARD1_HUMAN	O-acyl-ADP-ribose deacylase 1						purine nucleoside metabolic process (GO:0042278)		deacetylase activity (GO:0019213)|purine nucleoside binding (GO:0001883)										TAAGTGATCTAAAAAATGTGC	0.423																																					.		Atlas-Indel,Pindel	.											.,1	.	.	.	0			c.40-2T>-						.						56.0	59.0	58.0					6																	41039018		2203	4300	6503	SO:0001627	intron_variant	221443	exon4			.	AJ420538	CCDS34445.1	6p21.1	2013-03-14	2012-11-06	2012-11-06	ENSG00000124596	ENSG00000124596			21257	protein-coding gene	gene with protein product	"""terminal ADP-ribose protein glycohydrolase 1"""	614393	"""chromosome 6 open reading frame 130"""	C6orf130		21849506	Standard	NM_145063		Approved	MGC19570, dJ34B21.3, TARG1	uc003opm.3	Q9Y530	OTTHUMG00000014667	ENST00000479950.1:c.40-3T>-	chr6.hg19:g.41039018delA		147.0	0.0		339.0	139.0	NM_145063	A6NEK4|A8K4H4|Q96F23	Splice_Site	DEL	ENST00000479950.1	hg19	CCDS34445.1																																																																																			.	.		0.423	OARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040494.2	NM_145063	
DNMT3A	1788	hgsc.bcm.edu	37	2	25497864	25497864	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:25497864delG	ENST00000264709.3	-	6	922	c.585delC	c.(583-585)cccfs	p.P195fs	DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.P195fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	195					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGATGTAGTAGGGGTCCCCCG	0.701			"""Mis, F, N, S"""		AML																																p.Y196fs		Atlas-Indel,Pindel	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.586delT						.						39.0	37.0	38.0					2																	25497864		2203	4300	6503	SO:0001589	frameshift_variant	1788	exon6			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.585delC	chr2.hg19:g.25497864delG	ENSP00000264709:p.Pro195fs	126.0	0.0		136.0	53.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.701	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
CACNA2D3	55799	hgsc.bcm.edu	37	3	54354484	54354484	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:54354484delG	ENST00000474759.1	+	3	268	c.220delG	c.(220-222)gagfs	p.E74fs	CACNA2D3_ENST00000490478.1_5'UTR|CACNA2D3_ENST00000415676.2_Frame_Shift_Del_p.E74fs|CACNA2D3_ENST00000288197.5_Frame_Shift_Del_p.E74fs	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	74						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CAAAGAGTATGAGAAAGACGT	0.438																																					p.Y73X		Atlas-Indel,Pindel	.											.	CACNA2D3	159	.	0			c.219delT						.						62.0	57.0	58.0					3																	54354484		1913	4115	6028	SO:0001589	frameshift_variant	55799	exon3			.	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.220delG	chr3.hg19:g.54354484delG	ENSP00000419101:p.Glu74fs	84.0	0.0		85.0	38.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Frame_Shift_Del	DEL	ENST00000474759.1	hg19	CCDS54598.1																																																																																			.	.		0.438	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
SF3A1	10291	hgsc.bcm.edu	37	22	30736780	30736782	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:30736780_30736782delCTT	ENST00000215793.8	-	8	1245_1247	c.1091_1093delAAG	c.(1090-1095)gaaggg>ggg	p.E364del	SF3A1_ENST00000439242.1_In_Frame_Del_p.E299del	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	364					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						ACTTTCTGCCCTTCTTCTTCATC	0.571																																					p.364_365del		Atlas-Indel,Pindel	.											.	SF3A1	61	.	0			c.1092_1094del						.																																			SO:0001651	inframe_deletion	10291	exon8			.	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.1091_1093delAAG	chr22.hg19:g.30736786_30736788delCTT	ENSP00000215793:p.Glu364del	88.0	0.0		65.0	20.0	NM_005877	E9PAW1	In_Frame_Del	DEL	ENST00000215793.8	hg19	CCDS13875.1																																																																																			.	.		0.571	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877	
UPK3B	80761	hgsc.bcm.edu	37	7	76140138	76140139	+	Frame_Shift_Ins	INS	-	-	C	rs139989637|rs201668989	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:76140138_76140139insC	ENST00000257632.5	+	1	297_298	c.169_170insC	c.(169-171)gccfs	p.A57fs	UPK3B_ENST00000419923.2_Frame_Shift_Ins_p.A57fs|UPK3B_ENST00000394849.1_Intron|UPK3B_ENST00000448265.3_Frame_Shift_Ins_p.A57fs|UPK3B_ENST00000443097.2_Intron|UPK3B_ENST00000334348.3_Intron			Q9BT76	UPK3B_HUMAN	uroplakin 3B	57					negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				CTGGGCGCCCGCCCCCCTCCGA	0.708																																					p.A57fs		Atlas-Indel,Pindel	.											.	UPK3B	15	.	0			c.169_170insC						.																																			SO:0001589	frameshift_variant	80761	exon1			.	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"""uroplakin IIIb"""	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.175dupC	chr7.hg19:g.76140144_76140144dupC	ENSP00000257632:p.Ala57fs	169.0	0.0		182.0	63.0	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Frame_Shift_Ins	INS	ENST00000257632.5	hg19	CCDS5588.1																																																																																			.	.		0.708	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570	
SLITRK6	84189	hgsc.bcm.edu	37	13	86369655	86369655	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr13:86369655delG	ENST00000400286.2	-	2	1587	c.989delC	c.(988-990)cctfs	p.P330fs		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	330	LRRNT 2.				adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		ACAAGGAATAGGGCAGTAAGG	0.443																																					p.P330fs		Atlas-Indel,Pindel	.											.	SLITRK6	150	.	0			c.990delT						.						146.0	134.0	138.0					13																	86369655		1935	4130	6065	SO:0001589	frameshift_variant	84189	exon2			.	AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.989delC	chr13.hg19:g.86369655delG	ENSP00000383143:p.Pro330fs	61.0	0.0		62.0	26.0	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Frame_Shift_Del	DEL	ENST00000400286.2	hg19	CCDS41903.1																																																																																			.	.		0.443	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
ZNF503	84858	hgsc.bcm.edu	37	10	77159849	77159849	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr10:77159849delC	ENST00000372524.4	-	2	1085	c.599delG	c.(598-600)ggcfs	p.G204fs	ZNF503-AS2_ENST00000486015.1_RNA|RP11-399K21.11_ENST00000418818.2_lincRNA|ZNF503-AS2_ENST00000466942.2_RNA|ZNF503_ENST00000535216.1_Frame_Shift_Del_p.G204fs|ZNF503-AS2_ENST00000425916.3_RNA	NM_032772.4	NP_116161.2	Q96F45	ZN503_HUMAN	zinc finger protein 503	204	Gly-rich.				G1 to G0 transition involved in cell differentiation (GO:0070315)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|neural precursor cell proliferation (GO:0061351)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			lung(4)|ovary(1)|skin(1)	6	all_cancers(46;0.105)|all_epithelial(25;0.00449)|Prostate(51;0.0112)|Ovarian(15;0.088)					Cccgccgccgcccccgccacc	0.692																																					p.G200fs		Atlas-Indel,Pindel	.											.	ZNF503	25	.	0			c.600delC						.						2.0	2.0	2.0					10																	77159849		1491	3151	4642	SO:0001589	frameshift_variant	84858	exon2			.	AK127647	CCDS7350.1	10q22.3	2011-02-09			ENSG00000165655	ENSG00000165655		"""Zinc fingers, C2H2-type"""	23589	protein-coding gene	gene with protein product		613902				12477932	Standard	NM_032772		Approved	FLJ45745, MGC2555	uc001jxg.3	Q96F45	OTTHUMG00000018526	ENST00000372524.4:c.599delG	chr10.hg19:g.77159849delC	ENSP00000361602:p.Gly204fs	75.0	0.0		74.0	28.0	NM_032772	Q8NAC5|Q96E25|Q96IJ0	Frame_Shift_Del	DEL	ENST00000372524.4	hg19	CCDS7350.1																																																																																			.	.		0.692	ZNF503-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048826.1	NM_032772	
AKAP8	10270	hgsc.bcm.edu	37	19	15483896	15483896	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:15483896delG	ENST00000269701.2	-	5	687	c.627delC	c.(625-627)cccfs	p.P209fs		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	209					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						GGGGCACGAAGGGGTCGCTGC	0.731																																					p.F210fs	GBM(190;1671 2163 3274 27186 30476)	Atlas-Indel,Pindel	.											.	AKAP8	68	.	0			c.628delT						.						10.0	13.0	12.0					19																	15483896		2188	4271	6459	SO:0001589	frameshift_variant	10270	exon5			.	Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"""A-kinase anchor proteins"""	378	protein-coding gene	gene with protein product	"""A-kinase anchor protein, 95kDa"""	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.627delC	chr19.hg19:g.15483896delG	ENSP00000269701:p.Pro209fs	151.0	0.0		175.0	66.0	NM_005858		Frame_Shift_Del	DEL	ENST00000269701.2	hg19	CCDS12329.1																																																																																			.	.		0.731	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858	
SALL4	57167	hgsc.bcm.edu	37	20	50408677	50408678	+	Frame_Shift_Ins	INS	-	-	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:50408677_50408678insA	ENST00000217086.4	-	2	455_456	c.344_345insT	c.(343-345)ttcfs	p.F115fs	SALL4_ENST00000395997.3_Frame_Shift_Ins_p.F115fs|SALL4_ENST00000483130.1_5'UTR|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	115					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAGCTCCGGAGAAGTCTTCTGA	0.53																																					p.F115fs		Atlas-Indel,Pindel	.											SALL4,NS,carcinoma,0,1	SALL4	168	.	0			c.345_346insT						.																																			SO:0001589	frameshift_variant	57167	exon2			.	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.345dupT	chr20.hg19:g.50408679_50408679dupA	ENSP00000217086:p.Phe115fs	278.0	0.0		287.0	113.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Ins	INS	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.530	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
ALMS1	7840	hgsc.bcm.edu	37	2	73718037	73718038	+	Frame_Shift_Ins	INS	-	-	T			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:73718037_73718038insT	ENST00000264448.6	+	10	9059_9060	c.8948_8949insT	c.(8947-8952)cattttfs	p.HF2983fs	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Frame_Shift_Ins_p.HF2941fs	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2983					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						AATAAACACCATTTTCCCCTTC	0.391																																					p.H2983fs		Atlas-Indel,Pindel	.											.	ALMS1	384	.	0			c.8948_8949insT						.																																			SO:0001589	frameshift_variant	7840	exon10			.	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.8952dupT	chr2.hg19:g.73718041_73718041dupT	ENSP00000264448:p.His2983fs	187.0	0.0		193.0	80.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Frame_Shift_Ins	INS	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.391	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
PRR14	78994	hgsc.bcm.edu	37	16	30667498	30667498	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:30667498delG	ENST00000542965.2	+	11	2080	c.1624delG	c.(1624-1626)gggfs	p.G543fs	PRR14_ENST00000300835.4_Frame_Shift_Del_p.G543fs|FBRS_ENST00000356166.6_5'Flank			Q9BWN1	PRR14_HUMAN	proline rich 14	543										breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			CCGGGCTGCAGGGGGCAGGAC	0.637																																					p.A541fs		Atlas-Indel,Pindel	.											.	PRR14	45	.	0			c.1623delA						.						53.0	61.0	58.0					16																	30667498		2197	4300	6497	SO:0001589	frameshift_variant	78994	exon12			.	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.1624delG	chr16.hg19:g.30667498delG	ENSP00000441641:p.Gly543fs	91.0	0.0		86.0	38.0	NM_024031	Q8WTX2	Frame_Shift_Del	DEL	ENST00000542965.2	hg19	CCDS10687.1																																																																																			.	.		0.637	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031	
ASPM	259266	hgsc.bcm.edu	37	1	197070523	197070524	+	Frame_Shift_Ins	INS	-	-	T	rs587783274		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:197070523_197070524insT	ENST00000367409.4	-	18	8113_8114	c.7857_7858insA	c.(7855-7860)aaacagfs	p.Q2620fs	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2620			Q -> H (in dbSNP:rs12138336).		developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TCCTGAATCTGTTTTTTTATGT	0.347																																					p.Q2620fs		Atlas-Indel,Pindel	.											.,1	ASPM	444	.	0			c.7858_7859insA						.																																			SO:0001589	frameshift_variant	259266	exon18			.	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7858dupA	chr1.hg19:g.197070530_197070530dupT	ENSP00000356379:p.Gln2620fs	36.0	0.0		35.0	10.0	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Ins	INS	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.		0.347	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
NCOA1	8648	hgsc.bcm.edu	37	2	24952369	24952369	+	Splice_Site	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:24952369delG	ENST00000406961.1	+	17	3538		c.e17-1		NCOA1_ENST00000348332.3_Splice_Site|NCOA1_ENST00000407230.1_Splice_Site|NCOA1_ENST00000395856.3_Splice_Site|NCOA1_ENST00000405141.1_Splice_Site|NCOA1_ENST00000288599.5_Splice_Site|NCOA1_ENST00000538539.1_Splice_Site			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1						androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTCTAACAGGGGGGTGGAT	0.373			T	PAX3	alveolar rhadomyosarcoma																																.		Atlas-INDEL	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.2887-2G>-						.						72.0	72.0	72.0					2																	24952369		2203	4300	6503	SO:0001630	splice_region_variant	8648	exon15			.	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.2887-1G>-	chr2.hg19:g.24952369delG		129.0	0.0		125.0	11.0	NM_147233	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Splice_Site	DEL	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.		0.373	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	Intron
WRN	7486	hgsc.bcm.edu	37	8	30977943	30977943	+	Intron	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr8:30977943delA	ENST00000298139.5	+	21	2879					NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like						aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTAAATAGGTAAAAAAAATTT	0.358			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												.	Ovarian(18;161 598 2706 14834 27543)	Atlas-Indel,Pindel	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.2630+2A>-						.			4,4244		0,4,2120	31.0	32.0	31.0			5.8	1.0	8		33	3,8227		0,3,4112	no	intron	WRN	NM_000553.4		0,7,6232	A1A1,A1R,RR		0.0365,0.0942,0.0561			30977943	7,12471	2202	4297	6499	SO:0001627	intron_variant	7486	exon21	Familial Cancer Database	WS, Adult Progeria	.		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2630+3A>-	chr8.hg19:g.30977943delA		110.0	0.0		99.0	38.0	NM_000553	A1KYY9	Splice_Site	DEL	ENST00000298139.5	hg19	CCDS6082.1																																																																																			.	.		0.358	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
PTPRS	5802	hgsc.bcm.edu	37	19	5221076	5221076	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:5221076delG	ENST00000587303.1	-	19	3489	c.3390delC	c.(3388-3390)cccfs	p.P1130fs	PTPRS_ENST00000592099.1_Frame_Shift_Del_p.P699fs|PTPRS_ENST00000372412.4_Frame_Shift_Del_p.P1131fs|PTPRS_ENST00000348075.2_Frame_Shift_Del_p.P1108fs|PTPRS_ENST00000353284.2_Frame_Shift_Del_p.P699fs|PTPRS_ENST00000357368.4_Frame_Shift_Del_p.P1130fs|PTPRS_ENST00000588012.1_Frame_Shift_Del_p.P1108fs|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Frame_Shift_Del_p.P1126fs			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1130					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	CATCAGGCTTGGGGGCGACGC	0.637																																					p.K1131fs		Atlas-Indel,Pindel	.											.	PTPRS	169	.	0			c.3391delA						.						105.0	97.0	100.0					19																	5221076		2203	4300	6503	SO:0001589	frameshift_variant	5802	exon20			.	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.3390delC	chr19.hg19:g.5221076delG	ENSP00000467537:p.Pro1130fs	71.0	0.0		46.0	16.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Frame_Shift_Del	DEL	ENST00000587303.1	hg19	CCDS45930.1																																																																																			.	.		0.637	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
SPATA31A1	647060	hgsc.bcm.edu	37	9	39361342	39361342	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:39361342delA	ENST00000377647.3	+	4	3609	c.3580delA	c.(3580-3582)aaafs	p.K1194fs		NM_001085452.1	NP_001078921.1	Q5TZJ5	S31A1_HUMAN	SPATA31 subfamily A, member 1	1194					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAAAACAGTGAAAAACAGATC	0.448																																					p.V1193fs		Atlas-INDEL	.											.	.	.	.	0			c.3579delG						.						1.0	1.0	1.0					9																	39361342		77	181	258	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.3580delA	chr9.hg19:g.39361342delA	ENSP00000366875:p.Lys1194fs	146.0	0.0		163.0	28.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000377647.3	hg19	CCDS43808.1																																																																																			.	.		0.448	SPATA31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036910.1	NM_001085452	
TNIP1	10318	hgsc.bcm.edu	37	5	150410290	150410290	+	Frame_Shift_Del	DEL	C	C	-	rs199807288		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:150410290delC	ENST00000389378.2	-	18	2483	c.1895delG	c.(1894-1896)cgtfs	p.R632fs	TNIP1_ENST00000524280.1_Frame_Shift_Del_p.V536fs|TNIP1_ENST00000522226.1_Frame_Shift_Del_p.R632fs|TNIP1_ENST00000518977.1_Intron|TNIP1_ENST00000520931.1_Frame_Shift_Del_p.R579fs|TNIP1_ENST00000521591.1_Frame_Shift_Del_p.R632fs|TNIP1_ENST00000315050.7_Frame_Shift_Del_p.R632fs|TNIP1_ENST00000523200.1_Frame_Shift_Del_p.R568fs|TNIP1_ENST00000521423.1_5'Flank|TNIP1_ENST00000523338.1_Intron	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	632	Pro-rich.				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGCCCCTCACGGTCATTTTT	0.438																																					p.R632fs		Atlas-Indel,Pindel	.											.	TNIP1	51	.	0			c.1896delT						.						81.0	81.0	81.0					5																	150410290		2203	4300	6503	SO:0001589	frameshift_variant	10318	exon18			.	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.1895delG	chr5.hg19:g.150410290delC	ENSP00000374029:p.Arg632fs	155.0	0.0		158.0	58.0	NM_001258454	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Frame_Shift_Del	DEL	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.		0.438	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
HDAC5	10014	hgsc.bcm.edu	37	17	42157801	42157801	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr17:42157801delG	ENST00000393622.2	-	22	3124	c.2793delC	c.(2791-2793)cccfs	p.P931fs	HDAC5_ENST00000225983.6_Frame_Shift_Del_p.P932fs|HDAC5_ENST00000586802.1_Frame_Shift_Del_p.P931fs|HDAC5_ENST00000336057.5_Frame_Shift_Del_p.P846fs	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	931	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CGTCTCCAATGGGGGGGTCCA	0.607																																					p.I933fs		Atlas-Indel,Pindel	.											.	HDAC5	67	.	0			c.2797delA						.						103.0	98.0	99.0					17																	42157801		2203	4300	6503	SO:0001589	frameshift_variant	10014	exon22			.	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.2793delC	chr17.hg19:g.42157801delG	ENSP00000377244:p.Pro931fs	79.0	0.0		84.0	39.0	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Frame_Shift_Del	DEL	ENST00000393622.2	hg19	CCDS45696.1																																																																																			.	.		0.607	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053	
CBFA2T2	9139	hgsc.bcm.edu	37	20	32224505	32224505	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr20:32224505delA	ENST00000346541.3	+	10	1852	c.1315delA	c.(1315-1317)aaafs	p.K440fs	CBFA2T2_ENST00000375279.2_Frame_Shift_Del_p.K440fs|CBFA2T2_ENST00000359606.3_Frame_Shift_Del_p.K450fs|CBFA2T2_ENST00000543126.1_5'Flank|CBFA2T2_ENST00000492345.1_Frame_Shift_Del_p.K411fs|CBFA2T2_ENST00000342704.6_Frame_Shift_Del_p.K431fs|CBFA2T2_ENST00000397800.1_Frame_Shift_Del_p.K411fs	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	440					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						GGAGTTTTGGAAAAAAACAGG	0.448																																					p.W438X	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-Indel,Pindel	.											CBFA2T2_ENST00000342704,colon,carcinoma,0,2	CBFA2T2	93	.	0			c.1314delG						.																																			SO:0001589	frameshift_variant	9139	exon10			.	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"""Zinc fingers, MYND-type"""	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.1315delA	chr20.hg19:g.32224505delA	ENSP00000262653:p.Lys440fs	79.0	0.0		92.0	47.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Frame_Shift_Del	DEL	ENST00000346541.3	hg19	CCDS13221.1																																																																																			.	.		0.448	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999	
DHX9	1660	hgsc.bcm.edu	37	1	182812563	182812563	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:182812563delT	ENST00000367549.3	+	3	356	c.246delT	c.(244-246)gctfs	p.A82fs		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	82	Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						AAGTTCCAGCTTTTGGGGTAA	0.353																																					p.A82fs	Colon(69;210 1162 3697 13559 39565)	Atlas-Indel,Pindel	.											.	DHX9	114	.	0			c.245delC						.						122.0	116.0	118.0					1																	182812563		1837	4099	5936	SO:0001589	frameshift_variant	1660	exon3			.	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.246delT	chr1.hg19:g.182812563delT	ENSP00000356520:p.Ala82fs	70.0	0.0		82.0	32.0	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Frame_Shift_Del	DEL	ENST00000367549.3	hg19	CCDS41444.1																																																																																			.	.		0.353	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
NTS	4922	hgsc.bcm.edu	37	12	86276037	86276037	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:86276037delA	ENST00000256010.6	+	4	504	c.397delA	c.(397-399)aaafs	p.K133fs	NTS_ENST00000551529.1_Frame_Shift_Del_p.K58fs	NM_006183.4	NP_006174.1	P30990	NEUT_HUMAN	neurotensin	133					regulation of blood vessel size (GO:0050880)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)				large_intestine(2)|lung(6)	8						TGGAAATGACAAAAATGGAAA	0.323																																					p.D132fs		Atlas-Indel,Pindel	.											.	NTS	25	.	0			c.396delC						.						65.0	71.0	69.0					12																	86276037		2203	4293	6496	SO:0001589	frameshift_variant	4922	exon4			.		CCDS9029.1	12q21.31	2013-02-26			ENSG00000133636	ENSG00000133636		"""Endogenous ligands"""	8038	protein-coding gene	gene with protein product	"""neuromedin N"", ""pro-neurotensin/neuromedin"""	162650					Standard	NM_006183		Approved		uc001tag.3	P30990	OTTHUMG00000169832	ENST00000256010.6:c.397delA	chr12.hg19:g.86276037delA	ENSP00000256010:p.Lys133fs	372.0	0.0		378.0	122.0	NM_006183		Frame_Shift_Del	DEL	ENST00000256010.6	hg19	CCDS9029.1																																																																																			.	.		0.323	NTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406111.2		
CARS	833	hgsc.bcm.edu	37	11	3026609	3026612	+	Frame_Shift_Del	DEL	TCTC	TCTC	-	rs541100565		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:3026609_3026612delTCTC	ENST00000397111.5	-	19	2197_2200	c.1952_1955delGAGA	c.(1951-1956)agagaafs	p.RE651fs	CARS_ENST00000278224.9_Frame_Shift_Del_p.RE651fs|CARS_ENST00000380525.4_Frame_Shift_Del_p.RE734fs|CARS_ENST00000470221.2_5'UTR|CARS_ENST00000401769.3_Frame_Shift_Del_p.RE664fs|CARS_ENST00000397114.3_Frame_Shift_Del_p.RE641fs			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	651					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.R734T(1)|p.R651T(1)	CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	TCTCTTTTCTTCTCTCTCTTTTAA	0.397			T	ALK	ALCL																																p.734_735del	Ovarian(61;932 1157 5961 20446 52152)	Atlas-Indel,Pindel	.		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	CARS	114	.	2	Substitution - Missense(2)	lung(2)	c.2202_2205del						.																																			SO:0001589	frameshift_variant	833	exon20			.	AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	1493	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 1, cytoplasmic"""	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1952_1955delGAGA	chr11.hg19:g.3026613_3026616delTCTC	ENSP00000380300:p.Arg651fs	109.0	0.0		99.0	40.0	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Frame_Shift_Del	DEL	ENST00000397111.5	hg19	CCDS7742.1																																																																																			.	.		0.397	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751	
HYDIN	54768	hgsc.bcm.edu	37	16	71094473	71094474	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:71094473_71094474delTT	ENST00000393567.2	-	18	2612_2613	c.2462_2463delAA	c.(2461-2463)aaafs	p.K821fs	HYDIN_ENST00000448691.1_Frame_Shift_Del_p.K821fs|HYDIN_ENST00000541601.1_Frame_Shift_Del_p.K838fs|HYDIN_ENST00000538248.1_Frame_Shift_Del_p.K848fs|HYDIN_ENST00000321489.5_Frame_Shift_Del_p.K821fs|HYDIN_ENST00000448089.2_Frame_Shift_Del_p.K821fs	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	821					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGAAGAGTCTTTTAGGACGTA	0.475																																					p.848_849del		Atlas-INDEL	.											.	HYDIN	788	.	0			c.2544_2545del						.																																			SO:0001589	frameshift_variant	54768	exon18			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.2462_2463delAA	chr16.hg19:g.71094475_71094476delTT	ENSP00000377197:p.Lys821fs	156.0	0.0		133.0	18.0	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	hg19	CCDS59269.1																																																																																			.	.		0.475	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
TMEM225	338661	hgsc.bcm.edu	37	11	123754903	123754903	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr11:123754903delG	ENST00000375026.2	-	3	558	c.342delC	c.(340-342)ctcfs	p.L114fs		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	114					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						TGAGTGCCCAGAGCAGAGAGA	0.368																																					p.W115fs		Atlas-Indel,Pindel	.											.	TMEM225	56	.	0			c.343delT						.						108.0	103.0	105.0					11																	123754903		2202	4299	6501	SO:0001589	frameshift_variant	338661	exon3			.	AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"""PMP22 claudin domain containing"", ""protein phosphatase 1, regulatory subunit 154"""						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.342delC	chr11.hg19:g.123754903delG	ENSP00000364166:p.Leu114fs	61.0	0.0		65.0	24.0	NM_001013743		Frame_Shift_Del	DEL	ENST00000375026.2	hg19	CCDS31697.1																																																																																			.	.		0.368	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387260.1	NM_001013743	
CCBL2	56267	hgsc.bcm.edu	37	1	89453938	89453940	+	In_Frame_Del	DEL	AGA	AGA	-	rs146441129		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:89453938_89453940delAGA	ENST00000260508.4	-	2	431_433	c.94_96delTCT	c.(94-96)tctdel	p.S32del	CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_In_Frame_Del_p.S32del|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000321792.5_Intron|RBMXL1_ENST00000399794.2_5'UTR|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	32					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		TACCTACAGCAGAAGTAGAGAAT	0.35																																					p.32_33del		Atlas-Indel,Pindel	.											.	CCBL2	138	.	0			c.95_97del						.																																			SO:0001651	inframe_deletion	56267	exon2			.	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.94_96delTCT	chr1.hg19:g.89453938_89453940delAGA	ENSP00000260508:p.Ser32del	594.0	0.0		552.0	104.0	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	In_Frame_Del	DEL	ENST00000260508.4	hg19	CCDS30766.1																																																																																			.	.		0.350	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661	
NKX6-1	4825	hgsc.bcm.edu	37	4	85419145	85419145	+	Frame_Shift_Del	DEL	C	C	-	rs371770743		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:85419145delC	ENST00000295886.4	-	1	458	c.237delG	c.(235-237)gggfs	p.G79fs	NKX6-1_ENST00000515820.2_5'Flank	NM_006168.2	NP_006159.2	P78426	NKX61_HUMAN	NK6 homeobox 1	79					cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|cellular response to peptide hormone stimulus (GO:0071375)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|negative regulation of glial cell differentiation (GO:0045686)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|organ morphogenesis (GO:0009887)|pancreas development (GO:0031016)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of insulin secretion (GO:0032024)|positive regulation of neuron differentiation (GO:0045666)|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 B pancreatic cell development (GO:2000078)|regulation of axon extension (GO:0030516)|regulation of neuron migration (GO:2001222)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to drug (GO:0042493)|response to nicotine (GO:0035094)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	15		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)		GGGATGAGAGCCCCCCCGTGG	0.746																																					p.L80fs		Atlas-Indel,Pindel	.											.,1	NKX6-1	38	.	0			c.238delC						.						5.0	8.0	7.0					4																	85419145		1946	3968	5914	SO:0001589	frameshift_variant	4825	exon1			.	AH007313	CCDS3607.1	4q21.33	2012-03-09	2007-07-09	2002-10-04	ENSG00000163623	ENSG00000163623		"""Homeoboxes / ANTP class : NKL subclass"""	7839	protein-coding gene	gene with protein product		602563	"""NK homeobox (Drosophila), family 6, A"", ""NK6 transcription factor related, locus 1 (Drosophila)"""	NKX6A		9119408	Standard	NM_006168		Approved	Nkx6.1	uc003hpa.1	P78426	OTTHUMG00000130426	ENST00000295886.4:c.237delG	chr4.hg19:g.85419145delC	ENSP00000295886:p.Gly79fs	71.0	0.0		89.0	40.0	NM_006168		Frame_Shift_Del	DEL	ENST00000295886.4	hg19	CCDS3607.1																																																																																			.	.		0.746	NKX6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252814.2	NM_006168	
GJC2	57165	hgsc.bcm.edu	37	1	228345912	228345913	+	In_Frame_Ins	INS	-	-	GAG			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:228345912_228345913insGAG	ENST00000366714.2	+	2	628_629	c.453_454insGAG	c.(454-456)gag>GAGgag	p.152_152E>EE		NM_020435.3	NP_065168.2	Q5T442	CXG2_HUMAN	gap junction protein, gamma 2, 47kDa	152	Glu-rich.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|response to toxic substance (GO:0009636)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)	gap junction channel activity (GO:0005243)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7		Prostate(94;0.0405)				TGGGCCTGGGCgaggaggagga	0.787																																					p.G151delinsGE		Atlas-Indel,Pindel	.											.	GJC2	20	.	0			c.453_454insGAG						.																																			SO:0001652	inframe_insertion	57165	exon2			.	AF014643	CCDS1569.1	1q41-q42	2009-01-02	2007-12-14	2007-11-06	ENSG00000198835	ENSG00000198835		"""Ion channels / Gap junction proteins (connexins)"""	17494	protein-coding gene	gene with protein product	"""connexin 47"""	608803	"""gap junction protein, alpha 12, 47kDa"""	GJA12		19056803	Standard	NM_020435		Approved	CX47, CX46.6, SPG44	uc001hsk.3	Q5T442	OTTHUMG00000039771	ENST00000366714.2:c.472_474dupGAG	chr1.hg19:g.228345919_228345921dupGAG	ENSP00000355675:p.Glu158dup	349.0	0.0		364.0	88.0	NM_020435	O43440|Q7Z7J2|Q8IWJ9	In_Frame_Ins	INS	ENST00000366714.2	hg19	CCDS1569.1																																																																																			.	.		0.787	GJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095985.1	NM_020435	
PAPPA	5069	hgsc.bcm.edu	37	9	119130003	119130003	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:119130003delC	ENST00000328252.3	+	19	4944	c.4575delC	c.(4573-4575)atcfs	p.I1525fs	PAPPA_ENST00000534838.1_Frame_Shift_Del_p.I563fs	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1525	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						TGCGTGACATCCCCCACTGGC	0.572																																					p.I1525fs		Atlas-Indel,Pindel	.											.	PAPPA	243	.	0			c.4574delT						.						127.0	83.0	98.0					9																	119130003		2203	4300	6503	SO:0001589	frameshift_variant	5069	exon19			.		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.4575delC	chr9.hg19:g.119130003delC	ENSP00000330658:p.Ile1525fs	165.0	0.0		150.0	23.0	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Frame_Shift_Del	DEL	ENST00000328252.3	hg19	CCDS6813.1																																																																																			.	.		0.572	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
LILRA2	11027	hgsc.bcm.edu	37	19	55087325	55087325	+	Frame_Shift_Del	DEL	C	C	-	rs537955715		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:55087325delC	ENST00000251377.3	+	7	1137	c.1004delC	c.(1003-1005)gccfs	p.A335fs	LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000251376.3_Frame_Shift_Del_p.A335fs|LILRA2_ENST00000391738.3_Frame_Shift_Del_p.A335fs|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000391737.1_Frame_Shift_Del_p.A323fs			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	335	Ig-like C2-type 4.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CCCACAGTAGCCCCAGGAAAG	0.592																																					p.A335fs		Atlas-Indel,Pindel	.											.	LILRA2	99	.	0			c.1003delG						.						65.0	57.0	60.0					19																	55087325		2203	4300	6503	SO:0001589	frameshift_variant	11027	exon6			.	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1004delC	chr19.hg19:g.55087325delC	ENSP00000251377:p.Ala335fs	116.0	0.0		135.0	53.0	NM_001130917	O75020	Frame_Shift_Del	DEL	ENST00000251377.3	hg19	CCDS46179.1																																																																																			.	.		0.592	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816819	75816843	+	Intron	DEL	GAAAAATAAGCGATTGAACACTAGT	GAAAAATAAGCGATTGAACACTAGT	-	rs200555586|rs75261424|rs77365041	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	GAAAAATAAGCGATTGAACACTAGT	GAAAAATAAGCGATTGAACACTAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr12:75816819_75816843delGAAAAATAAGCGATTGAACACTAGT	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000320460.4_Frame_Shift_Del_p.KKNKRLNTS240fs|GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000435775.1_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)		p.K240N(1)		kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						GATTGGACAAGAAAAATAAGCGATTGAACACTAGTTTTTTATGGT	0.302																																					p.240_248del		Pindel	.											.	GLIPR1L2	54	.	1	Substitution - Missense(1)	large_intestine(1)	c.719_743del						.																																			SO:0001627	intron_variant	144321	exon4			.	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+50GAAAAATAAGCGATTGAACACTAGT>-	chr12.hg19:g.75816819_75816843delGAAAAATAAGCGATTGAACACTAGT		158.0	0.0		125.0	27.0	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Frame_Shift_Del	DEL	ENST00000550916.1	hg19	CCDS58258.1																																																																																			.	.		0.302	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
NPC1L1	29881	hgsc.bcm.edu	37	7	44556938	44556938	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:44556938delT	ENST00000289547.4	-	16	3291	c.3236delA	c.(3235-3237)tatfs	p.Y1079fs	NPC1L1_ENST00000381160.3_Frame_Shift_Del_p.Y1052fs|NPC1L1_ENST00000546276.1_Frame_Shift_Del_p.Y1006fs	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1079					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GGGCTTGTGATAGGCCATGAA	0.562																																					p.Y1079fs		Pindel	.											.	NPC1L1	141	.	0			c.3237delT						.						102.0	97.0	99.0					7																	44556938		2203	4300	6503	SO:0001589	frameshift_variant	29881	exon16			.		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3236delA	chr7.hg19:g.44556938delT	ENSP00000289547:p.Tyr1079fs	51.0	0.0		48.0	15.0	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Frame_Shift_Del	DEL	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.		0.562	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
ZNRF1	84937	hgsc.bcm.edu	37	16	75033762	75033762	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr16:75033762delG	ENST00000335325.4	+	1	835	c.193delG	c.(193-195)gggfs	p.G66fs	ZNRF1_ENST00000567962.1_Frame_Shift_Del_p.G66fs|ZNRF1_ENST00000320619.6_Frame_Shift_Del_p.G66fs|ZNRF1_ENST00000566250.1_Frame_Shift_Del_p.G66fs|WDR59_ENST00000562331.1_5'Flank	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase	66					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						CAGCACGGCCGGGGGGGTGCC	0.756																																					p.A64fs		Pindel	.											.	ZNRF1	6	.	0			c.192delC						.			23,3159		4,15,1572	3.0	4.0	4.0			2.8	1.0	16		3	35,6275		5,25,3125	no	frameshift	ZNRF1	NM_032268.4		9,40,4697	A1A1,A1R,RR		0.5547,0.7228,0.611			75033762	58,9434	1796	3541	5337	SO:0001589	frameshift_variant	84937	exon1			.	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"""RING-type (C3HC4) zinc fingers"""	18452	protein-coding gene	gene with protein product		612060	"""zinc and ring finger 1"""				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606	ENST00000335325.4:c.193delG	chr16.hg19:g.75033762delG	ENSP00000335091:p.Gly66fs	57.0	0.0		70.0	18.0	NM_032268	D3DUJ9|Q9H083	Frame_Shift_Del	DEL	ENST00000335325.4	hg19	CCDS10912.1																																																																																			.	.		0.756	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2		
JARID2	3720	hgsc.bcm.edu	37	6	15496635	15496636	+	Frame_Shift_Ins	INS	-	-	G			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:15496635_15496636insG	ENST00000341776.2	+	7	1423_1424	c.1179_1180insG	c.(1180-1182)gggfs	p.G394fs	JARID2_ENST00000397311.3_Frame_Shift_Ins_p.G222fs|JARID2_ENST00000541660.1_Frame_Shift_Ins_p.G356fs	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	394					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)	p.L393L(1)		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)				TGCTATCCCTCGGGGGGGCGTC	0.574																																					p.L393fs		Pindel	.											JARID2,NS,carcinoma,0,1	JARID2	135	.	1	Substitution - coding silent(1)	lung(1)	c.1179_1180insG						.																																			SO:0001589	frameshift_variant	3720	exon7			.	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.1186dupG	chr6.hg19:g.15496642_15496642dupG	ENSP00000341280:p.Gly394fs	246.0	0.0		254.0	55.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Frame_Shift_Ins	INS	ENST00000341776.2	hg19	CCDS4533.1																																																																																			.	.		0.574	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
DAZAP1	26528	hgsc.bcm.edu	37	19	1434830	1434830	+	Frame_Shift_Del	DEL	G	G	-	rs368917206		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr19:1434830delG	ENST00000233078.4	+	12	1304	c.1143delG	c.(1141-1143)tcgfs	p.S381fs	DAZAP1_ENST00000336761.6_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	381	Pro-rich.		S -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|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)		TGCCAGGGTcggggggccccc	0.711																																					p.S381fs		Pindel	.											DAZAP1,colon,carcinoma,0,1	DAZAP1	52	.	0			c.1142delC						.						12.0	16.0	15.0					19																	1434830		2200	4293	6493	SO:0001589	frameshift_variant	26528	exon12			.		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"""RNA binding motif (RRM) containing"""	2683	protein-coding gene	gene with protein product	"""deleted in azoospermia associated protein 1"""	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.1143delG	chr19.hg19:g.1434830delG	ENSP00000233078:p.Ser381fs	126.0	0.0		83.0	14.0	NM_018959	Q96MJ3|Q9NRR9	Frame_Shift_Del	DEL	ENST00000233078.4	hg19	CCDS12065.1																																																																																			.	.		0.711	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711	
COL28A1	340267	hgsc.bcm.edu	37	7	7412846	7412846	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:7412846delT	ENST00000399429.3	-	32	2831	c.2691delA	c.(2689-2691)aaafs	p.K897fs		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	897	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCAAGGCCACTTTTTTTACAC	0.478																																					p.V898fs		Pindel	.											.	COL28A1	113	.	0			c.2692delG						.						92.0	86.0	88.0					7																	7412846		1968	4159	6127	SO:0001589	frameshift_variant	340267	exon32			.	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2691delA	chr7.hg19:g.7412846delT	ENSP00000382356:p.Lys897fs	104.0	0.0		127.0	11.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Frame_Shift_Del	DEL	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.478	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
COL7A1	1294	hgsc.bcm.edu	37	3	48605066	48605066	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr3:48605066delC	ENST00000328333.8	-	108	8094	c.7987delG	c.(7987-7989)gagfs	p.E2663fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.E2631fs|COL7A1_ENST00000470076.1_5'Flank	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2663	Triple-helical region.				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)		ACACCAGGCTCCCCCTGGAGA	0.627																																					p.E2663fs		Pindel	.											.	COL7A1	320	.	0			c.7988delA						.						62.0	75.0	71.0					3																	48605066		2202	4300	6502	SO:0001589	frameshift_variant	1294	exon108			.	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.7987delG	chr3.hg19:g.48605066delC	ENSP00000332371:p.Glu2663fs	188.0	0.0		205.0	56.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.627	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
GTPBP1	9567	hgsc.bcm.edu	37	22	39125562	39125562	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr22:39125562delG	ENST00000216044.5	+	11	2045	c.1812delG	c.(1810-1812)gagfs	p.E604fs		NM_004286.4	NP_004277.2	O00178	GTPB1_HUMAN	GTP binding protein 1	604					GTP catabolic process (GO:0006184)|immune response (GO:0006955)|positive regulation of mRNA catabolic process (GO:0061014)|signal transduction (GO:0007165)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	18	Melanoma(58;0.04)					AACGAGACGAGGGGGGCCCGT	0.607																																					p.E604fs		Pindel	.											.	GTPBP1	51	.	0			c.1811delA						.						29.0	27.0	27.0					22																	39125562		2202	4300	6502	SO:0001589	frameshift_variant	9567	exon11			.	U87964	CCDS13977.2	22q13.1	2008-07-01			ENSG00000100226	ENSG00000100226			4669	protein-coding gene	gene with protein product		602245				9070279	Standard	XM_005261857		Approved	GP-1, HSPC018	uc003awg.3	O00178	OTTHUMG00000151002	ENST00000216044.5:c.1812delG	chr22.hg19:g.39125562delG	ENSP00000216044:p.Glu604fs	179.0	0.0		180.0	20.0	NM_004286	Q6IC67	Frame_Shift_Del	DEL	ENST00000216044.5	hg19	CCDS13977.2																																																																																			.	.		0.607	GTPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075532.1	NM_004286	
KCNH1	3756	hgsc.bcm.edu	37	1	210857113	210857113	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:210857113delC	ENST00000271751.4	-	11	2507	c.2480delG	c.(2479-2481)ggcfs	p.G829fs	KCNH1_ENST00000367007.4_Frame_Shift_Del_p.G802fs			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	829					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		ATCGCCCCCGCCCCCCTTGGG	0.652																																					p.G827fs		Pindel	.											.	KCNH1	199	.	0			c.2481delC						.						43.0	51.0	48.0					1																	210857113		2203	4300	6503	SO:0001589	frameshift_variant	3756	exon11			.	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2480delG	chr1.hg19:g.210857113delC	ENSP00000271751:p.Gly829fs	50.0	0.0		43.0	11.0	NM_172362	B1AQ26|O76035|Q14CL3	Frame_Shift_Del	DEL	ENST00000271751.4	hg19	CCDS1496.1																																																																																			.	.		0.652	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
TCP10L	140290	hgsc.bcm.edu	37	21	33949091	33949091	+	Frame_Shift_Del	DEL	C	C	-	rs373347740		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr21:33949091delC	ENST00000300258.3	-	5	754	c.641delG	c.(640-642)ggtfs	p.G214fs	LINC00846_ENST00000334165.4_lincRNA|TCP10L_ENST00000472557.1_Frame_Shift_Del_p.G128fs	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	214					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						TCTTCAGACACCCCCCCGTCT	0.478																																					p.G214fs		Pindel	.											.,2	TCP10L	24	.	0			c.642delT						.						118.0	108.0	112.0					21																	33949091		2203	4300	6503	SO:0001589	frameshift_variant	140290	exon5			.	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"""t-complex 10 (a murine tcp homolog)-like"", ""t-complex 10 (mouse)-like"""			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.641delG	chr21.hg19:g.33949091delC	ENSP00000300258:p.Gly214fs	102.0	0.0		106.0	40.0	NM_144659	Q53EW0|Q96LN5	Frame_Shift_Del	DEL	ENST00000300258.3	hg19	CCDS13616.1																																																																																			.	.		0.478	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659	
NES	10763	hgsc.bcm.edu	37	1	156642804	156642804	+	Frame_Shift_Del	DEL	G	G	-	rs372020167		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:156642804delG	ENST00000368223.3	-	4	1308	c.1176delC	c.(1174-1176)cccfs	p.P392fs		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	392	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTGAGGTGTGGGGGGGATGG	0.597																																					p.T393fs		Pindel	.											.	NES	196	.	0			c.1177delA						.						74.0	93.0	86.0					1																	156642804		2203	4299	6502	SO:0001589	frameshift_variant	10763	exon4			.	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.1176delC	chr1.hg19:g.156642804delG	ENSP00000357206:p.Pro392fs	90.0	0.0		84.0	21.0	NM_006617	O00552|Q3LIF5|Q5SYZ6	Frame_Shift_Del	DEL	ENST00000368223.3	hg19	CCDS1151.1																																																																																			.	.		0.597	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
FKBP15	23307	hgsc.bcm.edu	37	9	115941002	115941002	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr9:115941002delT	ENST00000238256.3	-	20	2111	c.1994delA	c.(1993-1995)aagfs	p.K665fs		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	665					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CTCTGTTTCCTTTTTTTGGTG	0.498																																					p.K665fs		Pindel	.											.	FKBP15	128	.	0			c.1995delG						.			21,3689		9,3,1843	51.0	47.0	49.0			-2.5	1.0	9		49	48,7884		17,14,3935	no	frameshift	FKBP15	NM_015258.1		26,17,5778	A1A1,A1R,RR		0.6051,0.566,0.5927			115941002	69,11573	1938	4146	6084	SO:0001589	frameshift_variant	23307	exon20			.	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.1994delA	chr9.hg19:g.115941002delT	ENSP00000238256:p.Lys665fs	52.0	0.0		59.0	12.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Frame_Shift_Del	DEL	ENST00000238256.3	hg19	CCDS48007.1																																																																																			.	.		0.498	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
PVRIG	79037	hgsc.bcm.edu	37	7	99817848	99817848	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:99817848delG	ENST00000317271.2	+	3	593	c.230delG	c.(229-231)tggfs	p.W77fs	AC005071.1_ENST00000410550.1_RNA|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA	NM_024070.3	NP_076975.2	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin domain containing	77						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)	11	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACTGTGAGCTGGGGGGGCCCC	0.662																																					p.W77fs		Pindel	.											.	PVRIG	20	.	0			c.229delT						.						16.0	16.0	16.0					7																	99817848		2201	4297	6498	SO:0001589	frameshift_variant	79037	exon3			.	BC001129	CCDS5690.1	7q22.1	2013-06-26			ENSG00000213413	ENSG00000213413			32190	protein-coding gene	gene with protein product						16926269	Standard	NM_024070		Approved	MGC2463, C7orf15	uc003uuf.1	Q6DKI7	OTTHUMG00000156798	ENST00000317271.2:c.230delG	chr7.hg19:g.99817848delG	ENSP00000316675:p.Trp77fs	46.0	0.0		55.0	11.0	NM_024070	D6W5U9|Q9BVK3	Frame_Shift_Del	DEL	ENST00000317271.2	hg19	CCDS5690.1																																																																																			.	.		0.662	PVRIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345870.2	NM_024070	
ANKRD30BL	554226	hgsc.bcm.edu	37	2	132912268	132912268	+	Frame_Shift_Del	DEL	T	T	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:132912268delT	ENST00000409867.1	-	4	830	c.581delA	c.(580-582)aatfs	p.N194fs	ANKRD30BL_ENST00000470729.1_5'UTR|RNU6-1132P_ENST00000459214.1_RNA			A7E2S9	A30BL_HUMAN	ankyrin repeat domain 30B-like	194										endometrium(1)|kidney(3)	4						TGCATTTGCATTTTTTGTCAG	0.318																																					.		Pindel	.											.	ANKRD30BL	36	.	0			.						.																																			SO:0001589	frameshift_variant	554226	.			.			2q21.2	2013-01-22	2010-06-14	2010-06-14	ENSG00000163046	ENSG00000163046		"""Ankyrin repeat domain containing"""	35167	protein-coding gene	gene with protein product			"""non-protein coding RNA 164"", ""ankyrin repeat domain 30B pseudogene 3"""	NCRNA00164, ANKRD30BP3		17114284	Standard	NR_027019		Approved		uc002tti.3	A7E2S9	OTTHUMG00000153491	ENST00000409867.1:c.581delA	chr2.hg19:g.132912268delT	ENSP00000386398:p.Asn194fs	348.0	0.0		320.0	70.0	.	B8ZZL7	RNA	DEL	ENST00000409867.1	hg19																																																																																				.	.		0.318	ANKRD30BL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331353.2	NR_027019	
ZNF236	7776	hgsc.bcm.edu	37	18	74587535	74587535	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr18:74587535delA	ENST00000253159.8	+	6	947	c.749delA	c.(748-750)gaafs	p.E250fs	ZNF236_ENST00000320610.9_Frame_Shift_Del_p.E252fs	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	250					cellular response to glucose stimulus (GO:0071333)|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(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		CACACAGGTGAAAAACCCCAT	0.527											OREG0025069	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E250fs		Pindel	.											.	ZNF236	325	.	0			c.748delG						.						123.0	126.0	125.0					18																	74587535		2013	4177	6190	SO:0001589	frameshift_variant	7776	exon6			.	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.749delA	chr18.hg19:g.74587535delA	ENSP00000253159:p.Glu250fs	117.0	0.0	1154	134.0	42.0	NM_007345	B2RTX9|Q9UL37	Frame_Shift_Del	DEL	ENST00000253159.8	hg19	CCDS42447.1																																																																																			.	.		0.527	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
ABLIM2	84448	hgsc.bcm.edu	37	4	8031388	8031389	+	Frame_Shift_Ins	INS	-	-	G	rs570874083|rs377709298		TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr4:8031388_8031389insG	ENST00000341937.5	-	11	1226_1227	c.1162_1163insC	c.(1162-1164)cgtfs	p.R388fs	ABLIM2_ENST00000361581.5_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000545242.1_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000447017.2_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000428004.2_Frame_Shift_Ins_p.R399fs|ABLIM2_ENST00000318888.4_Frame_Shift_Ins_p.R156fs|ABLIM2_ENST00000296372.8_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000407564.3_Frame_Shift_Ins_p.R388fs|ABLIM2_ENST00000515079.1_5'UTR|ABLIM2_ENST00000546334.1_Frame_Shift_Ins_p.R399fs|ABLIM2_ENST00000361737.5_Frame_Shift_Ins_p.R399fs|ABLIM2_ENST00000514025.1_Frame_Shift_Ins_p.R156fs|ABLIM2_ENST00000505872.1_Frame_Shift_Ins_p.R388fs	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	388					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						AGTACCTGGACGGCTGTAGTGC	0.53																																					p.R399fs		Pindel	.											.	ABLIM2	59	.	0			c.1196_1197insC						.																																			SO:0001589	frameshift_variant	84448	exon12			.	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"""actin binding LIM protein 2"""				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.1163dupC	chr4.hg19:g.8031390_8031390dupG	ENSP00000342813:p.Arg388fs	140.0	0.0		139.0	38.0	NM_001130087	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Frame_Shift_Ins	INS	ENST00000341937.5	hg19	CCDS47013.1																																																																																			.	.		0.530	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083	
DLK2	65989	hgsc.bcm.edu	37	6	43418413	43418413	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:43418413delG	ENST00000357338.3	-	6	1716	c.1016delC	c.(1015-1017)cctfs	p.P339fs	DLK2_ENST00000372488.3_Frame_Shift_Del_p.P339fs|DLK2_ENST00000372485.1_Frame_Shift_Del_p.P333fs|DLK2_ENST00000414245.1_Frame_Shift_Del_p.P333fs	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	339					negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			ACAGGGTCCAGGGGGGCAGAC	0.662																																					p.P339fs		Pindel	.											.	DLK2	22	.	0			c.1017delT						.						34.0	38.0	37.0					6																	43418413		2202	4297	6499	SO:0001589	frameshift_variant	65989	exon6			.	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.1016delC	chr6.hg19:g.43418413delG	ENSP00000349893:p.Pro339fs	222.0	0.0		599.0	71.0	NM_206539	B3KNZ7|Q5T3T8|Q9BQ54	Frame_Shift_Del	DEL	ENST00000357338.3	hg19	CCDS4897.1																																																																																			.	.		0.662	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
GPC1	2817	hgsc.bcm.edu	37	2	241390099	241390100	+	Intron	INS	-	-	G	rs563795742	byFrequency	TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr2:241390099_241390100insG	ENST00000264039.2	+	2	414				AC110619.2_ENST00000404891.1_3'UTR|AC110619.2_ENST00000404327.3_Frame_Shift_Ins_p.Q103fs	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1						axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		GGTGCTGGCTTGGGGGGGTGTG	0.629																																					.		Pindel	.											.	.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			.	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.167-8347->G	chr2.hg19:g.241390106_241390106dupG		170.0	0.0		171.0	23.0	.	B3KTD1|Q53QM4	RNA	INS	ENST00000264039.2	hg19	CCDS2534.1																																																																																			.	.		0.629	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
PLOD3	8985	hgsc.bcm.edu	37	7	100856126	100856126	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr7:100856126delC	ENST00000223127.3	-	8	1274	c.876delG	c.(874-876)gggfs	p.G292fs		NM_001084.4	NP_001075.1	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	292					basement membrane assembly (GO:0070831)|cellular protein modification process (GO:0006464)|cellular response to hormone stimulus (GO:0032870)|collagen fibril organization (GO:0030199)|endothelial cell morphogenesis (GO:0001886)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|lung morphogenesis (GO:0060425)|neural tube development (GO:0021915)|protein localization (GO:0008104)|vasodilation (GO:0042311)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen galactosyltransferase activity (GO:0050211)|procollagen glucosyltransferase activity (GO:0033823)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	31	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	ACCTCACCTGCCCCCCCGGGA	0.672																																					p.Q293fs		Pindel	.											.	PLOD3	79	.	0			c.877delC						.						28.0	29.0	29.0					7																	100856126		2203	4299	6502	SO:0001589	frameshift_variant	8985	exon8			.	AF046889	CCDS5715.1	7q22.1	2011-08-24			ENSG00000106397	ENSG00000106397	1.14.11.4		9083	protein-coding gene	gene with protein product	"""lysyl hydroxlase 3"""	603066				9724729, 9582318	Standard	NM_001084		Approved	LH3	uc003uyd.3	O60568	OTTHUMG00000157111	ENST00000223127.3:c.876delG	chr7.hg19:g.100856126delC	ENSP00000223127:p.Gly292fs	52.0	0.0		52.0	11.0	NM_001084	B2R6W6|Q540C3	Frame_Shift_Del	DEL	ENST00000223127.3	hg19	CCDS5715.1																																																																																			.	.		0.672	PLOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347470.1		
TNXB	7148	hgsc.bcm.edu	37	6	32029263	32029263	+	Frame_Shift_Del	DEL	C	C	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr6:32029263delC	ENST00000375244.3	-	21	7604	c.7403delG	c.(7402-7404)ggcfs	p.G2468fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.G2468fs			P22105	TENX_HUMAN	tenascin XB	2528	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGGCTCCAGGCCCCCCACGGT	0.687																																					p.G2468fs		Pindel	.											.	TNXB	553	.	0			c.7404delC						.						75.0	88.0	84.0					6																	32029263		1262	2532	3794	SO:0001589	frameshift_variant	7148	exon21			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7403delG	chr6.hg19:g.32029263delC	ENSP00000364393:p.Gly2468fs	131.0	0.0		198.0	30.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000375244.3	hg19																																																																																				.	.		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TMEM232	642987	hgsc.bcm.edu	37	5	110003053	110003054	+	Start_Codon_Ins	INS	-	-	A			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr5:110003053_110003054insA	ENST00000455884.2	-	0	50_51				TMEM232_ENST00000429839.2_Start_Codon_Ins|TMEM232_ENST00000515518.2_Intron			C9JQI7	TM232_HUMAN	transmembrane protein 232							integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						GGCATATTCATAAATCATAAAT	0.282																																					p.M1fs		Pindel	.											.	TMEM232	57	.	0			c.1_2insT						.																																			SO:0001582	initiator_codon_variant	642987	exon2			.	AK125070	CCDS47253.1, CCDS47253.2	5q22.1	2014-02-12	2009-10-02		ENSG00000186952	ENSG00000186952			37270	protein-coding gene	gene with protein product							Standard	NM_001039763		Approved	FLJ43080	uc011cvh.2	C9JQI7	OTTHUMG00000163297	ENST00000455884.2:c.2dupT	chr5.hg19:g.110003056_110003056dupA		263.0	0.0		237.0	63.0	NM_001039763	B4DKF4	Frame_Shift_Ins	INS	ENST00000455884.2	hg19	CCDS47253.2																																																																																			.	.		0.282	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
DNAH14	127602	hgsc.bcm.edu	37	1	225211543	225211543	+	Frame_Shift_Del	DEL	A	A	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:225211543delA	ENST00000445597.2	+	9	1391	c.1391delA	c.(1390-1392)gaafs	p.E464fs	DNAH14_ENST00000430092.1_Frame_Shift_Del_p.E445fs|DNAH14_ENST00000400952.3_Frame_Shift_Del_p.E445fs|DNAH14_ENST00000439375.2_Frame_Shift_Del_p.E445fs|DNAH14_ENST00000366849.1_Frame_Shift_Del_p.E422fs			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	464					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TTTTCAGTGGAAAAAAAGAAT	0.299																																					p.E445fs		Pindel	.											.	DNAH14	300	.	0			c.1333delG						.						83.0	68.0	72.0					1																	225211543		692	1590	2282	SO:0001589	frameshift_variant	127602	exon11			.	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.1391delA	chr1.hg19:g.225211543delA	ENSP00000409472:p.Glu464fs	224.0	0.0		250.0	23.0	NM_001145154	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Frame_Shift_Del	DEL	ENST00000445597.2	hg19																																																																																				.	.		0.299	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
IQCC	55721	hgsc.bcm.edu	37	1	32673443	32673443	+	Frame_Shift_Del	DEL	G	G	-			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:32673443delG	ENST00000291358.6	+	5	1182	c.1161delG	c.(1159-1161)ttgfs	p.L387fs	IQCC_ENST00000537469.1_Frame_Shift_Del_p.L467fs|RP4-622L5.7_ENST00000421616.1_RNA|RP4-622L5.7_ENST00000373604.4_RNA|DCDC2B_ENST00000409358.1_5'Flank	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	387										endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ATGGTACCTTGGGGGGGCCAG	0.552																																					p.L467fs		Pindel	.											.,1	IQCC	46	.	0			c.1400delT						.						82.0	89.0	87.0					1																	32673443		2203	4300	6503	SO:0001589	frameshift_variant	55721	exon5			.	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.1161delG	chr1.hg19:g.32673443delG	ENSP00000291358:p.Leu387fs	361.0	0.0		314.0	83.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Frame_Shift_Del	DEL	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.552	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134	
MMEL1	79258	hgsc.bcm.edu	37	1	2560839	2560840	+	Frame_Shift_Ins	INS	-	-	C			TCGA-4R-AA8I-01A-11D-A382-10	TCGA-4R-AA8I-10B-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8dba9681-e78c-40e4-a7d9-b031da622799	9ab82c20-518e-4e2e-9744-d813c8ecf079	g.chr1:2560839_2560840insC	ENST00000378412.3	-	2	245_246	c.84_85insG	c.(82-87)gggctgfs	p.L29fs	MMEL1_ENST00000511099.1_5'Flank|MMEL1_ENST00000288709.6_Frame_Shift_Ins_p.L20fs|MMEL1_ENST00000502556.1_Frame_Shift_Ins_p.L29fs			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	29						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		agcagcagcagcCCCCCCTCCA	0.723																																					p.L29fs		Pindel	.											.	MMEL1	64	.	0			c.85_86insG						.																																			SO:0001589	frameshift_variant	79258	exon2			.	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.85dupG	chr1.hg19:g.2560846_2560846dupC	ENSP00000367668:p.Leu29fs	258.0	0.0		246.0	63.0	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Frame_Shift_Ins	INS	ENST00000378412.3	hg19	CCDS30569.2																																																																																			.	.		0.723	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
